Scientific Computing and Data / High Performance Computing / Publications / Papers Published Through Minerva Supercomputing

Papers Published Through Minerva Supercomputing

2023

M. S. Breen et al., Large 22q13.3 deletions perturb peripheral transcriptomic and metabolomic profiles in Phelan-McDermid syndrome. Human Genetics and Genomics Advances 4, 100145 (2023).
M. S. Breilyn, E. E. Kenny, N. S. Abul-Husn, Diverse and unselected adults with clinically relevant ACADS variants lack evidence of metabolic disease. Mol Genet Metab 138, 106971 (2023).
M. Déjosez et al., Bat pluripotent stem cells reveal unusual entanglement between host and viruses. Cell 186, 957-974.e928 (2023).
S. Dyzenhaus et al., MRSA lineage USA300 isolated from bloodstream infections exhibit altered virulence regulation. Cell Host Microbe 31, 228-242.e228 (2023).
C. Ethan et al., Relationship of hepatitis C risk to hepatitis C test acceptance among adult patients participating in an ED hepatitis C screening programme. Emergency Medicine Journal 10.1136/emermed-2022-212726, emermed-2022-212726 (2023).
D. Greene et al., Genetic association analysis of 77,539 genomes reveals rare disease etiologies. Nature Medicine 29, 679-688 (2023).
K. Hou et al., Causal effects on complex traits are similar for common variants across segments of different continental ancestries within admixed individuals. Nature Genetics 10.1038/s41588-023-01338-6 (2023).
Y. Kong, E. A. Mead, G. Fang, Navigating the pitfalls of mapping DNA and RNA modifications. Nature Reviews Genetics 10.1038/s41576-022-00559-5 (2023).
K. R. Kulkarni et al., An Interpretable and Predictive Connectivity-Based Neural Signature for Chronic Cannabis Use. Biological Psychiatry: Cognitive Neuroscience and Neuroimaging 8, 320-330 (2023).
S. Lehrer, P. H. Rheinstein, Shingles vaccination reduces the risk of Parkinson’s disease. Chronic Dis Transl Med 9, 54-57 (2023).
S. Lehrer, P. H. Rheinstein, Androgen Deprivation Therapy Unrelated to Alzheimer’s Disease in the UK Biobank Cohort. Anticancer Res 43, 437-440 (2023).
J. E. Linder et al., Returning integrated genomic risk and clinical recommendations: The eMERGE study. Genet Med 25, 100006 (2023).
G. Qin et al., Distinct niche structures and intrinsic programs of fallopian tube and ovarian surface epithelial cells. iScience 26, 105861 (2023).
S. M. Rutledge et al., Association of HSD17B13 and PNPLA3 With Liver Enzymes and Fibrosis in Hispanic/Latino Individuals of Diverse Genetic Ancestries. Clin Gastroenterol Hepatol 10.1016/j.cgh.2022.12.025 (2023).
M. Sebastin et al., The TeleKidSeq pilot study: incorporating telehealth into clinical care of children from diverse backgrounds undergoing whole genome sequencing. Pilot and Feasibility Studies 9, 47 (2023).
X. Song et al., MiXcan: a framework for cell-type-aware transcriptome-wide association studies with an application to breast cancer. Nature Communications 14, 377 (2023).
C. M. Storey et al., Quantitative In Vivo Imaging of the Androgen Receptor Axis Reveals Degree of Prostate Cancer Radiotherapy Response. Mol Cancer Res 21, 307-315 (2023).
R. C. Thompson et al., Molecular states during acute COVID-19 reveal distinct etiologies of long-term sequelae. Nature Medicine 29, 236-246 (2023).
M. Verbitsky et al., Genomic Disorders in CKD across the Lifespan. J Am Soc Nephrol 34, 607-618 (2023).
R. Wang et al., Construction of a cross-species cell landscape at single-cell level. Nucleic Acids Res 51, 501-516 (2023).
P. Xu et al., Multi-omic integration reveals cell-type-specific regulatory networks of insulin resistance in distinct ancestry populations. Cell Syst 14, 41-57.e48 (2023).

2022

1. E. E. Abbott et al., Survival After Out-of-Hospital Cardiac Arrest: The Role of Racial Residential Segregation. Journal of Urban Health 99, 998-1011 (2022).
2. D. Ahn et al., Gαs slow conformational transition upon GTP binding and a novel Gαs regulator. bioRxiv 10.1101/2022.10.10.511514, 2022.2010.2010.511514 (2022).
3. C. J. Aranda et al., IgG memory B cells expressing IL4R and FCER2 are associated with atopic diseases. Allergy 10.1111/all.15601 (2022).
4. T. Aydillo et al., Transcriptome signatures preceding the induction of anti-stalk antibodies elicited after universal influenza vaccination. npj Vaccines 7, 160 (2022).
5. K. K. Badani et al., SARS-CoV-2 RNA Detected in Abdominal Insufflation Samples During Laparoscopic Surgery. European urology 81, 125-127 (2022).
6. S. Badrinath et al., A vaccine targeting resistant tumours by dual T cell plus NK cell attack. Nature 10.1038/s41586-022-04772-4 (2022).
7. A. M. Barrette et al., Anti-invasive efficacy and survival benefit of the YAP-TEAD inhibitor verteporfin in preclinical glioblastoma models. Neuro Oncol 24, 694-707 (2022).
8. R. Birnbaum, B. Mahjani, R. J. F. Loos, A. J. Sharp, Clinical Characterization of Copy Number Variants Associated With Neurodevelopmental Disorders in a Large-scale Multiancestry Biobank. JAMA Psychiatry 79, 250-259 (2022).
9. K. R. Bowles et al., Dysregulated coordination of MAPT exon 2 and exon 10 splicing underlies different tau pathologies in PSP and AD. Acta Neuropathologica 143, 225-243 (2022).
10. G. Butler-Laporte et al., The dynamic changes and sex differences of 147 immune-related proteins during acute COVID-19 in 580 individuals. Clin Proteomics 19, 34 (2022).
11. G. Carbonell et al., Quantitative chest computed tomography combined with plasma cytokines predict outcomes in COVID-19 patients. Heliyon 8, e10166 (2022).
12. S. Carcamo et al., Altered BAF occupancy and transcription factor dynamics in PBAF-deficient melanoma. Cell Reports 39 (2022).
13. J. M. Carreño et al., Activity of convalescent and vaccine serum against SARS-CoV-2 Omicron. Nature 602, 682-688 (2022).
14. S. T. Chen et al., Shift of lung macrophage composition is associated with COVID-19 disease severity and recovery. bioRxiv 10.1101/2022.01.11.475918, 2022.2001.2011.475918 (2022).
15. T.-Y. Chen et al., Extracellular vesicles carry distinct proteo-transcriptomic signatures that are different from their cancer cell of origin. iScience 25, 104414 (2022).
16. Cristiana Cruceanu, Ph.D. , et al., Cell-Type-Specific Impact of Glucocorticoid Receptor Activation on the Developing Brain: A Cerebral Organoid Study. American Journal of Psychiatry 179, 375-387 (2022).
17. W. H. Cuddleston et al., Spatiotemporal and genetic regulation of A-to-I editing throughout human brain development. Cell Rep 41, 111585 (2022).
18. W. H. Cuddleston et al., Cellular and genetic drivers of RNA editing variation in the human brain. Nature Communications 13, 2997 (2022).
19. O. Danziger, R. S. Patel, E. J. DeGrace, M. R. Rosen, B. R. Rosenberg, Inducible CRISPR activation screen for interferon-stimulated genes identifies OAS1 as a SARS-CoV-2 restriction factor. PLoS pathogens 18, e1010464-e1010464 (2022).
20. R. De Gasperi et al., Numb is required for optimal contraction of skeletal muscle. Journal of Cachexia, Sarcopenia and Muscle n/a (2022).
21. M. M. DeGrace et al., Defining the risk of SARS-CoV-2 variants on immune protection. Nature 605, 640-652 (2022).
22. N. Del Rossi, J. G. Chen, G.-C. Yuan, R. Dries, Analyzing Spatial Transcriptomics Data Using Giotto. Current Protocols 2, e405 (2022).
23. A. F. Di’Narzo et al., Integrative Analysis of the Inflammatory Bowel Disease Serum Metabolome Improves Our Understanding of Genetic Etiology and Points to Novel Putative Therapeutic Targets. Gastroenterology 162, 828-843.e811 (2022).
24. D. Dima et al., Subcortical volumes across the lifespan: Data from 18,605 healthy individuals aged 3–90 years. Human Brain Mapping 43, 452-469 (2022).
25. J. A. Duty et al., Discovery and intranasal administration of a SARS-CoV-2 broadly acting neutralizing antibody with activity against multiple Omicron subvariants. Med (N Y) 3, 705-721.e711 (2022).
26. P. Encinas et al., Evolution of influenza A virus in intensive and free-range swine farms in Spain. Virus Evol 7, veab099 (2022).
27. A. Escalera et al., Mutations in SARS-CoV-2 variants of concern link to increased spike cleavage and virus transmission. Cell host & microbe 30, 373-387.e377 (2022).
28. D. Esposito et al., ROCK1 mechano-signaling dependency of human malignancies driven by TEAD/YAP activation. Nature Communications 13, 703 (2022).
29. M. E. Farkouh et al., Anticoagulation in Patients With COVID-19: JACC Review Topic of the Week. Journal of the American College of Cardiology 79, 917-928 (2022).
30. K. Farrell et al., Genome-wide association study and functional validation implicates JADE1 in tauopathy. Acta neuropathologica 143, 33-53 (2022).
31. V. G. Fiore, X. Gu, Similar network compositions, but distinct neural dynamics underlying belief updating in environments with and without explicit outcomes. Neuroimage 247, 118821 (2022).
32. I. S. Forrest et al., Population-Based Penetrance of Deleterious Clinical Variants. JAMA 327, 350-359 (2022).
33. I. S. Forrest, G. N. Nadkarni, R. Do, Penetrance of Deleterious Clinical Variants—Reply. JAMA 327, 1927-1927 (2022).
34. S. Frangou et al., Hippocampal volume reduction is associated with direct measure of insulin resistance in adults. Neuroscience Research 174, 19-24 (2022).
35. S. Frangou et al., Cortical thickness across the lifespan: Data from 17,075 healthy individuals aged 3–90 years. Human Brain Mapping 43, 431-451 (2022).
36. X. Gao et al., Blocking PI3K p110β Attenuates Development of PTEN-Deficient Castration-Resistant Prostate Cancer. Molecular Cancer Research 20, 673-685 (2022).
37. P. Garg et al., A phenome-wide association study identifies effects of copy-number variation of VNTRs and multicopy genes on multiple human traits. The American Journal of Human Genetics 109, 1065-1076 (2022).
38. T. Ge et al., Development and validation of a trans-ancestry polygenic risk score for type 2 diabetes in diverse populations. Genome medicine 14, 70 (2022).
39. D. M. Gonzalez et al., Dissecting mechanisms of chamber-specific cardiac differentiation and its perturbation following retinoic acid exposure. Development 149 (2022).
40. E. E. Gonzalez-Kozlova, Molecular Profiling of Liquid Biopsies for Precision Oncology. Adv Exp Med Biol 1361, 235-247 (2022).
41. P. J. Halfmann et al., SARS-CoV-2 Omicron virus causes attenuated disease in mice and hamsters. Nature 603, 687-692 (2022).
42. S. C. Hanks et al., Extent to which array genotyping and imputation with large reference panels approximate deep whole-genome sequencing. American journal of human genetics 109, 1653-1666 (2022).
43. K. Y. He et al., Rare coding variants in RCN3 are associated with blood pressure. BMC genomics 23, 148 (2022).
44. M. M. Hernandez et al., RT-PCR/MALDI-TOF Diagnostic Target Performance Reflects Circulating SARS-CoV-2 Variant Diversity in New York City. J Mol Diagn 24, 738-749 (2022).
45. M. M. Hernandez et al., Robust clinical detection of SARS-CoV-2 variants by RT-PCR/MALDI-TOF multitarget approach. Journal of Medical Virology 94, 1606-1616 (2022).
46. M. M. Hernandez et al., A robust, highly multiplexed mass spectrometry assay to identify SARS-CoV-2 variants. medRxiv 10.1101/2022.05.28.22275691 (2022).
47. H. M. Highland et al., Predicted gene expression in ancestrally diverse populations leads to discovery of susceptibility loci for lifestyle and cardiometabolic traits. American journal of human genetics 109, 669-679 (2022).
48. G. Hindy et al., Rare coding variants in 35 genes associate with circulating lipid levels—A multi-ancestry analysis of 170,000 exomes. The American Journal of Human Genetics 109, 81-96 (2022).
49. G. E. Hoffman et al., Sex Differences in the Human Brain Transcriptome of Cases With Schizophrenia. Biological psychiatry 91, 92-101 (2022).
50. C. Hsuan, A. Zebrowski, M. P. Lin, D. G. Buckler, B. G. Carr, Emergency departments in the United States treating high proportions of patients with ambulatory care sensitive conditions: a retrospective cross-sectional analysis. BMC Health Services Research 22, 854 (2022).
51. L. Huang et al., TOP-LD: A tool to explore linkage disequilibrium with TOPMed whole-genome sequence data. American journal of human genetics 109, 1175-1181 (2022).
52. T. Jaquenoud, S. Keene, N. Shlayan, A. Federman, G. Pandey, An Effective Automated Algorithm to Isolate Patient Speech from Conversations with Clinicians. medRxiv 10.1101/2022.11.29.22282914, 2022.2011.2029.22282914 (2022).
53. S. F. Kazim et al., Chronic Intermittent Hypoxia Enhances Pathological Tau Seeding, Propagation, and Accumulation and Exacerbates Alzheimer-like Memory and Synaptic Plasticity Deficits and Molecular Signatures. Biological psychiatry 91, 346-358 (2022).
54. T. Kehrer et al., Impact of SARS-CoV-2 ORF6 and its variant polymorphisms on host responses and viral pathogenesis. bioRxiv 10.1101/2022.10.18.512708 (2022).
55. T. N. Kelly et al., Insights From a Large-Scale Whole-Genome Sequencing Study of Systolic Blood Pressure, Diastolic Blood Pressure, and Hypertension. Hypertension 79, 1656-1667 (2022).
56. A. Khan et al., Genome-wide polygenic score to predict chronic kidney disease across ancestries. Nature Medicine 28, 1412-1420 (2022).
57. E. Kirkpatrick Roubidoux et al., Novel Epitopes of the Influenza Virus N1 Neuraminidase Targeted by Human Monoclonal Antibodies. Journal of virology 96, e0033222-e0033222 (2022).
58. R. J. Klein et al., Prostate cancer polygenic risk score and prediction of lethal prostate cancer. NPJ Precis Oncol 6, 25-25 (2022).
59. Y. Kong et al., Critical assessment of DNA adenine methylation in eukaryotes using quantitative deconvolution. Science 375, 515-522 (2022).
60. N. Konstantinides et al., A complete temporal transcription factor series in the fly visual system. Nature 604, 316-322 (2022).
61. K. R. Kulkarni et al., An interpretable and predictive connectivity-based neural signature for chronic cannabis use. Biological Psychiatry: Cognitive Neuroscience and Neuroimaging https://doi.org/10.1016/j.bpsc.2022.04.009 (2022).
62. S. Lehrer, P. H. Rheinstein, Druggable genetic targets in endometrial cancer✰,✰✰. Cancer Treatment and Research Communications 30, 100502 (2022).
63. S. Lehrer, P. H. Rheinstein, Circulating Chlamydia Trachomatis Antigens in Subjects With Alzheimer’s Disease. In Vivo 36, 2650-2653 (2022).
64. S. Lehrer, P. H. Rheinstein, Vaccination Reduces Risk of Alzheimer’s Disease, Parkinson’s Disease and Other Neurodegenerative Disorders. Discov Med 34, 97-101 (2022).
65. S. Lehrer, P. H. Rheinstein, α-synuclein enfolds tyrosine hydroxylase and dopamine ß-hydroxylase, potentially reducing dopamine and norepinephrine synthesis. J Proteins Proteom 13, 109-115 (2022).
66. S. Lehrer, P. H. Rheinstein, Breast cancer and body weight changes of young women in the UK Biobank cohort. Cancer 128, 3573 (2022).
67. S. Lehrer, P. H. Rheinstein, Association of cannabis with chronic obstructive pulmonary disease and COVID-19 infection. Chronic Dis Transl Med 8, 238-241 (2022).
68. S. Lehrer, P. H. Rheinstein, Genome-wide association study of dermatophytosis in the UK Biobank cohort. J Eur Acad Dermatol Venereol 36, 2482-2487 (2022).
69. S. Lehrer, P. H. Rheinstein, EARS2 significantly coexpresses with PALB2 in breast and pancreatic cancer. Cancer Treat Res Commun 32, 100595 (2022).
70. S. Lehrer, P. H. Rheinstein, Cannabis smoking and age-related macular degeneration in the UK Biobank cohort. J Fr Ophtalmol 45, 756-761 (2022).
71. S. Lehrer, P. H. Rheinstein, The Association Between Selenium, Selenoprotein P (SEPP1), Fluid Intelligence, and Exercise in the UK Biobank Cohort. Cureus 14, e25353 (2022).
72. S. Lehrer, P. H. Rheinstein, RE: Nitrogen-Based Bisphosphonate Use and Ovarian Cancer Risk in Women Aged 50 Years and Older. J Natl Cancer Inst 114, 1425-1426 (2022).
73. S. Lehrer, P. H. Rheinstein, Neither tamoxifen nor aromatase inhibitors increase the risk of Parkinson disease in the UK Biobank cohort. Cancer 128, 2997-2998 (2022).
74. S. Lehrer, P. H. Rheinstein, Cannabis, Intraocular Pressure, and the Growth Arrest-Specific 7 (GAS7) Gene: A Retrospective Analysis. Cureus 14, e23919 (2022).
75. S. Lehrer, P. H. Rheinstein, Marijuana and Myocardial Infarction in the UK Biobank Cohort. Cureus 14, e22054 (2022).
76. S. Lehrer, P. H. Rheinstein, Constipation and Cigarette Smoking Are Independent Influences for Parkinson’s Disease. Cureus 14, e21689 (2022).
77. S. Lehrer, P. H. Rheinstein, Marijuana smoking and cataract. J Fr Ophtalmol 45, 267-271 (2022).
78. S. Lehrer, P. H. Rheinstein, Cannabis smoking and glaucoma in the UK Biobank cohort. J Fr Ophtalmol 45, 423-429 (2022).
79. S. Lehrer, P. H. Rheinstein, J. Schmeidler, A Component or Multiple Components of Bleeding Gums May Ameliorate Both Glaucoma and Alzheimer’s Disease. Cureus 14, e21004-e21004 (2022).
80. S. Li et al., Inpatient Administration of Alpha-1-Adrenergic Receptor Blocking Agents Reduces Mortality in Male COVID-19 Patients. Front Med (Lausanne) 9, 849222-849222 (2022).
81. Y.-C. Li, L. Wang, J. Law, T. M. Murali, G. Pandey, Integrating multimodal data through interpretable heterogeneous ensembles. bioRxiv 10.1101/2020.05.29.123497, 2020.2005.2029.123497 (2022).
82. D. Liu et al., Rare schizophrenia risk variant burden is conserved in diverse human populations. medRxiv 10.1101/2022.01.03.22268662, 2022.2001.2003.22268662 (2022).
83. R. A. Lizewski et al., SARS-CoV-2 Outbreak Dynamics in an Isolated US Military Recruit Training Center With Rigorous Prevention Measures. Epidemiology 33, 797-807 (2022).
84. T. J. Loftus et al., Artificial intelligence-enabled decision support in nephrology. Nature Reviews Nephrology 10.1038/s41581-022-00562-3 (2022).
85. R. W. Logan et al., Sex Differences in Molecular Rhythms in the Human Cortex. Biological psychiatry 91, 152-162 (2022).
86. S. I. Machlovi et al., APOE4 confers transcriptomic and functional alterations to primary mouse microglia. Neurobiology of Disease 164, 105615 (2022).
87. P. C. Mack et al., Longitudinal COVID-19-vaccination-induced antibody responses and Omicron neutralization in patients with lung cancer. Cancer Cell 10.1016/j.ccell.2022.04.012, S1535-6108(1522)00174-X (2022).
88. H. E. Maier et al., Protection Associated with Previous SARS-CoV-2 Infection in Nicaragua. N Engl J Med 387, 568-570 (2022).
89. G. A. Marx et al., Artificial intelligence-derived neurofibrillary tangle burden is associated with antemortem cognitive impairment. Acta Neuropathologica Communications 10, 157 (2022).
90. A. T. McKenzie et al., Interpretable deep learning of myelin histopathology in age-related cognitive impairment. bioRxiv 10.1101/2022.06.06.495016, 2022.2006.2006.495016 (2022).
91. S. Menez et al., Prognostic Significance of Urinary Biomarkers in Patients Hospitalized With COVID-19. Am J Kidney Dis 79, 257-267.e251 (2022).
92. G. Mestrallet, K. Sone, N. Bhardwaj, Strategies to overcome DC dysregulation in the tumor microenvironment. Front Immunol 13, 980709 (2022).
93. K. Mukherjee, J. J. Bieker, EKLF/Klf1 regulates erythroid transcription by its pioneering activity and selective control of RNA Pol II pause-release. Cell Rep 41, 111830 (2022).
94. S. Mukherjee et al., Germline Pathogenic Variants Impact Clinicopathology of Advanced Lung Cancer. Cancer Epidemiology, Biomarkers & Prevention 10.1158/1055-9965.Epi-21-1287, OF1-OF10 (2022).
95. N. Mullins et al., Dissecting the Shared Genetic Architecture of Suicide Attempt, Psychiatric Disorders, and Known Risk Factors. Biological psychiatry 91, 313-327 (2022).
96. T. Nakao et al., Mendelian randomization supports bidirectional causality between telomere length and clonal hematopoiesis of indeterminate potential. Sci Adv 8, eabl6579 (2022).
97. N. B. Olivero et al., Phylogenetic analysis and comparative genomics of SARS-CoV-2 from survivor and non-survivor COVID-19 patients in Cordoba, Argentina. BMC genomics 23, 510 (2022).
98. S. N. Olsen et al., MLL::AF9 degradation induces rapid changes in transcriptional elongation and subsequent loss of an active chromatin landscape. Molecular Cell 82, 1140-1155.e1111 (2022).
99. A. Ozonoff et al., Phenotypes of disease severity in a cohort of hospitalized COVID-19 patients: Results from the IMPACC study. EBioMedicine 83, 104208 (2022).
100. B. Pai et al., High-resolution transcriptomics informs glial pathology in human temporal lobe epilepsy. Acta Neuropathologica Communications 10, 149 (2022).
101. A. L. Pan et al., Dual-Specificity Protein Phosphatase 4 (DUSP4) Overexpression Improves Learning Behavior Selectively in Female 5xFAD Mice, and Reduces β-Amyloid Load in Males and Females. Cells 11 (2022).
102. R. Patel et al., Impact of body mass index on the efficacy of aromatase inhibitors in patients with metastatic breast cancer. Breast Cancer Research and Treatment 192, 313-319 (2022).
103. G. A. Pathak et al., A first update on mapping the human genetic architecture of COVID-19. Nature 608, E1-E10 (2022).
104. B. O. Petrazzini et al., Coronary Risk Estimation Based on Clinical Data in Electronic Health Records. Journal of the American College of Cardiology 79, 1155-1166 (2022).
105. J. D. Ramírez et al., Hotspots for SARS-CoV-2 Omicron variant spread: Lessons from New York City. Journal of medical virology 94, 2911-2914 (2022).
106. S. I. Ramos et al., An atlas of late prenatal human neurodevelopment resolved by single-nucleus transcriptomics. Nature Communications 13, 7671 (2022).
107. E. Reategui Schwarz et al., Everybody nose: molecular and clinical characteristics of nasal colonization during active methicillin-resistant Staphylococcus aureus bloodstream infection. BMC Infect Dis 22, 400-400 (2022).
108. D. Reyes-Dumeyer et al., The National Institute on Aging Late-Onset Alzheimer’s Disease Family Based Study: A resource for genetic discovery. Alzheimer’s & Dementia n/a (2022).
109. A. C. Ricardo et al., Hispanic ethnicity and mortality among critically ill patients with COVID-19. PloS one 17, e0268022-e0268022 (2022).
110. F. Richter et al., Neonatal outcomes during the COVID-19 pandemic in New York City. Pediatric research 91, 477-479 (2022).
111. L. Salas-Estrada, B. Fiorillo, M. Filizola, Metadynamics simulations leveraged by statistical analyses and artificial intelligence-based tools to inform the discovery of G protein-coupled receptor ligands. Front Endocrinol (Lausanne) 13, 1099715 (2022).
112. N. Sauerwald et al., Pre-infection antiviral innate immunity contributes to sex differences in SARS-CoV-2 infection. Cell Syst 13, 924-931.e924 (2022).
113. D. A. Schoenfeld et al., Loss of PBRM1 Alters Promoter Histone Modifications and Activates ALDH1A1 to Drive Renal Cell Carcinoma. Molecular Cancer Research 10.1158/1541-7786.Mcr-21-1039, OF1-OF15 (2022).
114. C. Seah et al., Modeling gene × environment interactions in PTSD using human neurons reveals diagnosis-specific glucocorticoid-induced gene expression. Nature Neuroscience 25, 1434-1445 (2022).
115. S. Sen et al., Structure-Based Discovery of a Novel Class of Small-Molecule Pure Antagonists of Integrin αVβ3. Journal of Chemical Information and Modeling 62, 5607-5621 (2022).
116. S. C. Shah et al., Breastfeeding Is Associated with Lower Likelihood of Helicobacter Pylori Colonization in Babies, Based on a Prospective USA Maternal-Infant Cohort. Dig Dis Sci 67, 5149-5157 (2022).
117. S. P. Smith et al., Enrichment analyses identify shared associations for 25 quantitative traits in over 600,000 individuals from seven diverse ancestries. The American Journal of Human Genetics 109, 871-884 (2022).
118. X. Song et al., MiXcan: a Framework for Cell-Type-Specific Transcriptome-Wide Association Studies with an Application to Breast Cancer. bioRxiv 10.1101/2022.03.15.484509, 2022.2003.2015.484509 (2022).
119. X. Song et al., SNPs at SMG7 Associated with Time from Biochemical Recurrence to Prostate Cancer Death. Cancer Epidemiology, Biomarkers & Prevention 10.1158/1055-9965.EPI-22-0053, OF1-OF7 (2022).
120. D. Stadlbauer et al., Antibodies targeting the neuraminidase active site inhibit influenza H3N2 viruses with an S245N glycosylation site. Nature Communications 13, 7864 (2022).
121. S. A. Suckiel et al., Perspectives of diverse Spanish- and English-speaking patients on the clinical use of polygenic risk scores. Genetics in Medicine 24, 1217-1226 (2022).
122. D. Sun et al., MacroH2A impedes metastatic growth by enforcing a discrete dormancy program in disseminated cancer cells. Sci Adv 8, eabo0876 (2022).
123. Z. Sun et al., Blood Transcriptomes of SARS-CoV-2-Infected Kidney Transplant Recipients Associated with Immune Insufficiency Proportionate to Severity. J Am Soc Nephrol 33, 2108-2122 (2022).
124. E. Takashita et al., Efficacy of Antibodies and Antiviral Drugs against Omicron BA.2.12.1, BA.4, and BA.5 Subvariants. N Engl J Med 387, 468-470 (2022).
125. J. Tan et al., Murine Broadly Reactive Antineuraminidase Monoclonal Antibodies Protect Mice from Recent Influenza B Virus Isolates and Partially Inhibit Virus Transmission in the Guinea Pig Model. mSphere 7, e0092721 (2022).
126. J. Tan et al., Human Anti-neuraminidase Antibodies Reduce Airborne Transmission of Clinical Influenza Virus Isolates in the Guinea Pig Model. Journal of Virology 96, e01421-01421 (2022).
127. G. B. Tantillo et al., Electroencephalography at the height of a pandemic: EEG findings in patients with COVID-19. Clin Neurophysiol 137, 102-112 (2022).
128. V. van der Heide et al., Limited extent and consequences of pancreatic SARS-CoV-2 infection. Cell reports 38, 110508-110508 (2022).
129. D. M. Walker et al., Sex-Specific Transcriptional Changes in Response to Adolescent Social Stress in the Brain’s Reward Circuitry. Biological psychiatry 91, 118-128 (2022).
130. C. Wang et al., Sex disparities in influenza: A multiscale network analysis. iScience 25, 104192 (2022).
131. M. Wang et al., Guidelines for bioinformatics of single-cell sequencing data analysis in Alzheimer’s disease: review, recommendation, implementation and application. Molecular Neurodegeneration 17, 17 (2022).
132. P. Wang et al., Disrupting the DREAM complex enables proliferation of adult human pancreatic β cells. The Journal of Clinical Investigation 132 (2022).
133. T. Wang et al., The Human Pangenome Project: a global resource to map genomic diversity. Nature 604, 437-446 (2022).
134. X. Wang et al., IL-17 Pathway Members as Potential Biomarkers of Effective Systemic Treatment and Cardiovascular Disease in Patients with Moderate-to-Severe Psoriasis. International journal of molecular sciences 23, 555 (2022).
135. N. M. Wickramasinghe et al., PPARdelta activation induces metabolic and contractile maturation of human pluripotent stem cell-derived cardiomyocytes. Cell stem cell 29, 559-576.e557 (2022).
136. A. P. Wingo et al., Brain microRNAs are associated with variation in cognitive trajectory in advanced age. Transl Psychiatry 12, 47 (2022).
137. T. S. Wingo et al., Integrating human brain proteomes with genome-wide association data implicates novel proteins in post-traumatic stress disorder. Molecular psychiatry 27, 3075-3084 (2022).
138. P. Xu et al., The landscape of human tissue and cell type specific expression and co-regulation of senescence genes. Molecular neurodegeneration 17, 5-5 (2022).
139. Z. Yi et al., Deep learning identified pathological abnormalities predictive of graft loss in kidney transplant biopsies. Kidney International 101, 288-298 (2022).
140. B. Zeng et al., Multi-ancestry eQTL meta-analysis of human brain identifies candidate causal variants for brain-related traits. Nature Genetics 10.1038/s41588-021-00987-9 (2022).
141. L. Zhang et al., Multiscale study of the oral and gut environments in children with high- and low-threshold peanut allergy. Journal of Allergy and Clinical Immunology 10.1016/j.jaci.2022.04.026 (2022).
142. A. B. Zheutlin et al., Improving postpartum hemorrhage risk prediction using longitudinal electronic medical records. Journal of the American Medical Informatics Association : JAMIA 29, 296-305 (2022).
143. R. W. Zhou et al., A local tumor microenvironment acquired super-enhancer induces an oncogenic driver in colorectal carcinoma. Nat Commun 13, 6041 (2022).

2021

1. 1. Zhou Y, Ramsey S, Provasi D, El Daibani A, Appourchaux K, et al. 2021. Predicted Mode of Binding to and Allosteric Modulation of the μ-Opioid Receptor by Kratom’s Alkaloids with Reported Antinociception In Vivo. Biochemistry 60:1420-9
 2. Zhao B, Li T, Yang Y, Wang X, Luo T, et al. 2021. Common genetic variation influencing human white matter microstructure. Science 372:eabf3736
 3. Zhang Z, Sun Z, Fu J, Lin Q, Banu K, et al. 2021. Recipient APOL1 risk alleles associate with death-censored renal allograft survival and rejection episodes. The Journal of Clinical Investigation 131
 4. Zhang J, Jun T, Frank J, Nirenberg S, Kovatch P, Huang K-l. 2021. Prediction of individual COVID-19 diagnosis using baseline demographics and lab data. Scientific Reports 11:13913
 5. Zeng B, Bendl J, Kosoy R, Fullard JF, Hoffman GE, Roussos P. 2021. Trans-ethnic eQTL meta-analysis of human brain reveals regulatory architecture and candidate causal variants for brain-related traits. medRxiv:2021.01.25.21250099
 6. Zazhytska M, Kodra A, Hoagland DA, Fullard JF, Shayya H, et al. 2021. Disruption of nuclear architecture as a cause of COVID-19 induced anosmia. bioRxiv:2021.02.09.430314
 7. Yoo S, Shi Z, Wen B, Kho S, Pan R, et al. 2021. A community effort to identify and correct mislabeled samples in proteogenomic studies. Patterns 2:100245
 8. Yi Z, Salem F, Menon MC, Keung K, Xi C, et al. 2021. Deep learning identifies pathological abnormalities predictive of graft loss in kidney transplant biopsies. bioRxiv:2021.04.18.440166
 9. Xue D, Bush WS, Renton AE, Marcora EA, Bis JC, et al. 2021. Large-scale sequencing studies expand the known genetic architecture of Alzheimer’s disease. Alzheimers Dement (Amst) 13:e12255-e
 10. Xu J, Yu X, Martin TC, Bansal A, Cheung K, et al. 2021. AKT Degradation Selectively Inhibits the Growth of PI3K/PTEN Pathway–Mutant Cancers with Wild-Type KRAS and BRAF by Destabilizing Aurora Kinase B. Cancer Discovery 11:3064-89
 11. Wu HM, Goate AM, O’Reilly PF. 2021. Heterogeneous effects of genetic risk for Alzheimer’s disease on the phenome. Transl Psychiatry 11:406-
 12. Wenger BM, Patel N, Lui M, Moscati A, Do R, et al. 2021. A genotype-first approach to exploring Mendelian cardiovascular traits with clear external manifestations. Genetics in medicine : official journal of the American College of Medical Genetics 23:94-102
 13. Webb BD, Hotchkiss H, Prasun P, Gelb BD, Satlin L. 2021. Biallelic loss-of-function variants in KCNJ16 presenting with hypokalemic metabolic acidosis. European Journal of Human Genetics
 14. Watnick D, Odgis JA, Suckiel SA, Gallagher KM, Teitelman N, et al. 2021. “Is that something that should concern me?”: a qualitative exploration of parent understanding of their child’s genomic test results. Human Genetics and Genomics Advances 2:100027
 15. Wanyan T, Honarvar H, Jaladanki SK, Zang C, Naik N, et al. 2021. Contrastive learning improves critical event prediction in COVID-19 patients. Patterns (N Y) 2:100389-
 16. Wang Z, Fan X, Shen Y, Pagadala MS, Signer R, et al. 2021. Non-cancer-related pathogenic germline variants and expression consequences in ten-thousand cancer genomes. Genome Medicine 13:147
 17. Wang Q, Zhang B, Yue Z. 2021. Disentangling the Molecular Pathways of Parkinson’s Disease using Multiscale Network Modeling. Trends in Neurosciences 44:182-8
 18. Wang M, Li A, Sekiya M, Beckmann ND, Quan X, et al. 2021. Transformative Network Modeling of Multi-omics Data Reveals Detailed Circuits, Key Regulators, and Potential Therapeutics for Alzheimer’s Disease. Neuron 109:257-72.e14
 19. Wang L-B, Karpova A, Gritsenko MA, Kyle JE, Cao S, et al. 2021. Proteogenomic and metabolomic characterization of human glioblastoma. Cancer Cell 39:509-28.e20
 20. Wang B, Glicksberg BS, Nadkarni GN, Vashishth D. 2021. Evaluation and management of COVID-19-related severity in people with type 2 diabetes. BMJ Open Diabetes Res Care 9:e002299
 21. Waller RG, Klein RJ, Vijai J, McKay JD, Clay-Gilmour A, et al. 2021. Sequencing at lymphoid neoplasm susceptibility loci maps six myeloma risk genes. Hum Mol Genet 30:1142-53
 22. Walker DM, Zhou X, Cunningham AM, Lipschultz AP, Ramakrishnan A, et al. 2021. Sex-Specific Transcriptional Changes in Response to Adolescent Social Stress in the Brain’s Reward Circuitry. Biological Psychiatry
 23. Wahane S, Zhou X, Zhou X, Guo L, Friedl M-S, et al. 2021. Diversified transcriptional responses of myeloid and glial cells in spinal cord injury shaped by HDAC3 activity. Sci Adv 7:eabd8811
 24. von Felden J, Garcia-Lezana T, Dogra N, Gonzalez-Kozlova E, Ahsen ME, et al. 2021. Unannotated small RNA clusters associated with circulating extracellular vesicles detect early stage liver cancer. Gut:gutjnl-2021-325036
 25. von Felden J, Craig AJ, Garcia-Lezana T, Labgaa I, Haber PK, et al. 2021. Mutations in circulating tumor DNA predict primary resistance to systemic therapies in advanced hepatocellular carcinoma. Oncogene 40:140-51
 26. Voloudakis G, Hoffman G, Venkatesh S, Lee KM, Dobrindt K, et al. 2021. IL10RB as a key regulator of COVID-19 host susceptibility and severity. medRxiv:2021.05.31.21254851
 27. Vialle RA, de Paiva Lopes K, Bennett DA, Crary JF, Raj T. 2021. The impact of genomic structural variation on the transcriptome, chromatin, and proteome in the human brain. medRxiv:2021.02.25.21252245
 28. Verbitsky M, Krithivasan P, Batourina E, Khan A, Graham SE, et al. 2021. Copy Number Variant Analysis and Genome-wide Association Study Identify Loci with Large Effect for Vesicoureteral Reflux. Journal of the American Society of Nephrology 32:805-20
 29. Vangeepuram N, Liu B, Chiu P-h, Wang L, Pandey G. 2021. Predicting youth diabetes risk using NHANES data and machine learning. Scientific Reports 11:11212
 30. Van Oekelen O, Gleason CR, Agte S, Srivastava K, Beach KF, et al. 2021. Highly variable SARS-CoV-2 spike antibody responses to two doses of COVID-19 RNA vaccination in patients with multiple myeloma. Cancer Cell 39:1028-30
 31. Van Oekelen O, Aleman A, Upadhyaya B, Schnakenberg S, Madduri D, et al. 2021. Neurocognitive and hypokinetic movement disorder with features of parkinsonism after BCMA-targeting CAR-T cell therapy. Nature Medicine 27:2099-103
 32. Vaid A, Johnson KW, Badgeley MA, Somani SS, Bicak M, et al. 2021. Using Deep-Learning Algorithms to Simultaneously Identify Right and Left Ventricular Dysfunction From the Electrocardiogram. JACC: Cardiovascular Imaging
 33. Vaid A, Jaladanki SK, Xu J, Teng S, Kumar A, et al. 2021. Federated Learning of Electronic Health Records to Improve Mortality Prediction in Hospitalized Patients With COVID-19: Machine Learning Approach. JMIR Med Inform 9:e24207-e
 34. Vaid A, Chan L, Chaudhary K, Jaladanki SK, Paranjpe I, et al. 2021. Predictive Approaches for Acute Dialysis Requirement and Death in COVID-19. Clinical Journal of the American Society of Nephrology 16:1158-68
 35. Tuminello S, Petralia F, Veluswamy R, Wang P, Flores R, Taioli E. 2021. Prognostic Value of the Tumor Immune Microenvironment for Early-stage, Non−Small Cell Lung Cancer. American Journal of Clinical Oncology 44:350-5
 36. Tourancheau A, Mead EA, Zhang X-S, Fang G. 2021. Discovering multiple types of DNA methylation from bacteria and microbiome using nanopore sequencing. Nat Methods 18:491-8
 37. Torrens L, Montironi C, Puigvehí M, Mesropian A, Leslie J, et al. 2021. Immunomodulatory Effects of Lenvatinib Plus Anti–Programmed Cell Death Protein 1 in Mice and Rationale for Patient Enrichment in Hepatocellular Carcinoma. Hepatology 74:2652-69
 38. Tomlinson JE, Wolfisberg R, Fahnøe U, Patel RS, Trivedi S, et al. 2021. Pathogenesis, MicroRNA-122 Gene-Regulation, and Protective Immune Responses After Acute Equine Hepacivirus Infection. Hepatology 74:1148-63
 39. Thompson RC, Simons NW, Wilkins L, Cheng E, Del Valle DM, et al. 2021. Acute COVID-19 gene-expression profiles show multiple etiologies of long-term sequelae. medRxiv:2021.10.04.21264434
 40. Thibado JK, Tano J-Y, Lee J, Salas-Estrada L, Provasi D, et al. 2021. Differences in interactions between transmembrane domains tune the activation of metabotropic glutamate receptors. Elife 10:e67027
 41. Tang L, Levy T, Guillory S, Halpern D, Zweifach J, et al. 2021. Prospective and detailed behavioral phenotyping in DDX3X syndrome. Molecular Autism 12:36
 42. Tan J, O’Dell G, Hernandez Matthew M, Sordillo Emilia M, Kahn Z, et al. 2021. Human anti-neuraminidase antibodies reduce airborne transmission of clinical influenza virus isolates in the guinea pig model. Journal of Virology 0:JVI.01421-21
 43. Sun X, Wang Q, Blennow K, Zetterberg H, McCarthy M, et al. 2021. Association of neurogranin gene expression with Alzheimer’s disease pathology in the perirhinal cortex. Alzheimers Dement (N Y) 7:e12162-e
 44. Sulaiman I, Chung M, Angel L, Tsay J-CJ, Wu BG, et al. 2021. Microbial signatures in the lower airways of mechanically ventilated COVID-19 patients associated with poor clinical outcome. Nature Microbiology 6:1245-58
 45. Suckiel SA, Odgis JA, Gallagher KM, Rodriguez JE, Watnick D, et al. 2021. GUÍA: a digital platform to facilitate result disclosure in genetic counseling. Genetics in Medicine 23:942-9
 46. Suárez-Fariñas M, Tokuyama M, Wei G, Huang R, Livanos A, et al. 2021. Intestinal Inflammation Modulates the Expression of ACE2 and TMPRSS2 and Potentially Overlaps With the Pathogenesis of SARS-CoV-2-related Disease. Gastroenterology 160:287-301.e20
 47. Strom N, Yu D, Gerring Z, Halvorsen M, Abdellaoui A, et al. 2021. Genome-wide association study identifies new locus associated with OCD.
 48. Stadlbauer D, Tan J, Jiang K, Hernandez MM, Fabre S, et al. 2021. Repeated cross-sectional sero-monitoring of SARS-CoV-2 in New York City. Nature 590:146-50
 49. Soper ER, Suckiel SA, Braganza GT, Kontorovich AR, Kenny EE, Abul-Husn NS. 2021. Genomic Screening Identifies Individuals at High Risk for Hereditary Transthyretin Amyloidosis. J Pers Med 11:49
 50. Song X, Ji J, Reva B, Joshi H, Calinawan AP, et al. 2021. Post-anticoagulant D-dimer is a highly prognostic biomarker of COVID-19 mortality. ERJ Open Res 7:00018-2021
 51. Song W-M, Agrawal P, Von Itter R, Fontanals-Cirera B, Wang M, et al. 2021. Network models of primary melanoma microenvironments identify key melanoma regulators underlying prognosis. Nature Communications 12:1214
 52. Soffer S, Glicksberg BS, Zimlichman E, Efros O, Levin MA, et al. 2021. The association between obesity and peak antibody titer response in COVID-19 infection. Obesity 29:1547-53
 53. Smith RHB, Khan ZM, Ung PM-U, Scopton AP, Silber L, et al. 2021. Type II Binders Targeting the “GLR-Out” Conformation of the Pseudokinase STRADα. Biochemistry 60:289-302
 54. Smith RG, Pishva E, Shireby G, Smith AR, Roubroeks JAY, et al. 2021. A meta-analysis of epigenome-wide association studies in Alzheimer’s disease highlights novel differentially methylated loci across cortex. Nature Communications 12:3517
 55. Silvas Jesus A, Vasquez Desarey M, Park J-G, Chiem K, Allué-Guardia A, et al. 2021. Contribution of SARS-CoV-2 Accessory Proteins to Viral Pathogenicity in K18 Human ACE2 Transgenic Mice. Journal of Virology 95:e00402-21
 56. Sieberts SK, Borzymowski H, Guan Y, Huang Y, Matzner A, et al. 2021. Developing better digital health measures of Parkinson’s disease using free living data and a crowdsourced data analysis challenge. medRxiv:2021.10.20.21265298
 57. Shuster A, O’Brien M, Luo Y, Berner LA, Perl O, et al. 2021. Emotional adaptation during a crisis: decline in anxiety and depression after the initial weeks of COVID-19 in the United States. Transl Psychiatry 11:435-
 58. Shemirani R, Wenric S, Kenny E, Ambite JL. 2021. EPS: automated feature selection in case–control studies using extreme pseudo-sampling. Bioinformatics 37:3372-3
 59. Shemirani R, Belbin GM, Avery CL, Kenny EE, Gignoux CR, Ambite JL. 2021. Rapid detection of identity-by-descent tracts for mega-scale datasets. Nature communications 12:3546-
 60. Selvan ME, Onel K, Gnjatic S, Klein RJ, Gümüş ZH. 2021. Germline rare deleterious variant load alters cancer risk, age of onset and tumor characteristics. medRxiv:2021.07.02.21259537
 61. Sealock JM, Lee YH, Moscati A, Venkatesh S, Voloudakis G, et al. 2021. Use of the PsycheMERGE Network to Investigate the Association Between Depression Polygenic Scores and White Blood Cell Count. JAMA Psychiatry 78:1365-74
 62. Schrode N, Seah C, Deans PJM, Hoffman G, Brennand KJ. 2021. Analysis framework and experimental design for evaluating synergy-driving gene expression. Nature Protocols 16:812-40
 63. Sayed Faten A, Kodama L, Fan L, Carling Gillian K, Udeochu Joe C, et al. 2021. AD-linked R47H-TREM2 mutation induces disease-enhancing microglial states via AKT hyperactivation. Science Translational Medicine 13:eabe3947
 64. Saxena M, van der Burg SH, Melief CJM, Bhardwaj N. 2021. Therapeutic cancer vaccines. Nature Reviews Cancer 21:360-78
 65. Satpathy S, Krug K, Jean Beltran PM, Savage SR, Petralia F, et al. 2021. A proteogenomic portrait of lung squamous cell carcinoma. Cell 184:4348-71.e40
 66. Ryu E, Jenkins GD, Wang Y, Olfson M, Talati A, et al. 2021. The importance of social activity to risk of major depression in older adults. Psychological Medicine:1-9
 67. Ruf-Zamojski F, Zhang Z, Zamojski M, Smith GR, Mendelev N, et al. 2021. Single nucleus multi-omics regulatory landscape of the murine pituitary. Nature Communications 12:2677
 68. Roubidoux EK, Carreño JM, McMahon M, Jiang K, van Bakel H, et al. 2021. Mutations in the Hemagglutinin Stalk Domain Do Not Permit Escape from a Protective, Stalk-Based Vaccine-Induced Immune Response in the Mouse Model. mBio 12:e03617-20
 69. Rodriguez OL, Sharp AJ, Watson CT. 2021. Limitations of lymphoblastoid cell lines for establishing genetic reference datasets in the immunoglobulin loci. PLoS One 16:e0261374-e
 70. Richter F, Strasser AS, Suarez-Farinas M, Zhao S, Nadkarni GN, et al. 2021. Neonatal outcomes during the COVID-19 pandemic in New York City. Pediatric Research
 71. Rao X, Thapa KS, Chen AB, Lin H, Gao H, et al. 2021. Allele-specific expression and high-throughput reporter assay reveal functional genetic variants associated with alcohol use disorders. Molecular psychiatry 26:1142-51
 72. Ramírez JD, Florez C, Muñoz M, Hernández C, Castillo A, et al. 2021. The arrival and spread of SARS-CoV-2 in Colombia. Journal of medical virology 93:1158-63
 73. Qian T, Fujiwara N, Koneru B, Ono A, Kubota N, et al. 2021. Molecular signature predictive of long-term liver fibrosis progression to inform anti-fibrotic drug development. Gastroenterology
 74. Pryce KD, Kang HJ, Sakloth F, Liu Y, Khan S, et al. 2021. A promising chemical series of positive allosteric modulators of the μ-opioid receptor that enhance the antinociceptive efficacy of opioids but not their adverse effects. Neuropharmacology 195:108673
 75. Preman P, Tcw J, Calafate S, Snellinx A, Alfonso-Triguero M, et al. 2021. Human iPSC-derived astrocytes transplanted into the mouse brain undergo morphological changes in response to amyloid-β plaques. Molecular neurodegeneration 16:68-
 76. Pinyol R, Torrecilla S, Wang H, Montironi C, Piqué-Gili M, et al. 2021. Molecular characterisation of hepatocellular carcinoma in patients with non-alcoholic steatohepatitis. Journal of Hepatology 75:865-78
 77. Pimenova AA, Herbinet M, Gupta I, Machlovi SI, Bowles KR, et al. 2021. Alzheimer’s-associated PU.1 expression levels regulate microglial inflammatory response. Neurobiology of disease 148:105217-
 78. Peng S, Zeng L, Haure-Mirande J-V, Wang M, Huffman DM, et al. 2021. Transcriptomic Changes Highly Similar to Alzheimer’s Disease Are Observed in a Subpopulation of Individuals During Normal Brain Aging. Front Aging Neurosci 13:711524-
 79. Pearson NM, Stolte C, Shi K, Beren F, Abul-Husn NS, et al. 2021. GenomeDiver: a platform for phenotype-guided medical genomic diagnosis. Genetics in Medicine 23:1998-2002
 80. Patiño LH, Ballesteros N, Muñoz M, Castañeda S, Hernández C, et al. 2021. SARS-CoV-2 in Transit: Characterization of SARS-CoV-2 Genomes From Venezuelan Migrants in Colombia. International Journal of Infectious Diseases 110:410-6
 81. Patel RS, Tomlinson JE, Divers TJ, Van de Walle GR, Rosenberg BR. 2021. Single-cell resolution landscape of equine peripheral blood mononuclear cells reveals diverse cell types including T-bet(+) B cells. BMC Biol 19:13-
 82. Patel AS, Yoo S, Kong R, Sato T, Sinha A, et al. 2021. Prototypical oncogene family Myc defines unappreciated distinct lineage states of small cell lung cancer. Sci Adv 7:eabc2578
 83. Paranjpe I, Chaudhary K, Johnson KW, Jaladanki SK, Zhao S, et al. 2021. Association of SARS-CoV-2 viral load at admission with in-hospital acute kidney injury: A retrospective cohort study. PLoS One 16:e0247366-e
 84. Pappas K, Martin TC, Wolfe AL, Nguyen CB, Su T, et al. 2021. NOTCH and EZH2 collaborate to repress PTEN expression in breast cancer. Communications Biology 4:312
 85. Odgis JA, Gallagher KM, Suckiel SA, Donohue KE, Ramos MA, et al. 2021. The NYCKidSeq project: study protocol for a randomized controlled trial incorporating genomics into the clinical care of diverse New York City children. Trials 22:56
 86. Novikova G, Kapoor M, Tcw J, Abud EM, Efthymiou AG, et al. 2021. Integration of Alzheimer’s disease genetics and myeloid genomics identifies disease risk regulatory elements and genes. Nature communications 12:1610-
 87. Nomura Y, Rompala G, Pritchett L, Aushev V, Chen J, Hurd YL. 2021. Natural disaster stress during pregnancy is linked to reprogramming of the placenta transcriptome in relation to anxiety and stress hormones in young offspring. Molecular Psychiatry 26:6520-30
 88. Nilsson-Payant BE, Uhl S, Grimont A, Doane AS, Cohen P, et al. 2021. The NF-κB Transcriptional Footprint Is Essential for SARS-CoV-2 Replication. Journal of Virology 95:e01257-21
 89. Niemi MEK, Karjalainen J, Liao RG, Neale BM, Daly M, et al. 2021. Mapping the human genetic architecture of COVID-19. Nature 600:472-7
 90. Nešić D, Bush M, Spasic A, Li J, Kamata T, et al. 2021. Electron microscopy shows that binding of monoclonal antibody PT25-2 primes integrin αIIbβ3 for ligand binding. Blood Adv 5:1781-90
 91. Neira V, Brito B, Agüero B, Berrios F, Valdés V, et al. 2021. A household case evidences shorter shedding of SARS-CoV-2 in naturally infected cats compared to their human owners. Emerg Microbes Infect 10:376-83
 92. Neff RA, Wang M, Vatansever S, Guo L, Ming C, et al. 2021. Molecular subtyping of Alzheimer’s disease using RNA sequencing data reveals novel mechanisms and targets. Sci Adv 7:eabb5398
 93. Navarro E, Udine E, Lopes KdP, Parks M, Riboldi G, et al. 2021. Dysregulation of mitochondrial and proteolysosomal genes in Parkinson’s disease myeloid cells. Nature Aging 1:850-63
 94. Natarajan P, Pampana A, Graham SE, Ruotsalainen SE, Perry JA, et al. 2021. Chromosome Xq23 is associated with lower atherogenic lipid concentrations and favorable cardiometabolic indices. Nature communications 12:2182-
 95. Na S, Chung D, Hula A, Perl O, Jung J, et al. 2021. Humans use forward thinking to exploit social controllability. Elife 10:e64983
 96. Mullins N, Forstner AJ, O’Connell KS, Coombes B, Coleman JRI, et al. 2021. Genome-wide association study of more than 40,000 bipolar disorder cases provides new insights into the underlying biology. Nature Genetics 53:817-29
 97. Mukherjee K, Xue L, Planutis A, Gnanapragasam MN, Chess A, Bieker JJ. 2021. EKLF/KLF1 expression defines a unique macrophage subset during mouse erythropoiesis. Elife 10:e61070
 98. Mukherjee K, Bieker JJ. 2021. Transcriptional Control of Gene Expression and the Heterogeneous Cellular Identity of Erythroblastic Island Macrophages. Front Genet 12:756028-
 99. Moon CY, Schilder BM, Raj T, Huang K-L. 2021. Phenome-wide and expression quantitative trait locus associations of coronavirus disease 2019 genetic risk loci. iScience 24:102550-
 100. Modabbernia A, Reichenberg A, Ing A, Moser DA, Doucet GE, et al. 2021. Linked patterns of biological and environmental covariation with brain structure in adolescence: a population-based longitudinal study. Molecular Psychiatry 26:4905-18
 101. Modabbernia A, Janiri D, Doucet GE, Reichenberg A, Frangou S. 2021. Multivariate Patterns of Brain-Behavior-Environment Associations in the Adolescent Brain and Cognitive Development Study. Biological psychiatry 89:510-20
 102. Mishra R, Bethunaickan R, Berthier CC, Yi Z, Strohl JJ, et al. 2021. Reversible dysregulation of renal circadian rhythm in lupus nephritis. Molecular Medicine 27:99
 103. Ming C, Wang M, Wang Q, Neff R, Wang E, et al. 2021. Whole genome sequencing–based copy number variations reveal novel pathways and targets in Alzheimer’s disease. Alzheimer’s & Dementia n/a
 104. Mezei M. 2021. Foldability and chameleon propensity of fold-switching protein sequences. Proteins: Structure, Function, and Bioinformatics 89:3-5
 105. Meyers JL, Zhang J, Chorlian DB, Pandey AK, Kamarajan C, et al. 2021. A genome-wide association study of interhemispheric theta EEG coherence: implications for neural connectivity and alcohol use behavior. Molecular Psychiatry 26:5040-52
 106. Melms JC, Biermann J, Huang H, Wang Y, Nair A, et al. 2021. A molecular single-cell lung atlas of lethal COVID-19. Nature 595:114-9
 107. Meliambro K, Li X, Salem F, Yi Z, Sun Z, et al. 2021. Molecular Analysis of the Kidney From a Patient With COVID-19-Associated Collapsing Glomerulopathy. Kidney medicine 3:653-8
 108. McInerney TW, Fulton-Howard B, Patterson C, Paliwal D, Jermiin LS, et al. 2021. A globally diverse reference alignment and panel for imputation of mitochondrial DNA variants. BMC Bioinformatics 22:417-
 109. Mahjani B, Klei L, Mattheisen M, Halvorsen MW, Reichenberg A, et al. 2021. The Genetic Architecture of Obsessive-Compulsive Disorder: Contribution of Liability to OCD From Alleles Across the Frequency Spectrum. American Journal of Psychiatry:appi.ajp.2021.21010101
 110. Mahjani B, De Rubeis S, Gustavsson Mahjani C, Mulhern M, Xu X, et al. 2021. Prevalence and phenotypic impact of rare potentially damaging variants in autism spectrum disorder. Molecular Autism 12:65
 111. Mahadevan NR, Knelson EH, Wolff JO, Vajdi A, Saigí M, et al. 2021. Intrinsic Immunogenicity of Small Cell Lung Carcinoma Revealed by Its Cellular Plasticity. Cancer Discovery 11:1952-69
 112. Lyons CE, Zhou X, Razzoli M, Chen M, Xia W, et al. 2021. Lifelong chronic psychosocial stress induces a proteomic signature of Alzheimer’s disease in wildtype mice. European Journal of Neuroscience n/a
 113. Livanos AE, Jha D, Cossarini F, Gonzalez-Reiche AS, Tokuyama M, et al. 2021. Intestinal Host Response to SARS-CoV-2 Infection and COVID-19 Outcomes in Patients With Gastrointestinal Symptoms. Gastroenterology 160:2435-50.e34
 114. Liu X, Verma A, Garcia G, Ramage H, Myers RL, et al. 2021. Targeting the Coronavirus Nucleocapsid Protein through GSK-3 Inhibition. medRxiv:2021.02.17.21251933
 115. Liu H, Plancarte M, Ball Erin E, Weiss Christopher M, Gonzales-Viera O, et al. 2021. Respiratory Tract Explant Infection Dynamics of Influenza A Virus in California Sea Lions, Northern Elephant Seals, and Rhesus Macaques. Journal of Virology 95:e00403-21
 116. Linderman MD, Paudyal C, Shakeel M, Kelley W, Bashir A, Gelb BD. 2021. NPSV: A simulation-driven approach to genotyping structural variants in whole-genome sequencing data. GigaScience 10
 117. Li Y-C, Hsu H-HL, Chun Y, Chiu P-H, Arditi Z, et al. 2021. Machine learning–driven identification of early-life air toxic combinations associated with childhood asthma outcomes. The Journal of Clinical Investigation 131
 118. Li W, Klein RJ. 2021. Genome-wide association study identifies a role for the progesterone receptor in benign prostatic hyperplasia risk. Prostate Cancer and Prostatic Diseases 24:492-8
 119. Li CW, Sachidanandam R, Jayaprakash A, Yi Z, Zhang W, et al. 2021. Identification of New Rare Variants Associated With Familial Autoimmune Thyroid Diseases by Deep Sequencing of Linked Loci. The Journal of Clinical Endocrinology & Metabolism 106:e4680-e7
 120. Letizia AG, Smith DR, Ge Y, Ramos I, Sealfon RSG, et al. 2021. Viable virus shedding during SARS-CoV-2 reinfection. Lancet Respir Med 9:e56-e7
 121. Letizia AG, Arnold CE, Adhikari BN, Voegtly LJ, Glang L, et al. 2021. Immunological and Genetic Investigation of SARS-CoV-2 Reinfection in an Otherwise Healthy, Young Marine Recruit. Pathogens 10:1589
 122. Lencz T, Yu J, Khan RR, Flaherty E, Carmi S, et al. 2021. Novel ultra-rare exonic variants identified in a founder population implicate cadherins in schizophrenia. Neuron 109:1465-78.e4
 123. Lehrer S, Rheinstein PH. 2021. Homozygosity for rs17775810 Minor Allele Associated With Reduced Mortality of COVID-19 in the UK Biobank Cohort. In Vivo 35:965-8
 124. Lehrer S, Rheinstein PH. 2021. Herpes Zoster Vaccination Reduces Risk of Dementia. In Vivo 35:3271-5
 125. Lehrer S, Rheinstein PH. 2021. FBXW7, L1CAM, and TGM2 in endometrial cancer. Cancer 127:4103-4
 126. Lehrer S, Rheinstein PH. 2021. Endometrial Cancer, BRCA1, and BRCA2 in the UK Biobank Cohort. American Journal of Clinical Oncology 44
 127. Lehrer S, Rheinstein PH. 2021. Common drugs, vitamins, nutritional supplements and COVID-19 mortality. Int J Funct Nutr 2:4
 128. Lehrer S, Rheinstein PH. 2021. Breast Cancer, Alzheimer’s Disease, and APOE4 Allele in the UK Biobank Cohort. J Alzheimers Dis Rep 5:49-53
 129. Lehrer S, Rheinstein PH. 2021. BIN1 rs744373 SNP and COVID‑19 mortality. World Acad Sci J 3:13
 130. Lehrer S, Rheinstein PH. 2021. Alzheimer’s Disease and Parkinson’s Disease May Result from Reactivation of Embryologic Pathways Silenced at Birth. Discov Med 31:89-94
 131. Lehrer S, Rheinstein PH. 2021. The actinomycin D molecule docks to a hydrophilic section of the SOX2 high-mobility group (HMG) domain. Neuro-Oncology 23:500-1
 132. Lehrer S, Rheinstein PH. 2021. ABO blood groups, COVID-19 infection and mortality. Blood Cells Mol Dis 89:102571-
 133. Lehrer S, Rheinstein P. 2021. Eyeglasses Reduce Risk of COVID-19 Infection. In Vivo 35:1581-2
 134. Lee WH, Antoniades M, Schnack HG, Kahn RS, Frangou S. 2021. Brain age prediction in schizophrenia: Does the choice of machine learning algorithm matter? Psychiatry Research: Neuroimaging 310:111270
 135. Lee W, Wang Z, Saffern M, Jun T, Huang K-L. 2021. Genomic and molecular features distinguish young adult cancer from later-onset cancer. Cell Rep 37:110005-
 136. Lee SE, Mushtaq A, Gitman M, Paniz-Mondolfi A, Chung M, et al. 2021. Lemierre’s syndrome associated with hypervirulent Klebsiella pneumoniae: A case report and genomic characterization of the isolate. IDCases 25:e01173-e
 137. Leader AM, Grout JA, Maier BB, Nabet BY, Park MD, et al. 2021. Single-cell analysis of human non-small cell lung cancer lesions refines tumor classification and patient stratification. Cancer Cell 39:1594-609.e12
 138. Landi I, Kaji DA, Cotter L, Van Vleck T, Belbin G, et al. 2021. Prognostic value of polygenic risk scores for adults with psychosis. Nature Medicine 27:1576-81
 139. Lagou V, Mägi R, Hottenga J-J, Grallert H, Perry JRB, et al. 2021. Sex-dimorphic genetic effects and novel loci for fasting glucose and insulin variability. Nature Communications 12:24
 140. Kvist-Hansen A, Kaiser H, Wang X, Krakauer M, Gørtz PM, et al. 2021. Neutrophil Pathways of Inflammation Characterize the Blood Transcriptomic Signature of Patients with Psoriasis and Cardiovascular Disease. Int J Mol Sci 22:10818
 141. Kulkarni KR, Schafer M, Berner L, Fiore VG, Heflin M, et al. 2021. An interpretable connectivity-based decoding model for classification of chronic marijuana use. bioRxiv:2021.05.04.442433
 142. Kontorovich AR, Tang Y, Patel N, Georgievskaya Z, Shadrina M, et al. 2021. Burden of Cardiomyopathic Genetic Variation in Lethal Pediatric Myocarditis. Circulation: Genomic and Precision Medicine 14:e003426
 143. Kontorovich AR, Patel N, Moscati A, Richter F, Peter I, et al. 2021. Myopathic Cardiac Genotypes Increase Risk for Myocarditis. JACC Basic Transl Sci 6:584-92
 144. Klei L, McClain LL, Mahjani B, Panayidou K, De Rubeis S, et al. 2021. How rare and common risk variation jointly affect liability for autism spectrum disorder. Molecular Autism 12:66
 145. Kirkpatrick Roubidoux E, McMahon M, Carreño JM, Capuano C, Jiang K, et al. 2021. Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. mSphere 6:e00958-20
 146. Kim ES, Tarassishin L, Eisele C, Barre A, Nair N, et al. 2021. Longitudinal Changes in Fecal Calprotectin Levels Among Pregnant Women With and Without Inflammatory Bowel Disease and Their Babies. Gastroenterology 160:1118-30.e3
 147. Khalil BD, Sanchez R, Rahman T, Rodriguez-Tirado C, Moritsch S, et al. 2021. A specific agonist of the orphan nuclear receptor NR2F1 suppresses metastasis through the induction of cancer cell dormancy. bioRxiv:2021.01.30.428967
 148. Kapoor M, Chao MJ, Johnson EC, Novikova G, Lai D, et al. 2021. Multi-omics integration analysis identifies novel genes for alcoholism with potential overlap with neurodegenerative diseases. Nature communications 12:5071-
 149. Kaiser H, Wang X, Kvist-Hansen A, Krakauer M, Gørtz PM, et al. 2021. Biomarkers of subclinical atherosclerosis in patients with psoriasis. Scientific Reports 11:21438
 150. Jun T, Nirenberg S, Weinberger T, Sharma N, Pujadas E, et al. 2021. Analysis of sex-specific risk factors and clinical outcomes in COVID-19. Communications Medicine 1:3
 151. Johnson JS, Cote AC, Dobbyn A, Sloofman LG, Xu J, et al. 2021. The Phenome-wide Consequences of Anorexia Nervosa Genes. medRxiv:2021.02.12.21250941
 152. Jin T, Rehani P, Ying M, Huang J, Liu S, et al. 2021. scGRNom: a computational pipeline of integrative multi-omics analyses for predicting cell-type disease genes and regulatory networks. Genome medicine 13:95-
 153. Javaid W, Ehni J, Gonzalez-Reiche AS, Carreño JM, Hirsch E, et al. 2021. Real-Time Investigation of a Large Nosocomial Influenza A Outbreak Informed by Genomic Epidemiology. Clin Infect Dis 73:e4375-e83
 154. Jatiani SS, Christie S, Leshchenko VV, Jain R, Kapoor A, et al. 2021. SOX11 Inhibitors Are Cytotoxic in Mantle Cell Lymphoma. Clinical Cancer Research 27:4652-63
 155. Jaladanki SK, Vaid A, Sawant AS, Xu J, Shah K, et al. 2021. Development of a federated learning approach to predict acute kidney injury in adult hospitalized patients with COVID-19 in New York City. medRxiv:2021.07.25.21261105
 156. Ishioka K, Yasuda H, Hamamoto J, Terai H, Emoto K, et al. 2021. Upregulation of FGF9 in Lung Adenocarcinoma Transdifferentiation to Small Cell Lung Cancer. Cancer Research 81:3916-29
 157. Huq AJ, Fulton-Howard B, Riaz M, Laws S, Sebra R, et al. 2021. Polygenic score modifies risk for Alzheimer’s disease in APOE ε4 homozygotes at phenotypic extremes. Alzheimers Dement (Amst) 13:e12226-e
 158. Huang Y, Tejero R, Lee VK, Brusco C, Hannah T, et al. 2021. Plexin-B2 facilitates glioblastoma infiltration by modulating cell biomechanics. Communications Biology 4:145
 159. Huang LO, Rauch A, Mazzaferro E, Preuss M, Carobbio S, et al. 2021. Genome-wide discovery of genetic loci that uncouple excess adiposity from its comorbidities. Nature Metabolism 3:228-43
 160. Huang D, Chowdhury S, Wang H, Savage SR, Ivey RG, et al. 2021. Multiomic analysis identifies CPT1A as a potential therapeutic target in platinum-refractory, high-grade serous ovarian cancer. Cell Reports Medicine 2:100471
 161. Huang C, Chen L, Savage SR, Eguez RV, Dou Y, et al. 2021. Proteogenomic insights into the biology and treatment of HPV-negative head and neck squamous cell carcinoma. Cancer Cell 39:361-79.e16
 162. Hu J, Benny P, Wang M, Ma Y, Lambertini L, et al. 2021. Intrauterine Growth Restriction Is Associated with Unique Features of the Reproductive Microbiome. Reproductive Sciences 28:828-37
 163. Horiuchi S, Wu H, Liu W-C, Schmitt N, Provot J, et al. 2021. Tox2 is required for the maintenance of GC TFH cells and the generation of memory TFH cells. Sci Adv 7:eabj1249
 164. Horgusluoglu E, Neff R, Song W-M, Wang M, Wang Q, et al. 2021. Integrative metabolomics-genomics approach reveals key metabolic pathways and regulators of Alzheimer’s disease. Alzheimer’s & Dementia n/a
 165. Holmes G, Gonzalez-Reiche AS, Saturne M, Motch Perrine SM, Zhou X, et al. 2021. Single-cell analysis identifies a key role for Hhip in murine coronal suture development. Nature Communications 12:7132
 166. Hoffman GE, Roussos P. 2021. Dream: powerful differential expression analysis for repeated measures designs. Bioinformatics (Oxford, England) 37:192-201
 167. Ho JSY, Mok BW-Y, Campisi L, Jordan T, Yildiz S, et al. 2021. TOP1 inhibition therapy protects against SARS-CoV-2-induced lethal inflammation. Cell 184:2618-32.e17
 168. Hirten RP, Danieletto M, Tomalin L, Choi KH, Zweig M, et al. 2021. Use of Physiological Data From a Wearable Device to Identify SARS-CoV-2 Infection and Symptoms and Predict COVID-19 Diagnosis: Observational Study. J Med Internet Res 23:e26107-e
 169. Hernandez MM, Gonzalez-Reiche AS, Alshammary H, Fabre S, Khan Z, et al. 2021. Molecular evidence of SARS-CoV-2 in New York before the first pandemic wave. Nature Communications 12:3463
 170. Hernandez MM, Gonzalez-Reiche AS, Alshammary H, Fabre S, Khan Z, et al. 2021. Before the Surge: Molecular Evidence of SARS-CoV-2 in New York City Prior to the First Report. medRxiv:2021.02.08.21251303
 171. Hernandez MM, Banu R, Gonzalez-Reiche AS, van de Guchte A, Khan Z, et al. 2021. Robust clinical detection of SARS-CoV-2 variants by RT-PCR/MALDI-TOF multitarget approach. Journal of Medical Virology n/a
 172. Hao K, Ermel R, Sukhavasi K, Cheng H, Ma L, et al. 2021. Integrative Prioritization of Causal Genes for Coronary Artery Disease. Circulation: Genomic and Precision Medicine 0:CIRCGEN.121.003365
 173. Gitman MR, Alburquerque B, Chung M, van de Guchte A, Sullivan MJ, et al. 2021. Modified methicillin-resistant Staphylococcus aureus detected in neonatal intensive care patients. J Antimicrob Chemother 76:2774-7
 174. Gillispie GJ, Sah E, Krishnamurthy S, Ahmidouch MY, Zhang B, Orr ME. 2021. Evidence of the Cellular Senescence Stress Response in Mitotically Active Brain Cells—Implications for Cancer and Neurodegeneration. Life 11:153
 175. Georges A, Yang M-L, Berrandou T-E, Bakker MK, Dikilitas O, et al. 2021. Genetic investigation of fibromuscular dysplasia identifies risk loci and shared genetics with common cardiovascular diseases. Nature Communications 12:6031
 176. Geanon D, Lee B, Gonzalez-Kozlova E, Kelly G, Handler D, et al. 2021. A streamlined whole blood CyTOF workflow defines a circulating immune cell signature of COVID-19. Cytometry A 99:446-61
 177. Garg P, Martin-Trujillo A, Rodriguez OL, Gies SJ, Hadelia E, et al. 2021. Pervasive cis effects of variation in copy number of large tandem repeats on local DNA methylation and gene expression. The American Journal of Human Genetics 108:809-24
 178. Gaglani S, Gonzalez-Kozlova E, Lundon DJ, Tewari AK, Dogra N, Kyprianou N. 2021. Exosomes as A Next-Generation Diagnostic and Therapeutic Tool in Prostate Cancer. Int J Mol Sci 22:10131
 179. Fulton-Howard B, Goate AM, Adelson RP, Koppel J, Gordon ML, et al. 2021. Greater effect of polygenic risk score for Alzheimer’s disease among younger cases who are apolipoprotein E-ε4 carriers. Neurobiology of aging 99:101.e1-.e9
 180. Fullard JF, Lee H-C, Voloudakis G, Suo S, Javidfar B, et al. 2021. Single-nucleus transcriptome analysis of human brain immune response in patients with severe COVID-19. Genome medicine 13:118-
 181. Fu JM, Satterstrom FK, Peng M, Brand H, Collins RL, et al. 2021. Rare coding variation illuminates the allelic architecture, risk genes, cellular expression patterns, and phenotypic context of autism. medRxiv:2021.12.20.21267194
 182. Fu J, Yi Z, Cai M, Yuan W, Zhang W, et al. 2021. Global transcriptomic changes in glomerular endothelial cells in mice with podocyte depletion and glomerulosclerosis. Cell Death & Disease 12:687
 183. Forrest IS, Chaudhary K, Vy HMT, Bafna S, Jordan DM, et al. 2021. Ancestrally and Temporally Diverse Analysis of Penetrance of Clinical Variants in 72,434 Individuals. medRxiv:2021.03.11.21253430
 184. Fiore VG, Guertler A-CV, Yu J-C, Tatineni CC, Gu X. 2021. A change of mind: Globus pallidus activity and effective connectivity during changes in choice selections. European Journal of Neuroscience 53:2774-87
 185. Fiore VG, DeFelice N, Glicksberg BS, Perl O, Shuster A, et al. 2021. Containment of COVID-19: Simulating the impact of different policies and testing capacities for contact tracing, testing, and isolation. PLoS One 16:e0247614-e
 186. Estill M, Ribeiro E, Francoeur NJ, Smith ML, Sebra R, et al. 2021. Long read, isoform aware sequencing of mouse nucleus accumbens after chronic cocaine treatment. Scientific Reports 11:6729
 187. Eric V, Yi V, Murdock D, Kalla SE, Wu T-J, et al. 2021. Neptune: an environment for the delivery of genomic medicine. Genetics in Medicine 23:1838-46
 188. Encinas P, del Real G, Dutta J, Khan Z, van Bakel H, et al. 2021. Evolution of influenza A virus in intensive and free-range swine farms in Spain. Virus Evolution 7
 189. Ellis RJ, Bara A, Vargas CA, Frick AL, Loh E, et al. 2021. Prenatal Δ9-Tetrahydrocannabinol Exposure in Males Leads to Motivational Disturbances Related to Striatal Epigenetic Dysregulation. Biological Psychiatry
 190. Doucet GE, Labache L, Thompson PM, Joliot M, Frangou S, Alzheimer’s Disease Neuroimaging I. 2021. Atlas55+: Brain Functional Atlas of Resting-State Networks for Late Adulthood. Cereb Cortex 31:1719-31
 191. Donohue KE, Dolan SM, Watnick D, Gallagher KM, Odgis JA, et al. 2021. Hope versus reality: Parent expectations of genomic testing. Patient Education and Counseling 104:2073-9
 192. Di Narzo AF, Hart A, Kosoy R, Peters L, Stojmirovic A, et al. 2021. Polygenic risk score for alcohol drinking behavior improves prediction of inflammatory bowel disease risk. Hum Mol Genet 30:514-23
 193. Di Narzo A, Frades I, Crane HM, Crane PK, Hulot J-S, et al. 2021. Meta-analysis of sample-level dbGaP data reveals novel shared genetic link between body height and Crohn’s disease. Human Genetics 140:865-77
 194. Deyssenroth MA, Rosa MJ, Eliot MN, Kelsey KT, Kloog I, et al. 2021. Placental gene networks at the interface between maternal PM2.5 exposure early in gestation and reduced infant birthweight. Environmental Research 199:111342
 195. Dellepiane S, Vaid A, Jaladanki SK, Coca S, Fayad ZA, et al. 2021. Acute Kidney Injury in Patients Hospitalized With COVID-19 in New York City: Temporal Trends From March 2020 to April 2021. Kidney Medicine 3:877-9
 196. Dayan I, Roth HR, Zhong A, Harouni A, Gentili A, et al. 2021. Federated learning for predicting clinical outcomes in patients with COVID-19. Nature Medicine 27:1735-43
 197. da Cruz HF, Pfahringer B, Martensen T, Schneider F, Meyer A, et al. 2021. Using interpretability approaches to update “black-box” clinical prediction models: an external validation study in nephrology. Artificial Intelligence in Medicine 111:101982
 198. Cuddleston R, Sloofman L, Liang L, Mossotto E, Fan X, et al. 2021. Expansion of RNA sequence diversity and RNA editing rates throughout human cortical development. bioRxiv:2021.06.10.447947
 199. Cruceanu C, Dony L, Krontira AC, Fischer DS, Roeh S, et al. 2021. Cell-Type-Specific Impact of Glucocorticoid Receptor Activation on the Developing Brain: A Cerebral Organoid Study. American Journal of Psychiatry:appi.ajp.2021.21010095
 200. Crawford AA, Bankier S, Altmaier E, Barnes CLK, Clark DW, et al. 2021. Variation in the SERPINA6/SERPINA1 locus alters morning plasma cortisol, hepatic corticosteroid binding globulin expression, gene expression in peripheral tissues, and risk of cardiovascular disease. Journal of Human Genetics 66:625-36
 201. Cohain AT, Barrington WT, Jordan DM, Beckmann ND, Argmann CA, et al. 2021. An integrative multiomic network model links lipid metabolism to glucose regulation in coronary artery disease. Nature Communications 12:547
 202. Cirnaru M-D, Song S, Tshilenge K-T, Corwin C, Mleczko J, et al. 2021. Unbiased identification of novel transcription factors in striatal compartmentation and striosome maturation. Elife 10:e65979
 203. Chen T-Y, Gonzalez-Kozlova E, Soleymani T, La Salvia S, Kyprianou N, et al. 2021. Extracellular Vesicles Carry Distinct Proteo-Transcriptomic Signatures That are Different from Their Cancer Cell of Origin. bioRxiv:2021.09.20.460963
 204. Chen H-H, Shaw DM, Petty LE, Graff M, Bohlender RJ, et al. 2021. Host genetic effects in pneumonia. Am J Hum Genet 108:194-201
 205. Chan L, Jaladanki SK, Somani S, Paranjpe I, Kumar A, et al. 2021. Outcomes of Patients on Maintenance Dialysis Hospitalized with COVID-19. Clinical Journal of the American Society of Nephrology 16:452-5
 206. Chan L, Chaudhary K, Saha A, Chauhan K, Vaid A, et al. 2021. AKI in Hospitalized Patients with COVID-19. Journal of the American Society of Nephrology 32:151-60
 207. Chakraborty S, DiBerto JF, Faouzi A, Bernhard SM, Gutridge AM, et al. 2021. A Novel Mitragynine Analog with Low-Efficacy Mu Opioid Receptor Agonism Displays Antinociception with Attenuated Adverse Effects. J Med Chem 64:13873-92
 208. Carreño JM, Alshammary H, Tcheou J, Singh G, Raskin A, et al. 2021. Activity of convalescent and vaccine serum against SARS-CoV-2 Omicron. Nature
 209. Carreño JM, Alshammary H, Singh G, Raskin A, Amanat F, et al. 2021. Evidence for retained spike-binding and neutralizing activity against emerging SARS-CoV-2 variants in serum of COVID-19 mRNA vaccine recipients. eBioMedicine 73
 210. Cao J, Huang M, Guo L, Zhu L, Hou J, et al. 2021. MicroRNA-195 rescues AD-associated lysosomal defects. Molecular Psychiatry 26:4563-
 211. Cao J, Huang M, Guo L, Zhu L, Hou J, et al. 2021. MicroRNA-195 rescues ApoE4-induced cognitive deficits and lysosomal defects in Alzheimer’s disease pathogenesis. Molecular psychiatry 26:4687-701
 212. Cao A, Li J, Asadi M, Basgen JM, Zhu B, et al. 2021. DACH1 protects podocytes from experimental diabetic injury and modulates PTIP-H3K4Me3 activity. The Journal of clinical investigation 131:e141279
 213. Britton GJ, Chen-Liaw A, Cossarini F, Livanos AE, Spindler MP, et al. 2021. Limited intestinal inflammation despite diarrhea, fecal viral RNA and SARS-CoV-2-specific IgA in patients with acute COVID-19. Scientific Reports 11:13308
 214. Bowles KR, Silva MC, Whitney K, Bertucci T, Berlind JE, et al. 2021. ELAVL4, splicing, and glutamatergic dysfunction precede neuron loss in MAPT mutation cerebral organoids. Cell 184:4547-63.e17
 215. Birnbaum R, Mahjani B, Loos RJF, Sharp AJ. 2021. A Survey of Copy Number Variants Associated with Neurodevelopmental Disorders in a Large-Scale, Multi-Ancestry Biobank. medRxiv:2021.06.09.21258554
 216. Bhattacharya D, Becker C, Readhead B, Goossens N, Novik J, et al. 2021. Repositioning of a novel GABA-B receptor agonist, AZD3355 (Lesogaberan), for the treatment of non-alcoholic steatohepatitis. Scientific Reports 11:20827
 217. Bhalla S, Melnekoff DT, Aleman A, Leshchenko V, Restrepo P, et al. 2021. Patient similarity network of newly diagnosed multiple myeloma identifies patient subgroups with distinct genetic features and clinical implications. Sci Adv 7:eabg9551-eabg
 218. Bendl J, Hauberg ME, Girdhar K, Im E, Vicari JM, et al. 2021. The three-dimensional landscape of chromatin accessibility in Alzheimer’s disease. bioRxiv:2021.01.11.426303
 219. Benchek P, Igo RP, Jr., Voss-Hoynes H, Wren Y, Miller G, et al. 2021. Association between genes regulating neural pathways for quantitative traits of speech and language disorders. NPJ genomic medicine 6:64-
 220. Belbin GM, Rutledge S, Dodatko T, Cullina S, Turchin MC, et al. 2021. Leveraging health systems data to characterize a large effect variant conferring risk for liver disease in Puerto Ricans. The American Journal of Human Genetics 108:2099-111
 221. Belbin GM, Cullina S, Wenric S, Soper ER, Glicksberg BS, et al. 2021. Toward a fine-scale population health monitoring system. Cell 184:2068-83.e11
 222. Beckmann ND, Comella PH, Cheng E, Lepow L, Beckmann AG, et al. 2021. Downregulation of exhausted cytotoxic T cells in gene expression networks of multisystem inflammatory syndrome in children. Nature Communications 12:4854
 223. Bar-Mashiah A, Soper ER, Cullina S, Belbin GM, Kenny EE, et al. 2021. CDH1 pathogenic variants and cancer risk in an unselected patient population. Familial Cancer
 224. Bao R, Ng A, Sasaki M, Esai Selvan M, Katti A, et al. 2021. Functional Common and Rare ERBB2 Germline Variants Cooperate in Familial and Sporadic Cancer Susceptibility. Cancer Prev Res (Phila) 14:441-54
 225. Banu K, Lin Q, Basgen JM, Planoutene M, Wei C, et al. 2021. AMPK mediates regulation of glomerular volume and podocyte survival. JCI Insight 6:e150004
 226. Ballesteros N, Muñoz M, Patiño LH, Hernández C, González-Casabianca F, et al. 2021. Deciphering the introduction and transmission of SARS-CoV-2 in the Colombian Amazon Basin. PLoS Negl Trop Dis 15:e0009327-e
 227. Aushev VN, Li Q, Deyssenroth M, Zhang W, Finik J, et al. 2021. Placental gene network modules are associated with maternal stress during pregnancy and infant temperament. The FASEB Journal 35:e21922
 228. Audrain M, Haure-Mirande J-V, Mleczko J, Wang M, Griffin JK, et al. 2021. Reactive or transgenic increase in microglial TYROBP reveals a TREM2-independent TYROBP–APOE link in wild-type and Alzheimer’s-related mice. Alzheimer’s & Dementia 17:149-63
 229. Andrews SJ, Fulton-Howard B, O’Reilly P, Marcora E, Goate AM, collaborators of the Alzheimer’s Disease Genetics C. 2021. Causal Associations Between Modifiable Risk Factors and the Alzheimer’s Phenome. Annals of neurology 89:54-65
 230. Amanat F, Thapa M, Lei T, Ahmed SMS, Adelsberg DC, et al. 2021. SARS-CoV-2 mRNA vaccination induces functionally diverse antibodies to NTD, RBD, and S2. Cell 184:3936-48.e10
 231. Aleman A, Upadhyaya B, Tuballes K, Kappes K, Gleason CR, et al. 2021. Variable cellular responses to SARS-CoV-2 in fully vaccinated patients with multiple myeloma. Cancer Cell 39:1442-4
 232. Aggarwala V, Mogno I, Li Z, Yang C, Britton GJ, et al. 2021. Precise quantification of bacterial strains after fecal microbiota transplantation delineates long-term engraftment and explains outcomes. Nature Microbiology 6:1309-18
 233. Abul-Husn NS, Soper ER, Braganza GT, Rodriguez JE, Zeid N, et al. 2021. Implementing genomic screening in diverse populations. Genome Medicine 13:17

2020

1. 1. Restrepo P YR, Laface I, Tsankova N, Nael K, Akturk G, Sebra R, Gnjatic S, Hormigo A, Losic B. 2020 Jan 6. Tumoral and immune heterogeneity in an anti-PD-1 responsive glioblastoma: a case study. Cold Spring Harb Mol Case Stud. pii: mcs.a004762
 2. Zhou Y, Ramsey S, Provasi D, El Daibani A, Appourchaux K, et al. 2020. Predicted Mode of Binding to and Allosteric Modulation of the μ-Opioid Receptor by Kratom’s Alkaloids with Reported Antinociception In Vivo. Biochemistry
 3. Zhou X, Wahane S, Friedl M-S, Kluge M, Friedel CC, et al. 2020. Microglia and macrophages promote corralling, wound compaction and recovery after spinal cord injury via Plexin-B2. Nature Neuroscience 23:337-50
 4. Zhang Z, Menon MC, Zhang W, Stahl E, Loza B-L, et al. 2020. Genome-wide non-HLA donor-recipient genetic differences influence renal allograft survival via early allograft fibrosis. Kidney International 98:758-68
 5. Zhang Q, Sidorenko J, Couvy-Duchesne B, Marioni RE, Wright MJ, et al. 2020. Risk prediction of late-onset Alzheimer’s disease implies an oligogenic architecture. Nature communications 11:4799
 6. Zhang Q, Sidorenko J, Couvy-Duchesne B, Marioni RE, Wright MJ, et al. 2020. Risk prediction of late-onset Alzheimer’s disease implies an oligogenic architecture. Nature Communications 11:4799
 7. Zhang J, Lee D, Dhiman V, Jiang P, Xu J, et al. 2020. An integrative ENCODE resource for cancer genomics. Nature Communications 11:3696
 8. Yazdani A, Mendez-Giraldez R, Yazdani A, Kosorok MR, Roussos P. 2020. Differential gene regulatory pattern in the human brain from schizophrenia using transcriptomic-causal network. BMC Bioinformatics 21:469-
 9. Yang J, Peng S, Zhang B, Houten S, Schadt E, et al. 2020. Human geroprotector discovery by targeting the converging subnetworks of aging and age-related diseases. GeroScience 42:353-72
 10. Yang C, Mogno I, Contijoch EJ, Borgerding JN, Aggarwala V, et al. 2020. Fecal IgA Levels Are Determined by Strain-Level Differences in Bacteroides ovatus and Are Modifiable by Gut Microbiota Manipulation. Cell host & microbe 27:467-75 e6
 11. Yaghootkar H, Zhang Y, Spracklen CN, Karaderi T, Huang LO, et al. 2020. Genetic Studies of Leptin Concentrations Implicate Leptin in the Regulation of Early Adiposity. Diabetes 69:2806-18
 12. Xie J, Liu L, Mladkova N, Li Y, Ren H, et al. 2020. The genetic architecture of membranous nephropathy and its potential to improve non-invasive diagnosis. Nature communications 11:1600
 13. Woo YJ, Roussos P, Haroutunian V, Katsel P, Gandy S, et al. 2020. Comparison of brain connectomes by MRI and genomics and its implication in Alzheimer’s disease. BMC medicine 18:23-
 14. Woo YJ, Roussos P, Haroutunian V, Katsel P, Gandy S, et al. 2020. Comparison of brain connectomes by MRI and genomics and its implication in Alzheimer’s disease. BMC medicine 18:23
 15. Wenger BM, Patel N, Lui M, Moscati A, Do R, et al. 2020. A genotype-first approach to exploring Mendelian cardiovascular traits with clear external manifestations. Genetics in Medicine
 16. Weiss K, Lazar HP, Kurolap A, Martinez AF, Paperna T, et al. 2020. The CHD4-related syndrome: a comprehensive investigation of theclinical spectrum, genotype–phenotype correlations, and molecular basis. Genetics in Medicine 22:389-97
 17. Wang L, Sebra RP, Sfakianos JP, Allette K, Wang W, et al. 2020. A reference profile-free deconvolution method to infer cancer cell-intrinsic subtypes and tumor-type-specific stromal profiles. Genome medicine 12:24-
 18. Wang H-Y, MacDonald ML, Borgmann-Winter KE, Banerjee A, Sleiman P, et al. 2020. mGluR5 hypofunction is integral to glutamatergic dysregulation in schizophrenia. Molecular psychiatry 25:750-60
 19. Wang C, Forst CV, Chou TW, Geber A, Wang M, et al. 2020. Cell-to-Cell Variation in Defective Virus Expression and Effects on Host Responses during Influenza Virus Infection. mBio 11
 20. Wang C, Forst CV, Chou T-w, Geber A, Wang M, et al. 2020. Cell-to-Cell Variation in Defective Virus Expression and Effects on Host Responses during Influenza Virus Infection. mBio 11:e02880-19
 21. Walker RW, Belbin GM, Sorokin EP, Van Vleck T, Wojcik GL, et al. 2020. A common variant in PNPLA3 is associated with age at diagnosis of NAFLD in patients from a multi-ethnic biobank. Journal of hepatology 72:1070-81
 22. Vuckovic D, Bao EL, Akbari P, Lareau CA, Mousas A, et al. 2020. The Polygenic and Monogenic Basis of Blood Traits and Diseases. Cell 182:1214-31.e11
 23. von Felden J, Garcia-Lezana T, Dogra N, Kozlova E, Ahsen ME, et al. 2020. Unannotated small RNA clusters in circulating extracellular vesicles detect early stage liver cancer. bioRxiv:2020.04.29.066183
 24. Vivas-Ruiz DE, Sandoval GA, Gonzalez-Kozlova E, Zarria-Romero J, Lazo F, et al. 2020. Fibrinogen-clotting enzyme, pictobin, from Bothrops pictus snake venom. Structural and functional characterization. International Journal of Biological Macromolecules 153:779-95
 25. Vatansever S, Schlessinger A, Wacker D, Kaniskan HÜ, Jin J, et al. 2020. Artificial intelligence and machine learning-aided drug discovery in central nervous system diseases: State-of-the-arts and future directions. Med Res Rev
 26. Vangeepuram N, Liu B, Chiu P-h, Wang L, Pandey G. 2020. Estimating youth diabetes risk using NHANES data and machine learning. medRxiv:19007872
 27. Urreizti R, Mayer K, Evrony GD, Said E, Castilla-Vallmanya L, et al. 2020. DPH1 syndrome: two novel variants and structural and functional analyses of seven missense variants identified in syndromic patients. European Journal of Human Genetics 28:64-75
 28. Tian F-Y, Everson TM, Lester B, Punshon T, Jackson BP, et al. 2020. Selenium-associated DNA methylation modifications in placenta and neurobehavioral development of newborns: An epigenome-wide study of two U.S. birth cohorts. Environment International 137:105508
 29. Surendran P, Feofanova EV, Lahrouchi N, Ntalla I, Karthikeyan S, et al. 2020. Discovery of rare variants associated with blood pressure regulation through meta-analysis of 1.3 million individuals. Nature Genetics 52:1314-32
 30. Stahl E, Roda G, Dobbyn A, Hu J, Zhang Z, et al. 2020. Collagenous Colitis Is Associated With HLA Signature and Shares Genetic Risks With Other Immune-Mediated Diseases. Gastroenterology 159:549-61.e8
 31. Song WM, Lin X, Liao X, Hu D, Lin J, et al. 2020. Multiscale network analysis reveals molecular mechanisms and key regulators of the tumor microenvironment in gastric cancer. International journal of cancer 146:1268-80
 32. Song W-M, Lin X, Liao X, Hu D, Lin J, et al. 2020. Multiscale network analysis reveals molecular mechanisms and key regulators of the tumor microenvironment in gastric cancer. International Journal of Cancer 146:1268-80
 33. Sieh W, Rothstein JH, Klein RJ, Alexeeff SE, Sakoda LC, et al. 2020. Identification of 31 loci for mammographic density phenotypes and their associations with breast cancer risk. Nature Communications 11:5116
 34. Sevim Bayrak C, Zhang P, Tristani-Firouzi M, Gelb BD, Itan Y. 2020. De novo variants in exomes of congenital heart disease patients identify risk genes and pathways. Genome Medicine 12:9
 35. Seiden AH, Richter F, Patel N, Rodriguez OL, Deikus G, et al. 2020. Elucidation of de novo small insertion/deletion biology with parent-of-origin phasing. Human Mutation 41:800-6
 36. Schneeberger PE, Kortüm F, Korenke GC, Alawi M, Santer R, et al. 2020. Biallelic MADD variants cause a phenotypic spectrum ranging from developmental delay to a multisystem disorder. Brain : a journal of neurology 143:2437-53
 37. Scarpa JR, Fatma M, Loh Y-HE, Traore SR, Stefan T, et al. 2020. Shared Transcriptional Signatures in Major Depressive Disorder and Mouse Chronic Stress Models. Biological Psychiatry 88:159-68
 38. Samuels BD, Aho R, Brinkley JF, Bugacov A, Feingold E, et al. 2020. FaceBase 3: analytical tools and FAIR resources for craniofacial and dental research. Development 147:dev191213
 39. Rubenstein AB, Smith GR, Raue U, Begue G, Minchev K, et al. 2020. Single-cell transcriptional profiles in human skeletal muscle. Scientific reports 10:229-
 40. Rodríguez-Espigares I, Torrens-Fontanals M, Tiemann JKS, Aranda-García D, Ramírez-Anguita JM, et al. 2020. GPCRmd uncovers the dynamics of the 3D-GPCRome. Nature Methods 17:777-87
 41. Rodríguez-Espigares I, Torrens-Fontanals M, Tiemann JKS, Aranda-García D, Ramírez-Anguita JM, et al. 2020. Publisher Correction: GPCRmd uncovers the dynamics of the 3D-GPCRome. Nature Methods 17:861-2
 42. Rodríguez Y, Gerona-Navarro G, Osman R, Zhou MM. 2020. In silico design and molecular basis for the selectivity of Olinone toward the first over the second bromodomain of BRD4. Proteins 88:414-30
 43. Rodríguez Y, Gerona-Navarro G, Osman R, Zhou M-M. 2020. In silico design and molecular basis for the selectivity of Olinone toward the first over the second bromodomain of BRD4. Proteins: Structure, Function, and Bioinformatics 88:414-30
 44. Rodriguez OL, Gibson WS, Parks T, Emery M, Powell J, et al. 2020. A Novel Framework for Characterizing Genomic Haplotype Diversity in the Human Immunoglobulin Heavy Chain Locus. Front Immunol 11:2136-
 45. Robinson JR, Carroll RJ, Bastarache L, Chen Q, Mou Z, et al. 2020. Association of Genetic Risk of Obesity with Postoperative Complications Using Mendelian Randomization. World Journal of Surgery 44:84-94
 46. Richter F, Morton SU, Kim SW, Kitaygorodsky A, Wasson LK, et al. 2020. Genomic analyses implicate noncoding de novo variants in congenital heart disease. Nature Genetics 52:769-77
 47. Ramdhani S, Navarro E, Udine E, Efthymiou AG, Schilder BM, et al. 2020. Tensor decomposition of stimulated monocyte and macrophage gene expression profiles identifies neurodegenerative disease-specific trans-eQTLs. PLOS Genetics 16:e1008549
 48. Perumal D, Imai N, Laganà A, Finnigan J, Melnekoff D, et al. 2020. Mutation-derived Neoantigen-specific T-cell Responses in Multiple Myeloma. Clinical Cancer Research 26:450
 49. Patel RS, Tomlinson JE, Divers TJ, Van de Walle GR, Rosenberg BR. 2020. Single cell resolution landscape of equine peripheral blood mononuclear cells reveals diverse immune cell subtypes including T-bet+ B cells. bioRxiv:2020.05.05.077362
 50. Papa L, Djedaini M, Martin TC, Zangui M, Beaumont KG, et al. 2020. Limited Mitochondrial Activity Coupled With Strong Expression of CD34, CD90 and EPCR Determines the Functional Fitness of ex vivo Expanded Human Hematopoietic Stem Cells. Front Cell Dev Biol 8:592348-
 51. Paniz-Mondolfi A, Muñoz M, Florez C, Gomez S, Rico A, et al. 2020. SARS-CoV-2 spread across the Colombian-Venezuelan border. Infect Genet Evol 86:104616-
 52. Oliveira PH, Ribis JW, Garrett EM, Trzilova D, Kim A, et al. 2020. Epigenomic characterization of Clostridioides difficile finds a conserved DNA methyltransferase that mediates sporulation and pathogenesis. Nature Microbiology 5:166-80
 53. Olin JW, Di Narzo AF, d’Escamard V, Kadian-Dodov D, Cheng H, et al. 2020. A plasma proteogenomic signature for fibromuscular dysplasia. Cardiovasc Res 116:63-77
 54. O’Donnell TJ, Rubinsteyn A, Laserson U. 2020. MHCflurry 2.0: Improved Pan-Allele Prediction of MHC Class I-Presented Peptides by Incorporating Antigen Processing. Cell Systems 11:42-8.e7
 55. O’Donnell T, Rubinsteyn A, Laserson U. 2020. A model of antigen processing improves prediction of MHC I-presented peptides. bioRxiv:2020.03.28.013714
 56. Ntalla I, Weng L-C, Cartwright JH, Hall AW, Sveinbjornsson G, et al. 2020. Multi-ancestry GWAS of the electrocardiographic PR interval identifies 202 loci underlying cardiac conduction. Nature Communications 11:2542
 57. Nešić D, Zhang Y, Spasic A, Li J, Provasi D, et al. 2020. Cryo-Electron Microscopy Structure of the αIIbβ3-Abciximab Complex. Arteriosclerosis, thrombosis, and vascular biology 40:624-37
 58. Nešić D, Zhang Y, Spasic A, Li J, Provasi D, et al. 2020. Cryo-Electron Microscopy Structure of the αIIbβ3-Abciximab Complex. Arteriosclerosis, Thrombosis, and Vascular Biology 40:624-37
 59. Nelson MI, Perofsky A, McBride DS, Rambo-Martin BL, Wilson MM, et al. 2020. A Heterogeneous Swine Show Circuit Drives Zoonotic Transmission of Influenza A Viruses in the United States. Journal of Virology 94:e01453-20
 60. Navarro E, Udine E, de Paiva Lopes K, Parks M, Riboldi G, et al. 2020. Discordant transcriptional signatures of mitochondrial genes in Parkinson’s disease human myeloid cells. bioRxiv:2020.07.20.212407
 61. Mzoughi S, Fong JY, Papadopoli D, Koh CM, Hulea L, et al. 2020. PRDM15 is a key regulator of metabolism critical to sustain B-cell lymphomagenesis. Nature Communications 11:3520
 62. Molina-Sánchez P, Ruiz de Galarreta M, Yao MA, Lindblad KE, Bresnahan E, et al. 2020. Cooperation Between Distinct Cancer Driver Genes Underlies Intertumor Heterogeneity in Hepatocellular Carcinoma. Gastroenterology 159:2203-20.e14
 63. Miorin L, Kehrer T, Sanchez-Aparicio MT, Zhang K, Cohen P, et al. 2020. SARS-CoV-2 Orf6 hijacks Nup98 to block STAT nuclear import and antagonize interferon signaling. Proceedings of the National Academy of Sciences 117:28344-54
 64. Mezei M, Baliram R, Ali MR, Zaidi M, Davies TF, Latif R. 2020. The Human TSHβ Subunit Proteins and Their Binding Sites on the TSH Receptor Using Molecular Dynamics Simulation. Endocrinology 161
 65. Mezei M. 2020. On predicting foldability of a protein from its sequence. Proteins: Structure, Function, and Bioinformatics 88:355-65
 66. Mei AH-C, Tung K, Han J, Perumal D, Laganà A, et al. 2020. MAGE-A inhibit apoptosis and promote proliferation in multiple myeloma through regulation of BIM and p21(Cip1). Oncotarget 11:727-39
 67. Martin-Trujillo A, Patel N, Richter F, Jadhav B, Garg P, et al. 2020. Rare genetic variation at transcription factor binding sites modulates local DNA methylation profiles. PLOS Genetics 16:e1009189
 68. Ma L, Chandel N, Ermel R, Sukhavasi K, Hao K, et al. 2020. Multiple independent mechanisms link gene polymorphisms in the region of ZEB2 with risk of coronary artery disease. Atherosclerosis 311:20-9
 69. Ma A, Stratikopoulos E, Park K-S, Wei J, Martin TC, et al. 2020. Discovery of a first-in-class EZH2 selective degrader. Nature Chemical Biology 16:214-22
 70. Losic B, Craig AJ, Villacorta-Martin C, Martins-Filho SN, Akers N, et al. 2020. Intratumoral heterogeneity and clonal evolution in liver cancer. Nature Communications 11:291
 71. Lombardi A, Concepcion E, Hou H, Arib H, Mezei M, et al. 2020. Retro-inverso D-peptides as a novel targeted immunotherapy for Type 1 diabetes. Journal of Autoimmunity 115:102543
 72. Livanos AE, Jha D, Cossarini F, Gonzalez-Reiche AS, Tokuyama M, et al. 2020. Gastrointestinal involvement attenuates COVID-19 severity and mortality. medRxiv:2020.09.07.20187666
 73. Li W, Klein RJ. 2020. Genome-wide association study identifies a role for the progesterone receptor in benign prostatic hyperplasia risk. Prostate Cancer and Prostatic Diseases
 74. Li W, Bicak M, Sjoberg DD, Vertosick E, Dahlin A, et al. 2020. Genome-wide association study identifies novel single nucleotide polymorphisms having age-specific effect on prostate-specific antigen levels. The Prostate 80:1405-12
 75. Letizia AG, Ramos I, Obla A, Goforth C, Weir DL, et al. 2020. SARS-CoV-2 Transmission among Marine Recruits during Quarantine. N Engl J Med 383:2407-16
 76. Lepack AE, Werner CT, Stewart AF, Fulton SL, Zhong P, et al. 2020. Dopaminylation of histone H3 in ventral tegmental area regulates cocaine seeking. Science 368:197-201
 77. Lee WH, Rodrigue A, Glahn DC, Bassett DS, Frangou S. 2020. Heritability and Cognitive Relevance of Structural Brain Controllability. Cerebral cortex (New York, N.Y. : 1991) 30:3044-54
 78. Lee JH, Ribeiro EA, Kim J, Ko B, Kronman H, et al. 2020. Dopaminergic Regulation of Nucleus Accumbens Cholinergic Interneurons Demarcates Susceptibility to Cocaine Addiction. Biological Psychiatry 88:746-57
 79. Leader AM, Grout JA, Chang C, Maier B, Tabachnikova A, et al. 2020. CITEseq analysis of non-small-cell lung cancer lesions reveals an axis of immune cell activation associated with tumor antigen load and TP53 mutations. bioRxiv:2020.07.16.207605
 80. Latif R, Morshed SA, Ma R, Tokat B, Mezei M, Davies TF. 2020. A Gq Biased Small Molecule Active at the TSH Receptor. Front Endocrinol (Lausanne) 11:372-
 81. Lamim Ribeiro JM, Provasi D, Filizola M. 2020. A combination of machine learning and infrequent metadynamics to efficiently predict kinetic rates, transition states, and molecular determinants of drug dissociation from G protein-coupled receptors. J Chem Phys 153:124105-
 82. Kozlenkov A, Vermunt MW, Apontes P, Li J, Hao K, et al. 2020. Evolution of regulatory signatures in primate cortical neurons at cell-type resolution. Proceedings of the National Academy of Sciences 117:28422-32
 83. Kovatch P, Gai L, Cho HM, Fluder E, Jiang D. Optimizing High-Performance Computing Systems for Biomedical Workloads. Proc. 2020 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), 2020:183-92:
 84. Kirkpatrick E, Henry C, McMahon M, Jiang K, Strohmeier S, et al. 2020. Characterization of Novel Cross-Reactive Influenza B Virus Hemagglutinin Head Specific Antibodies That Lack Hemagglutination Inhibition Activity. Journal of Virology 94:e01185-20
 85. Kerns SL, Fachal L, Dorling L, Barnett GC, Baran A, et al. 2020. Radiogenomics Consortium Genome-Wide Association Study Meta-Analysis of Late Toxicity After Prostate Cancer Radiotherapy. J Natl Cancer Inst 112:179-90
 86. Kennedy EM, Hermetz K, Burt A, Everson TM, Deyssenroth M, et al. 2020. Placental microRNA expression associates with birthweight through control of adipokines: results from two independent cohorts. Epigenetics:1-13
 87. Karakose E, Wang H, Inabnet W, Thakker RV, Libutti S, et al. 2020. Aberrant methylation underlies insulin gene expression in human insulinoma. Nature Communications 11:5210
 88. Kapoor A, Provasi D, Filizola M. 2020. Atomic-Level Characterization of the Methadone-Stabilized Active Conformation of µ-Opioid Receptor. Molecular Pharmacology 98:475
 89. Kapoor A, Provasi D, Filizola M. 2020. Atomic-Level Characterization of the Methadone-Stabilized Active Conformation of µ-Opioid Receptor. Molecular pharmacology 98:475-86
 90. Javaid W, Ehni J, Gonzalez-Reiche AS, Carreño JM, Hirsch E, et al. 2020. Real-Time Investigation of a Large Nosocomial Influenza A Outbreak Informed by Genomic Epidemiology. Clinical Infectious Diseases
 91. Javaid W, Ehni J, Gonzalez-Reiche AS, Carreno JM, Hirsch E, et al. 2020. Real Time Investigation of a large Nosocomial Influenza A Outbreak Informed by Genomic Epidemiology. medRxiv:2020.05.10.20096693
 92. Janiri D, Doucet GE, Pompili M, Sani G, Luna B, et al. 2020. Risk and protective factors for childhood suicidality: a US population-based study. The lancet. Psychiatry 7:317-26
 93. Issler O, van der Zee YY, Ramakrishnan A, Wang J, Tan C, et al. 2020. Sex-Specific Role for the Long Non-coding RNA LINC00473 in Depression. Neuron 106:912-26.e5
 94. Imai M, Yamashita M, Sakai-Tagawa Y, Iwatsuki-Horimoto K, Kiso M, et al. 2020. Influenza A variants with reduced susceptibility to baloxavir isolated from Japanese patients are fit and transmit through respiratory droplets. Nature Microbiology 5:27-33
 95. Hussey MR, Burt A, Deyssenroth MA, Jackson BP, Hao K, et al. 2020. Placental lncRNA expression associated with placental cadmium concentrations and birth weight. Environ Epigenet 6:dvaa003-dvaa
 96. Hur JY, Frost GR, Wu X, Crump C, Pan SJ, et al. 2020. The innate immunity protein IFITM3 modulates γ-secretase in Alzheimer’s disease. Nature
 97. Hur J-Y, Frost GR, Wu X, Crump C, Pan SJ, et al. 2020. The innate immunity protein IFITM3 modulates γ-secretase in Alzheimer’s disease. Nature 586:735-40
 98. Hu X, Provasi D, Ramsey S, Filizola M. 2020. Mechanism of μ-Opioid Receptor-Magnesium Interaction and Positive Allosteric Modulation. Biophysical journal 118:909-21
 99. Hu X, Provasi D, Ramsey S, Filizola M. 2020. Mechanism of μ-Opioid Receptor-Magnesium Interaction and Positive Allosteric Modulation. Biophysical Journal 118:909-21
 100. Horgusluoglu-Moloch E, Xiao G, Wang M, Wang Q, Zhou X, et al. 2020. Systems modeling of white matter microstructural abnormalities in Alzheimer’s disease. NeuroImage: Clinical 26:102203
 101. Holmes G, Gonzalez-Reiche AS, Lu N, Zhou X, Rivera J, et al. 2020. Integrated Transcriptome and Network Analysis Reveals Spatiotemporal Dynamics of Calvarial Suturogenesis. Cell Reports 32:107871
 102. Hoffman GE, Roussos P. 2020. Dream: powerful differential expression analysis for repeated measures designs. Bioinformatics
 103. Hoffman GE, Bendl J, Girdhar K, Roussos P. 2020. decorate: differential epigenetic correlation test. Bioinformatics 36:2856-61
 104. Ho JSY, Angel M, Ma Y, Sloan E, Wang G, et al. 2020. Hybrid Gene Origination Creates Human-Virus Chimeric Proteins during Infection. Cell 181:1502-17.e23
 105. Hernandez-Meza G, von Felden J, Gonzalez-Kozlova EE, Garcia-Lezana T, Peix J, et al. 2020. DNA methylation profiling of human hepatocarcinogenesis. Hepatology n/a
 106. Hernández Cordero AI, Li X, Yang CX, Milne S, Bossé Y, et al. 2020. Gene expression network analysis provides potential targets against SARS-CoV-2. Scientific Reports 10:21863
 107. Heindel DW, Koppolu S, Zhang Y, Kasper B, Meche L, et al. 2020. Glycomic analysis of host response reveals high mannose as a key mediator of influenza severity. Proceedings of the National Academy of Sciences 117:26926-35
 108. Hauberg ME, Creus-Muncunill J, Bendl J, Kozlenkov A, Zeng B, et al. 2020. Common schizophrenia risk variants are enriched in open chromatin regions of human glutamatergic neurons. Nature communications 11:5581-
 109. Harman RM, Patel RS, Fan JC, Park JE, Rosenberg BR, Van de Walle GR. 2020. Single-cell RNA sequencing of equine mesenchymal stromal cells from primary donor-matched tissue sources reveals functional heterogeneity in immune modulation and cell motility. Stem Cell Res Ther 11:524-
 110. Han L, Zhao X, Benton ML, Perumal T, Collins RL, et al. 2020. Functional annotation of rare structural variation in the human brain. Nature communications 11:2990-
 111. Gorski M, Jung B, Li Y, Matias-Garcia PR, Wuttke M, et al. 2020. Meta-analysis uncovers genome-wide significant variants for rapid kidney function decline. Kidney International
 112. Gordon DE, Watson A, Roguev A, Zheng S, Jang GM, et al. 2020. A Quantitative Genetic Interaction Map of HIV Infection. Molecular cell 78:197-209 e7
 113. Gonzalez-Reiche AS, Hernandez MM, Sullivan MJ, Ciferri B, Alshammary H, et al. 2020. Introductions and early spread of SARS-CoV-2 in the New York City area. Science 369:297-301
 114. Gill D, Arvanitis M, Carter P, Cordero AIH, Jo B, et al. 2020. ACE inhibition and cardiometabolic risk factors, lung ACE2 and TMPRSS2 gene expression, and plasma ACE2 levels: a Mendelian randomization study. Royal Society Open Science 7:200958
 115. Garg P, Martin-Trujillo A, Rodriguez OL, Gies SJ, Jadhav B, Sharp AJ. 2020. Pervasive cis effects of variation in copy number of large tandem repeats on local epigenetics and gene expression. bioRxiv:2020.12.16.423078
 116. Garg P, Jadhav B, Rodriguez OL, Patel N, Martin-Trujillo A, et al. 2020. A survey of rare epigenetic variation in 23,116 human genomes identifies disease-relevant epivariations and novel CGG expansions. bioRxiv:2020.03.25.007864
 117. Garg P, Jadhav B, Rodriguez OL, Patel N, Martin-Trujillo A, et al. 2020. A Survey of Rare Epigenetic Variation in 23,116 Human Genomes Identifies Disease-Relevant Epivariations and CGG Expansions. The American Journal of Human Genetics 107:654-69
 118. Fulton-Howard B, Goate AM, Adelson RP, Koppel J, Gordon ML, et al. 2020. Greater Effect of Polygenic Risk Score for Alzheimer’s Disease Among Younger Cases who are Apolipoprotein E-ε4 Carriers. Neurobiology of Aging
 119. Espeso-Gil S, Halene T, Bendl J, Kassim B, Ben Hutta G, et al. 2020. A chromosomal connectome for psychiatric and metabolic risk variants in adult dopaminergic neurons. Genome medicine 12:19-
 120. Esai Selvan M, Zauderer MG, Rudin CM, Jones S, Mukherjee S, et al. 2020. Inherited Rare, Deleterious Variants in ATM Increase Lung Adenocarcinoma Risk. Journal of Thoracic Oncology 15:1871-9
 121. Egervari G, Akpoyibo D, Rahman T, Fullard JF, Callens JE, et al. 2020. Chromatin accessibility mapping of the striatum identifies tyrosine kinase FYN as a therapeutic target for heroin use disorder. Nature communications 11:4634-
 122. Dogra N, Ahsen ME, Kozlova EE, Chen T-y, Allette K, et al. 2020. exRNA Signatures in Extracellular Vesicles and their Tumor-Lineage from Prostate Cancer. medRxiv:2020.09.28.20190009
 123. Dobrindt K, Hoagland DA, Seah C, Kassim B, O’Shea CP, et al. 2020. Common genetic variation in humans impacts in vitro susceptibility to SARS-CoV-2 infection. bioRxiv:2020.09.20.300574
 124. Do AN, Watson CT, Cohain AT, Griffin RS, Grishin A, et al. 2020. Dual transcriptomic and epigenomic study of reaction severity in peanut-allergic children. Journal of Allergy and Clinical Immunology 145:1219-30
 125. Deyssenroth MA, Marsit CJ, Chen J, Lambertini L. 2020. In-depth characterization of the placental imprintome reveals novel differentially methylated regions across birth weight categories. Epigenetics 15:47-60
 126. Deonaraine KK, Wang Q, Cheng H, Chan KL, Lin H-Y, et al. 2020. Sex-specific peripheral and central responses to stress-induced depression and treatment in a mouse model. Journal of Neuroscience Research 98:2541-53
 127. Clarkson-Townsend DA, Kennedy E, Everson TM, Deyssenroth MA, Burt AA, et al. 2020. Seasonally variant gene expression in full-term human placenta. The FASEB Journal 34:10431-42
 128. Chen S, Kasper B, Zhang B, Lashua LP, Ross TM, et al. 2020. Age-Dependent Glycomic Response to the 2009 Pandemic H1N1 Influenza Virus and Its Association with Disease Severity. J Proteome Res 19:4486-95
 129. Chen M-H, Raffield LM, Mousas A, Sakaue S, Huffman JE, et al. 2020. Trans-ethnic and Ancestry-Specific Blood-Cell Genetics in 746,667 Individuals from 5 Global Populations. Cell 182:1198-213.e14
 130. Chang H, Sewda A, Marquez-Luna C, White SR, Whitney BM, et al. 2020. Genetic architecture of cardiometabolic risks in people living with HIV. BMC Medicine 18:288
 131. Chami N, Preuss M, Walker RW, Moscati A, Loos RJF. 2020. The role of polygenic susceptibility to obesity among carriers of pathogenic mutations in MC4R in the UK Biobank population. PLOS Medicine 17:e1003196
 132. Cappuccio A, Jensen ST, Hartmann BM, Sealfon SC, Soumelis V, Zaslavsky E. 2020. Deciphering the combinatorial landscape of immunity. eLife 9:e62148
 133. Cao J, Huang M, Guo L, Zhu L, Hou J, et al. 2020. MicroRNA-195 rescues ApoE4-induced cognitive deficits and lysosomal defects in Alzheimer’s disease pathogenesis. Molecular Psychiatry
 134. Caban AB, Pak TR, Obla A, Dupper A, Chacko KI, et al. 2020. PathoSPOT genomic epidemiology reveals under-the-radar nosocomial outbreaks. medRxiv:2020.05.11.20098103
 135. Bubie A, Gonzalez-Kozlova E, Akers N, Villanueva A, Losic B. 2020. Tumor fitness, immune exhaustion and clinical outcomes: impact of immune checkpoint inhibitors. Scientific reports 10:5062-
 136. Britton GJ, Chen-Liaw A, Cossarini F, Livanos AE, Spindler MP, et al. 2020. SARS-CoV-2-specific IgA and limited inflammatory cytokines are present in the stool of select patients with acute COVID-19. medRxiv:2020.09.03.20183947
 137. Breen MS, Garg P, Tang L, Mendonca D, Levy T, et al. 2020. Episignatures Stratifying Helsmoortel-Van Der Aa Syndrome Show Modest Correlation with Phenotype. The American Journal of Human Genetics 107:555-63
 138. Bicak M, Wang X, Gao X, Xu X, Vaananen R-M, et al. 2020. Prostate cancer risk SNP rs10993994 is a trans-eQTL for SNHG11 mediated through MSMB. Human Molecular Genetics
 139. Bicak M, Wang X, Gao X, Xu X, Väänänen R-M, et al. 2020. Prostate cancer risk SNP rs10993994 is a trans-eQTL for SNHG11 mediated through MSMB. Human Molecular Genetics 29:1581-91
 140. Bicak M, Lückerath K, Kalidindi T, Phelps ME, Strand S-E, et al. 2020. Genetic signature of prostate cancer mouse models resistant to optimized hK2 targeted α-particle therapy. Proc Natl Acad Sci U S A 117:15172-81
 141. Berbel Caban A, Pak TR, Obla A, Dupper AC, Chacko KI, et al. 2020. PathoSPOT genomic epidemiology reveals under-the-radar nosocomial outbreaks. Genome medicine 12:96-
 142. Beckmann ND, Lin W-J, Wang M, Cohain AT, Charney AW, et al. 2020. Multiscale causal networks identify VGF as a key regulator of Alzheimer’s disease. Nature Communications 11:3942
 143. Basak S, Kumar A, Ramsey S, Gibbs E, Kapoor A, et al. 2020. High-resolution structures of multiple 5-HT3AR-setron complexes reveal a novel mechanism of competitive inhibition. eLife 9:e57870
 144. Barretto N, Zhang H, Powell SK, Fernando MB, Zhang S, et al. 2020. ASCL1- and DLX2-induced GABAergic neurons from hiPSC-derived NPCs. Journal of neuroscience methods 334:108548
 145. Barbar L, Jain T, Zimmer M, Kruglikov I, Sadick JS, et al. 2020. CD49f Is a Novel Marker of Functional and Reactive Human iPSC-Derived Astrocytes. Neuron 107:436-53.e12
 146. Aydillo T, Gonzalez-Reiche AS, Aslam S, van de Guchte A, Khan Z, et al. 2020. Shedding of Viable SARS-CoV-2 after Immunosuppressive Therapy for Cancer. New England Journal of Medicine 383:2586-8
 147. Aschenbrenner AJ, James BD, McDade E, Wang G, Lim YY, et al. 2020. Awareness of genetic risk in the Dominantly Inherited Alzheimer Network (DIAN). Alzheimer’s & Dementia 16:219-28
 148. Andrews SJ, Goate A, Anstey KJ. 2020. Association between alcohol consumption and Alzheimer’s disease: A Mendelian randomization study. Alzheimers Dement 16:345-53
 149. Andrews SJ, Fulton-Howard B, Patterson C, McFall GP, Gross A, et al. 2020. Mitonuclear interactions influence Alzheimer’s disease risk. Neurobiology of Aging 87:138.e7-.e14
 150. Andrews SJ, Fulton-Howard B, O’Reilly P, Marcora E, Goate AM, collaborators of the Alzheimer’s Disease Genetics C. 2020. Causal associations between modifiable risk factors and the Alzheimer’s phenome. Annals of Neurology n/a
 151. Andrews SJ, Fulton-Howard B, Goate A. 2020. Interpretation of risk loci from genome-wide association studies of Alzheimer’s disease. The Lancet Neurology 19:326-35
 152. Allen RJ, Guillen-Guio B, Oldham JM, Ma S-F, Dressen A, et al. 2020. Genome-Wide Association Study of Susceptibility to Idiopathic Pulmonary Fibrosis. Am J Respir Crit Care Med 201:564-74
 153. Agüero B, Mena J, Berrios F, Tapia R, Salinas C, et al. 2020. First report of porcine respirovirus 1 in South America. Veterinary Microbiology 246:108726

2019

1. 1. Abbas A, Romigh T, Eng C. PTEN interacts with RNA polymerase II to dephosphorylate polymerase II C-terminal domain. Oncotarget; Vol 10, No 48. 2019.
 2. Abul-Husn NS, Soper ER, Odgis JA, Cullina S, Bobo D, Moscati A, et al. Exome sequencing reveals a high prevalence of BRCA1 and BRCA2 founder variants in a diverse population-based biobank. Genome Medicine. 2019;12(1):2. doi: 10.1186/s13073-019-0691-1.
 3. Abul-Husn NS, Soper ER, Odgis JA, Cullina S, Bobo D, Moscati A, et al. Exome sequencing reveals a high prevalence of BRCA1 and BRCA2 founder variants in a diverse population-based biobank. Genome medicine. 2019;12(1):2-. doi: 10.1186/s13073-019-0691-1. PubMed PMID: 31892343.
 4. Adelson RP, Renton AE, Li W, Barzilai N, Atzmon G, Goate AM, et al. Empirical design of a variant quality control pipeline for whole genome sequencing data using replicate discordance. Scientific Reports. 2019;9(1):16156. doi: 10.1038/s41598-019-52614-7.
 5. Ahsen ME, Chun Y, Grishin A, Grishina G, Stolovitzky G, Pandey G, et al. NeTFactor, a framework for identifying transcriptional regulators of gene expression-based biomarkers. Scientific Reports. 2019;9(1):12970. doi: 10.1038/s41598-019-49498-y.
 6. Ali MR, Mezei M. Observation of quantum signature in rivastigmine chemical bond break-up and quantum energetics, spectral studies of anti-Alzheimer inhibitors. Journal of Biomolecular Structure and Dynamics. 2019:1-11. doi: 10.1080/07391102.2019.1708462.
 7. Andrews SJ, Fulton-Howard B, Patterson C, McFall GP, Gross A, Michaelis EK, et al. Mitonuclear interactions influence Alzheimer’s disease risk. Neurobiology of Aging. 2019. doi: https://doi.org/10.1016/j.neurobiolaging.2019.09.007.
 8. Andrews SJ, Goate A. Mendelian randomization indicates that TNF is not causally associated with Alzheimer’s disease. Neurobiology of Aging. 2019;84:241.e1-.e3. doi: https://doi.org/10.1016/j.neurobiolaging.2019.09.003.
 9. Andrews SJ, Goate A, Anstey KJ. Association between alcohol consumption and Alzheimer’s disease: A Mendelian randomization study. Alzheimer’s & Dementia. 2019. doi: https://doi.org/10.1016/j.jalz.2019.09.086.
 10. Au – Wu M, Au – Kriti D, Au – van Bakel H, Au – Jabs EW, Au – Holmes G. Laser Capture Microdissection of Mouse Embryonic Cartilage and Bone for Gene Expression Analysis. JoVE. 2019(154):e60503. doi: doi:10.3791/60503.
 11. Baker E, Sims R, Leonenko G, Frizzati A, Harwood JC, Grozeva D, et al. Gene-based analysis in HRC imputed genome wide association data identifies three novel genes for Alzheimer’s disease. PloS one. 2019;14(7):e0218111-e. doi: 10.1371/journal.pone.0218111. PubMed PMID: 31283791.
 12. Bangi E, Ang C, Smibert P, Uzilov AV, Teague AG, Antipin Y, et al. A personalized platform identifies trametinib plus zoledronate for a patient with KRAS-mutant metastatic colorectal cancer. Science advances. 2019;5(5):eaav6528-eaav. doi: 10.1126/sciadv.aav6528. PubMed PMID: 31131321.
 13. Basak S, Gicheru Y, Kapoor A, Mayer ML, Filizola M, Chakrapani S. Molecular mechanism of setron-mediated inhibition of full-length 5-HT(3A) receptor. Nature communications. 2019;10(1):3225-. doi: 10.1038/s41467-019-11142-8. PubMed PMID: 31324772.
 14. Beaulaurier J, Schadt EE, Fang G. Deciphering bacterial epigenomes using modern sequencing technologies. Nature Reviews Genetics. 2019;20(3):157-72. doi: 10.1038/s41576-018-0081-3.
 15. Bergervoet SA, Pritz-Verschuren SBE, Gonzales JL, Bossers A, Poen MJ, Dutta J, et al. Circulation of low pathogenic avian influenza (LPAI) viruses in wild birds and poultry in the Netherlands, 2006–2016. Scientific Reports. 2019;9(1):13681. doi: 10.1038/s41598-019-50170-8.
 16. Bis JC, Jian X, Kunkle BW, Chen Y, Hamilton-Nelson KL, Bush WS, et al. Correction: Whole exome sequencing study identifies novel rare and common Alzheimer’s-Associated variants involved in immune response and transcriptional regulation. Molecular Psychiatry. 2019. doi: 10.1038/s41380-019-0529-7.
 17. Bowles KR, Tcw J, Qian L, Jadow BM, Goate AM. Reduced variability of neural progenitor cells and improved purity of neuronal cultures using magnetic activated cell sorting. PloS one. 2019;14(3):e0213374-e. doi: 10.1371/journal.pone.0213374. PubMed PMID: 30917153.
 18. Brazel DM, Jiang Y, Hughey JM, Turcot V, Zhan X, Gong J, et al. Exome Chip Meta-analysis Fine Maps Causal Variants and Elucidates the Genetic Architecture of Rare Coding Variants in Smoking and Alcohol Use. Biological Psychiatry. 2019;85(11):946-55. doi: https://doi.org/10.1016/j.biopsych.2018.11.024.
 19. Breen MS, Bierer LM, Daskalakis NP, Bader HN, Makotkine I, Chattopadhyay M, et al. Differential transcriptional response following glucocorticoid activation in cultured blood immune cells: a novel approach to PTSD biomarker development. Translational Psychiatry. 2019;9(1):201. doi: 10.1038/s41398-019-0539-x.
 20. Breen MS, Browne A, Hoffman GE, Stathopoulos S, Brennand K, Buxbaum JD, et al. Transcriptional signatures of participant-derived neural progenitor cells and neurons implicate altered Wnt signaling in Phelan McDermid syndrome and autism. bioRxiv. 2019:855163. doi: 10.1101/855163.
 21. Breen MS, Dobbyn A, Li Q, Roussos P, Hoffman GE, Stahl E, et al. Global landscape and genetic regulation of RNA editing in cortical samples from individuals with schizophrenia. Nature Neuroscience. 2019;22(9):1402-12. doi: 10.1038/s41593-019-0463-7.
 22. Breen MS, Thomas KGF, Baldwin DS, Lipinska G. Modelling PTSD diagnosis using sleep, memory, and adrenergic metabolites: An exploratory machine-learning study. Human Psychopharmacology: Clinical and Experimental. 2019;34(2):e2691. doi: 10.1002/hup.2691.
 23. Britton GJ, Contijoch EJ, Mogno I, Vennaro OH, Llewellyn SR, Ng R, et al. Microbiotas from Humans with Inflammatory Bowel Disease Alter the Balance of Gut Th17 and RORγt(+) Regulatory T Cells and Exacerbate Colitis in Mice. Immunity. 2019;50(1):212-24.e4. doi: 10.1016/j.immuni.2018.12.015. PubMed PMID: 30650377.
 24. Bubie A, Gonzalez-Kozlova E, Akers N, Villanueva A, Losic B. Tumor fitness, immune exhaustion and clinical outcomes: impact of immune checkpoint inhibitors. bioRxiv. 2019:679886. doi: 10.1101/679886.
 25. Chen B, Wang M, Gan L, Zhang B, Desnick RJ, Yasuda M. Characterization of the hepatic transcriptome following phenobarbital induction in mice with AIP. Molecular Genetics and Metabolism. 2019. doi: https://doi.org/10.1016/j.ymgme.2018.12.010.
 26. Cheng H, Wang L, Wang D, Zhang J, Cheng L, Yao P, et al. Bio3Air, an integrative system for monitoring individual-level air pollutant exposure with high time and spatial resolution. Ecotoxicology and Environmental Safety. 2019;169:756-63. doi: https://doi.org/10.1016/j.ecoenv.2018.11.067.
 27. Choi H, Song W-m, Wang M, Sram RJ, Zhang B. Benzo[a]pyrene is associated with dysregulated myelo-lymphoid hematopoiesis in asthmatic children. Environment International. 2019;128:218-32. doi: https://doi.org/10.1016/j.envint.2019.04.052.
 28. Clark DW, Okada Y, Moore KHS, Mason D, Pirastu N, Gandin I, et al. Associations of autozygosity with a broad range of human phenotypes. Nature communications. 2019;10(1):4957-. doi: 10.1038/s41467-019-12283-6. PubMed PMID: 31673082.
 29. Clarkson-Townsend DA, Everson TM, Deyssenroth MA, Burt AA, Hermetz KE, Hao K, et al. Maternal circadian disruption is associated with variation in placental DNA methylation. PLOS ONE. 2019;14(4):e0215745. doi: 10.1371/journal.pone.0215745.
 30. Contijoch EJ, Britton GJ, Yang C, Mogno I, Li Z, Ng R, et al. Gut microbiota density influences host physiology and is shaped by host and microbial factors. eLife. 2019;8:e40553. doi: 10.7554/eLife.40553. PubMed PMID: 30666957.
 31. Copin R, Sause WE, Fulmer Y, Balasubramanian D, Dyzenhaus S, Ahmed JM, et al. Sequential evolution of virulence and resistance during clonal spread of community-acquired methicillin-resistant Staphylococcus aureus</em&gt. Proceedings of the National Academy of Sciences. 2019;116(5):1745. doi: 10.1073/pnas.1814265116.
 32. Copin R, Sause WE, Fulmer Y, Balasubramanian D, Dyzenhaus S, Ahmed JM, et al. Sequential evolution of virulence and resistance during clonal spread of community-acquired methicillin-resistant Staphylococcus aureus. Proceedings of the National Academy of Sciences of the United States of America. 2019;116(5):1745-54. Epub 2019/01/11. doi: 10.1073/pnas.1814265116. PubMed PMID: 30635416.
 33. Dallner OS, Marinis JM, Lu Y-H, Birsoy K, Werner E, Fayzikhodjaeva G, et al. Dysregulation of a long noncoding RNA reduces leptin leading to a leptin-responsive form of obesity. Nature Medicine. 2019;25(3):507-16. doi: 10.1038/s41591-019-0370-1.
 34. Damrauer SM, Chaudhary K, Cho JH, Liang LW, Argulian E, Chan L, et al. Association of the V122I Hereditary Transthyretin Amyloidosis Genetic Variant With Heart Failure Among Individuals of African or Hispanic/Latino Ancestry. JAMA. 2019;322(22):2191-202. doi: 10.1001/jama.2019.17935.
 35. Davenport B, Eberlein J, van der Heide V, Jhun K, Nguyen TT, Victorino F, et al. Aging of Antiviral CD8+ Memory T Cells Fosters Increased Survival, Metabolic Adaptations, and Lymphoid Tissue Homing. The Journal of Immunology. 2019;202(2):460. doi: 10.4049/jimmunol.1801277.
 36. Daya M, Rafaels N, Brunetti TM, Chavan S, Levin AM, Shetty A, et al. Association study in African-admixed populations across the Americas recapitulates asthma risk loci in non-African populations. Nature Communications. 2019;10(1):880. doi: 10.1038/s41467-019-08469-7.
 37. Di Narzo AF, Brodmerkel C, Telesco SE, Argmann C, Peters LA, Li K, et al. High-Throughput Identification of the Plasma Proteomic Signature of Inflammatory Bowel Disease. Journal of Crohn’s & colitis. 2019;13(4):462-71. Epub 2018/11/15. doi: 10.1093/ecco-jcc/jjy190. PubMed PMID: 30445421.
 38. Do AN, Watson CT, Cohain AT, Griffin RS, Grishin A, Wood RA, et al. Dual transcriptomic and epigenomic study of reaction severity in peanut allergic children. Journal of Allergy and Clinical Immunology. 2019. doi: https://doi.org/10.1016/j.jaci.2019.10.040.
 39. Doucet GE, Lee WH, Frangou S. Evaluation of the spatial variability in the major resting-state networks across human brain functional atlases. Human brain mapping. 2019;40(15):4577-87. Epub 2019/07/19. doi: 10.1002/hbm.24722. PubMed PMID: 31322303.
 40. Doucet GE, Luber MJ, Balchandani P, Sommer IE, Frangou S. Abnormal auditory tonotopy in patients with schizophrenia. npj Schizophrenia. 2019;5(1):16. doi: 10.1038/s41537-019-0084-x.
 41. Doucet GE, Moser DA, Rodrigue A, Bassett DS, Glahn DC, Frangou S. Person-Based Brain Morphometric Similarity is Heritable and Correlates With Biological Features. Cerebral cortex (New York, NY : 1991). 2019;29(2):852-62. doi: 10.1093/cercor/bhy287. PubMed PMID: 30462205.
 42. Dumitrescu L, Barnes LL, Thambisetty M, Beecham G, Kunkle B, Bush WS, et al. Sex differences in the genetic predictors of Alzheimer’s pathology. Brain. 2019;142(9):2581-9. doi: 10.1093/brain/awz206.
 43. Dupper AC, Sullivan MJ, Chacko KI, Mishkin A, Ciferri B, Kumaresh A, et al. Blurred Molecular Epidemiological Lines Between the Two Dominant Methicillin-Resistant Staphylococcus aureus Clones. Open forum infectious diseases. 2019;6(9):ofz302-ofz. doi: 10.1093/ofid/ofz302. PubMed PMID: 31660395.
 44. Edwards TL, Giri A, Hellwege JN, Hartmann KE, Stewart EA, Jeff JM, et al. A Trans-Ethnic Genome-Wide Association Study of Uterine Fibroids. Frontiers in Genetics. 2019;10:511.
 45. Erzurumluoglu AM, Liu M, Jackson VE, Barnes DR, Datta G, Melbourne CA, et al. Meta-analysis of up to 622,409 individuals identifies 40 novel smoking behaviour associated genetic loci. Molecular Psychiatry. 2019. doi: 10.1038/s41380-018-0313-0.
 46. Esai Selvan M, Klein RJ, Gümüş ZH. Rare, Pathogenic Germline Variants in Fanconi Anemia Genes Increase Risk for Squamous Lung Cancer. Clinical Cancer Research. 2019;25(5):1517. doi: 10.1158/1078-0432.CCR-18-2660.
 47. Everson TM, Marable C, Deyssenroth MA, Punshon T, Jackson BP, Lambertini L, et al. Placental Expression of Imprinted Genes, Overall and in Sex-Specific Patterns, Associated with Placental Cadmium Concentrations and Birth Size. Environmental health perspectives. 2019;127(5):57005-. doi: 10.1289/EHP4264. PubMed PMID: 31082282.
 48. Farrelly LA, Thompson RE, Zhao S, Lepack AE, Lyu Y, Bhanu NV, et al. Histone serotonylation is a permissive modification that enhances TFIID binding to H3K4me3. Nature. 2019;567(7749):535-9. Epub 2019/03/13. doi: 10.1038/s41586-019-1024-7. PubMed PMID: 30867594.
 49. Fernandez-Jimenez R, Jaslow R, Bansilal S, Santana M, Diaz-Munoz R, Latina J, et al. Child Health Promotion in Underserved Communities. Journal of the American College of Cardiology. 2019;73(16):2011. doi: 10.1016/j.jacc.2019.01.057.
 50. Filizola M. Insights from molecular dynamics simulations to exploit new trends for the development of improved opioid drugs. Neuroscience Letters. 2019;700:50-5. doi: https://doi.org/10.1016/j.neulet.2018.02.037.
 51. Flaherty E, Zhu S, Barretto N, Cheng E, Deans PJM, Fernando MB, et al. Neuronal impact of patient-specific aberrant NRXN1α splicing. Nature Genetics. 2019;51(12):1679-90. doi: 10.1038/s41588-019-0539-z.
 52. Flannick J, Mercader JM, Fuchsberger C, Udler MS, Mahajan A, Wessel J, et al. Exome sequencing of 20,791 cases of type 2 diabetes and 24,440 controls. Nature. 2019;570(7759):71-6. Epub 2019/05/22. doi: 10.1038/s41586-019-1231-2. PubMed PMID: 31118516.
 53. Frades I RB, Amadori L, Koplev S, Talukdar HA, Crane HM, Crane PK,, Kovacic JC DJ, Giannarelli C, Björkegren JLM, Peter I. Systems Pharmacology Identifies an Arterial Wall Regulatory Gene Network Mediating Coronary Artery Disease Side Effects of Antiretroviral Therapy. Circ Genom Precis Med. 2019. Epub 2019 May 6. doi: doi: 10.1161/CIRCGEN.118.002390. PubMed Central PMCID: PMCPMID: 31059280
 54. Franzmeier N, Ren J, Damm A, Monté-Rubio G, Boada M, Ruiz A, et al. The BDNF(Val66Met) SNP modulates the association between beta-amyloid and hippocampal disconnection in Alzheimer’s disease. Molecular psychiatry. 2019:10.1038/s41380-019-0404-6. doi: 10.1038/s41380-019-0404-6. PubMed PMID: 30899092.
 55. Frolinger T, Sims S, Smith C, Wang J, Cheng H, Faith J, et al. The gut microbiota composition affects dietary polyphenols-mediated cognitive resilience in mice by modulating the bioavailability of phenolic acids. Scientific Reports. 2019;9(1):3546. doi: 10.1038/s41598-019-39994-6.
 56. Fu J, Akat KM, Sun Z, Zhang W, Schlondorff D, Liu Z, et al. Single-Cell RNA Profiling of Glomerular Cells Shows Dynamic Changes in Experimental Diabetic Kidney Disease. Journal of the American Society of Nephrology. 2019;30(4):533. doi: 10.1681/ASN.2018090896.
 57. Fullard JF, Charney AW, Voloudakis G, Uzilov AV, Haroutunian V, Roussos P. Assessment of somatic single-nucleotide variation in brain tissue of cases with schizophrenia. Translational psychiatry. 2019;9(1):21-. doi: 10.1038/s41398-018-0342-0. PubMed PMID: 30655504.
 58. Furusawa Y, Yamada S, da Silva Lopes TJ, Dutta J, Khan Z, Kriti D, et al. Influenza Virus Polymerase Mutation Stabilizes a Foreign Gene Inserted into the Virus Genome by Enhancing the Transcription/Replication Efficiency of the Modified Segment. mBio. 2019;10(5):e01794-19. doi: 10.1128/mBio.01794-19.
 59. Garg P, Sharp AJ. Screening for rare epigenetic variations in autism and schizophrenia. Human Mutation. 2019;0(0). doi: 10.1002/humu.23740.
 60. Golden CEM, Breen MS, Koro L, Sonar S, Niblo K, Browne A, et al. Deletion of the KH1 Domain of Fmr1 Leads to Transcriptional Alterations and Attentional Deficits in Rats. Cerebral cortex (New York, NY : 1991). 2019;29(5):2228-44. doi: 10.1093/cercor/bhz029. PubMed PMID: 30877790.
 61. Grove J, Ripke S, Als TD, Mattheisen M, Walters RK, Won H, et al. Identification of common genetic risk variants for autism spectrum disorder. Nature genetics. 2019;51(3):431-44. Epub 2019/02/25. doi: 10.1038/s41588-019-0344-8. PubMed PMID: 30804558.
 62. Gruber C, Calis J, Buta S, Evrony G, Martin J, Uhl S, et al. Complex Autoinflammatory Syndrome Unveils Fundamental Principles of JAK1 Transcriptional and Biochemical Function. bioRxiv. 2019:807669. doi: 10.1101/807669.
 63. Hernandez I, Luna G, Rauch JN, Reis SA, Giroux M, Karch CM, et al. A farnesyltransferase inhibitor activates lysosomes and reduces tau pathology in mice with tauopathy. Science Translational Medicine. 2019;11(485):eaat3005. doi: 10.1126/scitranslmed.aat3005.
 64. Hirten RP, Grinspan A, Fu S-C, Luo Y, Suarez-Farinas M, Rowland J, et al. Microbial Engraftment and Efficacy of Fecal Microbiota Transplant for Clostridium Difficile in Patients With and Without Inflammatory Bowel Disease. Inflammatory Bowel Diseases. 2019;25(6):969-79. doi: 10.1093/ibd/izy398. PubMed PMID: 30852592.
 65. Hoffman GE, Bendl J, Girdhar K, Schadt EE, Roussos P. Functional interpretation of genetic variants using deep learning predicts impact on chromatin accessibility and histone modification. Nucleic acids research. 2019;47(20):10597-611. doi: 10.1093/nar/gkz808. PubMed PMID: 31544924.
 66. Hoffman GE, Bendl J, Voloudakis G, Montgomery KS, Sloofman L, Wang Y-C, et al. CommonMind Consortium provides transcriptomic and epigenomic data for Schizophrenia and Bipolar Disorder. Scientific Data. 2019;6(1):180. doi: 10.1038/s41597-019-0183-6.
 67. Holt RJ, Young RM, Crespo B, Ceroni F, Curry CJ, Bellacchio E, et al. De Novo Missense Variants in FBXW11 Cause Diverse Developmental Phenotypes Including Brain, Eye, and Digit Anomalies. The American Journal of Human Genetics. 2019;105(3):640-57. doi: https://doi.org/10.1016/j.ajhg.2019.07.005.
 68. Homan P, Levy I, Feltham E, Gordon C, Hu J, Li J, et al. Neural computations of threat in the aftermath of combat trauma. Nature Neuroscience. 2019;22(3):470-6. doi: 10.1038/s41593-018-0315-x.
 69. Hu J, Ly J, Zhang W, Huang Y, Glover V, Peter I, et al. Microbiota of newborn meconium is associated with maternal anxiety experienced during pregnancy. Developmental Psychobiology. 2019;0(0). doi: 10.1002/dev.21837. PubMed PMID: 30908632.
 70. Hu W, Jiang C, Guan D, Dierickx P, Zhang R, Moscati A, et al. Patient Adipose Stem Cell-Derived Adipocytes Reveal Genetic Variation that Predicts Antidiabetic Drug Response. Cell Stem Cell. 2019;24(2):299-308.e6. doi: https://doi.org/10.1016/j.stem.2018.11.018.
 71. Hu X, Provasi D, Ramsey S, Filizola M. Mechanism of μ-Opioid Receptor-Magnesium Interaction and Positive Allosteric Modulation. Biophysical Journal. 2019. doi: https://doi.org/10.1016/j.bpj.2019.10.007.
 72. Hu X, Wang Y, Hunkele A, Provasi D, Pasternak GW, Filizola M. Kinetic and thermodynamic insights into sodium ion translocation through the μ-opioid receptor from molecular dynamics and machine learning analysis. PLOS Computational Biology. 2019;15(1):e1006689. doi: 10.1371/journal.pcbi.1006689.
 73. Huang F, Wang M, Liu R, Wang J-Z, Schadt E, Haroutunian V, et al. CDT2-controlled cell cycle reentry regulates the pathogenesis of Alzheimer’s disease. Alzheimer’s & Dementia. 2019;15(2):217-31. doi: https://doi.org/10.1016/j.jalz.2018.08.013.
 74. Hughes TE, Del Rosario JS, Kapoor A, Yazici AT, Yudin Y, Fluck EC, 3rd, et al. Structure-based characterization of novel TRPV5 inhibitors. eLife. 2019;8:e49572. doi: 10.7554/eLife.49572. PubMed PMID: 31647410.
 75. Jadhav B, Monajemi R, Gagalova KK, Ho D, Draisma HHM, van de Wiel MA, et al. RNA-Seq in 296 phased trios provides a high-resolution map of genomic imprinting. BMC biology. 2019;17(1):50-. doi: 10.1186/s12915-019-0674-0. PubMed PMID: 31234833.
 76. Janiri D, Moser DA, Doucet GE, Luber MJ, Rasgon A, Lee WH, et al. Shared Neural Phenotypes for Mood and Anxiety Disorders: A Meta-analysis of 226 Task-Related Functional Imaging Studies. JAMA psychiatry. 2019:1-8. doi: 10.1001/jamapsychiatry.2019.3351. PubMed PMID: 31664439.
 77. Jiang P, Scarpa JR, Gao VD, Vitaterna MH, Kasarskis A, Turek FW. Parkinson’s Disease is Associated with Dysregulations of a Dopamine-Modulated Gene Network Relevant to Sleep and Affective Neurobehaviors in the Striatum. Scientific Reports. 2019;9(1):4808. doi: 10.1038/s41598-019-41248-4.
 78. Johnson EC, St. Pierre CL, Meyers JL, Aliev F, McCutcheon VV, Lai D, et al. The Genetic Relationship Between Alcohol Consumption and Aspects of Problem Drinking in an Ascertained Sample. Alcoholism: Clinical and Experimental Research. 2019;43(6):1113-25. doi: 10.1111/acer.14064.
 79. Kalayci S, Selvan ME, Ramos I, Cotsapas C, Harris E, Kim E-Y, et al. ImmuneRegulation: a web-based tool for identifying human immune regulatory elements. Nucleic acids research. 2019;47(W1):W142-W50. doi: 10.1093/nar/gkz450. PubMed PMID: 31114925.
 80. Kapoor M, Wang J-C, Farris SP, Liu Y, McClintick J, Gupta I, et al. Analysis of whole genome-transcriptomic organization in brain to identify genes associated with alcoholism. Translational psychiatry. 2019;9(1):89-. doi: 10.1038/s41398-019-0384-y. PubMed PMID: 30765688.
 81. Karch CM, Kao AW, Karydas A, Onanuga K, Martinez R, Argouarch A, et al. A Comprehensive Resource for Induced Pluripotent Stem Cells from Patients with Primary Tauopathies. Stem cell reports. 2019;13(5):939-55. Epub 2019/10/17. doi: 10.1016/j.stemcr.2019.09.006. PubMed PMID: 31631020.
 82. Katsel P, Roussos P, Fam P, Khan S, Tan W, Hirose T, et al. The expression of long noncoding RNA NEAT1 is reduced in schizophrenia and modulates oligodendrocytes transcription. NPJ schizophrenia. 2019;5(1):3-. doi: 10.1038/s41537-019-0071-2. PubMed PMID: 30696826.
 83. Kennedy E, Everson TM, Punshon T, Jackson BP, Hao K, Lambertini L, et al. Copper associates with differential methylation in placentae from two US birth cohorts. Epigenetics. 2019:1-16. doi: 10.1080/15592294.2019.1661211.
 84. Kerns SL, Fachal L, Dorling L, Barnett GC, Baran A, Peterson DR, et al. Radiogenomics Consortium Genome-Wide Association Study Meta-Analysis of Late Toxicity After Prostate Cancer Radiotherapy. JNCI: Journal of the National Cancer Institute. 2019. doi: 10.1093/jnci/djz075.
 85. Kowalski MH, Qian H, Hou Z, Rosen JD, Tapia AL, Shan Y, et al. Use of >100,000 NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium whole genome sequences improves imputation quality and detection of rare variant associations in admixed African and Hispanic/Latino populations. PLoS genetics. 2019;15(12):e1008500-e. doi: 10.1371/journal.pgen.1008500. PubMed PMID: 31869403.
 86. Kraja AT, Liu C, Fetterman JL, Graff M, Have CT, Gu C, et al. Associations of Mitochondrial and Nuclear Mitochondrial Variants and Genes with Seven Metabolic Traits. The American Journal of Human Genetics. 2019;104(1):112-38. doi: https://doi.org/10.1016/j.ajhg.2018.12.001.
 87. Kronman H, Richter F, Labonté B, Chandra R, Zhao S, Hoffman G, et al. Biology and Bias in Cell Type-Specific RNAseq of Nucleus Accumbens Medium Spiny Neurons. Scientific Reports. 2019;9(1):8350. doi: 10.1038/s41598-019-44798-9.
 88. Kunkle BW, Grenier-Boley B, Sims R, Bis JC, Damotte V, Naj AC, et al. Author Correction: Genetic meta-analysis of diagnosed Alzheimer’s disease identifies new risk loci and implicates Aβ, tau, immunity and lipid processing. Nature Genetics. 2019;51(9):1423-4. doi: 10.1038/s41588-019-0495-7.
 89. Kunkle BW, Grenier-Boley B, Sims R, Bis JC, Damotte V, Naj AC, et al. Genetic meta-analysis of diagnosed Alzheimer’s disease identifies new risk loci and implicates Aβ, tau, immunity and lipid processing. Nature Genetics. 2019;51(3):414-30. doi: 10.1038/s41588-019-0358-2.
 90. Lachance V, Wang Q, Sweet E, Choi I, Cai C-Z, Zhuang X-X, et al. Autophagy protein NRBF2 has reduced expression in Alzheimer’s brains and modulates memory and amyloid-beta homeostasis in mice. Molecular Neurodegeneration. 2019;14(1):43. doi: 10.1186/s13024-019-0342-4.
 91. Lai D, Wetherill L, Bertelsen S, Carey CE, Kamarajan C, Kapoor M, et al. Genome-wide association studies of alcohol dependence, DSM-IV criterion count and individual criteria. Genes, Brain and Behavior. 2019;0(0). doi: 10.1111/gbb.12579. PubMed PMID: 31090166.
 92. Lai D, Wetherill L, Kapoor M, Johnson EC, Schwandt M, Ramchandani VA, et al. Genome-wide association studies of the self-rating of effects of ethanol (SRE). Addiction Biology. 2019;n/a(n/a):e12800. doi: 10.1111/adb.12800.
 93. Lambertini L, Li Q, Ma Y, Zhang W, Hao K, Marsit C, et al. Placental imprinted gene expression mediates the effects of maternal psychosocial stress during pregnancy on fetal growth. Journal of Developmental Origins of Health and Disease. 2019;10(2):196-205. Epub 2019/04/10. doi: 10.1017/S2040174418000545.
 94. Lamim Ribeiro JM, Filizola M. Allostery in G protein-coupled receptors investigated by molecular dynamics simulations. Current Opinion in Structural Biology. 2019;55:121-8. doi: https://doi.org/10.1016/j.sbi.2019.03.016.
 95. Latif R, Mezei M, Morshed SA, Ma R, Ehrlich R, Davies TF. A Modifying Autoantigen in Graves’ Disease. Endocrinology. 2019;160(5):1008-20. doi: 10.1210/en.2018-01048.
 96. Laverty KU, Stout JM, Sullivan MJ, Shah H, Gill N, Holbrook L, et al. A physical and genetic map of Cannabis sativa identifies extensive rearrangements at the THC/CBD acid synthase loci. Genome research. 2019;29(1):146-56. doi: 10.1101/gr.242594.118. PubMed PMID: 30409771.
 97. Leandro J, Violante S, Argmann CA, Hagen J, Dodatko T, Bender A, et al. Mild inborn errors of metabolism in commonly used inbred mouse strains. Molecular Genetics and Metabolism. 2019;126(4):388-96. doi: https://doi.org/10.1016/j.ymgme.2019.01.021.
 98. Li J, Fukase Y, Shang Y, Zou W, Muñoz-Félix JM, Buitrago L, et al. Novel Pure αVβ3 Integrin Antagonists That Do Not Induce Receptor Extension, Prime the Receptor, or Enhance Angiogenesis at Low Concentrations. ACS Pharmacology & Translational Science. 2019;2(6):387-401. doi: 10.1021/acsptsci.9b00041.
 99. Li YI, Wong G, Humphrey J, Raj T. Prioritizing Parkinson’s disease genes using population-scale transcriptomic data. Nature communications. 2019;10(1):994-. doi: 10.1038/s41467-019-08912-9. PubMed PMID: 30824768.
 100. Li Z, Chen H, Zhong F, Zhang W, Lee K, He JC. Expression of Glutamate Receptor Subtype 3 Is Epigenetically Regulated in Podocytes under Diabetic Conditions. Kidney Diseases. 2019;5(1):34-42. doi: 10.1159/000492933.
 101. Lin BM, Nadkarni GN, Tao R, Graff M, Fornage M, Buyske S, et al. Genetics of Chronic Kidney Disease Stages Across Ancestries: The PAGE Study. Frontiers in genetics. 2019;10:494-. doi: 10.3389/fgene.2019.00494. PubMed PMID: 31178898.
 102. Liu Y, Wang M, Marcora EM, Zhang B, Goate AM. Promoter DNA hypermethylation – Implications for Alzheimer’s disease. Neuroscience Letters. 2019;711:134403. doi: https://doi.org/10.1016/j.neulet.2019.134403.
 103. Lorsch ZS, Hamilton PJ, Ramakrishnan A, Parise EM, Salery M, Wright WJ, et al. Stress resilience is promoted by a Zfp189-driven transcriptional network in prefrontal cortex. Nature Neuroscience. 2019;22(9):1413-23. doi: 10.1038/s41593-019-0462-8.
 104. M. M. Exploiting Sparse Statistics for a Sequence-Based Prediction of the Effect of Mutations. Algorithms. 2019;12(10):214.
 105. Ma A, Stratikopoulos E, Park K-S, Wei J, Martin TC, Yang X, et al. Discovery of a first-in-class EZH2 selective degrader. Nature Chemical Biology. 2019. doi: 10.1038/s41589-019-0421-4.
 106. Ma Y, Angel M, Wang G, Ho JSY, Zhao N, Noel J, et al. Discovery of UFO Proteins: Human-Virus Chimeric Proteins Generated During Influenza Virus Infection. bioRxiv. 2019:597617. doi: 10.1101/597617.
 107. Manservisi F, Lesseur C, Panzacchi S, Mandrioli D, Falcioni L, Bua L, et al. The Ramazzini Institute 13-week pilot study glyphosate-based herbicides administered at human-equivalent dose to Sprague Dawley rats: effects on development and endocrine system. Environmental health : a global access science source. 2019;18(1):15-. doi: 10.1186/s12940-019-0453-y. PubMed PMID: 30857531.
 108. Mao W, Zaslavsky E, Hartmann BM, Sealfon SC, Chikina M. Pathway-level information extractor (PLIER) for gene expression data. Nature Methods. 2019;16(7):607-10. doi: 10.1038/s41592-019-0456-1.
 109. Marioni RE, Harris SE, Zhang Q, McRae AF, Hagenaars SP, Hill WD, et al. Correction: GWAS on family history of Alzheimer’s disease. Translational Psychiatry. 2019;9(1):161. doi: 10.1038/s41398-019-0498-2.
 110. Meng F, Wu L, Dong L, Mitchell AV, James Block C, Liu J, et al. EGFL9 promotes breast cancer metastasis by inducing cMET activation and metabolic reprogramming. Nature communications. 2019;10(1):5033-. doi: 10.1038/s41467-019-13034-3. PubMed PMID: 31695034.
 111. Mervish NA, Hu J, Hagan LA, Arora M, Frau C, Choi J, et al. Associations of the Oral Microbiota with Obesity and Menarche in Inner City Girls. Journal of childhood obesity. 2019;4(1):2. Epub 2019/03/13. doi: 10.21767/2572-5394.100068. PubMed PMID: 31535093.
 112. Meyers JL, Chorlian DB, Johnson EC, Pandey AK, Kamarajan C, Salvatore JE, et al. Association of Polygenic Liability for Alcohol Dependence and EEG Connectivity in Adolescence and Young Adulthood. Brain sciences. 2019;9(10):280. doi: 10.3390/brainsci9100280. PubMed PMID: 31627376.
 113. Moon J-Y, Louie TL, Jain D, Sofer T, Schurmann C, Below JE, et al. A Genome-Wide Association Study Identifies Blood Disorder–Related Variants Influencing Hemoglobin A1c With Implications for Glycemic Status in U.S. Hispanics/Latinos. Diabetes Care. 2019;42(9):1784. doi: 10.2337/dc19-0168.
 114. Morris AP, Le TH, Wu H, Akbarov A, van der Most PJ, Hemani G, et al. Trans-ethnic kidney function association study reveals putative causal genes and effects on kidney-specific disease aetiologies. Nature communications. 2019;10(1):29-. doi: 10.1038/s41467-018-07867-7. PubMed PMID: 30604766.
 115. Motch Perrine SM, Wu M, Stephens NB, Kriti D, van Bakel H, Jabs EW, et al. Mandibular dysmorphology due to abnormal embryonic osteogenesis in FGFR2-related craniosynostosis mice. Disease Models &amp; Mechanisms. 2019;12(5):dmm038513. doi: 10.1242/dmm.038513.
 116. Noordam R, Bos MM, Wang H, Winkler TW, Bentley AR, Kilpeläinen TO, et al. Multi-ancestry sleep-by-SNP interaction analysis in 126,926 individuals reveals lipid loci stratified by sleep duration. Nature communications. 2019;10(1):5121-. doi: 10.1038/s41467-019-12958-0. PubMed PMID: 31719535.
 117. Ntranos A, Ntranos V, Bonnefil V, Liu J, Kim-Schulze S, He Y, et al. Fumarates target the metabolic-epigenetic interplay of brain-homing T cells in multiple sclerosis. Brain. 2019;142(3):647-61. doi: 10.1093/brain/awy344.
 118. Olin JW, Di Narzo AF, d’Escamard V, Kadian-Dodov D, Cheng H, Georges A, et al. A plasma proteogenomic signature for fibromuscular dysplasia. Cardiovascular Research. 2019;116(1):63-77. doi: 10.1093/cvr/cvz219.
 119. Peña CJ, Smith M, Ramakrishnan A, Cates HM, Bagot RC, Kronman HG, et al. Early life stress alters transcriptomic patterning across reward circuitry in male and female mice. Nature Communications. 2019;10(1):5098. doi: 10.1038/s41467-019-13085-6.
 120. Peng S, Deyssenroth MA, Di Narzo AF, Cheng H, Zhang Z, Lambertini L, et al. Genetic regulation of the placental transcriptome underlies birth weight and risk of childhood obesity. PLOS Genetics. 2019;14(12):e1007799. doi: 10.1371/journal.pgen.1007799.
 121. Pertesi M, Vallée M, Wei X, Revuelta MV, Galia P, Demangel D, et al. Exome sequencing identifies germline variants in DIS3 in familial multiple myeloma. Leukemia. 2019. doi: 10.1038/s41375-019-0452-6.
 122. Preische O, Schultz SA, Apel A, Kuhle J, Kaeser SA, Barro C, et al. Serum neurofilament dynamics predicts neurodegeneration and clinical progression in presymptomatic Alzheimer’s disease. Nature Medicine. 2019;25(2):277-83. doi: 10.1038/s41591-018-0304-3.
 123. Qadeer ZA, Valle-Garcia D, Hasson D, Sun Z, Cook A, Nguyen C, et al. ATRX In-Frame Fusion Neuroblastoma Is Sensitive to EZH2 Inhibition via Modulation of Neuronal Gene Signatures. Cancer Cell. 2019;36(5):512-27.e9. doi: https://doi.org/10.1016/j.ccell.2019.09.002.
 124. Ramírez AS, Kowal J, Locher KP. Cryo–electron microscopy structures of human oligosaccharyltransferase complexes OST-A and OST-B. Science. 2019;366(6471):1372. doi: 10.1126/science.aaz3505.
 125. Ramos I, Smith G, Ruf-Zamojski F, Martínez-Romero C, Fribourg M, Carbajal EA, et al. Innate Immune Response to Influenza Virus at Single-Cell Resolution in Human Epithelial Cells Revealed Paracrine Induction of Interferon Lambda 1. Journal of Virology. 2019;93(20):e00559-19. doi: 10.1128/JVI.00559-19.
 126. Rao X, Thapa KS, Chen AB, Lin H, Gao H, Reiter JL, et al. Allele-specific expression and high-throughput reporter assay reveal functional genetic variants associated with alcohol use disorders. Molecular Psychiatry. 2019. doi: 10.1038/s41380-019-0508-z.
 127. Rejwan Ali M, Sadoqi M, Boutajangout A, Mezei M. Virtual screening of a natural compound library at orthosteric and allosteric binding sites of the neurotensin receptor. Journal of Biomolecular Structure and Dynamics. 2019;37(17):4494-506. doi: 10.1080/07391102.2018.1552200.
 128. Ribeiro JML, Filizola M. Insights From Molecular Dynamics Simulations of a Number of G-Protein Coupled Receptor Targets for the Treatment of Pain and Opioid Use Disorders. Frontiers in molecular neuroscience. 2019;12:207-. doi: 10.3389/fnmol.2019.00207. PubMed PMID: 31507375.
 129. Richter F, Hoffman GE, Manheimer KB, Patel N, Sharp AJ, McKean D, et al. ORE identifies extreme expression effects enriched for rare variants. Bioinformatics. 2019. doi: 10.1093/bioinformatics/btz202.
 130. Rodriguez OL, Ritz A, Sharp AJ, Bashir A. MsPAC: a tool for haplotype-phased structural variant detection. Bioinformatics. 2019. doi: 10.1093/bioinformatics/btz618.
 131. Ruf-Zamojski F, Ge Y, Pincas H, Shan J, Song Y, Hines N, et al. Cytogenetic, Genomic, and Functional Characterization of Pituitary Gonadotrope Cell Lines. Journal of the Endocrine Society. 2019;3(5):902-20. doi: 10.1210/js.2019-00064.
 132. Sato T, Yoo S, Kong R, Sinha A, Chandramani-Shivalingappa P, Patel A, et al. Epigenomic profiling discovers trans-lineage SOX2 partnerships driving tumor heterogeneity in lung squamous cell carcinoma. Cancer Research. 2019:canres.2132.019. doi: 10.1158/0008-5472.CAN-19-2132.
 133. Satterstrom FK, Kosmicki JA, Wang J, Breen MS, De Rubeis S, An J-Y, et al. Large-scale exome sequencing study implicates both developmental and functional changes in the neurobiology of autism. bioRxiv. 2019:484113. doi: 10.1101/484113.
 134. Sause WE, Balasubramanian D, Irnov I, Copin R, Sullivan MJ, Sommerfield A, et al. The purine biosynthesis regulator PurR moonlights as a virulence regulator in Staphylococcus aureus</em&gt. Proceedings of the National Academy of Sciences. 2019;116(27):13563. doi: 10.1073/pnas.1904280116.
 135. Schrode N, Ho S-M, Yamamuro K, Dobbyn A, Huckins L, Matos MR, et al. Synergistic effects of common schizophrenia risk variants. Nature Genetics. 2019;51(10):1475-85. doi: 10.1038/s41588-019-0497-5.
 136. Seifert LL, Si C, Saha D, Sadic M, de Vries M, Ballentine S, et al. The ETS transcription factor ELF1 regulates a broadly antiviral program distinct from the type I interferon response. PLOS Pathogens. 2019;15(11):e1007634. doi: 10.1371/journal.ppat.1007634.
 137. Sewda A, White SR, Erazo M, Hao K, García-Fructuoso G, Fernández-Rodriguez I, et al. Nonsyndromic craniosynostosis: novel coding variants. Pediatric Research. 2019;85(4):463-8. doi: 10.1038/s41390-019-0274-2. PubMed PMID: 30651579.
 138. Shen Q, Xiao G, Zheng Y, Wang J, Liu Y, Zhu X, et al. ARMBIS: accurate and robust matching of brain image sequences from multiple modal imaging techniques. Bioinformatics. 2019;35(24):5281-9. doi: 10.1093/bioinformatics/btz404.
 139. Sprooten E, O’Halloran R, Dinse J, Lee WH, Moser DA, Doucet GE, et al. Depth-dependent intracortical myelin organization in the living human brain determined by in vivo ultra-high field magnetic resonance imaging. NeuroImage. 2019;185:27-34. Epub 2018/10/09. doi: 10.1016/j.neuroimage.2018.10.023. PubMed PMID: 30312809.
 140. Srinivasan S, Stephens C, Wilson E, Panchadsaram J, DeVoss K, Koistinen H, et al. Prostate Cancer Risk-Associated Single-Nucleotide Polymorphism Affects Prostate-Specific Antigen Glycosylation and Its Function. Clinical Chemistry. 2019;65(1):e1. doi: 10.1373/clinchem.2018.295790.
 141. Stefan-Lifshitz M, Karakose E, Cui L, Ettela A, Yi Z, Zhang W, et al. Epigenetic modulation of β cells by interferon-α via PNPT1/mir-26a/TET2 triggers autoimmune diabetes. JCI insight. 2019;4(5):e126663. doi: 10.1172/jci.insight.126663. PubMed PMID: 30721151.
 142. Steinbach N, Hasson D, Mathur D, Stratikopoulos EE, Sachidanandam R, Bernstein E, et al. PTEN interacts with the transcription machinery on chromatin and regulates RNA polymerase II-mediated transcription. Nucleic Acids Research. 2019. doi: 10.1093/nar/gkz272.
 143. Sullivan MJ, Altman DR, Chacko KI, Ciferri B, Webster E, Pak TR, et al. A Complete Genome Screening Program of Clinical Methicillin-Resistant Staphylococcus aureus Isolates Identifies the Origin and Progression of a Neonatal Intensive Care Unit Outbreak. Journal of clinical microbiology. 2019;57(12):e01261-19. doi: 10.1128/JCM.01261-19. PubMed PMID: 31578260.
 144. Sung YJ, de las Fuentes L, Winkler TW, Chasman DI, Bentley AR, Kraja AT, et al. A multi-ancestry genome-wide study incorporating gene–smoking interactions identifies multiple new loci for pulse pressure and mean arterial pressure. Human Molecular Genetics. 2019;28(15):2615-33. doi: 10.1093/hmg/ddz070.
 145. Takada K, Kawakami C, Fan S, Chiba S, Zhong G, Gu C, et al. A humanized MDCK cell line for the efficient isolation and propagation of human influenza viruses. Nature Microbiology. 2019;4(8):1268-73. doi: 10.1038/s41564-019-0433-6.
 146. Tejero R, Huang Y, Katsyv I, Kluge M, Lin J-Y, Tome-Garcia J, et al. Gene signatures of quiescent glioblastoma cells reveal mesenchymal shift and interactions with niche microenvironment. EBioMedicine. 2019;42:252-69. doi: 10.1016/j.ebiom.2019.03.064. PubMed PMID: 30952620.
 147. The Genetics of Glaucoma in People of African Descent C. Association of Genetic Variants With Primary Open-Angle Glaucoma Among Individuals With African Ancestry. JAMA. 2019;322(17):1682-91. doi: 10.1001/jama.2019.16161.
 148. Tin A, Marten J, Halperin Kuhns VL, Li Y, Wuttke M, Kirsten H, et al. Target genes, variants, tissues and transcriptional pathways influencing human serum urate levels. Nature Genetics. 2019;51(10):1459-74. doi: 10.1038/s41588-019-0504-x.
 149. Torres J, Hu J, Seki A, Eisele C, Nair N, Huang R, et al. Infants born to mothers with IBD present with altered gut microbiome that transfers abnormalities of the adaptive immune system to germ-free mice. Gut. 2019:gutjnl-2018-317855. doi: 10.1136/gutjnl-2018-317855. PubMed PMID: 31036757.
 150. Urreizti R, Mayer K, Evrony GD, Said E, Castilla-Vallmanya L, Cody NAL, et al. DPH1 syndrome: two novel variants and structural and functional analyses of seven missense variants identified in syndromic patients. European Journal of Human Genetics. 2019. doi: 10.1038/s41431-019-0374-9.
 151. Van Vleck TT, Chan L, Coca SG, Craven CK, Do R, Ellis SB, et al. Augmented intelligence with natural language processing applied to electronic health records for identifying patients with non-alcoholic fatty liver disease at risk for disease progression. International Journal of Medical Informatics. 2019;129:334-41. doi: https://doi.org/10.1016/j.ijmedinf.2019.06.028.
 152. Vangeepuram N, Liu B, Chiu P-h, Wang L, Pandey G. Predicting youth diabetes risk using NHANES data and machine learning. medRxiv. 2019:19007872. doi: 10.1101/19007872.
 153. Vasily NA, Kalpana G, Susan LT, Humberto P, Jr., Regina MS, Marilie DG, et al. Tumor expression of environmental chemical-responsive genes and breast cancer mortality. Endocrine-Related Cancer. 2019;26(12):843-51. doi: 10.1530/ERC-19-0357.
 154. Verheije R, Kupchik GS, Isidor B, Kroes HY, Lynch SA, Hawkes L, et al. Heterozygous loss-of-function variants of MEIS2 cause a triad of palatal defects, congenital heart defects, and intellectual disability. European Journal of Human Genetics. 2019;27(2):278-90. doi: 10.1038/s41431-018-0281-5.
 155. Vishnu A, Belbin GM, Wojcik GL, Bottinger EP, Gignoux CR, Kenny EE, et al. The role of country of birth, and genetic and self-identified ancestry, in obesity susceptibility among African and Hispanic Americans. The American Journal of Clinical Nutrition. 2019. doi: 10.1093/ajcn/nqz098.
 156. Vöglein J, Paumier K, Jucker M, Preische O, McDade E, Hassenstab J, et al. Clinical, pathophysiological and genetic features of motor symptoms in autosomal dominant Alzheimer’s disease. Brain. 2019;142(5):1429-40. doi: 10.1093/brain/awz050.
 157. Wang H, Nandakumar P, Tekola-Ayele F, Tayo BO, Ware EB, Gu CC, et al. Combined linkage and association analysis identifies rare and low frequency variants for blood pressure at 1q31. European Journal of Human Genetics. 2019;27(2):269-77. doi: 10.1038/s41431-018-0277-1.
 158. Wang L, Cheng H, Wang D, Zhao B, Zhang J, Cheng L, et al. Airway microbiome is associated with respiratory functions and responses to ambient particulate matter exposure. Ecotoxicology and Environmental Safety. 2019;167:269-77. doi: https://doi.org/10.1016/j.ecoenv.2018.09.079.
 159. Wang P, Karakose E, Liu H, Swartz E, Ackeifi C, Zlatanic V, et al. Combined Inhibition of DYRK1A, SMAD, and Trithorax Pathways Synergizes to Induce Robust Replication in Adult Human Beta Cells. Cell Metabolism. 2019;29(3):638-52.e5. doi: https://doi.org/10.1016/j.cmet.2018.12.005.
 160. Wang Q, Zhang Y, Wang M, Song W-M, Shen Q, McKenzie A, et al. The landscape of multiscale transcriptomic networks and key regulators in Parkinson’s disease. Nature Communications. 2019;10(1):5234. doi: 10.1038/s41467-019-13144-y.
 161. Wang S, Zhang C, Hasson D, Desai A, SenBanerjee S, Magnani E, et al. Epigenetic Compensation Promotes Liver Regeneration. Developmental Cell. 2019;50(1):43-56.e6. doi: https://doi.org/10.1016/j.devcel.2019.05.034.
 162. Warrington NM, Beaumont RN, Horikoshi M, Day FR, Helgeland Ø, Laurin C, et al. Maternal and fetal genetic effects on birth weight and their relevance to cardio-metabolic risk factors. Nature Genetics. 2019;51(5):804-14. doi: 10.1038/s41588-019-0403-1.
 163. Watkins WS, Hernandez EJ, Wesolowski S, Bisgrove BW, Sunderland RT, Lin E, et al. De novo and recessive forms of congenital heart disease have distinct genetic and phenotypic landscapes. Nature Communications. 2019;10(1):4722. doi: 10.1038/s41467-019-12582-y.
 164. Weiss K, Lazar HP, Kurolap A, Martinez AF, Paperna T, Cohen L, et al. The CHD4-related syndrome: a comprehensive investigation of theclinical spectrum, genotype–phenotype correlations, and molecular basis. Genetics in Medicine. 2019. doi: 10.1038/s41436-019-0612-0.
 165. Wetherill L, Lai D, Johnson EC, Anokhin A, Bauer L, Bucholz KK, et al. Genome-wide association study identifies loci associated with liability to alcohol and drug dependence that is associated with variability in reward-related ventral striatum activity in African- and European-Americans. Genes, Brain and Behavior. 2019;0(0):e12580. doi: 10.1111/gbb.12580. PubMed PMID: 31099175.
 166. Wetherill L, Lai D, Johnson EC, Anokhin A, Bauer L, Bucholz KK, et al. ERRATUM: Genome-wide association study identifies loci associated with liability to alcohol and drug dependence that is associated with variability in reward-related ventral striatum activity in African- and European-Americans. Genes, Brain and Behavior. 2019;18(8):e12608. doi: 10.1111/gbb.12608.
 167. Wingo AP, Dammer EB, Breen MS, Logsdon BA, Duong DM, Troncosco JC, et al. Large-scale proteomic analysis of human brain identifies proteins associated with cognitive trajectory in advanced age. Nature Communications. 2019;10(1):1619. doi: 10.1038/s41467-019-09613-z.
 168. Wojcik GL, Graff M, Nishimura KK, Tao R, Haessler J, Gignoux CR, et al. Genetic analyses of diverse populations improves discovery for complex traits. Nature. 2019;570(7762):514-8. doi: 10.1038/s41586-019-1310-4.
 169. Wuttke M, Li Y, Li M, Sieber KB, Feitosa MF, Gorski M, et al. A catalog of genetic loci associated with kidney function from analyses of a million individuals. Nature genetics. 2019;51(6):957-72. Epub 2019/05/31. doi: 10.1038/s41588-019-0407-x. PubMed PMID: 31152163.
 170. Yang J, Peng S, Zhang B, Houten S, Schadt E, Zhu J, et al. Human geroprotector discovery by targeting the converging subnetworks of aging and age-related diseases. GeroScience. 2019. doi: 10.1007/s11357-019-00106-x.
 171. Yang X, Yuan T, Ma R, Chacko KI, Smith M, Deikus G, et al. Mce3R Stress-Resistance Pathway Is Vulnerable to Small-Molecule Targeting That Improves Tuberculosis Drug Activities. ACS Infectious Diseases. 2019. doi: 10.1021/acsinfecdis.9b00099.
 172. Zhang W, Voloudakis G, Rajagopal VM, Readhead B, Dudley JT, Schadt EE, et al. Integrative transcriptome imputation reveals tissue-specific and shared biological mechanisms mediating susceptibility to complex traits. Nature communications. 2019;10(1):3834-. doi: 10.1038/s41467-019-11874-7. PubMed PMID: 31444360.
 173. Zhang Z, Cheng H, Hong X, Narzo AFD, Franzén O, Peng S, et al., editors. EnsembleCNV: an ensemble machine learning algorithm to identify and genotype copy number variation using SNP array data. Nucleic acids research; 2019.
 174. Zhao L, He Z, Zhang D, Wang GT, Renton AE, Vardarajan BN, et al. A Rare Variant Nonparametric Linkage Method for Nuclear and Extended Pedigrees with Application to Late-Onset Alzheimer Disease via WGS Data. The American Journal of Human Genetics. 2019;105(4):822-35. doi: https://doi.org/10.1016/j.ajhg.2019.09.006.
 175. Zheutlin AB, Dennis J, Karlsson Linnér R, Moscati A, Restrepo N, Straub P, et al. Penetrance and Pleiotropy of Polygenic Risk Scores for Schizophrenia in 106,160 Patients Across Four Health Care Systems. The American journal of psychiatry. 2019;176(10):846-55. Epub 2019/08/16. doi: 10.1176/appi.ajp.2019.18091085. PubMed PMID: 31416338.
 176. Zhong G, Fan S, Lopes TJS, Le MQ, van Bakel H, Dutta J, et al. Isolation of Highly Pathogenic H5N1 Influenza Viruses in 2009-2013 in Vietnam. Frontiers in microbiology. 2019;10:1411-. doi: 10.3389/fmicb.2019.01411. PubMed PMID: 31293548.

2018

1. Altman DR, Sullivan MJ, Chacko KI, Balasubramanian D, Pak TR, Sause WE, et al. Genome Plasticity of agr-Defective Staphylococcus aureus during Clinical Infection. Infection and immunity. 2018;86(10):e00331-18. doi: 10.1128/IAI.00331-18. PubMed PMID: 30061376.

2. Audrain M, Haure-Mirande J-V, Wang M, Kim SH, Fanutza T, Chakrabarty P, et al. Integrative approach to sporadic Alzheimer’s disease: deficiency of TYROBP in a tauopathy mouse model reduces C1q and normalizes clinical phenotype while increasing spread and state of phosphorylation of tau. Molecular Psychiatry. 2018. doi: 10.1038/s41380-018-0258-3.

3. Aushev VN, Lee E, Zhu J, Gopalakrishnan K, Li Q, Teitelbaum SL, et al. Novel Predictors of Breast Cancer Survival Derived from miRNA Activity Analysis. Clinical Cancer Research. 2018;24(3):581.

4. Ayata P, Badimon A, Strasburger HJ, Duff MK, Montgomery SE, Loh Y-HE, et al. Epigenetic regulation of brain region-specific microglia clearance activity. Nature Neuroscience. 2018;21(8):1049-60. doi: 10.1038/s41593-018-0192-3.

5. Barbosa M, Joshi RS, Garg P, Martin-Trujillo A, Patel N, Jadhav B, et al. Identification of rare de novo epigenetic variations in congenital disorders. bioRxiv. 2018.

6. Barbosa M, Joshi RS, Garg P, Martin-Trujillo A, Patel N, Jadhav B, et al. Identification of rare de novo epigenetic variations in congenital disorders. Nature communications. 2018;9(1):2064-. doi: 10.1038/s41467-018-04540-x. PubMed PMID: 29802345.

7. Bonnemaijer PWM, Iglesias AI, Nadkarni GN, Sanyiwa AJ, Hassan HG, Cook C, et al. Genome-wide association study of primary open-angle glaucoma in continental and admixed African populations. Human Genetics. 2018;137(10):847-62. doi: 10.1007/s00439-018-1943-7.

8. Cates HM, Heller EA, Lardner CK, Purushothaman I, Peña CJ, Walker DM, et al. Transcription Factor E2F3a in Nucleus Accumbens Affects Cocaine Action via Transcription and Alternative Splicing. Biological Psychiatry. 2018;84(3):167-79. doi: https://doi.org/10.1016/j.biopsych.2017.11.027.

9. Cates HM, Li X, Purushothaman I, Kennedy PJ, Shen L, Shaham Y, et al. Genome-wide transcriptional profiling of central amygdala and orbitofrontal cortex during incubation of methamphetamine craving. Neuropsychopharmacology. 2018;43(12):2426-34. doi: 10.1038/s41386-018-0158-x.

10. Chacko K, Sullivan M, Beckford C, Altman D, Ciferri B, Pak T, et al. The genetic basis of emerging vancomycin, linezolid, and daptomycin heteroresistance in a case of persistent Enterococcus faecium bacteremia. Antimicrobial Agents and Chemotherapy. 2018.

11. Chacko KI, Sullivan MJ, Beckford C, Altman DR, Ciferri B, Pak TR, et al. Genetic Basis of Emerging Vancomycin, Linezolid, and Daptomycin Heteroresistance in a Case of Persistent Enterococcus faecium Bacteremia. Antimicrobial agents and chemotherapy. 2018;62(4):e02007-17. doi: 10.1128/AAC.02007-17. PubMed PMID: 29339387.

12. Chen L, He Z, Iuga AC, Martins Filho SN, Faith JJ, Clemente JC, et al. Diet Modifies Colonic Microbiota and CD4+ T-Cell Repertoire to Induce Flares of Colitis in Mice With Myeloid-Cell Expression of Interleukin 23. Gastroenterology. 2018;155(4):1177-91.e16. doi: https://doi.org/10.1053/j.gastro.2018.06.034.

13. Chen LA, Hourigan SK, Grigoryan Z, Gao Z, Clemente JC, Rideout JR, et al. Decreased Fecal Bacterial Diversity and Altered Microbiome in Children Colonized With Clostridium difficile. Journal of Pediatric Gastroenterology and Nutrition. 2018;Publish Ahead of Print.

14. Clemente JC, Manasson J, Scher JU. The role of the gut microbiome in systemic inflammatory disease. BMJ. 2018;360.

15. Cruchaga C, Del-Aguila JL, Saef B, Black K, Fernandez MV, Budde J, et al. Polygenic risk score of sporadic late-onset Alzheimer’s disease reveals a shared architecture with the familial and early-onset forms. Alzheimer’s & Dementia. 2018;14(2):205-14. doi: https://doi.org/10.1016/j.jalz.2017.08.013.

16. D’Avola D, Villacorta-Martin C, Martins-Filho SN, Craig A, Labgaa I, von Felden J, et al. High-density single cell mRNA sequencing to characterize circulating tumor cells in hepatocellular carcinoma. Scientific Reports. 2018;8(1):11570. doi: 10.1038/s41598-018-30047-y.

17. Davenport B, Eberlein J, van der Heide V, Jhun K, Nguyen TT, Victorino F, et al. Aging of Antiviral CD8+ Memory T Cells Fosters Increased Survival, Metabolic Adaptations, and Lymphoid Tissue Homing. The Journal of Immunology. 2018:ji1801277. doi: 10.4049/jimmunol.1801277.

18. Deyssenroth MA, Gennings C, Liu SH, Peng S, Hao K, Lambertini L, et al. Intrauterine multi-metal exposure is associated with reduced fetal growth through modulation of the placental gene network. Environment International. 2018;120:373-81. doi: https://doi.org/10.1016/j.envint.2018.08.010.

19. Dong L, Wu N, Wang S, Cheng Y, Han L, Zhao J, et al. Detection of novel germline mutations in six breast cancer predisposition genes by targeted next-generation sequencing. Human Mutation. 2018;39(10):1442-55. doi: 10.1002/humu.23597.

20. Esai Selvan M, Klein RJ, Gumus ZH. Rare, pathogenic germline variants in Fanconi Anemia genes increase risk for squamous lung cancer. Clinical Cancer Research. 2018:clincanres.2660.018. doi: 10.1158/1078-0432.CCR-18-2660.

21. Evangelou E, Warren HR, Mosen-Ansorena D, Mifsud B, Pazoki R, Gao H, et al. Genetic analysis of over 1 million people identifies 535 new loci associated with blood pressure traits. Nature genetics. 2018;50(10):141225. Epub 2018/09/17. doi: 10.1038/s41588-018-0205-x. PubMed PMID: 30224653.

22. Fazlollahi M, Chun Y, Grishin A, Wood RA, Burks AW, Dawson P, et al. Early-life gut microbiome and egg allergy. Allergy. 2018;73(7):1515-24. doi: 10.1111/all.13389.

23. Fazlollahi M, Chun Y, Grishin A, Wood RA, Burks AW, Dawson P, et al. Early‐life gut microbiome and egg allergy. Allergy. 2018;0(0). doi: 10.1111/all.13389.

24. Fazlollahi M, Lee TD, Andrade J, Oguntuyo K, Chun Y, Grishina G, et al. The nasal microbiome in asthma. Journal of Allergy and Clinical Immunology. 2018;142(3):834-43.e2. doi: https://doi.org/10.1016/j.jaci.2018.02.020.

25. Fernández-Rhodes L, Howard AG, Graff M, Isasi CR, Highland HM, Young KL, et al. Complex patterns of direct and indirect association between the transcription Factor-7 like 2 gene, body mass index and type 2 diabetes diagnosis in adulthood in the Hispanic Community Health Study/Study of Latinos. BMC obesity. 2018;5:26-. doi: 10.1186/s40608-018-0200-x. PubMed PMID: 30305909.

26. Filizola M. Insights from molecular dynamics simulations to exploit new trends for the development of improved opioid drugs. Neuroscience Letters. 2018. doi: https://doi.org/10.1016/j.neulet.2018.02.037.

27. Fu J, Wang Z, Lee K, Wei C, Liu Z, Zhang M, et al. Transcriptomic analysis uncovers novel synergistic mechanisms in combination therapy for lupus nephritis. Kidney International. 2018;93(2):416-29. doi: https://doi.org/10.1016/j.kint.2017.08.031.

28. Fu J, Wei C, Zhang W, Schlondorff D, Wu J, Cai M, et al. Gene expression profiles of glomerular endothelial cells support their role in the glomerulopathy of diabetic mice. Kidney International. 2018;94(2):326-45. doi: 10.1016/j.kint.2018.02.028.

29. Galatioto J, Caescu CI, Hansen J, Cook JR, Miramontes I, Iyengar R, et al. Cell Type–Specific Contributions of the Angiotensin II Type 1a Receptor to Aorta Homeostasis and Aneurysmal Disease—Brief ReportHighlights</span&gt. Arteriosclerosis, Thrombosis, and Vascular Biology. 2018;38(3):588.

30. Galsky MD, Wang H, Hahn NM, Twardowski P, Pal SK, Albany C, et al. Phase 2 Trial of Gemcitabine, Cisplatin, plus Ipilimumab in Patients with Metastatic Urothelial Cancer and Impact of DNA Damage Response Gene Mutations on Outcomes. European Urology. 2018;73(5):751-9. doi: https://doi.org/10.1016/j.eururo.2017.12.001.

31. Gandal MJ, Zhang P, Hadjimichael E, Walker RL, Chen C, Liu S, et al. Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder. Science. 2018;362(6420):eaat8127. doi: 10.1126/science.aat8127.

32. Gaspari S, Purushothaman I, Cogliani V, Sakloth F, Neve RL, Howland D, et al. Suppression of RGSz1 function optimizes the actions of opioid analgesics by mechanisms that involve the Wnt/β-catenin pathway. Proceedings of the National Academy of Sciences. 2018;115(9):E2085. doi: 10.1073/pnas.1707887115.

33. Gaspari S, Purushothaman I, Cogliani V, Sakloth F, Neve RL, Howland D, et al. Suppression of RGSz1 function optimizes the actions of opioid analgesics by mechanisms that involve the Wnt/beta-catenin pathway. Proceedings of the National Academy of Sciences of the United States of America. 2018;115(9):E2085-e94. Epub 2018/02/15. doi: 10.1073/pnas.1707887115. PubMed PMID: 29440403.

34. Gilsbach R, Schwaderer M, Preissl S, Grüning BA, Kranzhöfer D, Schneider P, et al. Distinct epigenetic programs regulate cardiac myocyte development and disease in the human heart in vivo. Nature Communications. 2018;9(1):391. doi: 10.1038/s41467-017-02762-z.

35. Girdhar K, Hoffman GE, Jiang Y, Brown L, Kundakovic M, Hauberg ME, et al. Cell-specific histone modification maps in the human frontal lobe link schizophrenia risk to the neuronal epigenome. Nature Neuroscience.
2018;21(8):1126-36. doi: 10.1038/s41593-018-0187-0.

36. Gómez S, Garrido-Garcia A, Garcia-Gerique L, Lemos I, Suñol M, de Torres C, et al. A novel method for rapid molecular subgrouping of medulloblastoma. Clinical Cancer Research. 2018.

37. Gómez S, Garrido-Garcia A, Garcia-Gerique L, Lemos I, Suñol M, de Torres C, et al. A Novel Method for Rapid Molecular Subgrouping of Medulloblastoma. Clinical Cancer Research. 2018;24(6):1355. doi: 10.1158/1078-0432.CCR-17-2243.

38. Gong J, Nishimura KK, Fernandez-Rhodes L, Haessler J, Bien S, Graff M, et al. Trans-ethnic analysis of metabochip data identifies two new loci associated with BMI. International journal of obesity (2005).
2018;42(3):384-90. Epub 2017/12/21. doi: 10.1038/ijo.2017.304. PubMed PMID: 29381148.

39. Haure-Mirande J-V, Wang M, Audrain M, Fanutza T, Kim SH, Heja S, et al. Integrative approach to sporadic Alzheimer’s disease: deficiency of TYROBP in cerebral Aβ amyloidosis mouse normalizes clinical phenotype and complement subnetwork molecular pathology without reducing Aβ burden. Molecular Psychiatry. 2018. doi: 10.1038/s41380-018-0255-6.

40. Hefti MM, Farrell K, Kim S, Bowles KR, Fowkes ME, Raj T, et al. High-resolution temporal and regional mapping of MAPT expression and splicing in human brain development. PLOS ONE. 2018;13(4):e0195771. doi: 10.1371/journal.pone.0195771.

41. Hodonsky CJ, Schurmann C, Schick UM, Kocarnik J, Tao R, van Rooij FJA, et al. Generalization and fine mapping of red blood cell trait genetic associations to multi-ethnic populations: The PAGE study. American Journal of Hematology. 2018;93(8):1061-73. doi: 10.1002/ajh.25161.

42. Holmes G, Rourke C, Motch Perrine SM, Lu N, van Bakel H, Richtsmeier JT, et al. Midface and upper airway dysgenesis in FGFR2-related craniosynostosis involves multiple tissue-specific and cell cycle effects. Development. 2018;145(19):dev166488. doi: 10.1242/dev.166488.

43. Hong J, Hatchell KE, Bradfield JP, Andrew B, Alessandra C, Chao-Qiang L, et al. Trans-ethnic Evaluation Identifies Novel Low Frequency Loci Associated with 25-Hydroxyvitamin D Concentrations. The Journal of Clinical Endocrinology & Metabolism. 2018:jc.2017-01802-jc.2017-. doi: 10.1210/jc.2017-01802.

44. Hong J, Hatchell KE, Bradfield JP, Bjonnes A, Chesi A, Lai C-Q, et al. Transethnic Evaluation Identifies Low-Frequency Loci Associated With 25-Hydroxyvitamin D Concentrations. The Journal of Clinical Endocrinology & Metabolism. 2018;103(4):1380-92. doi: 10.1210/jc.2017-01802.

45. Hu Y, Raffield LM, Polfus LM, Moscati A, Nadkarni G, Preuss MH, et al. A common TCN1 loss-of-function variant is associated with lower vitamin B12 concentration in African Americans. Blood. 2018;131(25):2859. doi: 10.1182/blood-2018-03-841023.

46. Huang F, Wang M, Liu R, Wang J-Z, Schadt E, Haroutunian V, et al. CDT2-controlled cell cycle reentry regulates the pathogenesis of Alzheimer’s disease. Alzheimer’s & Dementia. 2018. doi: https://doi.org/10.1016/j.jalz.2018.08.013.

47. Hughes TET, Lodowski DT, Huynh KW, Yazici A, Del Rosario J, Kapoor A, et al. Structural basis of TRPV5 channel inhibition by econazole revealed by cryo-EM. Nature Structural & Molecular Biology. 2018;25(1):53-60. doi: 10.1038/s41594-017-0009-1.

48. Kajiwara Y, Wang E, Wang M, Sin WC, Brennand KJ, Schadt E, et al. GJA1 (connexin43) is a key regulator of Alzheimer’s disease pathogenesis. Acta neuropathologica communications. 2018;6(1):144-. doi: 10.1186/s40478-018-0642-x. PubMed PMID: 30577786.

49. Kalayci S, Esai Selvan M, Ramos I, Cotsapas C, Montgomery RR, Poland G, et al. ImmuneRegulation: A web-based tool for identifying human immune regulatory elements. bioRxiv. 2018:468124. doi: 10.1101/468124.

50. Kalayci S, Gümüş ZH. Exploring Biological Networks in 3D, Stereoscopic 3D, and Immersive 3D with iCAVE. Current Protocols in Bioinformatics. 2018;61(1):8.27.1-8..6. doi: 10.1002/cpbi.47.

51. Kasarskis A, Di Narzo AF, Kidd B, Argmann C, Dudley J, Cho J, et al. High-Throughput Identification of the Plasma Proteomic Signature of Inflammatory Bowel Disease. 2018. doi: 10.1093/ecco-jcc/jjy190.

52. Keenan AB, Jenkins SL, Jagodnik KM, Koplev S, He E, Torre D, et al. The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations. Cell Systems. 2018;6(1):13-24. doi: https://doi.org/10.1016/j.cels.2017.11.001.

53. Kozlenkov A, Li J, Apontes P, Hurd YL, Byne WM, Koonin EV, et al. A unique role for DNA (hydroxy)methylation in epigenetic regulation of human inhibitory neurons. Science advances. 2018;4(9):eaau6190-eaau. doi: 10.1126/sciadv.aau6190. PubMed PMID: 30263963.

54. Labgaa I, Villacorta-Martin C, D’Avola D, Craig AJ, von Felden J, Martins-Filho SN, et al. A pilot study of ultra-deep targeted sequencing of plasma DNA identifies driver mutations in hepatocellular carcinoma. Oncogene. 2018;37(27):3740-52. Epub 2018/04/09. doi: 10.1038/s41388-018-0206-3. PubMed PMID: 29628508.

55. Laverty KU, Stout JM, Sullivan MJ, Shah H, Gill N, Holbrook L, et al. A physical and genetic map of Cannabis sativa identifies extensive rearrangement at the THC/CBD acid synthase locus. Genome Research. 2018.

56. Li H, Zhang W, Zhong F, Das GC, Xie Y, Li Z, et al. Epigenetic regulation of RCAN1 expression in kidney disease and its role in podocyte injury. Kidney International. 2018;94(6):1160-76. doi: 10.1016/j.kint.2018.07.023.

57. Li W, Middha M, Bicak M, Sjoberg DD, Vertosick E, Dahlin A, et al. Genome-wide Scan Identifies Role for AOX1 in Prostate Cancer Survival. European Urology. 2018;74(6):710-9. doi: 10.1016/j.eururo.2018.06.021.

58. Ligthart S, Vaez A, Võsa U, Stathopoulou MG, de Vries PS, Prins BP, et al. Genome Analyses of >200,000 Individuals Identify 58 Loci for Chronic Inflammation and Highlight Pathways that Link Inflammation and Complex Disorders. American journal of human genetics. 2018;103(5):691-706. Epub 2018/11/01. doi: 10.1016/j.ajhg.2018.09.009. PubMed PMID: 30388399.

59. Linde N, Casanova-Acebes M, Sosa MS, Mortha A, Rahman A, Farias E, et al. Macrophages orchestrate breast cancer early dissemination and metastasis. Nature Communications. 2018;9(1):21. doi: 10.1038/s41467-017-02481-5.

60. Llewellyn SR, Britton GJ, Contijoch EJ, Vennaro OH, Mortha A, Colombel J-F, et al. Interactions Between Diet and the Intestinal Microbiota Alter Intestinal Permeability and Colitis Severity in Mice. Gastroenterology. 2018;154(4):1037-46.e2. doi: https://doi.org/10.1053/j.gastro.2017.11.030.

61. Lorsch ZS, Hamilton PJ, Ramakrishnan A, Parise EM, Wright WJ, Salery M, et al. Zfp189 Mediates Stress Resilience Through a CREB-Regulated Transcriptional Network in Prefrontal Cortex. bioRxiv. 2018:403733. doi: 10.1101/403733.

62. Lorsch ZS, Loh Y-HE, Purushothaman I, Walker DM, Parise EM, Salery M, et al. Estrogen receptor α drives pro-resilient transcription in mouse models of depression. Nature Communications. 2018;9(1):1116. doi: 10.1038/s41467-018-03567-4.

63. Mahajan A, Taliun D, Thurner M, Robertson NR, Torres JM, Rayner NW, et al. Fine-mapping type 2 diabetes loci to single-variant resolution using high-density imputation and islet-specific epigenome maps. Nature genetics. 2018;50(11):1505-13. Epub 2018/10/08. doi: 10.1038/s41588-018-0241-6. PubMed PMID: 30297969.

64. Mahajan A, Wessel J, Willems SM, Zhao W, Robertson NR, Chu AY, et al. Refining the accuracy of validated target identification through coding variant fine-mapping in type 2 diabetes. Nature genetics. 2018;50(4):559-71. Epub 2018/04/09. doi: 10.1038/s41588-018-0084-1. PubMed PMID: 29632382.

65. Manasson J, Shen N, Garcia Ferrer Helga R, Ubeda C, Iraheta I, Heguy A, et al. Gut Microbiota Perturbations in Reactive Arthritis and Postinfectious Spondyloarthritis. Arthritis & Rheumatology. 2018;70(2):242-54. doi: 10.1002/art.40359.

66. Manheimer Kathryn B, Patel N, Richter F, Gorham J, Tai Angela C, Homsy J, et al. Robust identification of deletions in exome and genome sequence data based on clustering of Mendelian errors. Human Mutation. 2018;39(6):870-81. doi: 10.1002/humu.23419.

67. Manheimer KB, Patel N, Richter F, Gorham J, Tai AC, Homsy J, et al. Robust identification of deletions in exome and genome sequence data based on clustering of Mendelian errors. Human Mutation. 2018;39(6):870-81. doi: 10.1002/humu.23419.

68. Manheimer KB, Richter F, Edelmann LJ, D’Souza SL, Shi L, Shen Y, et al. Robust identification of mosaic variants in congenital heart disease. Human Genetics. 2018;137(2):183-93. doi: 10.1007/s00439-018-1871-6.

69. Marino KA, Filizola M. Investigating Small-Molecule Ligand Binding to G Protein-Coupled Receptors with Biased or Unbiased Molecular Dynamics Simulations. Methods in molecular biology (Clifton, NJ). 2018;1705:351-64. doi: 10.1007/978-1-4939-7465-8_17. PubMed PMID: PMC5745006.

70. Martinelli S, Krumbach OHF, Pantaleoni F, Coppola S, Amin E, Pannone L, et al. Functional Dysregulation of CDC42 Causes Diverse Developmental Phenotypes. American journal of human genetics. 2018;102(2):309-20. Epub 2018/01/25. doi: 10.1016/j.ajhg.2017.12.015. PubMed PMID: 29394990.

71. Mayourian J, Ceholski DK, Gonzalez DM, Cashman TJ, Sahoo S, Hajjar RJ, et al. Physiologic, Pathologic, and Therapeutic Paracrine Modulation of Cardiac Excitation-Contraction Coupling. Circulation research. 2018;122(1):167-83. doi: 10.1161/CIRCRESAHA.117.311589. PubMed PMID: 29301848.

72. McDonald D, Hyde E, Debelius JW, Morton JT, Gonzalez A, Ackermann G, et al. American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems. 2018;3(3):e00031-18. doi: 10.1128/mSystems.00031-18.

73. McKenzie AT, Wang M, Hauberg ME, Fullard JF, Kozlenkov A, Keenan A, et al. Brain Cell Type Specific Gene Expression and Co-expression Network Architectures. Scientific Reports. 2018;8(1):8868. doi: 10.1038/s41598-018-27293-5.

74. Mena J, Brito B, Moreira R, Tadich T, González I, Cruces J, et al. Reemergence of H3N8 Equine Influenza A virus in Chile, 2018. Transboundary and Emerging Diseases. 2018;65(6):1408-15. doi: 10.1111/tbed.12984.

75. Meral D, Provasi D, Filizola M. An efficient strategy to estimate thermodynamics and kinetics of G protein-coupled receptor activation using metadynamics and maximum caliber. The Journal of Chemical Physics. 2018;149(22):224101. doi: 10.1063/1.5060960.

76. Meral D, Provasi D, Prada-Gracia D, Möller J, Marino K, Lohse MJ, et al. Molecular details of dimerization kinetics reveal negligible populations of transient µ-opioid receptor homodimers at physiological concentrations. Scientific Reports. 2018;8(1):7705. doi: 10.1038/s41598-018-26070-8.

77. Mezei M. Revisiting Chameleon Sequences in the Protein Data Bank. Algorithms. 2018;11(8). doi: 10.3390/a11080114.

78. Miller ML, Chadwick B, Dickstein DL, Purushothaman I, Egervari G, Rahman T, et al. Adolescent exposure to Δ9-tetrahydrocannabinol alters the transcriptional trajectory and dendritic architecture of prefrontal pyramidal neurons. Molecular Psychiatry. 2018. doi: 10.1038/s41380-018-0243-x.

79. Miller ML, Ren Y, Szutorisz H, Warren NA, Tessereau C, Egervari G, et al. Ventral striatal regulation of CREM mediates impulsive action and drug addiction vulnerability. Molecular psychiatry. 2018;23(5):1328-35. Epub 2017/04/25. doi: 10.1038/mp.2017.80. PubMed PMID: 28439100.

80. Nielsen JB, Fritsche LG, Zhou W, Teslovich TM, Holmen OL, Gustafsson S, et al. Genome-wide Study of Atrial Fibrillation Identifies Seven Risk Loci and Highlights Biological Pathways and Regulatory Elements Involved in Cardiac Development. The American Journal of Human Genetics. 2018;102(1):103-15. doi: https://doi.org/10.1016/j.ajhg.2017.12.003.

81. Pandey G, Pandey OP, Rogers AJ, Ahsen ME, Hoffman GE, Raby BA, et al. A Nasal Brush-based Classifier of Asthma Identified by Machine Learning Analysis of Nasal RNA Sequence Data. Scientific Reports. 2018;8(1):8826. doi: 10.1038/s41598-018-27189-4.

82. Polfus LM, Raffield LM, Wheeler MM, Tracy RP, Lange LA, Lettre G, et al. Whole genome sequence association with E-selectin levels reveals loss-of-function variant in African Americans. Human Molecular Genetics. 2018:ddy360-ddy. doi: 10.1093/hmg/ddy360.

83. Qian T, Zhu S, Hao K, Hoshida Y, Shen Y, Yu J. GIGSEA: genotype imputed gene set enrichment analysis using GWAS summary level data. Bioinformatics. 2018;35(1):160-3. doi: 10.1093/bioinformatics/bty529.

84. Rahman AH, Lavin Y, Kobayashi S, Leader A, Merad M. High-dimensional single cell mapping of cerium distribution in the lung immune microenvironment of an active smoker. Cytometry Part B: Clinical Cytometry. 2018;94(6):941-5. doi: 10.1002/cyto.b.21545.

85. Raj T, Li YI, Wong G, Humphrey J, Wang M, Ramdhani S, et al. Integrative transcriptome analyses of the aging brain implicate altered splicing in Alzheimer’s disease susceptibility. Nature Genetics. 2018;50(11):1584-92. doi: 10.1038/s41588-018-0238-1.

86. Rajarajan P, Borrman T, Liao W, Schrode N, Flaherty E, Casiño C, et al. Neuron-specific signatures in the chromosomal connectome associated with schizophrenia risk. Science. 2018;362(6420):eaat4311. doi: 10.1126/science.aat4311.

87. Ramdhani S, Navarro E, Udine E, Schilder BM, Parks M, Raj T. Tensor Decomposition of Stimulated Monocyte and Macrophage Gene Expression Profiles Identifies Neurodegenerative Disease-specific Trans-eQTLs. bioRxiv. 2018:499509. doi: 10.1101/499509.

88. Rathore N, Ramani SR, Pantua H, Payandeh J, Bhangale T, Wuster A, et al. Paired Immunoglobulin-like Type 2 Receptor Alpha G78R variant alters ligand binding and confers protection to Alzheimer’s disease. PLoS genetics. 2018;14(11):e1007427-e. doi: 10.1371/journal.pgen.1007427. PubMed PMID: 30388101.

89. Readhead B, Hartley BJ, Eastwood BJ, Collier DA, Evans D, Farias R, et al. Expression-based drug screening of neural progenitor cells from individuals with schizophrenia. Nature Communications. 2018;9(1):4412. doi: 10.1038/s41467-018-06515-4.

90. Reiner J, Pisani L, Qiao W, Singh R, Yang Y, Shi L, et al. Cytogenomic identification and long-read single molecule real-time (SMRT) sequencing of a Bardet-Biedl Syndrome 9 (BBS9) deletion. NPJ genomic medicine. 2018;3:3-. doi: 10.1038/s41525-017-0042-3. PubMed PMID: 29367880.

91. Rejwan Ali M, Sadoqi M, Boutajangout A, Mezei M. Virtual screening of a natural compound library at orthosteric and allosteric binding sites of the neurotensin receptor. Journal of Biomolecular Structure and Dynamics. 2018:1-13. doi: 10.1080/07391102.2018.1552200.

92. Ren C, Zhang G, Han F, Fu S, Cao Y, Zhang F, et al. Spatially constrained tandem bromodomain inhibition bolsters sustained repression of BRD4 transcriptional activity for TNBC cell growth. Proceedings of the National Academy of Sciences. 2018;115(31):7949. doi: 10.1073/pnas.1720000115.

93. Ribeiro EA, Salery M, Scarpa JR, Calipari ES, Hamilton PJ, Ku SM, et al. Transcriptional and physiological adaptations in nucleus accumbens somatostatin interneurons that regulate behavioral responses to cocaine. Nature communications. 2018;9(1):3149-. doi: 10.1038/s41467-018-05657-9. PubMed PMID: 30089879.

94. Rimondi A, Gonzalez-Reiche AS, Olivera VS, Decarre J, Castresana GJ, Romano M, et al. Evidence of a fixed internal gene constellation in influenza A viruses isolated from wild birds in Argentina (2006-2016). Emerging microbes & infections. 2018;7(1):194-. doi: 10.1038/s41426-018-0190-2. PubMed PMID: 30482896.

95. Roselli C, Chaffin MD, Weng L-C, Aeschbacher S, Ahlberg G, Albert CM, et al. Multi-ethnic genome-wide association study for atrial fibrillation. Nature genetics. 2018;50(9):1225-33. Epub 2018/06/11. doi: 10.1038/s41588-018-0133-9. PubMed PMID: 29892015.

96. Saccone NL, Emery LS, Sofer T, Gogarten SM, Becker DM, Bottinger EP, et al. Genome-Wide Association Study of Heavy Smoking and Daily/Nondaily Smoking in the Hispanic Community Health Study/Study of Latinos (HCHS/SOL). Nicotine & Tobacco Research. 2018;20(4):448-57. doi: 10.1093/ntr/ntx107.

97. Sekiya M, Wang M, Fujisaki N, Sakakibara Y, Quan X, Ehrlich ME, et al. Integrated biology approach reveals molecular and pathological interactions among Alzheimer’s Aβ42, Tau, TREM2, and TYROBP in Drosophila models. Genome Medicine. 2018;10(1):26. doi: 10.1186/s13073-018-0530-9.

98. Snoek R, van Setten J, Keating BJ, Israni AK, Jacobson PA, Oetting WS, et al. NPHP1 (Nephrocystin-1) Gene Deletions Cause Adult-Onset ESRD. Journal of the American Society of Nephrology. 2018;29(6):1772. doi: 10.1681/ASN.2017111200.

99. Stanescu A, Pandey G. Developing parsimonious ensembles using ensemble diversity within a reinforcement learning framework. eprint arXiv:180502103. 2018:arXiv:1805.02103.

100. Strub T, Ghiraldini FG, Carcamo S, Li M, Wroblewska A, Singh R, et al. SIRT6 haploinsufficiency induces BRAF(V600E) melanoma cell resistance to MAPK inhibitors via IGF signalling. Nature communications. 2018;9(1):3440-. doi: 10.1038/s41467-018-05966-z. PubMed PMID: 30143629.

101. Sulaiman I, Wu BG, Li Y, Scott AS, Malecha P, Scaglione B, et al. Evaluation of the airway microbiome in nontuberculous mycobacteria disease. European Respiratory Journal. 2018;52(4):1800810. doi: 10.1183/13993003.00810-2018.

102. Sun Z, Filipescu D, Andrade J, Gaspar-Maia A, Ueberheide B, Bernstein E. Transcription-associated histone pruning demarcates macroH2A chromatin domains. Nature Structural & Molecular Biology. 2018;25(10):958-70. doi: 10.1038/s41594-018-0134-5.

103. Sung YJ, Winkler TW, de Las Fuentes L, Bentley AR, Brown MR, Kraja AT, et al. A Large-Scale Multi-ancestry Genome-wide Study Accounting for Smoking Behavior Identifies Multiple Significant Loci for Blood Pressure. American journal of human genetics. 2018;102(3):375-400. Epub 2018/02/15. doi: 10.1016/j.ajhg.2018.01.015. PubMed PMID: 29455858.

104. Tome-Garcia J, Erfani P, Nudelman G, Tsankov AM, Katsyv I, Tejero R, et al. Analysis of chromatin accessibility uncovers TEAD1 as a regulator of migration in human glioblastoma. Nature Communications. 2018;9(1):4020. doi: 10.1038/s41467-018-06258-2.

105. Tsay J-CJ, Wu BG, Badri MH, Clemente JC, Shen N, Meyn P, et al. Airway Microbiota Is Associated with Upregulation of the PI3K Pathway in Lung Cancer. American Journal of Respiratory and Critical Care Medicine. 2018;198(9):1188-98. doi: 10.1164/rccm.201710-2118OC.

106. Turcot V, Lu Y, Highland HM, Schurmann C, Justice AE, Fine RS, et al. Protein-altering variants associated with body mass index implicate pathways that control energy intake and expenditure in obesity. Nature Genetics. 2018;50(1):26-41. doi: 10.1038/s41588-017-0011-x.

107. van Setten J, Brody JA, Jamshidi Y, Swenson BR, Butler AM, Campbell H, et al. PR interval genome-wide association meta-analysis identifies 50 loci associated with atrial and atrioventricular electrical activity. Nature communications. 2018;9(1):2904-. doi: 10.1038/s41467-018-04766-9. PubMed PMID: 30046033.

108. van Weeghel M, Houtkooper RH, Denis S, Wanders RJ, Des Rosiers C, Abdurrachim D, et al. Increased cardiac fatty acid oxidation in a mouse model with decreased malonyl-CoA sensitivity of CPT1B. Cardiovascular Research. 2018;114(10):1324-34. doi: 10.1093/cvr/cvy089.

109. Venkatesh D, Poen MJ, Bestebroer TM, Scheuer RD, Vuong O, Chkhaidze M, et al. Avian Influenza Viruses in Wild Birds: Virus Evolution in a Multihost Ecosystem. Journal of virology. 2018;92(15):e00433-18. doi: 10.1128/JVI.00433-18. PubMed PMID: 29769347.

110. Verghese DA, Chun N, Paz K, Fribourg M, Woodruff TM, Flynn R, et al. C5aR1 regulates T follicular helper differentiation and chronic graft-versus-host disease bronchiolitis obliterans. JCI insight. 2018;3(24):e124646. doi: 10.1172/jci.insight.124646. PubMed PMID: 30568034.

111. Verheije R, Kupchik GS, Isidor B, Kroes HY, Lynch SA, Hawkes L, et al. Heterozygous loss-of-function variants of MEIS2 cause a triad of palatal defects, congenital heart defects, and intellectual disability. European Journal of Human Genetics. 2018. doi: 10.1038/s41431-018-0281-5.

112. Vincek AS, Patel J, Jaganathan A, Green A, Pierre-Louis V, Arora V, et al. Inhibitor of CBP Histone Acetyltransferase Downregulates p53 Activation and Facilitates Methylation at Lysine 27 on Histone H3. Molecules (Basel, Switzerland). 2018;23(8):1930. doi: 10.3390/molecules23081930. PubMed PMID: 30072621.

113. Voorhees IEH, Dalziel BD, Glaser A, Dubovi EJ, Murcia PR, Newbury S, et al. Multiple Incursions and Recurrent Epidemic Fade-Out of H3N2 Canine Influenza A Virus in the United States. Journal of Virology. 2018;92(16):e00323-18. doi: 10.1128/JVI.00323-18.

114. Walker DM, Cates HM, Loh Y-HE, Purushothaman I, Ramakrishnan A, Cahill KM, et al. Cocaine Self-administration Alters Transcriptome-wide Responses in the Brain’s Reward Circuitry. Biological Psychiatry. 2018;84(12):867-80. doi: https://doi.org/10.1016/j.biopsych.2018.04.009.

115. Waller RG, Darlington TM, Wei X, Madsen MJ, Thomas A, Curtin K, et al. Novel pedigree analysis implicates DNA repair and chromatin remodeling in multiple myeloma risk. PLOS Genetics. 2018;14(2):e1007111. doi: 10.1371/journal.pgen.1007111.

116. Wang L, Law J, Kale S, Murali T, Pandey G. Large-scale protein function prediction using heterogeneous ensembles [version 1; referees: 2 approved]. 2018;7(1577). doi: 10.12688/f1000research.16415.1.

117. Wang M, Beckmann ND, Roussos P, Wang E, Zhou X, Wang Q, et al. The Mount Sinai cohort of large-scale genomic, transcriptomic and proteomic data in Alzheimer’s disease. Scientific Data. 2018;5:180185. doi: 10.1038/sdata.2018.185 https://www.nature.com/articles/sdata2018185 – supplementary-information.

118. Wang P, Karakose E, Liu H, Swartz E, Ackeifi C, Zlatanic V, et al. Combined Inhibition of DYRK1A, SMAD, and Trithorax Pathways Synergizes to Induce Robust Replication in Adult Human Beta Cells. Cell Metabolism. 2018. doi: https://doi.org/10.1016/j.cmet.2018.12.005.

119. Wang W, Wei C, Li P, Wang L, Li W, Chen K, et al. Integrative analysis of mRNA and lncRNA profiles identified pathogenetic lncRNAs in esophageal squamous cell carcinoma. Gene. 2018;661:169-75. doi: https://doi.org/10.1016/j.gene.2018.03.066.

120. Wei C, Banu K, Garzon F, Basgen JM, Philippe N, Yi Z, et al. SHROOM3-FYN Interaction Regulates Nephrin Phosphorylation and Affects Albuminuria in Allografts. Journal of the American Society of Nephrology. 2018;29(11):2641. doi: 10.1681/ASN.2018060573.

121. Wei X, Calvo-Vidal MN, Chen S, Wu G, Revuelta MV, Sun J, et al. Germline Lysine-Specific Demethylase 1 (LSD1/KDM1A) Mutations Confer Susceptibility to Multiple Myeloma. Cancer Research. 2018;78(10):2747. doi: 10.1158/0008-5472.CAN-17-1900.

122. Wu BG, Sulaiman I, Wang J, Shen N, Clemente JC, Li Y, et al. Severe Obstructive Sleep Apnea Is Associated with Alterations in the Nasal Microbiome and an Increase in Inflammation. American Journal of Respiratory and Critical Care Medicine. 2018;199(1):99-109. doi: 10.1164/rccm.201801-0119OC.

123. Xu P-X, Xu J, Li J, Loh Y-HE, Zhang T, Jiang H, et al. Brg1 controls neurosensory cell fate commitment and differentiation in the mammalian inner ear. bioRxiv. 2018:434159. doi: 10.1101/434159.

124. Yan J, Li J, Hu J, Zhang L, Wei C, Sultana N, et al. Smad4 deficiency impairs chondrocyte hypertrophy via the Runx2 transcription factor in mouse skeletal development. Journal of Biological Chemistry. 2018;293(24):9162-75.

125. Zakirova Z, Fanutza T, Bonet J, Readhead B, Zhang W, Yi Z, et al. Mutations in THAP1/DYT6 reveal that diverse dystonia genes disrupt similar neuronal pathways and functions. PLOS Genetics. 2018;14(1):e1007169. doi: 10.1371/journal.pgen.1007169.

126. Zhao N, Sebastiano V, Moshkina N, Mena N, Hultquist J, Jimenez-Morales D, et al. Influenza virus infection causes global RNAPII termination defects. Nature Structural & Molecular Biology. 2018;25(9):885-93. doi: 10.1038/s41594-018-0124-7.

127. Zhong F, Chen H, Xie Y, Azeloglu EU, Wei C, Zhang W, et al. Protein S Protects against Podocyte Injury in Diabetic Nephropathy. Journal of the American Society of Nephrology. 2018;29(5):1397. doi: 10.1681/ASN.2017030234.

128. Zhou X, Wang M, Katsyv I, Irie H, Zhang B. EMUDRA: Ensemble of Multiple Drug Repositioning Approaches to improve prediction accuracy. Bioinformatics. 2018;34(18):3151-9. doi: 10.1093/bioinformatics/bty325.

2017

1. Zhao Y, Song W-M, Zhang F, Zhou M-M, Zhang W, Walsh MJ, et al. Distinct distributions of genomic features of the 5’ and 3’ partners of coding somatic cancer gene fusions: arising mechanisms and functional implications. Oncotarget. 2017;8(40):66769-83. doi: 10.18632/oncotarget.10734. PubMed PMID: PMC5620135.
2. Zhao W, Rasheed A, Tikkanen E, Lee J-J, Butterworth AS, Howson JMM, et al. Identification of new susceptibility loci for type 2 diabetes and shared etiological pathways with coronary heart disease. Nature Genetics. 2017;49:1450. doi: 10.1038/ng.3943
https://www.nature.com/articles/ng.3943 – supplementary-information.
3. Zhang Z, Hao K, Ross MJ, Murphy B, Menon MC. APOL1 G2 risk allele—clarifying nomenclature. Kidney International. 2017;92(2):518-9. doi: https://doi.org/10.1016/j.kint.2017.05.009.
4. Zhang P, Chu T, Dedousis N, Mantell BS, Sipula I, Li L, et al. DNA methylation alters transcriptional rates of differentially expressed genes and contributes to pathophysiology in mice fed a high fat diet. Molecular Metabolism. 2017;6(4):327-39. doi: 10.1016/j.molmet.2017.02.001. PubMed PMID: PMC5369282.
5. Zhang J, Peng S, Cheng H, Nomura Y, Di Narzo AF, Hao K. Genetic Pleiotropy between Nicotine Dependence and Respiratory Outcomes. Scientific Reports. 2017;7(1):16907. doi: 10.1038/s41598-017-16964-4.
6. Zhang H, Fillmore Brainson C, Koyama S, Redig AJ, Chen T, Li S, et al. Lkb1 inactivation drives lung cancer lineage switching governed by Polycomb Repressive Complex 2. Nature Communications. 2017;8:14922. doi: 10.1038/ncomms14922
https://www.nature.com/articles/ncomms14922 – supplementary-information.
7. Zafar H, Shang Y, Li J, David GA, Fernandez JP, Molina H, et al. αIIbβ3 binding to a fibrinogen fragment lacking the γ-chain dodecapeptide is activation dependent and EDTA inducible. Blood Advances. 2017;1(7):417-28. doi: 10.1182/bloodadvances.2017004689. PubMed PMID: PMC5738983.
8. Yoo S, Wang W, Wang Q, Fiel MI, Lee E, Hiotis SP, et al. A pilot systematic genomic comparison of recurrence risks of hepatitis B virus-associated hepatocellular carcinoma with low- and high-degree liver fibrosis. BMC Medicine. 2017;15(1):214. doi: 10.1186/s12916-017-0973-7.
9. Yano H, Provasi D, Cai NS, Filizola M, Ferré S, Javitch JA. Development of novel biosensors to study receptor-mediated activation of the G-protein α subunits Gs and Golf. Journal of Biological Chemistry. 2017;292(49):19989-98.
10. Yang Z, Jin M, Zhang Z, Lu J, Hao K. Classification Based on Feature Extraction For Hepatocellular Carcinoma Diagnosis Using High-throughput Dna Methylation Sequencing Data. Procedia Computer Science. 2017;107:412-7. doi: https://doi.org/10.1016/j.procs.2017.03.130.
11. Yang Y, Botton MR, Scott ER, Scott SA. Sequencing the CYP2D6 gene: from variant allele discovery to clinical pharmacogenetic testing. Pharmacogenomics. 2017;18(7):673-85. doi: 10.2217/pgs-2017-0033.
12. Yang S, Hemarajata P, Hindler J, Li F, Adisetiyo H, Aldrovandi G, et al. Evolution and Transmission of Carbapenem-Resistant Klebsiella pneumoniae Expressing the blaOXA-232 Gene During an Institutional Outbreak Associated With Endoscopic Retrograde Cholangiopancreatography. Clinical Infectious Diseases. 2017;64(7):894-901. doi: 10.1093/cid/ciw876.
13. Yang J, Hagen J, Guntur KV, Allette K, Schuyler S, Ranjan J, et al. A next generation sequencing based approach to identify extracellular vesicle mediated mRNA transfers between cells. BMC Genomics. 2017;18:987. doi: 10.1186/s12864-017-4359-1. PubMed PMID: PMC5741891.
14. Yang B, Zhou W, Jiao J, Nielsen JB, Mathis MR, Heydarpour M, et al. Protein-altering and regulatory genetic variants near GATA4 implicated in bicuspid aortic valve. Nature Communications. 2017;8:15481. doi: 10.1038/ncomms15481. PubMed PMID: PMC5458508.
15. Xiong Y, Soumillon M, Wu J, Hansen J, Hu B, van Hasselt JGC, et al. A Comparison of mRNA Sequencing with Random Primed and 3′-Directed Libraries. Scientific Reports. 2017;7(1):14626. doi: 10.1038/s41598-017-14892-x.
16. Wheeler E, Leong A, Liu C-T, Hivert M-F, Strawbridge RJ, Podmore C, et al. Impact of common genetic determinants of Hemoglobin A1c on type 2 diabetes risk and diagnosis in ancestrally diverse populations: A transethnic genome-wide meta-analysis. PLOS Medicine. 2017;14(9):e1002383. doi: 10.1371/journal.pmed.1002383.
17. Wei C, Li L, Menon MC, Zhang W, Fu J, Kidd B, et al. Genomic Analysis of Kidney Allograft Injury Identifies Hematopoietic Cell Kinase as a Key Driver of Renal Fibrosis. Journal of the American Society of Nephrology. 2017;28(5):1385-93.
18. Webb TR, Erdmann J, Stirrups KE, Stitziel NO, Masca NGD, Jansen H, et al. Systematic Evaluation of Pleiotropy Identifies 6 Further Loci Associated With Coronary Artery Disease. Journal of the American College of Cardiology. 2017;69(7):823-36. doi: 10.1016/j.jacc.2016.11.056. PubMed PMID: PMC5314135.
19. Webb BD, Metikala S, Wheeler PG, Sherpa MD, Houten SM, Horb ME, et al. Heterozygous Pathogenic Variant in DACT1 Causes an Autosomal-Dominant Syndrome with Features Overlapping Townes–Brocks Syndrome. Human mutation. 2017;38(4):373-7. doi: 10.1002/humu.23171. PubMed PMID: PMC5390682.
20. Watson CT, Cohain AT, Griffin RS, Chun Y, Grishin A, Hacyznska H, et al. Integrative transcriptomic analysis reveals key drivers of acute peanut allergic reactions. Nature Communications. 2017;8(1):1943. doi: 10.1038/s41467-017-02188-7.
21. Watson C, Cohain A, Griffin R, Beckmann N, Grishin A, Haczynska H, et al. Analysis of Serial Peripheral Blood Transcriptomes from Peanut Allergic Children Undergoing Double-blind, Placebo-controlled Oral Food Challenges Reveals Key Drivers of the Acute Allergic Response to Peanut. Journal of Allergy and Clinical Immunology. 2017;139(2):AB189. doi: 10.1016/j.jaci.2016.12.615.
22. Wang H, Bender A, Wang P, Karakose E, Inabnet WB, Libutti SK, et al. Insights into beta cell regeneration for diabetes via integration of molecular landscapes in human insulinomas. Nature Communications. 2017;8:767. doi: 10.1038/s41467-017-00992-9. PubMed PMID: PMC5626682.
23. Wan L, Wen H, Li Y, Lyu J, Xi Y, Hoshii T, et al. ENL links histone acetylation to oncogenic gene expression in acute myeloid leukaemia. Nature. 2017;543(7644):265-9. Epub 2017/02/28. doi: 10.1038/nature21687. PubMed PMID: 28241141; PubMed Central PMCID: PMCPMC5372383.
24. Wain LV, Vaez A, Jansen R, Joehanes R, van der Most PJ, Erzurumluoglu AM, et al. Novel Blood Pressure Locus and Gene Discovery Using Genome-Wide Association Study and Expression Data Sets From Blood and the KidneyNovelty and Significance</span&gt. Hypertension. 2017;70(3):e4.
25. Wain LV, Shrine N, Soler Artigas M, Erzurumluoglu AM, Noyvert B, Bossini-Castillo L, et al. Genome-wide association analyses for lung function and chronic obstructive pulmonary disease identify new loci and potential druggable targets. Nature genetics. 2017;49(3):416-25. doi: 10.1038/ng.3787. PubMed PMID: PMC5326681.
26. Vatansever S, Gumus Z, Erman B. The Effects Of Oncogenic G12D Mutation On K-Ras Structure, Conformation And Dynamics. bioRxiv. 2017.
27. van Rooij FJA, Qayyum R, Smith AV, Zhou Y, Trompet S, Tanaka T, et al. Genome-wide Trans-ethnic Meta-analysis Identifies Seven Genetic Loci Influencing Erythrocyte Traits and a Role for RBPMS in Erythropoiesis. American Journal of Human Genetics. 2017;100(1):51-63. doi: 10.1016/j.ajhg.2016.11.016. PubMed PMID: PMC5223059.
28. Uzilov AV, Cheesman KC, Fink MY, Newman LC, Pandya C, Lalazar Y, et al. Identification of a novel RASD1 somatic mutation in a USP8-mutated corticotroph adenoma. Cold Spring Harbor Molecular Case Studies. 2017;3(3):a001602. doi: 10.1101/mcs.a001602. PubMed PMID: PMC5411693.
29. Tsao AS, Wistuba I, Xia D, Byers L, Diao L, Wang J, et al. Germline and Somatic Smoothened Mutations in Non–Small-Cell Lung Cancer Are Potentially Responsive to Hedgehog Inhibitor Vismodegib. JCO Precision Oncology. 2017;1(1):1-10. doi: 10.1200/PO.17.00149.
30. Tosto G, Bird TD, Tsuang D, Bennett DA, Boeve BF, Cruchaga C, et al. Polygenic risk scores in familial Alzheimer disease. Neurology. 2017;88(12):1180.
31. Torrecilla S, Sia D, Harrington AN, Zhang Z, Cabellos L, Cornella H, et al. Trunk mutational events present minimal intra- and inter-tumoral heterogeneity in hepatocellular carcinoma. Journal of Hepatology. 2017;67(6):1222-31. doi: https://doi.org/10.1016/j.jhep.2017.08.013.
32. Tome-Garcia J, Tejero R, Nudelman G, Yong RL, Sebra R, Wang H, et al. Prospective Isolation and Comparison of Human Germinal Matrix and Glioblastoma EGFR(+) Populations with Stem Cell Properties. Stem Cell Reports. 2017;8(5):1421-9. doi: 10.1016/j.stemcr.2017.03.019. PubMed PMID: PMC5425658.
33. Tcw J, Wang M, Pimenova AA, Bowles KR, Hartley BJ, Lacin E, et al. An Efficient Platform for Astrocyte Differentiation from Human Induced Pluripotent Stem Cells. Stem Cell Reports. 2017;9(2):600-14. doi: 10.1016/j.stemcr.2017.06.018. PubMed PMID: PMC5550034.
34. Tamburini S, Clemente JC. Neonatal gut microbiota induces lung immunity against pneumonia. Nature Reviews Gastroenterology &Amp; Hepatology. 2017;14:263. doi: 10.1038/nrgastro.2017.34.
35. Stein L, Thaler A, Liang JW, Tuhrim S, Dhamoon AS, Dhamoon MS. Intermediate‐Term Risk of Stroke Following Cardiac Procedures in a Nationally Representative Data Set. Journal of the American Heart Association. 2017;6(12).
36. Shen L, Zhu J, Robert Li S-Y, Fan X. Detect differentially methylated regions using non-homogeneous hidden Markov model for methylation array data. Bioinformatics. 2017;33(23):3701-8. doi: 10.1093/bioinformatics/btx467.
37. Shen L. End-to-end Training for Whole Image Breast Cancer Diagnosis using An All Convolutional Design2017.
38. Sheen J-H, Strainic MG, Liu J, Zhang W, Yi Z, Medof ME, et al. TLR-Induced Murine Dendritic Cell (DC) Activation Requires DC-Intrinsic Complement. The Journal of Immunology. 2017;199(1):278.
39. Shameer K, Glicksberg BS, Hodos R, Johnson KW, Badgeley MA, Readhead B, et al. Systematic analyses of drugs and disease indications in RepurposeDB reveal pharmacological, biological and epidemiological factors influencing drug repositioning. Briefings in Bioinformatics. 2017:bbw136-bbw. doi: 10.1093/bib/bbw136.
40. Segal LN, Clemente JC, Li Y, Ruan C, Cao J, Danckers M, et al. Anaerobic Bacterial Fermentation Products Increase Tuberculosis Risk in Antiretroviral-Drug-Treated HIV Patients. Cell Host & Microbe. 2017;21(4):530-7.e4. doi: https://doi.org/10.1016/j.chom.2017.03.003.
41. Scott SA, Owusu Obeng A, Botton MR, Yang Y, Scott ER, Ellis SB, et al. Institutional profile: translational pharmacogenomics at the Icahn School of Medicine at Mount Sinai. Pharmacogenomics. 2017;18(15):1381-6. doi: 10.2217/pgs-2017-0137.
42. Scott RA, Scott LJ, Mägi R, Marullo L, Gaulton KJ, Kaakinen M, et al. An Expanded Genome-Wide Association Study of Type 2 Diabetes in Europeans. Diabetes. 2017;66(11):2888.
43. Sanderson SC, Linderman MD, Suckiel SA, Zinberg R, Wasserstein M, Kasarskis A, et al. Psychological and behavioural impact of returning personal results from whole-genome sequencing: the HealthSeq project. European Journal of Human Genetics. 2017;25(3):280-92. doi: 10.1038/ejhg.2016.178. PubMed PMID: PMC5315514.
44. Saccone NL, Emery LS, Sofer T, Gogarten SM, Becker DM, Bottinger EP, et al. Genome-Wide Association Study of Heavy Smoking and Daily/Nondaily Smoking in the Hispanic Community Health Study/Study of Latinos (HCHS/SOL). Nicotine & Tobacco Research. 2017:ntx107-ntx. doi: 10.1093/ntr/ntx107.
45. Romero Navarro JA, Phillips-Mora W, Arciniegas-Leal A, Mata-Quirós A, Haiminen N, Mustiga G, et al. Application of Genome Wide Association and Genomic Prediction for Improvement of Cacao Productivity and Resistance to Black and Frosty Pod Diseases. Frontiers in Plant Science. 2017;8:1905. doi: 10.3389/fpls.2017.01905. PubMed PMID: PMC5694496.
46. Ridge PG, Karch CM, Hsu S, Arano I, Teerlink CC, Ebbert MTW, et al. Linkage, whole genome sequence, and biological data implicate variants in RAB10 in Alzheimer’s disease resilience. Genome Medicine. 2017;9(1):100. doi: 10.1186/s13073-017-0486-1.
47. Ribeiro EA, Scarpa JR, Garamszegi SP, Kasarskis A, Mash DC, Nestler EJ. Gene Network Dysregulation in Dorsolateral Prefrontal Cortex Neurons of Humans with Cocaine Use Disorder. Scientific Reports. 2017;7:5412. doi: 10.1038/s41598-017-05720-3. PubMed PMID: PMC5511210.
48. Rialdi A, Hultquist J, Jimenez-Morales D, Peralta Z, Campisi L, Fenouil R, et al. The RNA Exosome Syncs IAV-RNAPII Transcription to Promote Viral Ribogenesis and Infectivity. Cell. 2017;169(4):679-92.e14. doi: https://doi.org/10.1016/j.cell.2017.04.021.
49. Rengasamy M, Zhang F, Vashisht A, Song W-M, Aguilo F, Sun Y, et al. The PRMT5/WDR77 complex regulates alternative splicing through ZNF326 in breast cancer. Nucleic Acids Research. 2017;45(19):11106-20. doi: 10.1093/nar/gkx727. PubMed PMID: PMC5737218.
50. Ramesh M, Hamm D, Simchoni N, Cunningham-Rundles C. Clonal and constricted T cell repertoire in Common Variable Immune Deficiency. Clinical immunology (Orlando, Fla). 2017;178:1-9. Epub 2015/01/14. doi: 10.1016/j.clim.2015.01.002. PubMed PMID: 25596453.
51. Rahman Adeeb H, Lavin Y, Kobayashi S, Leader A, Merad M. High‐dimensional single cell mapping of cerium distribution in the lung immune microenvironment of an active smoker. Cytometry Part B: Clinical Cytometry. 2017;0(0). doi: 10.1002/cyto.b.21545.
52. Qi H, Casalena G, Shi S, Yu L, Ebefors K, Sun Y, et al. Glomerular Endothelial Mitochondrial Dysfunction Is Essential and Characteristic of Diabetic Kidney Disease Susceptibility. Diabetes. 2017;66(3):763-78. doi: 10.2337/db16-0695. PubMed PMID: PMC5319717.
53. Polubriaginof F, Vanguri R, Quinnies K, Belbin G, Yahi A, Salmasian H, et al. Estimate of disease heritability using 7.4 million familial relationships inferred from electronic health records. bioRxiv. 2017.
54. Pollak J, Rai KG, Funk CC, Arora S, Lee E, Zhu J, et al. Ion channel expression patterns in glioblastoma stem cells with functional and therapeutic implications for malignancy. PLOS ONE. 2017;12(3):e0172884. doi: 10.1371/journal.pone.0172884.
55. Petralia F, Aushev VN, Gopalakrishnan K, Kappil M, W. Khin N, Chen J, et al. A new method to study the change of miRNA–mRNA interactions due to environmental exposures. Bioinformatics. 2017;33(14):i199-i207. doi: 10.1093/bioinformatics/btx256.
56. Peters LA, Perrigoue J, Mortha A, Iuga A, Song W-m, Neiman EM, et al. A functional genomics predictive network model identifies regulators of inflammatory bowel disease. Nature Genetics. 2017;49:1437. doi: 10.1038/ng.3947
https://www.nature.com/articles/ng.3947 – supplementary-information.
57. Peng S, Deyssenroth MA, Di Narzo AF, Lambertini L, Marsit CJ, Chen J, et al. Expression quantitative trait loci (eQTLs) in human placentas suggest developmental origins of complex diseases. Human Molecular Genetics. 2017;26(17):3432-41. doi: 10.1093/hmg/ddx265.
58. Pena CJ, Kronman HG, Walker DM, Cates HM, Bagot RC, Purushothaman I, et al. Early life stress confers lifelong stress susceptibility in mice via ventral tegmental area OTX2. Science. 2017;356(6343):1185-8. Epub 2017/06/18. doi: 10.1126/science.aan4491. PubMed PMID: 28619944; PubMed Central PMCID: PMCPMC5539403.
59. Peña CJ, Kronman HG, Walker DM, Cates HM, Bagot RC, Purushothaman I, et al. Early life stress confers lifelong stress susceptibility in mice via ventral tegmental area OTX2. Science. 2017;356(6343):1185.
60. Pappas K, Xu J, Zairis S, Resnick-Silverman L, Abate F, Steinbach N, et al. p53 Maintains Baseline Expression of Multiple Tumor Suppressor Genes. Molecular Cancer Research. 2017;15(8):1051.
61. Pandya C, Uzilov AV, Bellizzi J, Lau CY, Moe AS, Strahl M, et al. Genomic profiling reveals mutational landscape in parathyroid carcinomas. JCI Insight. 2017;2(6):e92061. doi: 10.1172/jci.insight.92061. PubMed PMID: PMC5358487.
62. Pandey G, Pandey OP, Rogers AJ, Hoffman GE, Raby BA, Weiss ST, et al. A Novel Nasal Brush-based Classifier of Asthma Identified by Machine Learning Analysis of Nasal RNA Sequence Data. bioRxiv. 2017.
63. Pak TR, Chacko KI, O’Donnell T, Huprikar SS, van Bakel H, Kasarskis A, et al. Estimating Local Costs Associated With Clostridium difficile Infection Using Machine Learning and Electronic Medical Records. Infection Control & Hospital Epidemiology. 2017;38(12):1478-86. Epub 2017/11/06. doi: 10.1017/ice.2017.214.
64. Ortiz-Virumbrales M, Moreno CL, Kruglikov I, Marazuela P, Sproul A, Jacob S, et al. CRISPR/Cas9-Correctable mutation-related molecular and physiological phenotypes in iPSC-derived Alzheimer’s PSEN2(N141I) neurons. Acta Neuropathologica Communications. 2017;5:77. doi: 10.1186/s40478-017-0475-z. PubMed PMID: PMC5660456.
65. O’Connell PJ, Zhang W, Ge Y, Menon MC, Murphy B. Biopsy transcriptome expression profiling: proper validation is key – Authors’ reply. The Lancet. 2017;389(10069):601. doi: https://doi.org/10.1016/S0140-6736(17)30283-0.
66. Ng MCY, Graff M, Lu Y, Justice AE, Mudgal P, Liu C-T, et al. Discovery and fine-mapping of adiposity loci using high density imputation of genome-wide association studies in individuals of African ancestry: African Ancestry Anthropometry Genetics Consortium. PLOS Genetics. 2017;13(4):e1006719. doi: 10.1371/journal.pgen.1006719.
67. Nelson CP, Goel A, Butterworth AS, Kanoni S, Webb TR, Marouli E, et al. Association analyses based on false discovery rate implicate new loci for coronary artery disease. Nature Genetics. 2017;49:1385. doi: 10.1038/ng.3913
https://www.nature.com/articles/ng.3913 – supplementary-information.
68. Nadkarni GN, Galarneau G, Ellis SB, Nadukuru R, Zhang J, Scott SA, et al. Apolipoprotein L1 Variants and Blood Pressure Traits in African Americans. Journal of the American College of Cardiology. 2017;69(12):1564-74. doi: https://doi.org/10.1016/j.jacc.2017.01.040.
69. Moser DA, Doucet GE, Ing A, Dima D, Schumann G, Bilder RM, et al. An integrated brain–behavior model for working memory. Molecular Psychiatry. 2017. doi: 10.1038/mp.2017.247
https://www.nature.com/articles/mp2017247 – supplementary-information.
70. Monsell SE, Mock C, Fardo DW, Bertelsen S, Cairns NJ, Roe CM, et al. Genetic Comparison of Symptomatic and Asymptomatic Persons With Alzheimer Disease Neuropathology. Alzheimer Disease & Associated Disorders. 2017;31(3).
71. Miller ML, Ren Y, Szutorisz H, Warren NA, Tessereau C, Egervári G, et al. Ventral striatal regulation of CREM mediates impulsive action and drug addiction vulnerability. Molecular psychiatry. 2017:10.1038/mp.2017.80. doi: 10.1038/mp.2017.80. PubMed PMID: PMC5656565.
72. Mezei M. Using Force-Field Grids for Sampling Translation/Rotation of Partially Rigid Macromolecules. Algorithms. 2017;10(1). doi: 10.3390/a10010006.
73. Meyers JL, Zhang J, Wang JC, Su J, Kuo SI, Kapoor M, et al. An endophenotype approach to the genetics of alcohol dependence: a genome wide association study of fast beta EEG in families of African ancestry. Molecular Psychiatry. 2017;22:1767. doi: 10.1038/mp.2016.239
https://www.nature.com/articles/mp2016239 – supplementary-information.
74. McKenzie AT, Moyon S, Wang M, Katsyv I, Song W-M, Zhou X, et al. Multiscale network modeling of oligodendrocytes reveals molecular components of myelin dysregulation in Alzheimer’s disease. Molecular Neurodegeneration. 2017;12(1):82. doi: 10.1186/s13024-017-0219-3.
75. Mayourian J, Cashman TJ, Ceholski DK, Johnson BV, Sachs D, Kaji DA, et al. Experimental and Computational Insight Into Human Mesenchymal Stem Cell Paracrine Signaling and Heterocellular Coupling Effects on Cardiac Contractility and ArrhythmogenicityNovelty and Significance</span&gt. Circulation Research. 2017;121(4):411.
76. Mathers AJ, Stoesser N, Chai W, Carroll J, Barry K, Cherunvanky A, et al. Chromosomal Integration of the Klebsiella pneumoniae Carbapenemase Gene, blaKPC, in Klebsiella Species Is Elusive but Not Rare. Antimicrobial Agents and Chemotherapy. 2017;61(3).
77. Martín-Martínez M, Pérez-Gordillo FL, Álvarez de la Rosa D, Rodríguez Y, Gerona-Navarro G, González-Muñiz R, et al. Modulating Mineralocorticoid Receptor with Non-steroidal Antagonists. New Opportunities for the Development of Potent and Selective Ligands without Off-Target Side Effects. Journal of Medicinal Chemistry. 2017;60(7):2629-50. doi: 10.1021/acs.jmedchem.6b01065.
78. Martin AR, Gignoux CR, Walters RK, Wojcik GL, Neale BM, Gravel S, et al. Human Demographic History Impacts Genetic Risk Prediction across Diverse Populations. American Journal of Human Genetics. 2017;100(4):635-49. doi: 10.1016/j.ajhg.2017.03.004. PubMed PMID: PMC5384097.
79. Marouli E, Graff M, Medina-Gomez C, Lo KS, Wood AR, Kjaer TR, et al. Rare and low-frequency coding variants alter human adult height. Nature. 2017;542:186. doi: 10.1038/nature21039
https://www.nature.com/articles/nature21039 – supplementary-information.
80. Marino Kristen A, Shang Y, Filizola M. Insights into the function of opioid receptors from molecular dynamics simulations of available crystal structures. British Journal of Pharmacology. 2017;0(0). doi: 10.1111/bph.13774.
81. Marino KA, Shang Y, Filizola M. Insights into the function of opioid receptors from molecular dynamics simulations of available crystal structures. British Journal of Pharmacology. 2017:n/a-n/a. doi: 10.1111/bph.13774.
82. Macé A, Tuke MA, Deelen P, Kristiansson K, Mattsson H, Nõukas M, et al. CNV-association meta-analysis in 191,161 European adults reveals new loci associated with anthropometric traits. Nature Communications. 2017;8(1):744. doi: 10.1038/s41467-017-00556-x.
83. Loh YE, Koemeter-Cox A, Finelli MJ, Shen L, Friedel RH, Zou H. Comprehensive mapping of 5-hydroxymethylcytosine epigenetic dynamics in axon regeneration. Epigenetics. 2017;12(2):77-92. Epub 2016/12/06. doi: 10.1080/15592294.2016.1264560. PubMed PMID: 27918235; PubMed Central PMCID: PMCPMC5330438.
84. Loh YE, Feng J, Nestler E, Shen L. Bioinformatic Analysis for Profiling Drug-induced Chromatin Modification Landscapes in Mouse Brain Using ChlP-seq Data. Bio Protoc. 2017;7(3). Epub 2017/05/19. doi: 10.21769/BioProtoc.2123. PubMed PMID: 28516124; PubMed Central PMCID: PMCPMC5432020.
85. Llewellyn SR, Britton GJ, Contijoch EJ, Mortha A, Colombel J-F, Grinspan A, et al. Deciphering the combinatorial influence of diet and the microbiota on experimental colitis. bioRxiv. 2017.
86. Liu DJ, Peloso GM, Yu H, Butterworth AS, Wang X, Mahajan A, et al. Exome-wide association study of plasma lipids in >300,000 individuals. Nature Genetics. 2017;49:1758. doi: 10.1038/ng.3977
https://www.nature.com/articles/ng.3977 – supplementary-information.
87. Lim ET, Uddin M, De Rubeis S, Chan Y, Kamumbu AS, Zhang X, et al. Rates, distribution and implications of postzygotic mosaic mutations in autism spectrum disorder. Nature Neuroscience. 2017;20:1217. doi: 10.1038/nn.4598
https://www.nature.com/articles/nn.4598 – supplementary-information.
88. Liang J, Le TH, Edwards DRV, Tayo BO, Gaulton KJ, Smith JA, et al. Single-trait and multi-trait genome-wide association analyses identify novel loci for blood pressure in African-ancestry populations. PLOS Genetics. 2017;13(5):e1006728. doi: 10.1371/journal.pgen.1006728.
89. Li YI, Wong G, Humphrey J, Raj T. Prioritizing Parkinson’s Disease genes using population-scale transcriptomic data. bioRxiv. 2017:231001. doi: 10.1101/231001.
90. Li Y, Lucas-Osma AM, Black S, Bandet MV, Stephens MJ, Vavrek R, et al. Pericytes impair capillary blood flow and motor function after chronic spinal cord injury. Nature medicine. 2017;23(6):733-41. doi: 10.1038/nm.4331. PubMed PMID: PMC5716958.
91. Li M, Li Y, Weeks O, Mijatovic V, Teumer A, Huffman JE, et al. SOS2 and ACP1 Loci Identified through Large-Scale Exome Chip Analysis Regulate Kidney Development and Function. Journal of the American Society of Nephrology : JASN. 2017;28(3):981-94. doi: 10.1681/ASN.2016020131. PubMed PMID: PMC5328154.
92. Li L, Greene I, Readhead B, Menon MC, Kidd BA, Uzilov AV, et al. Novel Therapeutics Identification for Fibrosis in Renal Allograft Using Integrative Informatics Approach. Scientific Reports. 2017;7:39487. doi: 10.1038/srep39487. PubMed PMID: PMC5209709.
93. Li J, Rodriguez Y, Cheng C, Zeng L, Wong EYM, Xu CY, et al. EYA1’s Conformation Specificity in Dephosphorylating Phosphothreonine in Myc and Its Activity on Myc Stabilization in Breast Cancer. Molecular and Cellular Biology. 2017;37(1):e00499-16. doi: 10.1128/MCB.00499-16. PubMed PMID: PMC5192086.
94. Li H, Cai J, Chen R, Zhao Z, Ying Z, Wang L, et al. Particulate Matter Exposure and Stress Hormone Levels. Circulation. 2017;136(7):618.
95. Levin MA, Joseph TT, Jeff JM, Nadukuru R, Ellis SB, Bottinger EP, et al. iGAS: A framework for using electronic intraoperative medical records for genomic discovery. Journal of Biomedical Informatics. 2017;67:80-9. doi: https://doi.org/10.1016/j.jbi.2017.02.005.
96. Lee E, Pain M, Wang H, Herman JA, Toledo CM, DeLuca JG, et al. Sensitivity to BUB1B Inhibition Defines an Alternative Classification of Glioblastoma. Cancer Research. 2017;77(20):5518.
97. Lavin Y, Kobayashi S, Leader A, Amir E-aD, Elefant N, Bigenwald C, et al. Innate Immune Landscape in Early Lung Adenocarcinoma by Paired Single-Cell Analyses. Cell. 2017;169(4):750-65.e17. doi: https://doi.org/10.1016/j.cell.2017.04.014.
98. Laganà A, Perumal D, Melnekoff D, Readhead B, Kidd BA, Leshchenko V, et al. Integrative network analysis identifies novel drivers of pathogenesis and progression in newly diagnosed multiple myeloma. Leukemia. 2017;32:120. doi: 10.1038/leu.2017.197
https://www.nature.com/articles/leu2017197 – supplementary-information.
99. Labonte B, Engmann O, Purushothaman I, Menard C, Wang J, Tan C, et al. Sex-specific transcriptional signatures in human depression. Nat Med. 2017;23(9):1102-11. Epub 2017/08/22. doi: 10.1038/nm.4386. PubMed PMID: 28825715; PubMed Central PMCID: PMCPMC5734943.
100. Labonté B, Engmann O, Purushothaman I, Menard C, Wang J, Tan C, et al. Sex-specific transcriptional signatures in human depression. Nature Medicine. 2017;23:1102. doi: 10.1038/nm.4386
https://www.nature.com/articles/nm.4386 – supplementary-information.
101. Kozlenkov A, Jaffe AE, Timashpolsky A, Apontes P, Rudchenko S, Barbu M, et al. DNA Methylation Profiling of Human Prefrontal Cortex Neurons in Heroin Users Shows Significant Difference between Genomic Contexts of Hyper- and Hypomethylation and a Younger Epigenetic Age. Genes. 2017;8(6):152. doi: 10.3390/genes8060152. PubMed PMID: PMC5485516.
102. Kotini AG, Chang C-J, Chow A, Yuan H, Ho T-C, Wang T, et al. Stage-specific human induced pluripotent stem cells map the progression of myeloid transformation to transplantable leukemia. Cell stem cell. 2017;20(3):315-28.e7. doi: 10.1016/j.stem.2017.01.009. PubMed PMID: PMC5337161.
103. Kapoor A, Martinez-Rosell G, Provasi D, de Fabritiis G, Filizola M. Dynamic and Kinetic Elements of µ-Opioid Receptor Functional Selectivity. Scientific Reports. 2017;7(1):11255. doi: 10.1038/s41598-017-11483-8.
104. Justice AE, Winkler TW, Feitosa MF, Graff M, Fisher VA, Young K, et al. Genome-wide meta-analysis of 241,258 adults accounting for smoking behaviour identifies novel loci for obesity traits. Nature Communications. 2017;8:14977. doi: 10.1038/ncomms14977. PubMed PMID: PMC5414044.
105. Johnston HR, Hu Y-J, Gao J, O’Connor TD, Abecasis GR, Wojcik GL, et al. Identifying tagging SNPs for African specific genetic variation from the African Diaspora Genome. Scientific Reports. 2017;7:46398. doi: 10.1038/srep46398
https://www.nature.com/articles/srep46398 – supplementary-information.
106. Jin SC, Homsy J, Zaidi S, Lu Q, Morton S, DePalma SR, et al. Contribution of rare inherited and de novo variants in 2,871 congenital heart disease probands. Nature Genetics. 2017;49:1593. doi: 10.1038/ng.3970
https://www.nature.com/articles/ng.3970 – supplementary-information.
107. Jiang Y, Loh YE, Rajarajan P, Hirayama T, Liao W, Kassim BS, et al. The methyltransferase SETDB1 regulates a large neuron-specific topological chromatin domain. Nat Genet. 2017;49(8):1239-50. Epub 2017/07/04. doi: 10.1038/ng.3906. PubMed PMID: 28671686; PubMed Central PMCID: PMCPMC5560095.
108. Jiang Y, Loh Y-HE, Rajarajan P, Hirayama T, Liao W, Kassim BS, et al. Kmt1e regulates a large neuron-specific topological chromatin domain. Nature genetics. 2017;49(8):1239-50. doi: 10.1038/ng.3906. PubMed PMID: PMC5560095.
109. Jason F, Fuchsberger C, Mahajan A, Teslovich TM, Agarwala V, Gaulton KJ, et al. Sequence data and association statistics from 12,940 type 2 diabetes cases and controls. Scientific Data. 2017;4:170179. doi: 10.1038/sdata.2017.179. PubMed PMID: PMC5735917.
110. Ito K, Park SH, Katsyv I, Zhang W, De Angelis C, Schiff R, et al. PTK6 regulates growth and survival of endocrine therapy-resistant ER+ breast cancer cells. npj Breast Cancer. 2017;3(1):45. doi: 10.1038/s41523-017-0047-1.
111. Ibi D, de la Fuente Revenga M, Kezunovic N, Muguruza C, Saunders JM, Gaitonde SA, et al. Antipsychotic-induced Hdac2 transcription via NF-κB leads to synaptic and cognitive side effects. Nature Neuroscience. 2017;20:1247. doi: 10.1038/nn.4616
https://www.nature.com/articles/nn.4616 – supplementary-information.
112. Huang K-l, Marcora E, Pimenova AA, Di Narzo AF, Kapoor M, Jin SC, et al. A common haplotype lowers PU.1 expression in myeloid cells and delays onset of Alzheimer’s disease. Nature neuroscience. 2017;20(8):1052-61. doi: 10.1038/nn.4587. PubMed PMID: PMC5759334.
113. Hong X, Hao K, Ji H, Peng S, Sherwood B, Di Narzo A, et al. Genome-wide approach identifies a novel gene-maternal pre-pregnancy BMI interaction on preterm birth. Nature Communications. 2017;8:15608. doi: 10.1038/ncomms15608
https://www.nature.com/articles/ncomms15608 – supplementary-information.
114. Homan P, Reddan MC, Brosch T, Koenigsberg HW, Schiller D. Aberrant link between empathy and social attribution style in borderline personality disorder. Journal of Psychiatric Research. 2017;94:163-71. doi: https://doi.org/10.1016/j.jpsychires.2017.07.012.
115. Homan P, Ely BA, Yuan M, Brosch T, Ng J, Trope Y, et al. Aversive smell associations shape social judgment. Neurobiology of Learning and Memory. 2017;144:86-95. doi: https://doi.org/10.1016/j.nlm.2017.07.004.
116. Hogstad B, Berres M-L, Chakraborty R, Tang J, Bigenwald C, Serasinghe M, et al. RAF/MEK/extracellular signal–related kinase pathway suppresses dendritic cell migration and traps dendritic cells in Langerhans cell histiocytosis lesions. The Journal of Experimental Medicine. 2017.
117. Hoffman GE, Hartley BJ, Flaherty E, Ladran I, Gochman P, Ruderfer DM, et al. Transcriptional signatures of schizophrenia in hiPSC-derived NPCs and neurons are concordant with post-mortem adult brains. Nature Communications. 2017;8(1):2225. doi: 10.1038/s41467-017-02330-5.
118. Hellwege JN, Jeff JM, Wise LA, Gallagher CS, Wellons M, Hartmann KE, et al. A multi-stage genome-wide association study of uterine fibroids in African Americans. Human Genetics. 2017;136(10):1363-73. doi: 10.1007/s00439-017-1836-1. PubMed PMID: PMC5628188.
119. Heaton BE, Kennedy EM, Dumm RE, Harding AT, Sacco MT, Sachs D, et al. A CRISPR activation screen identifies a pan-avian influenza virus inhibitory host factor. Cell reports. 2017;20(7):1503-12. doi: 10.1016/j.celrep.2017.07.060. PubMed PMID: PMC5568676.
120. He Z, Zhang D, Renton AE, Li B, Zhao L, Wang GT, et al. The Rare-Variant Generalized Disequilibrium Test for Association Analysis of Nuclear and Extended Pedigrees with Application to Alzheimer Disease WGS Data. American Journal of Human Genetics. 2017;100(2):193-204. doi: 10.1016/j.ajhg.2016.12.001. PubMed PMID: PMC5294711.
121. Haure-Mirande J-V, Audrain M, Fanutza T, Kim SH, Klein WL, Glabe C, et al. Deficiency of TYROBP, an adapter protein for TREM2 and CR3 receptors, is neuroprotective in a mouse model of early Alzheimer’s pathology. Acta Neuropathologica. 2017;134(5):769-88. doi: 10.1007/s00401-017-1737-3. PubMed PMID: PMC5645450.
122. Hartmann BM, Albrecht RA, Zaslavsky E, Nudelman G, Pincas H, Marjanovic N, et al. Pandemic H1N1 influenza A viruses suppress immunogenic RIPK3-driven dendritic cell death. Nature Communications. 2017;8(1):1931. doi: 10.1038/s41467-017-02035-9.
123. Haro C, García‐Carpintero S, Rangel‐Zúñiga Oriol A, Alcalá‐Díaz Juan F, Landa Blanca B, Clemente José C, et al. Consumption of Two Healthy Dietary Patterns Restored Microbiota Dysbiosis in Obese Patients with Metabolic Dysfunction. Molecular Nutrition & Food Research. 2017;61(12):1700300. doi: 10.1002/mnfr.201700300.
124. Hammerstad SS, Stefan M, Blackard J, Owen RP, Lee HJ, Concepcion E, et al. Hepatitis C Virus E2 Protein Induces Upregulation of IL-8 Pathways and Production of Heat Shock Proteins in Human Thyroid Cells. The Journal of Clinical Endocrinology and Metabolism. 2017;102(2):689-97. doi: 10.1210/jc.2016-3403. PubMed PMID: PMC5413166.
125. Hamlin RE, Rahman A, Pak TR, Maringer K, Mena I, Bernal-Rubio D, et al. High-dimensional CyTOF analysis of dengue virus–infected human DCs reveals distinct viral signatures. JCI Insight. 2017;2(13):e92424. doi: 10.1172/jci.insight.92424. PubMed PMID: PMC5499363.
126. Graff M, Scott RA, Justice AE, Young KL, Feitosa MF, Barata L, et al. Genome-wide physical activity interactions in adiposity ― A meta-analysis of 200,452 adults. PLOS Genetics. 2017;13(4):e1006528. doi: 10.1371/journal.pgen.1006528.
127. Graff M, Emery LS, Justice AE, Parra E, Below JE, Palmer ND, et al. Genetic architecture of lipid traits in the Hispanic community health study/study of Latinos. Lipids in Health and Disease. 2017;16:200. doi: 10.1186/s12944-017-0591-6. PubMed PMID: PMC5639746.
128. Gorski M, van der Most PJ, Teumer A, Chu AY, Li M, Mijatovic V, et al. 1000 Genomes-based meta-analysis identifies 10 novel loci for kidney function. Scientific Reports. 2017;7:45040. doi: 10.1038/srep45040
https://www.nature.com/articles/srep45040 – supplementary-information.
129. Gong J, Nishimura KK, Fernandez-Rhodes L, Haessler J, Bien S, Graff M, et al. Trans-ethnic analysis of metabochip data identifies two new loci associated with BMI. International Journal Of Obesity. 2017. doi: 10.1038/ijo.2017.304
https://www.nature.com/articles/ijo2017304 – supplementary-information.
130. Ghersi D, Parakh A, Mezei M. Comparison of a quantum random number generator with pseudorandom number generators for their use in molecular Monte Carlo simulations. Journal of Computational Chemistry. 2017;38(31):2713-20. doi: 10.1002/jcc.25065.
131. Fulton BO, Sachs D, Schwarz MC, Palese P, Evans MJ. Transposon Mutagenesis of the Zika Virus Genome Highlights Regions Essential for RNA Replication and Restricted for Immune Evasion. Journal of Virology. 2017;91(15):e00698-17. doi: 10.1128/JVI.00698-17. PubMed PMID: PMC5512254.
132. Fu R, Wang P, Ma W, Taguchi A, Wong C-H, Zhang Q, et al. A statistical method for detecting differentially expressed SNVs based on next-generation RNA-seq data. Biometrics. 2017;73(1):42-51. doi: 10.1111/biom.12548. PubMed PMID: PMC5151178.
133. Forst CV, Zhou B, Wang M, Chou T-W, Mason G, Song W-m, et al. Integrative gene network analysis identifies key signatures, intrinsic networks and host factors for influenza virus A infections. npj Systems Biology and Applications. 2017;3(1):35. doi: 10.1038/s41540-017-0036-x.
134. Fontanals-Cirera B, Hasson D, Vardabasso C, Di Micco R, Agrawal P, Chowdhury A, et al. Harnessing BET Inhibitor Sensitivity Reveals AMIGO2 as a Melanoma Survival Gene. Molecular Cell. 2017;68(4):731-44.e9. doi: https://doi.org/10.1016/j.molcel.2017.11.004.
135. Flannick J, Fuchsberger C, Mahajan A, Teslovich TM, Agarwala V, Gaulton KJ, et al. Sequence data and association statistics from 12,940 type 2 diabetes cases and controls. Scientific Data. 2017;4:170179. doi: 10.1038/sdata.2017.179
https://www.nature.com/articles/sdata2017179 – supplementary-information.
136. Flaherty E, Deranieh RM, Artimovich E, Lee IS, Siegel AJ, Levy DL, et al. Patient-derived hiPSC neurons with heterozygous CNTNAP2 deletions display altered neuronal gene expression and network activity. npj Schizophrenia. 2017;3(1):35. doi: 10.1038/s41537-017-0033-5.
137. Fernández-Rhodes L, Gong J, Haessler J, Franceschini N, Graff M, Nishimura KK, et al. Trans-ethnic fine-mapping of genetic loci for body mass index in the diverse ancestral populations of the Population Architecture using Genomics and Epidemiology (PAGE) Study reveals evidence for multiple signals at established loci. Human Genetics. 2017;136(6):771-800. doi: 10.1007/s00439-017-1787-6.
138. Fernández MV, Kim JH, Budde JP, Black K, Medvedeva A, Saef B, et al. Analysis of neurodegenerative Mendelian genes in clinically diagnosed Alzheimer Disease. PLOS Genetics. 2017;13(11):e1007045. doi: 10.1371/journal.pgen.1007045.
139. Feng J, Pena CJ, Purushothaman I, Engmann O, Walker D, Brown AN, et al. Tet1 in Nucleus Accumbens Opposes Depression- and Anxiety-Like Behaviors. Neuropsychopharmacology. 2017;42(8):1657-69. Epub 2017/01/12. doi: 10.1038/npp.2017.6. PubMed PMID: 28074830; PubMed Central PMCID: PMCPMC5518912.
140. Engmann O, Labonte B, Mitchell A, Bashtrykov P, Calipari ES, Rosenbluh C, et al. Cocaine-Induced Chromatin Modifications Associate With Increased Expression and Three-Dimensional Looping of Auts2. Biol Psychiatry. 2017;82(11):794-805. Epub 2017/06/05. doi: 10.1016/j.biopsych.2017.04.013. PubMed PMID: 28577753; PubMed Central PMCID: PMCPMC5671915.
141. Eisfeld AJ, Halfmann PJ, Wendler JP, Kyle JE, Burnum-Johnson KE, Peralta Z, et al. Multi-platform ‘Omics Analysis of Human Ebola Virus Disease Pathogenesis. Cell host & microbe. 2017;22(6):817-29.e8. Epub 2017/11/16. doi: 10.1016/j.chom.2017.10.011. PubMed PMID: 29154144.
142. Douvaras P, Sun B, Wang M, Kruglikov I, Lallos G, Zimmer M, et al. Directed Differentiation of Human Pluripotent Stem Cells to Microglia. Stem Cell Reports. 2017;8(6):1516-24. doi: 10.1016/j.stemcr.2017.04.023. PubMed PMID: PMC5470097.
143. Dong L, Meng F, Wu L, Mitchell AV, Block CJ, Zhang B, et al. Cooperative oncogenic effect and cell signaling crosstalk of co-occurring HER2 and mutant PIK3CA in mammary epithelial cells. International Journal of Oncology. 2017;51(4):1320-30. doi: 10.3892/ijo.2017.4108. PubMed PMID: PMC5592866.
144. Dole NS, Mazur CM, Acevedo C, Lopez JP, Monteiro DA, Fowler TW, et al. Osteocyte-Intrinsic TGF-β Signaling Regulates Bone Quality through Perilacunar/Canalicular Remodeling. Cell reports. 2017;21(9):2585-96. doi: 10.1016/j.celrep.2017.10.115. PubMed PMID: 29186693.
145. Di Narzo AF, Telesco SE, Brodmerkel C, Argmann C, Peters LA, Li K, et al. High-Throughput Characterization of Blood Serum Proteomics of IBD Patients with Respect to Aging and Genetic Factors. PLOS Genetics. 2017;13(1):e1006565. doi: 10.1371/journal.pgen.1006565.
146. Deyssenroth MA, Peng S, Hao K, Lambertini L, Marsit CJ, Chen J. Whole-transcriptome analysis delineates the human placenta gene network and its associations with fetal growth. BMC Genomics. 2017;18(1):520. doi: 10.1186/s12864-017-3878-0.
147. Descalzi G, Mitsi V, Purushothaman I, Gaspari S, Avrampou K, Loh YE, et al. Neuropathic pain promotes adaptive changes in gene expression in brain networks involved in stress and depression. Sci Signal. 2017;10(471). Epub 2017/03/23. doi: 10.1126/scisignal.aaj1549. PubMed PMID: 28325815; PubMed Central PMCID: PMCPMC5524975.
148. Deming Y, Li Z, Kapoor M, Harari O, Del-Aguila JL, Black K, et al. Genome-wide association study identifies four novel loci associated with Alzheimer’s endophenotypes and disease modifiers. Acta Neuropathologica. 2017;133(5):839-56. doi: 10.1007/s00401-017-1685-y.
149. Degli Esposti D, Aushev VN, Lee E, Cros M-P, Zhu J, Herceg Z, et al. miR-500a-5p regulates oxidative stress response genes in breast cancer and predicts cancer survival. Scientific Reports. 2017;7(1):15966. doi: 10.1038/s41598-017-16226-3.
150. Dahl C, Stanislawski M, Iszatt N, Mandal S, Lozupone C, Clemente JC, et al. Gut microbiome of mothers delivering prematurely shows reduced diversity and lower relative abundance of Bifidobacterium and Streptococcus. PLOS ONE. 2017;12(10):e0184336. doi: 10.1371/journal.pone.0184336.
151. Christophersen IE, Rienstra M, Roselli C, Yin X, Geelhoed B, Barnard J, et al. Large-scale analyses of common and rare variants identify 12 new loci associated with atrial fibrillation. Nature genetics. 2017;49(6):946-52. doi: 10.1038/ng.3843. PubMed PMID: PMC5585859.
152. Choi H, Song W-M, Zhang B. Linking childhood allergic asthma phenotypes with endotype through integrated systems biology: current evidence and research needs. Reviews on Environmental Health2017. p. 55.
153. Cheung KL, Zhang F, Jaganathan A, Sharma R, Zhang Q, Konuma T, et al. Distinct Roles of Brd2 and Brd4 in Potentiating the Transcriptional Program for Th17 Cell Differentiation. Molecular cell. 2017;65(6):1068-80.e5. doi: 10.1016/j.molcel.2016.12.022. PubMed PMID: PMC5357147.
154. Cheung K, Lu G, Sharma R, Vincek A, Zhang R, Plotnikov AN, et al. BET N-terminal bromodomain inhibition selectively blocks Th17 cell differentiation and ameliorates colitis in mice. Proceedings of the National Academy of Sciences. 2017;114(11):2952.
155. Chen Y, Camacho SC, Silvers TR, Razak ARA, Gabrail NY, Gerecitano JF, et al. Inhibition of the Nuclear Export Receptor XPO1 as a Therapeutic Target for Platinum-Resistant Ovarian Cancer. Clinical Cancer Research. 2017;23(6):1552.
156. Chan Y-FY, Wang P, Rogers L, Tignor N, Zweig M, Hershman SG, et al. The Asthma Mobile Health Study, a large-scale clinical observational study using ResearchKit. Nature Biotechnology. 2017;35:354. doi: 10.1038/nbt.3826
https://www.nature.com/articles/nbt.3826 – supplementary-information.
157. Cates HM, Heller EA, Lardner CK, Purushothaman I, Peña CJ, Walker DM, et al. Transcription Factor E2F3a in Nucleus Accumbens Affects Cocaine Action via Transcription and Alternative Splicing. Biological Psychiatry. 2017. doi: https://doi.org/10.1016/j.biopsych.2017.11.027.
158. Cates H, Heller E, Lardner C, Purushothaman I, Jensen Pena C, Walker D, et al. E2F3a in nucleus accumbens affects cocaine action via transcription and alternative splicing2017.
159. Carcamo-Orive I, Hoffman GE, Cundiff P, Beckmann ND, D’Souza SL, Knowles JW, et al. Analysis of Transcriptional Variability in a Large Human iPSC Library Reveals Genetic and Non-genetic Determinants of Heterogeneity. Cell stem cell. 2017;20(4):518-32.e9. Epub 2016/12/22. doi: 10.1016/j.stem.2016.11.005. PubMed PMID: 28017796.
160. Boorsma CE, van der Veen TA, Putri KSS, de Almeida A, Draijer C, Mauad T, et al. A Potent Tartrate Resistant Acid Phosphatase Inhibitor to Study the Function of TRAP in Alveolar Macrophages. Scientific Reports. 2017;7(1):12570. doi: 10.1038/s41598-017-12623-w.
161. Bobeck EN, Gomes I, Pena D, Cummings KA, Clem RL, Mezei M, et al. The BigLEN-GPR171 Peptide Receptor System Within the Basolateral Amygdala Regulates Anxiety-Like Behavior and Contextual Fear Conditioning. Neuropsychopharmacology. 2017;42:2527. doi: 10.1038/npp.2017.79
https://www.nature.com/articles/npp201779 – supplementary-information.
162. Bichoupan K, Tandon N, Martel-Laferriere V, Patel NM, Sachs D, Ng M, et al. Factors associated with success of telaprevir- and boceprevir-based triple therapy for hepatitis C virus infection. World Journal of Hepatology. 2017;9(11):551-61. doi: 10.4254/wjh.v9.i11.551. PubMed PMID: PMC5395804.
163. Belbin GM, Odgis J, Sorokin EP, Yee M-C, Kohli S, Glicksberg BS, et al. Genetic identification of a common collagen disease in Puerto Ricans via identity-by-descent mapping in a health system. eLife. 2017;6:e25060. doi: 10.7554/eLife.25060.
164. Bashir A, Attie O, Sullivan M, Sebra R, Singh KV, Altman D, et al. Genomic confirmation of vancomycin-resistant Enterococcus transmission from deceased donor to liver transplant recipient. PLOS ONE. 2017;12(3):e0170449. doi: 10.1371/journal.pone.0170449.
165. Bardot E, Calderon D, Santoriello F, Han S, Cheung K, Jadhav B, et al. Foxa2 identifies a cardiac progenitor population with ventricular differentiation potential. Nature Communications. 2017;8:14428. doi: 10.1038/ncomms14428
https://www.nature.com/articles/ncomms14428 – supplementary-information.
166. Balan S, Finnigan J, Bhardwaj N. Dendritic Cell Strategies for Eliciting Mutation-Derived Tumor Antigen Responses in Patients. The Cancer Journal. 2017;23(2).
167. Ali MR, Sadoqi M, Møller SG, Boutajangout A, Mezei M. Assessing the binding of cholinesterase inhibitors by docking and molecular dynamics studies. Journal of Molecular Graphics and Modelling. 2017;76:36-42. doi: https://doi.org/10.1016/j.jmgm.2017.06.027.
168. Akerman I, Tu Z, Beucher A, Rolando DMY, Sauty-Colace C, Benazra M, et al. Human Pancreatic β Cell lncRNAs Control Cell-Specific Regulatory Networks. Cell Metabolism. 2017;25(2):400-11. doi: 10.1016/j.cmet.2016.11.016. PubMed PMID: PMC5300904.
169. Aguilo F, Zakirova Z, Nolan K, Wagner R, Sharma R, Hogan M, et al. THAP1: Role in Mouse Embryonic Stem Cell Survival and Differentiation. Stem Cell Reports. 2017;9(1):92-107. doi: 10.1016/j.stemcr.2017.04.032. PubMed PMID: PMC5511047.
170. Aguado LC, Schmid S, May J, Sabin LR, Panis M, Blanco-Melo D, et al. RNase III nucleases from diverse kingdoms serve as antiviral effectors. Nature. 2017;547(7661):114-7. doi: 10.1038/nature22990. PubMed PMID: PMC5846625.

2016

1. Zubair N, Graff M, Luis Ambite J, Bush WS, Kichaev G, Lu Y, et al. Fine-mapping of lipid regions in global populations discovers ethnic-specific signals and refines previously identified lipid loci. Human Molecular Genetics. 2016;25(24):5500-12. doi: 10.1093/hmg/ddw358. PubMed PMID: PMC5721937.
2. Zhou F, Wang W, Shen C, Li H, Zuo X, Zheng X, et al. Epigenome-Wide Association Analysis Identified Nine Skin DNA Methylation Loci for Psoriasis. Journal of Investigative Dermatology. 2016;136(4):779-87. doi: https://doi.org/10.1016/j.jid.2015.12.029.
3. Zhao Y, Song W-M, Zhang F, Zhou M-M, Zhang W, Walsh MJ, et al. Distinct distributions of genomic features of the 5′ and 3′ partners of coding somatic cancer gene fusions: arising mechanisms and functional implications. Oncotarget. 2016;8(40):66769-83. doi: 10.18632/oncotarget.10734. PubMed PMID: 28977995.
4. Zhao Y, Forst CV, Sayegh CE, Wang IM, Yang X, Zhang B. Molecular and Genetic Inflammation Networks in Major Human Diseases. Molecular bioSystems. 2016;12(8):2318-41. doi: 10.1039/c6mb00240d. PubMed PMID: PMC4955784.
5. Zhao W, Ho L, Wang J, Bi W, Yemul S, Ward L, et al. In Silico Modelling of Novel Drug Ligands Associated with Abnormal Tau Phosphorylation: Implications for Concussion Associated Tauopathy Intervention(). Journal of cellular biochemistry. 2016;117(10):2241-8. doi: 10.1002/jcb.25521. PubMed PMID: PMC4988328.
6. Zhang F, Ren C, Lau KK, Zheng Z, Lu G, Yi Z, et al. A network medicine approach to build a comprehensive atlas for the prognosis of human cancer. Briefings in Bioinformatics. 2016;17(6):1044-59. doi: 10.1093/bib/bbw076.
7. Zhang DY, Goossens N, Guo J, Tsai M-c, Chou H-I, Altunkaynak C, et al. A hepatic stellate cell gene expression signature associated with outcomes in hepatitis C cirrhosis and hepatocellular carcinoma after curative resection. Gut. 2016;65(10):1754-64. doi: 10.1136/gutjnl-2015-309655. PubMed PMID: PMC4848165.
8. Zhang DY, Goossens N, Guo J, Tsai M-C, Chou H-I, Altunkaynak C, et al. A hepatic stellate cell gene expression signature associated with outcomes in hepatitis C cirrhosis and hepatocellular carcinoma after curative resection. Gut. 2016;65(10):1754-64. Epub 2015/06/04. doi: 10.1136/gutjnl-2015-309655. PubMed PMID: 26045137.
9. Zhang B, Tran L, Emilsson V, Zhu J. Characterization of Genetic Networks Associated with Alzheimer’s Disease. In: Castrillo JI, Oliver SG, editors. Systems Biology of Alzheimer’s Disease. New York, NY: Springer New York; 2016. p. 459-77.
10. Yuan H, Liu H, Liu Z, Owzar K, Han Y, Su L, et al. A Novel Genetic Variant in Long Non-coding RNA Gene NEXN-AS1 is Associated with Risk of Lung Cancer. Scientific Reports. 2016;6:34234. doi: 10.1038/srep34234. PubMed PMID: PMC5054367.
11. Yang X, Li F, Konze KD, Meslamani J, Ma A, Brown PJ, et al. Structure–Activity Relationship Studies for Enhancer of Zeste Homologue 2 (EZH2) and Enhancer of Zeste Homologue 1 (EZH1) Inhibitors. Journal of Medicinal Chemistry. 2016;59(16):7617-33. doi: 10.1021/acs.jmedchem.6b00855.
12. Yang J, Huang T, Song W-m, Petralia F, Mobbs CV, Zhang B, et al. Discover the network mechanisms underlying the connections between aging and age-related diseases. Scientific Reports. 2016;6:32566. doi: 10.1038/srep32566
https://www.nature.com/articles/srep32566 – supplementary-information.
13. Yang J, Huang T, Petralia F, Long Q, Zhang B, Argmann C, et al. Corrigendum: Synchronized age-related gene expression changes across multiple tissues in human and the link to complex diseases. Scientific Reports. 2016;6:19384. doi: 10.1038/srep19384.
14. Whalen S, Pandey OP, Pandey G. Predicting protein function and other biomedical characteristics with heterogeneous ensembles. Methods (San Diego, Calif). 2016;93:92-102. doi: 10.1016/j.ymeth.2015.08.016. PubMed PMID: PMC4718788.
15. Watson CT, Roussos P, Garg P, Ho DJ, Azam N, Katsel PL, et al. Genome-wide12 DNA methylation profiling in the superior temporal gyrus reveals epigenetic signatures associated with Alzheimer’s disease. Genome Medicine. 2016;8:5. doi: 10.1186/s13073-015-0258-8. PubMed PMID: PMC4719699.
16. Wardman JH, Gomes I, Bobeck EN, Stockert JA, Kapoor A, Bisignano P, et al. Identification of a small-molecule ligand that activates the neuropeptide receptor GPR171 and increases food intake. Science signaling. 2016;9(430):ra55-ra. doi: 10.1126/scisignal.aac8035. PubMed PMID: PMC5150984.
17. Wang T, Santos JH, Feng J, Fargo DC, Shen L, Riadi G, et al. A Novel Analytical Strategy to Identify Fusion Transcripts between Repetitive Elements and Protein Coding-Exons Using RNA-Seq. PLoS ONE. 2016;11(7):e0159028. doi: 10.1371/journal.pone.0159028. PubMed PMID: PMC4945064.
18. Wang Q, Lin L, Yoo S, Wang W, Blank S, Fiel MI, et al. Impact of non-neoplastic vs intratumoural hepatitis B viral DNA and replication on hepatocellular carcinoma recurrence. British Journal of Cancer. 2016;115(7):841-7. doi: 10.1038/bjc.2016.239. PubMed PMID: PMC5046201.
19. Wang M, Roussos P, McKenzie A, Zhou X, Kajiwara Y, Brennand KJ, et al. Integrative network analysis of nineteen brain regions identifies molecular signatures and networks underlying selective regional vulnerability to Alzheimer’s disease. Genome Medicine. 2016;8(1):104. doi: 10.1186/s13073-016-0355-3.
20. Wang L, Oh WK, Zhu J. Disease-specific classification using deconvoluted whole blood gene expression. Scientific Reports. 2016;6:32976. doi: 10.1038/srep32976
https://www.nature.com/articles/srep32976 – supplementary-information.
21. Vedanthan R, Bansilal S, Soto AV, Kovacic JC, Latina J, Jaslow R, et al. Family-Based Approaches to Cardiovascular Health Promotion. Journal of the American College of Cardiology. 2016;67(14):1725-37. doi: https://doi.org/10.1016/j.jacc.2016.01.036.
22. Uzilov AV, Ding W, Fink MY, Antipin Y, Brohl AS, Davis C, et al. Development and clinical application of an integrative genomic approach to personalized cancer therapy. Genome Medicine. 2016;8:62. doi: 10.1186/s13073-016-0313-0. PubMed PMID: PMC4888213.
23. Topol A, Zhu S, Hartley BJ, English J, Hauberg ME, Readhead B, et al. Dysregulation of miRNA-9 in a subset of schizophrenia patient-derived neural progenitor cells. Cell reports. 2016;15(5):1024-36. doi: 10.1016/j.celrep.2016.03.090. PubMed PMID: PMC4856588.
24. Tignor N, Wang PEI, Genes N, Rogers L, Hershman SG, Scott ER, et al. METHODS FOR CLUSTERING TIME SERIES DATA ACQUIRED FROM MOBILE HEALTH APPS. Biocomputing 2017: WORLD SCIENTIFIC; 2016. p. 300-11.
25. Tan PS, Nakagawa S, Goossens N, Venkatesh A, Huang T, Ward SC, et al. Clinicopathological indices to predict hepatocellular carcinoma molecular classification. Liver international : official journal of the International Association for the Study of the Liver. 2016;36(1):108-18. Epub 2015/06/29. doi: 10.1111/liv.12889. PubMed PMID: 26058462.
26. Tamburini S, Shen N, Wu HC, Clemente JC. The microbiome in early life: implications for health outcomes. Nature Medicine. 2016;22:713. doi: 10.1038/nm.4142.
27. Tamburini S, Clemente JC. Zooming in on Inflammatory Bowel Disease: Microbial and Proteomic Features Associated With IBD in Colonic Microenvironments. Cellular and Molecular Gastroenterology and Hepatology. 2016;2(5):540-1. doi: 10.1016/j.jcmgh.2016.07.001. PubMed PMID: PMC5042882.
28. Tajuddin Salman M, Schick Ursula M, Eicher John D, Chami N, Giri A, Brody Jennifer A, et al. Large-Scale Exome-wide Association Analysis Identifies Loci for White Blood Cell Traits and Pleiotropy with Immune-Mediated Diseases. American Journal of Human Genetics. 2016;99(1):22-39. doi: 10.1016/j.ajhg.2016.05.003. PubMed PMID: PMC5005433.
29. Sung YJ, Winkler TW, Manning AK, Aschard H, Gudnason V, Harris TB, et al. An Empirical Comparison of Joint and Stratified Frameworks for Studying G × E Interactions: Systolic Blood Pressure and Smoking in the CHARGE Gene-Lifestyle Interactions Working Group. Genetic Epidemiology. 2016;40(5):404-15. doi: 10.1002/gepi.21978.
30. Sun H, Martin JA, Werner CT, Wang ZJ, Damez-Werno DM, Scobie KN, et al. BAZ1B in Nucleus Accumbens Regulates Reward-Related Behaviors in Response to Distinct Emotional Stimuli. J Neurosci. 2016;36(14):3954-61. Epub 2016/04/08. doi: 10.1523/jneurosci.3254-15.2016. PubMed PMID: 27053203; PubMed Central PMCID: PMCPMC4821908.
31. Suckiel SA, Linderman MD, Sanderson SC, Diaz GA, Wasserstein M, Kasarskis A, et al. Impact of Genomic Counseling on Informed Decision-Making among ostensibly Healthy Individuals Seeking Personal Genome Sequencing: the HealthSeq Project. Journal of Genetic Counseling. 2016;25(5):1044-53. doi: 10.1007/s10897-016-9935-z.
32. Stoesser N, Sheppard AE, Peirano G, Sebra RP, Lynch T, Anson LW, et al. First Report of bla(IMP-14) on a Plasmid Harboring Multiple Drug Resistance Genes in Escherichia coli Sequence Type 131. Antimicrobial Agents and Chemotherapy. 2016;60(8):5068-71. doi: 10.1128/AAC.00840-16. PubMed PMID: PMC4958194.
33. Stoesser N, Sheppard AE, Peirano G, Sebra R, Lynch T, Anson L, et al. Complete Sequencing of Plasmids Containing bla(OXA-163) and bla(OXA-48) in Escherichia coli Sequence Type 131. Antimicrobial Agents and Chemotherapy. 2016;60(11):6948-51. doi: 10.1128/AAC.01130-16. PubMed PMID: PMC5075115.
34. Stoesser N, Sheppard AE, Pankhurst L, De Maio N, Moore CE, Sebra R, et al. Evolutionary History of the Global Emergence of the Escherichia coli Epidemic Clone ST131. mBio. 2016;7(2).
35. Stanescu ANA, Pandey G. LEARNING PARSIMONIOUS ENSEMBLES FOR UNBALANCED COMPUTATIONAL GENOMICS PROBLEMS. Pacific Symposium on Biocomputing Pacific Symposium on Biocomputing. 2016;22:288-99. PubMed PMID: PMC5147733.
36. Smith SG, Zhou M-M. Bromodomains as targets for therapeutic intervention. Drug Discovery Today: Technologies. 2016;19:1-2. doi: https://doi.org/10.1016/j.ddtec.2016.09.002.
37. Shukla-Dave A, Castillo-Martin M, Chen M, Lobo J, Gladoun N, Collazo-Lorduy A, et al. Ornithine Decarboxylase Is Sufficient for Prostate Tumorigenesis via Androgen Receptor Signaling. The American Journal of Pathology. 2016;186(12):3131-45. doi: https://doi.org/10.1016/j.ajpath.2016.08.021.
38. Shoemaker LD, Clark MJ, Patwardhan A, Chandratillake G, Garcia S, Chen R, et al. Disease Variant Landscape of a Large Multiethnic Population of Moyamoya Patients by Exome Sequencing. G3: Genes|Genomes|Genetics. 2016;6(1):41-9. doi: 10.1534/g3.115.020321. PubMed PMID: PMC4704723.
39. Sheppard AE, Stoesser N, Wilson DJ, Sebra R, Kasarskis A, Anson LW, et al. Nested Russian Doll-Like Genetic Mobility Drives Rapid Dissemination of the Carbapenem Resistance Gene blaKPC. Antimicrobial Agents and Chemotherapy. 2016;60(6):3767-78.
40. Sheppard AE, Stoesser N, Sebra R, Kasarskis A, Deikus G, Anson L, et al. Complete Genome Sequence of KPC-Producing Klebsiella pneumoniae Strain CAV1193. Genome Announcements. 2016;4(1):e01649-15. doi: 10.1128/genomeA.01649-15. PubMed PMID: PMC4732343.
41. Shen EY, Jiang Y, Javidfar B, Kassim B, Loh YE, Ma Q, et al. Neuronal Deletion of Kmt2a/Mll1 Histone Methyltransferase in Ventral Striatum is Associated with Defective Spike-Timing-Dependent Striatal Synaptic Plasticity, Altered Response to Dopaminergic Drugs, and Increased Anxiety. Neuropsychopharmacology. 2016;41(13):3103-13. Epub 2016/08/04. doi: 10.1038/npp.2016.144. PubMed PMID: 27485686; PubMed Central PMCID: PMCPMC5101561.
42. Shang Y, Yeatman HR, Provasi D, Alt A, Christopoulos A, Canals M, et al. Proposed Mode of Binding and Action of Positive Allosteric Modulators at Opioid Receptors. ACS Chemical Biology. 2016;11(5):1220-9. doi: 10.1021/acschembio.5b00712.
43. Shameer K, Johnson KW, Yahi A, Miotto R, Li LI, Ricks D, et al. PREDICTIVE MODELING OF HOSPITAL READMISSION RATES USING ELECTRONIC MEDICAL RECORD-WIDE MACHINE LEARNING: A CASE-STUDY USING MOUNT SINAI HEART FAILURE COHORT. Pacific Symposium on Biocomputing Pacific Symposium on Biocomputing. 2016;22:276-87. PubMed PMID: PMC5362124.
44. Segal LN, Clemente JC, Wu BG, Wikoff WR, Gao Z, Li Y, et al. Randomised, double-blind, placebo-controlled trial with azithromycin selects for anti-inflammatory microbial metabolites in the emphysematous lung. Thorax. 2016.
45. Segal LN, Clemente JC, Tsay J-CJ, Koralov SB, Keller BC, Wu BG, et al. Enrichment of the lung microbiome with oral taxa is associated with lung inflammation of a Th17 phenotype. Nature microbiology. 2016;1:16031-. doi: 10.1038/nmicrobiol.2016.31. PubMed PMID: PMC5010013.
46. Schneider S, Provasi D, Filizola M. How Oliceridine (TRV-130) Binds and Stabilizes a μ-Opioid Receptor Conformational State That Selectively Triggers G Protein Signaling Pathways. Biochemistry. 2016;55(46):6456-66. doi: 10.1021/acs.biochem.6b00948.
47. Schmidt B, Wei L, DePeralta DK, Hoshida Y, Tan PS, Sun X, et al. Molecular subclasses of hepatocellular carcinoma predict sensitivity to fibroblast growth factor receptor inhibition. International journal of cancer. 2016;138(6):1494-505. Epub 2015/11/09. doi: 10.1002/ijc.29893. PubMed PMID: 26481559.
48. Scarpa JR, Jiang P, Losic B, Readhead B, Gao VD, Dudley JT, et al. Systems Genetic Analyses Highlight a TGFβ-FOXO3 Dependent Striatal Astrocyte Network Conserved across Species and Associated with Stress, Sleep, and Huntington’s Disease. PLOS Genetics. 2016;12(7):e1006137. doi: 10.1371/journal.pgen.1006137.
49. Sanderson SC, Linderman MD, Suckiel SA, Diaz GA, Zinberg RE, Ferryman K, et al. Motivations, concerns and preferences of personal genome sequencing research participants: Baseline findings from the HealthSeq project. European Journal of Human Genetics. 2016;24(1):14-20. doi: 10.1038/ejhg.2015.118. PubMed PMID: PMC4795230.
50. Salmon H, Idoyaga J, Rahman A, Leboeuf M, Remark R, Jordan S, et al. Expansion and activation of CD103(+) dendritic cell progenitors at the tumor site enhances tumor responses to therapeutic PD-L1 and BRAF inhibition. Immunity. 2016;44(4):924-38. doi: 10.1016/j.immuni.2016.03.012. PubMed PMID: PMC4980762.
51. Roussos P, Guennewig B, Kaczorowski DC, Barry G, Brennand KJ. Activity-Dependent Changes in Gene Expression in Schizophrenia Human-Induced Pluripotent Stem Cell Neurons. JAMA psychiatry. 2016;73(11):1180-8. doi: 10.1001/jamapsychiatry.2016.2575. PubMed PMID: PMC5437975.
52. Rialdi A, Campisi L, Zhao N, Lagda AC, Pietzsch C, Ho JSY, et al. Topoisomerase 1 inhibition suppresses inflammatory genes and protects from death by inflammation. Science (New York, NY). 2016;352(6289):aad7993-aad. doi: 10.1126/science.aad7993. PubMed PMID: PMC5193222.
53. Ren C, Smith SG, Yap K, Li S, Li J, Mezei M, et al. Structure-Guided Discovery of Selective Antagonists for the Chromodomain of Polycomb Repressive Protein CBX7. ACS Medicinal Chemistry Letters. 2016;7(6):601-5. doi: 10.1021/acsmedchemlett.6b00042.
54. Quilez J, Guilmatre A, Garg P, Highnam G, Gymrek M, Erlich Y, et al. Polymorphic tandem repeats within gene promoters act as modifiers of gene expression and DNA methylation in humans. Nucleic Acids Research. 2016;44(8):3750-62. doi: 10.1093/nar/gkw219. PubMed PMID: PMC4857002.
55. Qiao W, Yang Y, Sebra R, Mendiratta G, Gaedigk A, Desnick RJ, et al. Long-Read Single Molecule Real-Time Full Gene Sequencing of Cytochrome P450-2D6. Human mutation. 2016;37(3):315-23. Epub 2015/12/18. doi: 10.1002/humu.22936. PubMed PMID: 26602992.
56. Qiao W, Wang J, Pullman BS, Chen R, Yang Y, Scott SA. The CYP2D6 VCF Translator. The Pharmacogenomics Journal. 2016;17:301. doi: 10.1038/tpj.2016.14.
57. Pfau ML, Purushothaman I, Feng J, Golden SA, Aleyasin H, Lorsch ZS, et al. Integrative Analysis of Sex-Specific microRNA Networks Following Stress in Mouse Nucleus Accumbens. Frontiers in Molecular Neuroscience. 2016;9:144. doi: 10.3389/fnmol.2016.00144. PubMed PMID: PMC5179560.
58. Petralia F, Song W-M, Tu Z, Wang P. New Method for Joint Network Analysis Reveals Common and Different Coexpression Patterns among Genes and Proteins in Breast Cancer. Journal of Proteome Research. 2016;15(3):743-54. doi: 10.1021/acs.jproteome.5b00925.
59. Perumal D, Kuo P-Y, Leshchenko VV, Jiang Z, Divakar SKA, Cho HJ, et al. Dual Targeting of CDK4 and ARK5 Using a Novel Kinase Inhibitor ON123300 Exerts Potent Anticancer Activity against Multiple Myeloma. Cancer Research. 2016;76(5):1225.
60. Pattaro C, Teumer A, Gorski M, Chu AY, Li M, Mijatovic V, et al. Genetic associations at 53 loci highlight cell types and biological pathways relevant for kidney function. Nature communications. 2016;7:10023-. doi: 10.1038/ncomms10023. PubMed PMID: PMC4735748.
61. Pak TR, Kasarskis A. Reply to Lesho. Clinical Infectious Diseases. 2016;62(8):1053-. doi: 10.1093/cid/ciw010.
62. Osman R, Mezei M, Engel S. The role of protein “Stability patches” in molecular recognition: A case study of the human growth hormone-receptor complex. Journal of Computational Chemistry. 2016;37(10):913-9. doi: 10.1002/jcc.24276.
63. O’Connell PJ, Zhang W, Menon MC, Yi Z, Schröppel B, Gallon L, et al. Biopsy transcriptome expression profiling to identify kidney transplants at risk of chronic injury: a multicentre, prospective study. The Lancet. 2016;388(10048):983-93. doi: https://doi.org/10.1016/S0140-6736(16)30826-1.
64. Nakagawa S, Wei L, Song WM, Higashi T, Ghoshal S, Kim RS, et al. Molecular liver cancer prevention in cirrhosis by organ transcriptome analysis and lysophosphatidic acid pathway inhibition. Cancer cell. 2016;30(6):879-90. doi: 10.1016/j.ccell.2016.11.004. PubMed PMID: PMC5161110.
65. Moyon S, Huynh JL, Dutta D, Zhang F, Ma D, Yoo S, et al. Functional characterization of DNA methylation in the oligodendrocyte lineage. Cell reports. 2016;15(4):748-60. doi: 10.1016/j.celrep.2016.03.060. PubMed PMID: PMC5063656.
66. Mezei M. Use of an interface contact statistics to rescore protein‐protein docked ensembles2016.
67. Mertins P, Mani DR, Ruggles KV, Gillette MA, Clauser KR, Wang P, et al. Proteogenomics connects somatic mutations to signalling in breast cancer. Nature. 2016;534:55. doi: 10.1038/nature18003
https://www.nature.com/articles/nature18003 – supplementary-information.
68. Meng Q, Ying Z, Noble E, Zhao Y, Agrawal R, Mikhail A, et al. Systems Nutrigenomics Reveals Brain Gene Networks Linking Metabolic and Brain Disorders. EBioMedicine. 2016;7:157-66. doi: 10.1016/j.ebiom.2016.04.008. PubMed PMID: PMC4909610.
69. Mena I, Nelson MI, Quezada-Monroy F, Dutta J, Cortes-Fernández R, Lara-Puente JH, et al. Origins of the 2009 H1N1 influenza pandemic in swine in Mexico. eLife. 2016;5:e16777. doi: 10.7554/eLife.16777. PubMed PMID: PMC4957980.
70. Melo R, Fieldhouse R, Melo A, Correia JDG, Cordeiro MNDS, Gümüş ZH, et al. A Machine Learning Approach for Hot-Spot Detection at Protein-Protein Interfaces. International Journal of Molecular Sciences. 2016;17(8):1215. doi: 10.3390/ijms17081215. PubMed PMID: PMC5000613.
71. McKenzie AT, Katsyv I, Song W-M, Wang M, Zhang B. DGCA: A comprehensive R package for Differential Gene Correlation Analysis. BMC Systems Biology. 2016;10:106. doi: 10.1186/s12918-016-0349-1. PubMed PMID: PMC5111277.
72. Mathias RA, Taub MA, Gignoux CR, Fu W, Musharoff S, O’Connor TD, et al. A continuum of admixture in the Western Hemisphere revealed by the African Diaspora genome. Nature Communications. 2016;7:12522. doi: 10.1038/ncomms12522
https://www.nature.com/articles/ncomms12522 – supplementary-information.
73. Marino KA, Prada-Gracia D, Provasi D, Filizola M. Impact of Lipid Composition and Receptor Conformation on the Spatio-temporal Organization of μ-Opioid Receptors in a Multi-component Plasma Membrane Model. PLOS Computational Biology. 2016;12(12):e1005240. doi: 10.1371/journal.pcbi.1005240.
74. Ma M, Wang C, Glicksberg BS, Schadt EE, Li SD, Chen R. IDENTIFY CANCER DRIVER GENES THROUGH SHARED MENDELIAN DISEASE PATHOGENIC VARIANTS AND CANCER SOMATIC MUTATIONS. Biocomputing 2017: WORLD SCIENTIFIC; 2016. p. 473-84.
75. Luo W, Obeidat Me, Di Narzo AF, Chen R, Sin DD, Paré PD, et al. Airway Epithelial Expression Quantitative Trait Loci Reveal Genes Underlying Asthma and Other Airway Diseases. American Journal of Respiratory Cell and Molecular Biology. 2016;54(2):177-87. doi: 10.1165/rcmb.2014-0381OC. PubMed PMID: PMC4821039.
76. Lu AT, Hannon E, Levine ME, Hao K, Crimmins EM, Lunnon K, et al. Genetic variants near MLST8 and DHX57 affect the epigenetic age of the cerebellum. Nature Communications. 2016;7:10561. doi: 10.1038/ncomms10561. PubMed PMID: PMC4740877.
77. Long Q, Argmann C, Houten SM, Huang T, Peng S, Zhao Y, et al. Inter-tissue coexpression network analysis reveals DPP4 as an important gene in heart to blood communication. Genome Medicine. 2016;8:15. doi: 10.1186/s13073-016-0268-1. PubMed PMID: PMC4746932.
78. Loley C, Alver M, Assimes TL, Bjonnes A, Goel A, Gustafsson S, et al. No Association of Coronary Artery Disease with X-Chromosomal Variants in Comprehensive International Meta-Analysis. Scientific Reports. 2016;6:35278. doi: 10.1038/srep35278
https://www.nature.com/articles/srep35278 – supplementary-information.
79. Loh YH, Shen L. Analysis and Visualization of ChIP-Seq and RNA-Seq Sequence Alignments Using ngs.plot. Methods Mol Biol. 2016;1415:371-83. Epub 2016/04/27. doi: 10.1007/978-1-4939-3572-7_18. PubMed PMID: 27115642.
80. Liu P, Ping Y, Ma M, Zhang D, Liu C, Zaidi S, et al. Anabolic actions of Notch on mature bone. Proceedings of the National Academy of Sciences of the United States of America. 2016;113(15):E2152-E61. doi: 10.1073/pnas.1603399113. PubMed PMID: PMC4839423.
81. Liu C-T, Raghavan S, Maruthur N, Kabagambe Edmond K, Hong J, Ng Maggie C, et al. Trans-ethnic Meta-analysis and Functional Annotation Illuminates the Genetic Architecture of Fasting Glucose and Insulin. American Journal of Human Genetics. 2016;99(1):56-75. doi: 10.1016/j.ajhg.2016.05.006. PubMed PMID: PMC5005440.
82. Liu C, Kraja AT, Smith JA, Brody JA, Franceschini N, Bis JC, et al. Meta-analysis identifies common and rare variants influencing blood pressure and overlapping with metabolic trait loci. Nature genetics. 2016;48(10):1162-70. doi: 10.1038/ng.3660. PubMed PMID: PMC5320952.
83. Li Q, Lee CH, Peters LA, Mastropaolo LA, Thoeni C, Elkadri A, et al. Variants in TRIM22 that Affect NOD2 Signaling Are Associated With Very Early Onset Inflammatory Bowel Disease. Gastroenterology. 2016;150(5):1196-207. doi: 10.1053/j.gastro.2016.01.031. PubMed PMID: PMC4842103.
84. Li CW, Menconi F, Osman R, Mezei M, Jacobson EM, Concepcion E, et al. Identifying a Small Molecule Blocking Antigen Presentation in Autoimmune Thyroiditis. The Journal of Biological Chemistry. 2016;291(8):4079-90. doi: 10.1074/jbc.M115.694687. PubMed PMID: PMC4759184.
85. Lessard S, Manning AK, Low-Kam C, Auer PL, Giri A, Graff M, et al. Testing the role of predicted gene knockouts in human anthropometric trait variation. Human Molecular Genetics. 2016;25(10):2082-92. doi: 10.1093/hmg/ddw055. PubMed PMID: PMC5062577.
86. Lepack AE, Bagot RC, Pena CJ, Loh YE, Farrelly LA, Lu Y, et al. Aberrant H3.3 dynamics in NAc promote vulnerability to depressive-like behavior. Proc Natl Acad Sci U S A. 2016;113(44):12562-7. Epub 2016/11/03. doi: 10.1073/pnas.1608270113. PubMed PMID: 27791098; PubMed Central PMCID: PMCPMC5098673.
87. Lee E, Ito K, Zhao Y, Schadt EE, Irie HY, Zhu J. Inferred miRNA activity identifies miRNA-mediated regulatory networks underlying multiple cancers. Bioinformatics. 2016;32(1):96-105. doi: 10.1093/bioinformatics/btv531. PubMed PMID: PMC5006235.
88. Latif R, Realubit RB, Karan C, Mezei M, Davies TF. TSH Receptor Signaling Abrogation by a Novel Small Molecule. Frontiers in Endocrinology. 2016;7:130. doi: 10.3389/fendo.2016.00130. PubMed PMID: PMC5037132.
89. Laitman BM, Asp L, Mariani JN, Zhang J, Liu J, Sawai S, et al. The Transcriptional Activator Krüppel-like Factor-6 Is Required for CNS Myelination. PLOS Biology. 2016;14(5):e1002467. doi: 10.1371/journal.pbio.1002467.
90. Kruegel AC, Gassaway MM, Kapoor A, Váradi A, Majumdar S, Filizola M, et al. Synthetic and Receptor Signaling Explorations of the Mitragyna Alkaloids: Mitragynine as an Atypical Molecular Framework for Opioid Receptor Modulators. Journal of the American Chemical Society. 2016;138(21):6754-64. doi: 10.1021/jacs.6b00360.
91. Kozlenkov A, Wang M, Roussos P, Rudchenko S, Barbu M, Bibikova M, et al. Substantial DNA methylation differences between two major neuronal subtypes in human brain. Nucleic Acids Research. 2016;44(6):2593-612. doi: 10.1093/nar/gkv1304. PubMed PMID: PMC4824074.
92. Kosoy R, Agashe C, Grishin A, Leung DY, Wood RA, Sicherer SH, et al. Transcriptional Profiling of Egg Allergy and Relationship to Disease Phenotype. PLOS ONE. 2016;11(10):e0163831. doi: 10.1371/journal.pone.0163831.
93. Kocabayoglu P, Zhang DY, Kojima K, Hoshida Y, Friedman SL. Induction and contribution of beta platelet-derived growth factor signalling by hepatic stellate cells to liver regeneration after partial hepatectomy in mice. Liver international : official journal of the International Association for the Study of the Liver. 2016;36(6):874-82. Epub 2015/09/21. doi: 10.1111/liv.12933. PubMed PMID: 26256287.
94. Kilpeläinen TO, Carli JFM, Skowronski AA, Sun Q, Kriebel J, Feitosa MF, et al. Genome-wide meta-analysis uncovers novel loci influencing circulating leptin levels. Nature Communications. 2016;7:10494. doi: 10.1038/ncomms10494
https://www.nature.com/articles/ncomms10494 – supplementary-information.
95. Kidd BA, Wroblewska A, Boland MR, Agudo J, Merad M, Tatonetti NP, et al. Mapping the effects of drugs on the immune system. Nature biotechnology. 2016;34(1):47-54. doi: 10.1038/nbt.3367. PubMed PMID: PMC4706827.
96. Khan JA, Mendelson A, Kunisaki Y, Birbrair A, Kou Y, Arnal-Estapé A, et al. Fetal liver hematopoietic stem cell niches associate with portal vessels. Science (New York, NY). 2016;351(6269):176-80. doi: 10.1126/science.aad0084. PubMed PMID: PMC4706788.
97. Katsyv I, Wang M, Song WM, Zhou X, Zhao Y, Park S, et al. EPRS is a critical regulator of cell proliferation and estrogen signaling in ER(+) breast cancer. Oncotarget. 2016;7(43):69592-605. doi: 10.18632/oncotarget.11870. PubMed PMID: PMC5342500.
98. Kapoor M, Chou YL, Edenberg HJ, Foroud T, Martin NG, Madden PAF, et al. Genome-wide polygenic scores for age at onset of alcohol dependence and association with alcohol-related measures. Translational Psychiatry. 2016;6(3):e761. doi: 10.1038/tp.2016.27. PubMed PMID: PMC4872451.
99. Kamlesh KY, Khader S, Ben R, Shalini SY, Li L, Andrew K, et al. Systems Medicine Approaches to Improving Understanding, Treatment, and Clinical Management of Neuroendocrine Prostate Cancer. Current Pharmaceutical Design. 2016;22(34):5234-48. doi: http://dx.doi.org/10.2174/1381612822666160513145924.
100. Kajiwara Y, McKenzie A, Dorr N, Gama Sosa MA, Elder G, Schmeidler J, et al. The human-specific CASP4 gene product contributes to Alzheimer-related synaptic and behavioural deficits. Human Molecular Genetics. 2016;25(19):4315-27. doi: 10.1093/hmg/ddw265. PubMed PMID: PMC5291199.
101. Hoffman KW, Sachs D, Bardina SV, Michlmayr D, Rodriguez CA, Sum J, et al. Differences in Early Cytokine Production Are Associated With Development of a Greater Number of Symptoms Following West Nile Virus Infection. The Journal of Infectious Diseases. 2016;214(4):634-43. doi: 10.1093/infdis/jiw179. PubMed PMID: PMC4957436.
102. Hoarau G, Mukherjee PK, Gower-Rousseau C, Hager C, Chandra J, Retuerto MA, et al. Bacteriome and Mycobiome Interactions Underscore Microbial Dysbiosis in Familial Crohn’s Disease. mBio. 2016;7(5):e01250-16. doi: 10.1128/mBio.01250-16. PubMed PMID: PMC5030358.
103. Heck MM, Thalgott M, Schmid SC, Oh WK, Gong Y, Wang L, et al. A 2-Gene Panel Derived From Prostate Cancer-Enhanced Transcripts in Whole Blood Is Prognostic for Survival and Predicts Treatment Benefit in Metastatic Castration-Resistant Prostate Cancer. The Prostate. 2016;76(13):1160-8. doi: 10.1002/pros.23202.
104. Heaton NS, Moshkina N, Fenouil R, Gardner TJ, Aguirre S, Shah PS, et al. Limiting influenza virus, HIV and dengue virus infection by targeting viral proteostasis. Immunity. 2016;44(1):46-58. doi: 10.1016/j.immuni.2015.12.017. PubMed PMID: PMC4878455.
105. Haro C, Garcia-Carpintero S, Alcala-Diaz JF, Gomez-Delgado F, Delgado-Lista J, Perez-Martinez P, et al. The gut microbial community in metabolic syndrome patients is modified by diet. The Journal of Nutritional Biochemistry. 2016;27:27-31. doi: https://doi.org/10.1016/j.jnutbio.2015.08.011.
106. Hamilton JR, Sachs D, Lim JK, Langlois RA, Palese P, Heaton NS. Club cells surviving influenza A virus infection induce temporary nonspecific antiviral immunity. Proceedings of the National Academy of Sciences of the United States of America. 2016;113(14):3861-6. doi: 10.1073/pnas.1522376113. PubMed PMID: PMC4833272.
107. Halene TB, Kozlenkov A, Jiang Y, Mitchell A, Javidfar B, Dincer A, et al. NeuN(+) Neuronal Nuclei in Non-Human Primate Prefrontal Cortex and Subcortical White Matter After Clozapine Exposure. Schizophrenia research. 2016;170(0):235-44. doi: 10.1016/j.schres.2015.12.016. PubMed PMID: PMC4740223.
108. Hakenberg J, Cheng W-Y, Thomas P, Wang Y-C, Uzilov AV, Chen R. Integrating 400 million variants from 80,000 human samples with extensive annotations: towards a knowledge base to analyze disease cohorts. BMC Bioinformatics. 2016;17:24. doi: 10.1186/s12859-015-0865-9. PubMed PMID: PMC4706706.
109. Goossens N, Hoshida Y, Song WM, Jung M, Morel P, Nakagawa S, et al. Nonalcoholic Steatohepatitis Is Associated With Increased Mortality in Obese Patients Undergoing Bariatric Surgery. Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association. 2016;14(11):1619-28. Epub 2015/10/20. doi: 10.1016/j.cgh.2015.10.010. PubMed PMID: 26492845.
110. Goossens N, Hoshida Y, Song WM, Jung M, Morel P, Nakagawa S, et al. Non-alcoholic Steatohepatitis is Associated with Increased Mortality in Obese Patients Undergoing Bariatric Surgery. Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association. 2016;14(11):1619-28. doi: 10.1016/j.cgh.2015.10.010. PubMed PMID: PMC4838546.
111. Gonzalo B, Dusan B-B, Marcelo Cortez San M, Víctor N, Harm van B, Michele T, et al. Avian Influenza Virus H5 Strain with North American and Eurasian Lineage Genes in an Antarctic Penguin. Emerging Infectious Disease journal. 2016;22(12):2221. doi: 10.3201/eid2212.161076.
112. Gong Y, Wang L, Chippada-Venkata U, Dai X, Oh WK, Zhu J. Constructing Bayesian networks by integrating gene expression and copy number data identifies NLGN4Y as a novel regulator of prostate cancer progression. Oncotarget. 2016;7(42):68688-707. doi: 10.18632/oncotarget.11925. PubMed PMID: PMC5356583.
113. Glicksberg BS, Li L, Badgeley MA, Shameer K, Kosoy R, Beckmann ND, et al. Comparative analyses of population-scale phenomic data in electronic medical records reveal race-specific disease networks. Bioinformatics. 2016;32(12):i101-i10. doi: 10.1093/bioinformatics/btw282. PubMed PMID: PMC4908366.
114. Gajzer D, Ross J, Winder L, Navada S, Zhang W, Silverman L, et al. Epigenetic and molecular signatures of cord blood CD34+ cells treated with histone deacetylase inhibitors. Vox Sanguinis. 2016;110(1):79-89. doi: 10.1111/vox.12303.
115. Gacias M, Gaspari S, Santos P-MG, Tamburini S, Andrade M, Zhang F, et al. Microbiota-driven transcriptional changes in prefrontal cortex override genetic differences in social behavior. eLife. 2016;5:e13442. doi: 10.7554/eLife.13442. PubMed PMID: PMC4880443.
116. Fuchsberger C, Flannick J, Teslovich TM, Mahajan A, Agarwala V, Gaulton KJ, et al. The genetic architecture of type 2 diabetes. Nature. 2016;536(7614):41-7. doi: 10.1038/nature18642. PubMed PMID: PMC5034897.
117. Fu J, Wei C, Lee K, Zhang W, He W, Chuang P, et al. Comparison of Glomerular and Podocyte mRNA Profiles in Streptozotocin-Induced Diabetes. Journal of the American Society of Nephrology : JASN. 2016;27(4):1006-14. Epub 2015/08/11. doi: 10.1681/ASN.2015040421. PubMed PMID: 26264855.
118. Fromer M, Roussos P, Sieberts SK, Johnson JS, Kavanagh DH, Perumal TM, et al. Gene Expression Elucidates Functional Impact of Polygenic Risk for Schizophrenia. Nature neuroscience. 2016;19(11):1442-53. doi: 10.1038/nn.4399. PubMed PMID: PMC5083142.
119. Franzén O, Ermel R, Cohain A, Akers NK, Di Narzo A, Talukdar HA, et al. Cardiometabolic Risk Loci Share Downstream Cis- and Trans-Gene Regulation Across Tissues and Diseases. Science (New York, NY). 2016;353(6301):827-30. doi: 10.1126/science.aad6970. PubMed PMID: PMC5534139.
120. Franceschini N, Carty CL, Lu Y, Tao R, Sung YJ, Manichaikul A, et al. Variant Discovery and Fine Mapping of Genetic Loci Associated with Blood Pressure Traits in Hispanics and African Americans. PLOS ONE. 2016;11(10):e0164132. doi: 10.1371/journal.pone.0164132.
121. Epel ES, Puterman E, Lin J, Blackburn EH, Lum PY, Beckmann ND, et al. Meditation and vacation effects have an impact on disease-associated molecular phenotypes. Translational Psychiatry. 2016;6:e880. doi: 10.1038/tp.2016.164
https://www.nature.com/articles/tp2016164 – supplementary-information.
122. Ely BA, Xu J, Goodman WK, Lapidus KA, Gabbay V, Stern ER. Resting-State Functional Connectivity of the Human Habenula in Healthy Individuals: Associations with Subclinical Depression. Human brain mapping. 2016;37(7):2369-84. doi: 10.1002/hbm.23179. PubMed PMID: PMC4905808.
123. Eicher John D, Chami N, Kacprowski T, Nomura A, Chen M-H, Yanek Lisa R, et al. Platelet-Related Variants Identified by Exomechip Meta-analysis in 157,293 Individuals. American Journal of Human Genetics. 2016;99(1):40-55. doi: 10.1016/j.ajhg.2016.05.005. PubMed PMID: PMC5005441.
124. E Cahill M, Bagot R, Gancarz A, Walker D, Sun H, Wang Z, et al. Bidirectional Synaptic Structural Plasticity after Chronic Cocaine Administration Occurs through Rap1 Small GTPase Signaling2016. 566-82 p.
125. Dominguez-Bello MG, De Jesus-Laboy KM, Shen N, Cox LM, Amir A, Gonzalez A, et al. Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer. Nature medicine. 2016;22(3):250-3. doi: 10.1038/nm.4039. PubMed PMID: PMC5062956.
126. Di Narzo AF, Peters LA, Argmann C, Stojmirovic A, Perrigoue J, Li K, et al. Blood and Intestine eQTLs from an Anti-TNF-Resistant Crohn’s Disease Cohort Inform IBD Genetic Association Loci. Clinical and Translational Gastroenterology. 2016;7(6):e177. doi: 10.1038/ctg.2016.34. PubMed PMID: PMC4931595.
127. Di Cecilia S, Zhang F, Sancho A, Li S, Aguiló F, Sun Y, et al. RBM5-AS1 Is Critical for Self-Renewal of Colon Cancer Stem-like Cells. Cancer Research. 2016;76(19):5615. doi: 10.1158/0008-5472.CAN-15-1824.
128. Damez-Werno DM, Sun H, Scobie KN, Shao N, Rabkin J, Dias C, et al. Histone arginine methylation in cocaine action in the nucleus accumbens. Proc Natl Acad Sci U S A. 2016;113(34):9623-8. Epub 2016/08/11. doi: 10.1073/pnas.1605045113. PubMed PMID: 27506785; PubMed Central PMCID: PMCPMC5003250.
129. Crowley RS, Riley AP, Sherwood AM, Groer CE, Shivaperumal N, Biscaia M, et al. Synthetic Studies of Neoclerodane Diterpenes from Salvia divinorum: Identification of a Potent and Centrally Acting μ Opioid Analgesic with Reduced Abuse Liability. Journal of Medicinal Chemistry. 2016;59(24):11027-38. doi: 10.1021/acs.jmedchem.6b01235.
130. Collazo-Lorduy A, Castillo-Martin M, Wang L, Patel V, Iyer G, Jordan E, et al. Urachal Carcinoma Shares Genomic Alterations with Colorectal Carcinoma and May Respond to Epidermal Growth Factor Inhibition. European urology. 2016;70(5):771-5. doi: 10.1016/j.eururo.2016.04.037. PubMed PMID: PMC5489411.
131. Cohain A, Divaraniya AA, Zhu K, Scarpa JR, Kasarskis A, Zhu J, et al. EXPLORING THE REPRODUCIBILITY OF PROBABILISTIC CAUSAL MOLECULAR NETWORK MODELS. Pacific Symposium on Biocomputing Pacific Symposium on Biocomputing. 2016;22:120-31. PubMed PMID: PMC5161348.
132. Clemente JC, Dominguez-Bello MG. Safety of vaginal microbial transfer in infants delivered by caesarean, and expected health outcomes. BMJ. 2016;352.
133. Chudnovskiy A, Mortha A, Kana V, Kennard A, Ramirez JD, Rahman A, et al. Host-protozoan interactions protect from mucosal infections through activation of the inflammasome. Cell. 2016;167(2):444-56.e14. doi: 10.1016/j.cell.2016.08.076. PubMed PMID: PMC5129837.
134. Choi SG, Wang Q, Jia J, Chikina M, Pincas H, Dolios G, et al. Characterization of Gonadotrope Secretoproteome Identifies Neurosecretory Protein VGF-derived Peptide Suppression of Follicle-stimulating Hormone Gene Expression. The Journal of Biological Chemistry. 2016;291(40):21322-34. doi: 10.1074/jbc.M116.740365. PubMed PMID: PMC5076536.
135. Cheng W-Y, Hakenberg J, Li SD, Chen R. DIVAS: a centralized genetic variant repository representing 150 000 individuals from multiple disease cohorts. Bioinformatics. 2016;32(1):151-3. doi: 10.1093/bioinformatics/btv511. PubMed PMID: PMC4681987.
136. Chen R, Shi L, Hakenberg J, Naughton B, Sklar P, Zhang J, et al. Analysis of 589,306 genomes identifies individuals resilient to severe Mendelian childhood diseases. Nature Biotechnology. 2016;34:531. doi: 10.1038/nbt.3514
https://www.nature.com/articles/nbt.3514 – supplementary-information.
137. Chen P, Yi Z, Zhang W, Klotman ME, Chen BK. HIV infection-induced transcriptional program in renal tubular epithelial cells activates a CXCR2-driven CD4+ T-cell chemotactic response. AIDS (London, England). 2016;30(12):1877-88. doi: 10.1097/QAD.0000000000001153. PubMed PMID: 27163710.
138. Chen B, Solis-Villa C, Hakenberg J, Qiao W, Srinivasan RR, Yasuda M, et al. Acute Intermittent Porphyria: Predicted Pathogenicity of HMBS Variants Indicates Extremely Low Penetrance of the Autosomal Dominant Disease. Human mutation. 2016;37(11):1215-22. doi: 10.1002/humu.23067. PubMed PMID: PMC5063710.
139. Chami N, Chen M-H, Slater Andrew J, Eicher John D, Evangelou E, Tajuddin Salman M, et al. Exome Genotyping Identifies Pleiotropic Variants Associated with Red Blood Cell Traits. American Journal of Human Genetics. 2016;99(1):8-21. doi: 10.1016/j.ajhg.2016.05.007. PubMed PMID: PMC5005438.
140. Bunyavanich S, Shen N, Grishin A, Wood R, Burks A, Dawson P, et al. Early-life gut microbiome composition and milk allergy resolution2016.
141. Bien SA, Wojcik GL, Zubair N, Gignoux CR, Martin AR, Kocarnik JM, et al. Strategies for Enriching Variant Coverage in Candidate Disease Loci on a Multiethnic Genotyping Array. PLOS ONE. 2016;11(12):e0167758. doi: 10.1371/journal.pone.0167758.
142. Below JE, Parra EJ, Gamazon ER, Torres J, Krithika S, Candille S, et al. Meta-analysis of lipid-traits in Hispanics identifies novel loci, population-specific effects, and tissue-specific enrichment of eQTLs. Scientific Reports. 2016;6:19429. doi: 10.1038/srep19429
https://www.nature.com/articles/srep19429 – supplementary-information.
143. Baharian S, Barakatt M, Gignoux CR, Shringarpure S, Errington J, Blot WJ, et al. The Great Migration and African-American Genomic Diversity. PLOS Genetics. 2016;12(5):e1006059. doi: 10.1371/journal.pgen.1006059.
144. Bagot RC, Cates HM, Purushothaman I, Lorsch ZS, Walker DM, Wang J, et al. Circuit-wide transcriptional profiling reveals brain region-specific gene networks regulating depression susceptibility. Neuron. 2016;90(5):969-83. doi: 10.1016/j.neuron.2016.04.015. PubMed PMID: PMC4896746.
145. Bagot R, Cates H, Purushothaman I, Vialou V, Heller E, Yieh L, et al. Ketamine and Imipramine Reverse Transcriptional Signatures of Susceptibility and Induce Resilience-Specific Gene Expression Profiles2016.
146. Bagot R, Cates H, Purushothaman I, Lorsch Zachary S, Walker D, Wang J, et al. Circuit-wide Transcriptional Profiling Reveals Brain Region-Specific Gene Networks Regulating Depression Susceptibility2016.
147. Badgeley MA, Shameer K, Glicksberg BS, Tomlinson MS, Levin MA, McCormick PJ, et al. EHDViz: clinical dashboard development using open-source technologies. BMJ Open. 2016;6(3):e010579. doi: 10.1136/bmjopen-2015-010579. PubMed PMID: PMC4809078.
148. Ayers KL, Mirshahi UL, Wardeh AH, Murray MF, Hao K, Glicksberg BS, et al. A loss of function variant in CASP7 protects against Alzheimer’s disease in homozygous APOE ε4 allele carriers. BMC Genomics. 2016;17(Suppl 2):445. doi: 10.1186/s12864-016-2725-z. PubMed PMID: PMC4928152.
149. Argmann CA, Houten SM, Zhu J, Schadt EE. A next generation multiscale view of inborn errors of metabolism. Cell metabolism. 2016;23(1):13-26. doi: 10.1016/j.cmet.2015.11.012. PubMed PMID: PMC4715559.
150. Aguilo F, Li S, Balasubramaniyan N, Sancho A, Benko S, Zhang F, et al. Deposition of 5-Methylcytosine on Enhancer RNAs Enables the Coactivator Function of PGC-1α. Cell reports. 2016;14(3):479-92. Epub 2016/01/07. doi: 10.1016/j.celrep.2015.12.043. PubMed PMID: 26774474.
151. Coding Variation in ANGPTL4, LPL, and SVEP1 and the Risk of Coronary Disease. New England Journal of Medicine. 2016;374(12):1134-44. doi: 10.1056/NEJMoa1507652.

2015

1. Zhu J, Chen C, Yang B, Guo Y, Ai H, Ren J, et al. A systems genetics study of swine illustrates mechanisms underlying human phenotypic traits. BMC Genomics. 2015;16(1):88. doi: 10.1186/s12864-015-1240-y.
2. Zhang Z, Hao K. SAAS-CNV: A Joint Segmentation Approach on Aggregated and Allele Specific Signals for the Identification of Somatic Copy Number Alterations with Next-Generation Sequencing Data. PLoS computational biology. 2015;11(11):e1004618-e. doi: 10.1371/journal.pcbi.1004618. PubMed PMID: 26583378.
3. Zhang G, Smith SG, Zhou M-M. Discovery of Chemical Inhibitors of Human Bromodomains. Chemical Reviews. 2015;115(21):11625-68. doi: 10.1021/acs.chemrev.5b00205.
4. Yoo S, Takikawa S, Geraghty P, Argmann C, Campbell J, Lin L, et al. Integrative Analysis of DNA Methylation and Gene Expression Data Identifies EPAS1 as a Key Regulator of COPD. PLOS Genetics. 2015;11(1):e1004898. doi: 10.1371/journal.pgen.1004898.
5. Yang Y, Sebra R, Pullman BS, Qiao W, Peter I, Desnick RJ, et al. Quantitative and multiplexed DNA methylation analysis using long-read single-molecule real-time bisulfite sequencing (SMRT-BS). BMC genomics. 2015;16(1):350-. doi: 10.1186/s12864-015-1572-7. PubMed PMID: 25943404.
6. Yang J, Huang T, Petralia F, Long Q, Zhang B, Argmann C, et al. Synchronized age-related gene expression changes across multiple tissues in human and the link to complex diseases. Scientific Reports. 2015;5:15145. doi: 10.1038/srep15145
https://www.nature.com/articles/srep15145 – supplementary-information.
7. Xu K, Schadt EE, Pollard KS, Roussos P, Dudley JT. Genomic and Network Patterns of Schizophrenia Genetic Variation in Human Evolutionary Accelerated Regions. Molecular Biology and Evolution. 2015;32(5):1148-60. doi: 10.1093/molbev/msv031.
8. Winkler TW, Justice AE, Graff M, Barata L, Feitosa MF, Chu S, et al. The Influence of Age and Sex on Genetic Associations with Adult Body Size and Shape: A Large-Scale Genome-Wide Interaction Study. PLOS Genetics. 2015;11(10):e1005378. doi: 10.1371/journal.pgen.1005378.
9. Wessel J, Chu AY, Willems SM, Wang S, Yaghootkar H, Brody JA, et al. Low-frequency and rare exome chip variants associate with fasting glucose and type 2 diabetes susceptibility. Nature Communications. 2015;6:5897. doi: 10.1038/ncomms6897
https://www.nature.com/articles/ncomms6897 – supplementary-information.
10. Webb BD, Wheeler PG, Hagen JJ, Cohen N, Linderman MD, Diaz GA, et al. Novel, compound heterozygous, single-nucleotide variants in MARS2 associated with developmental delay, poor growth, and sensorineural hearing loss. Human mutation. 2015;36(6):587-92. Epub 2015/04/08. doi: 10.1002/humu.22781. PubMed PMID: 25754315.
11. Webb BD, Wheeler PG, Hagen JJ, Cohen N, Linderman MD, Diaz GA, et al. Novel, Compound Heterozygous, Single Nucleotide Variants in MARS2 Associated with Developmental Delay, Poor Growth, and Sensorineural Hearing Loss. Human mutation. 2015;36(6):587-92. doi: 10.1002/humu.22781. PubMed PMID: PMC4439286.
12. Wang Z, Rajaraman P, Melin BS, Chung CC, Zhang W, McKean-Cowdin R, et al. Further Confirmation of Germline Glioma Risk Variant rs78378222 in TP53 and Its Implication in Tumor Tissues via Integrative Analysis of TCGA Data. Human mutation. 2015;36(7):684-8. Epub 2015/05/18. doi: 10.1002/humu.22799. PubMed PMID: 25907361.
13. Wang M, Zhao Y, Zhang B. Efficient Test and Visualization of Multi-Set Intersections. Scientific Reports. 2015;5:16923. doi: 10.1038/srep16923
https://www.nature.com/articles/srep16923 – supplementary-information.
14. Wang L, Gong Y, Chippada-Venkata U, Heck MM, Retz M, Nawroth R, et al. A robust blood gene expression-based prognostic model for castration-resistant prostate cancer. BMC Medicine. 2015;13:201. doi: 10.1186/s12916-015-0442-0. PubMed PMID: PMC4546313.
15. Wang J, Liao J, Zhang J, Cheng W-Y, Hakenberg J, Ma M, et al. ClinLabGeneticist: a tool for clinical management of genetic variants from whole exome sequencing in clinical genetic laboratories. Genome Medicine. 2015;7(1):77. doi: 10.1186/s13073-015-0207-6. PubMed PMID: PMC4558641.
16. Vilhjálmsson BJ, Yang J, Finucane HK, Gusev A, Lindström S, Ripke S, et al. Modeling Linkage Disequilibrium Increases Accuracy of Polygenic Risk Scores. American journal of human genetics. 2015;97(4):576-92. Epub 2015/10/01. doi: 10.1016/j.ajhg.2015.09.001. PubMed PMID: 26430803.
17. Vardabasso C, Gaspar-Maia A, Hasson D, Pünzeler S, Valle-Garcia D, Straub T, et al. Histone Variant H2A.Z.2 Mediates Proliferation and Drug Sensitivity of Malignant Melanoma. Molecular cell. 2015;59(1):75-88. Epub 2015/06/04. doi: 10.1016/j.molcel.2015.05.009. PubMed PMID: 26051178.
18. Udler MS, Nadkarni GN, Belbin G, Lotay V, Wyatt C, Gottesman O, et al. Effect of Genetic African Ancestry on eGFR and Kidney Disease. Journal of the American Society of Nephrology : JASN. 2015;26(7):1682-92. doi: 10.1681/ASN.2014050474. PubMed PMID: PMC4483587.
19. Topol A, Zhu S, Tran N, Simone A, Fang G, Brennand KJ. Altered WNT signaling in hiPSC NPCs derived from four schizophrenia patients. Biological psychiatry. 2015;78(6):e29-e34. doi: 10.1016/j.biopsych.2014.12.028. PubMed PMID: PMC4520784.
20. Topol A, English JA, Flaherty E, Rajarajan P, Hartley BJ, Gupta S, et al. Increased abundance of translation machinery in stem cell–derived neural progenitor cells from four schizophrenia patients. Translational Psychiatry. 2015;5(10):e662. doi: 10.1038/tp.2015.118. PubMed PMID: PMC4930118.
21. Tong J, Xie J, Ren H, Liu J, Zhang W, Wei C, et al. Comparison of Glomerular Transcriptome Profiles of Adult-Onset Steroid Sensitive Focal Segmental Glomerulosclerosis and Minimal Change Disease. PLOS ONE. 2015;10(11):e0140453. doi: 10.1371/journal.pone.0140453.
22. Tomer Y, Dolan LM, Kahaly G, Divers J, D’Agostino RB, Jr., Imperatore G, et al. Genome wide identification of new genes and pathways in patients with both autoimmune thyroiditis and type 1 diabetes. Journal of autoimmunity. 2015;60:32-9. Epub 2015/04/27. doi: 10.1016/j.jaut.2015.03.006. PubMed PMID: 25936594.
23. Toledo CM, Ding Y, Hoellerbauer P, Davis RJ, Basom R, Girard EJ, et al. Genome-wide CRISPR-Cas9 screens reveal loss of redundancy between PKMYT1 and WEE1 in Glioblastoma stem-like cells. Cell reports. 2015;13(11):2425-39. doi: 10.1016/j.celrep.2015.11.021. PubMed PMID: PMC4691575.
24. The Genomes Project C. A global reference for human genetic variation. Nature. 2015;526:68. doi: 10.1038/nature15393
https://www.nature.com/articles/nature15393 – supplementary-information.
25. Teixeira A, Yen B, Gusella GL, Thomas AG, Mullen MP, Aberg J, et al. Prothymosin α Variants Isolated From CD8(+) T Cells and Cervicovaginal Fluid Suppress HIV-1 Replication Through Type I Interferon Induction. The Journal of Infectious Diseases. 2015;211(9):1467-75. doi: 10.1093/infdis/jiu643. PubMed PMID: PMC4425839.
26. Sun H, Damez-Werno DM, Scobie KN, Shao NY, Dias C, Rabkin J, et al. ACF chromatin-remodeling complex mediates stress-induced depressive-like behavior. Nat Med. 2015;21(10):1146-53. Epub 2015/09/22. doi: 10.1038/nm.3939. PubMed PMID: 26390241; PubMed Central PMCID: PMCPMC4598281.
27. Song W-M, Zhang B. Multiscale Embedded Gene Co-expression Network Analysis. PLOS Computational Biology. 2015;11(11):e1004574. doi: 10.1371/journal.pcbi.1004574.
28. Smith CC, Zhang C, Lin K, Lasater EA, Zhang Y, Massi E, et al. Characterizing and Overriding the Structural Mechanism of the Quizartinib-resistant FLT3 “Gatekeeper” F691L Mutation with PLX3397. Cancer discovery. 2015;5(6):668-79. doi: 10.1158/2159-8290.CD-15-0060. PubMed PMID: PMC4522415.
29. Simchoni N, Cunningham-Rundles C. TLR7- and TLR9-Responsive Human B Cells Share Phenotypic and Genetic Characteristics. The Journal of Immunology. 2015;194(7):3035. doi: 10.4049/jimmunol.1402690.
30. Sia D, Losic B, Moeini A, Cabellos L, Hao K, Revill K, et al. Massive parallel sequencing uncovers actionable FGFR2–PPHLN1 fusion and ARAF mutations in intrahepatic cholangiocarcinoma. Nature Communications. 2015;6:6087. doi: 10.1038/ncomms7087
https://www.nature.com/articles/ncomms7087 – supplementary-information.
31. Shungin D, Winkler TW, Croteau-Chonka DC, Ferreira T, Locke AE, Mägi R, et al. New genetic loci link adipose and insulin biology to body fat distribution. Nature. 2015;518(7538):187-96. doi: 10.1038/nature14132. PubMed PMID: 25673412.
32. Shen N, Clemente JC. Engineering the Microbiome: a Novel Approach to Immunotherapy for Allergic and Immune Diseases. Current Allergy and Asthma Reports. 2015;15(7):39. doi: 10.1007/s11882-015-0538-9.
33. Shen L. Automatic genome segmentation with HMM-ANN hybrid models. bioRxiv. 2015. doi: 10.1101/034579.
34. Shang Y, Filizola M. Opioid receptors: Structural and mechanistic insights into pharmacology and signaling. European journal of pharmacology. 2015;763(0 0):206-13. doi: 10.1016/j.ejphar.2015.05.012. PubMed PMID: PMC4584181.
35. Schneider S, Provasi D, Filizola M. The Dynamic Process of Drug-GPCR Binding at Either Orthosteric or Allosteric Sites Evaluated by Metadynamics. Methods in molecular biology (Clifton, NJ). 2015;1335:277-94. doi: 10.1007/978-1-4939-2914-6_18. PubMed PMID: PMC4703114.
36. Schliekelman MJ, Taguchi A, Zhu J, Dai X, Rodriguez J, Celiktas M, et al. Molecular portraits of epithelial, mesenchymal and hybrid states in lung adenocarcinoma and their relevance to survival. Cancer research. 2015;75(9):1789-800. doi: 10.1158/0008-5472.CAN-14-2535. PubMed PMID: PMC4846295.
37. Sanderson SC, Linderman MD, Zinberg R, Bashir A, Kasarskis A, Zweig M, et al. How do students react to analyzing their own genomes in a whole-genome sequencing course?: outcomes of a longitudinal cohort study. Genetics In Medicine. 2015;17:866. doi: 10.1038/gim.2014.203
https://www.nature.com/articles/gim2014203 – supplementary-information.
38. Sancho A, Li S, Paul T, Zhang F, Aguilo F, Vashisht A, et al. CHD6 regulates the topological arrangement of the CFTR locus. Human molecular genetics. 2015;24(10):2724-32. Epub 2015/01/28. doi: 10.1093/hmg/ddv032. PubMed PMID: 25631877.
39. Rivas MA, Pirinen M, Conrad DF, Lek M, Tsang EK, Karczewski KJ, et al. Impact of predicted protein-truncating genetic variants on the human transcriptome. Science (New York, NY). 2015;348(6235):666-9. doi: 10.1126/science.1261877. PubMed PMID: PMC4537935.
40. Ren C, Morohashi K, Plotnikov AN, Jakoncic J, Smith SG, Li J, et al. Small Molecule Modulators of Methyl-Lysine Binding for the CBX7 Chromodomain. Chemistry & biology. 2015;22(2):161-8. doi: 10.1016/j.chembiol.2014.11.021. PubMed PMID: PMC4336573.
41. Readhead B, Haure-Mirande JV, Zhang B, Haroutunian V, Gandy S, Schadt EE, et al. Molecular systems evaluation of oligomerogenic APPE693Q and fibrillogenic APPKM670/671NL/PSEN1Δexon9 mouse models identifies shared features with human Alzheimer’s brain molecular pathology. Molecular Psychiatry. 2015;21:1099. doi: 10.1038/mp.2015.167
https://www.nature.com/articles/mp2015167 – supplementary-information.
42. Provasi D, Boz MB, Johnston JM, Filizola M. Preferred Supramolecular Organization and Dimer Interfaces of Opioid Receptors from Simulated Self-Association. PLOS Computational Biology. 2015;11(3):e1004148. doi: 10.1371/journal.pcbi.1004148.
43. Pierson E, the GC, Koller D, Battle A, Mostafavi S. Sharing and Specificity of Co-expression Networks across 35 Human Tissues. PLOS Computational Biology. 2015;11(5):e1004220. doi: 10.1371/journal.pcbi.1004220.
44. Petralia F, Wang P, Yang J, Tu Z. Integrative random forest for gene regulatory network inference. Bioinformatics. 2015;31(12):i197-i205. doi: 10.1093/bioinformatics/btv268. PubMed PMID: PMC4542785.
45. Pereira E, Camacho-Vanegas O, Anand S, Sebra R, Catalina Camacho S, Garnar-Wortzel L, et al. Personalized Circulating Tumor DNA Biomarkers Dynamically Predict Treatment Response and Survival In Gynecologic Cancers. PLoS ONE. 2015;10(12):e0145754. doi: 10.1371/journal.pone.0145754. PubMed PMID: PMC4696808.
46. Pak TR, Kasarskis A. How Next-Generation Sequencing and Multiscale Data Analysis Will Transform Infectious Disease Management. Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America. 2015;61(11):1695-702. doi: 10.1093/cid/civ670. PubMed PMID: PMC4643486.
47. Pak TR, Altman DR, Attie O, Sebra R, Hamula CL, Lewis M, et al. Whole-Genome Sequencing Identifies Emergence of a Quinolone Resistance Mutation in a Case of Stenotrophomonas maltophilia Bacteremia. Antimicrobial Agents and Chemotherapy. 2015;59(11):7117. doi: 10.1128/AAC.01723-15.
48. Pak TR, Altman DR, Attie O, Sebra R, Hamula CL, Lewis M, et al. Whole-Genome Sequencing Identifies Emergence of a Quinolone Resistance Mutation in a Case of Stenotrophomonas maltophilia Bacteremia. Antimicrobial Agents and Chemotherapy. 2015;59(11):7117-20. doi: 10.1128/AAC.01723-15. PubMed PMID: PMC4604410.
49. Obregon-Tito AJ, Tito RY, Metcalf J, Sankaranarayanan K, Clemente JC, Ursell LK, et al. Subsistence strategies in traditional societies distinguish gut microbiomes. Nature Communications. 2015;6:6505. doi: 10.1038/ncomms7505
https://www.nature.com/articles/ncomms7505 – supplementary-information.
50. Nonnenmacher M, van Bakel H, Hajjar RJ, Weber T. High capsid-genome correlation facilitates creation of AAV libraries for directed evolution. Molecular therapy : the journal of the American Society of Gene Therapy. 2015;23(4):675-82. Epub 2015/02/10. doi: 10.1038/mt.2015.3. PubMed PMID: 25586687.
51. Nonnenmacher M, van Bakel H, Hajjar RJ, Weber T. High Capsid–Genome Correlation Facilitates Creation of AAV Libraries for Directed Evolution. Molecular Therapy. 2015;23(4):675-82. doi: 10.1038/mt.2015.3. PubMed PMID: PMC4395795.
52. Noh KM, Maze I, Zhao D, Xiang B, Wenderski W, Lewis PW, et al. ATRX tolerates activity-dependent histone H3 methyl/phos switching to maintain repetitive element silencing in neurons. Proc Natl Acad Sci U S A. 2015;112(22):6820-7. Epub 2014/12/30. doi: 10.1073/pnas.1411258112. PubMed PMID: 25538301; PubMed Central PMCID: PMCPMC4460490.
53. Nikpay M, Goel A, Won H-H, Hall LM, Willenborg C, Kanoni S, et al. A comprehensive 1000 Genomes-based genome-wide association meta-analysis of coronary artery disease. Nature genetics. 2015;47(10):1121-30. doi: 10.1038/ng.3396. PubMed PMID: PMC4589895.
54. Narzo AFD, Kozlenkov A, Ge Y, Zhang B, Sanelli L, May Z, et al. Decrease of mRNA Editing after Spinal Cord Injury is Caused by Down-regulation of ADAR2 that is Triggered by Inflammatory Response. Scientific Reports. 2015;5:12615. doi: 10.1038/srep12615. PubMed PMID: PMC4519770.
55. Mitsi V, Terzi D, Purushothaman I, Manouras L, Gaspari S, Neve RL, et al. RGS9-2–controlled adaptations in the striatum determine the onset of action and efficacy of antidepressants in neuropathic pain states. Proc Natl Acad Sci U S A. 2015;112(36):E5088-97. Epub 2015/08/26. doi: 10.1073/pnas.1504283112. PubMed PMID: 26305935; PubMed Central PMCID: PMCPMC4568688.
56. Miltiadous O, Sia D, Hoshida Y, Fiel MI, Harrington AN, Thung SN, et al. Progenitor cell markers predict outcome of patients with hepatocellular carcinoma beyond Milan criteria undergoing liver transplantation. Journal of Hepatology. 2015;63(6):1368-77. doi: https://doi.org/10.1016/j.jhep.2015.07.025.
57. Miller MS, Rialdi A, Ho JSY, Tilove M, Martinez-Gil L, Moshkina NP, et al. Senataxin suppresses the antiviral transcriptional response and controls viral biogenesis. Nature immunology. 2015;16(5):485-94. Epub 2015/03/30. doi: 10.1038/ni.3132. PubMed PMID: 25822250.
58. Mezei M. Use of circular variance to quantify the deviation of a macromolecule from the spherical shape. Journal of mathematical chemistry. 2015;53(10):2184-90. doi: 10.1007/s10910-015-0540-4. PubMed PMID: PMC4684833.
59. Mezei M. Statistical Properties of Protein-Protein Interfaces. Algorithms. 2015;8(2). doi: 10.3390/a8020092.
60. Menon MC, Chuang PY, Li Z, Wei C, Zhang W, Luan Y, et al. Intronic locus determines SHROOM3 expression and potentiates renal allograft fibrosis. The Journal of Clinical Investigation. 2015;125(1):208-21. doi: 10.1172/JCI76902. PubMed PMID: PMC4382250.
61. Menon MC, Chuang PY, Li Z, Wei C, Zhang W, Luan Y, et al. Intronic locus determines SHROOM3 expression and potentiates renal allograft fibrosis. The Journal of clinical investigation. 2015;125(1):208-21. Epub 2014/12/01. doi: 10.1172/JCI76902. PubMed PMID: 25437874.
62. Meng F, Speyer CL, Zhang B, Zhao Y, Chen W, Gorski DH, et al. PDGFRα and β Play Critical Roles in Mediating Foxq1-Driven Breast Cancer Stemness and Chemoresistance. Cancer research. 2015;75(3):584-93. doi: 10.1158/0008-5472.CAN-13-3029. PubMed PMID: PMC4384815.
63. Maze I, Wenderski W, Noh KM, Bagot RC, Tzavaras N, Purushothaman I, et al. Critical Role of Histone Turnover in Neuronal Transcription and Plasticity. Neuron. 2015;87(1):77-94. Epub 2015/07/04. doi: 10.1016/j.neuron.2015.06.014. PubMed PMID: 26139371; PubMed Central PMCID: PMCPMC4491146.
64. Mathers AJ, Stoesser N, Sheppard AE, Pankhurst L, Giess A, Yeh AJ, et al. Klebsiella pneumoniae Carbapenemase (KPC)-Producing K. pneumoniae at a Single Institution: Insights into Endemicity from Whole-Genome Sequencing. Antimicrobial Agents and Chemotherapy. 2015;59(3):1656-63.
65. Ma M, Ru Y, Chuang L-S, Hsu N-Y, Shi L-S, Hakenberg J, et al. Disease-associated variants in different categories of disease located in distinct regulatory elements. BMC Genomics. 2015;16(Suppl 8):S3-S. doi: 10.1186/1471-2164-16-S8-S3. PubMed PMID: PMC4480828.
66. Locke AE, Kahali B, Berndt SI, Justice AE, Pers TH, Day FR, et al. Genetic studies of body mass index yield new insights for obesity biology. Nature. 2015;518(7538):197-206. doi: 10.1038/nature14177. PubMed PMID: PMC4382211.
67. Liu J, Magri L, Zhang F, Marsh NO, Albrecht S, Huynh JL, et al. Chromatin landscape defined by repressive histone methylation during oligodendrocyte differentiation. The Journal of neuroscience : the official journal of the Society for Neuroscience. 2015;35(1):352-65. doi: 10.1523/JNEUROSCI.2606-14.2015. PubMed PMID: 25568127.
68. Linderman MD, Bashir A, Diaz GA, Kasarskis A, Sanderson SC, Zinberg RE, et al. Preparing the next generation of genomicists: a laboratory-style course in medical genomics. BMC Medical Genomics. 2015;8(1):47. doi: 10.1186/s12920-015-0124-y.
69. Lin X, Zhao Y, Song W-m, Zhang B. Molecular classification and prediction in gastric cancer. Computational and Structural Biotechnology Journal. 2015;13:448-58. doi: 10.1016/j.csbj.2015.08.001. PubMed PMID: PMC4556804.
70. Li L, Cheng W-Y, Glicksberg BS, Gottesman O, Tamler R, Chen R, et al. Identification of type 2 diabetes subgroups through topological analysis of patient similarity. Science translational medicine. 2015;7(311):311ra174-311ra174. doi: 10.1126/scitranslmed.aaa9364. PubMed PMID: PMC4780757.
71. Latif R, Ali MR, Mezei M, Davies TF. Transmembrane Domains of Attraction on the TSH Receptor. Endocrinology. 2015;156(2):488-98. doi: 10.1210/en.2014-1509. PubMed PMID: PMC4298320.
72. Latif R, Ali MR, Ma R, David M, Morshed SA, Ohlmeyer M, et al. New Small Molecule Agonists to the Thyrotropin Receptor. Thyroid. 2015;25(1):51-62. doi: 10.1089/thy.2014.0119. PubMed PMID: PMC4291085.
73. Kwon Y-J, Petrie K, Leibovitch BA, Zeng L, Mezei M, Howell L, et al. Selective inhibition of SIN3 corepressor with avermectins as a novel therapeutic strategy in triple negative breast cancer. Molecular cancer therapeutics. 2015;14(8):1824-36. doi: 10.1158/1535-7163.MCT-14-0980-T. PubMed PMID: PMC4529816.
74. Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, et al. Integrative analysis of 111 reference human epigenomes. Nature. 2015;518(7539):317-30. Epub 2015/02/20. doi: 10.1038/nature14248. PubMed PMID: 25693563; PubMed Central PMCID: PMCPMC4530010.
75. Kocabayoglu P, Lade A, Lee YA, Dragomir A-C, Sun X, Fiel MI, et al. β-PDGF receptor expressed by hepatic stellate cells regulates fibrosis in murine liver injury, but not carcinogenesis. Journal of hepatology. 2015;63(1):141-7. Epub 2015/02/09. doi: 10.1016/j.jhep.2015.01.036. PubMed PMID: 25678385.
76. King LY, Canasto-Chibuque C, Johnson KB, Yip S, Chen X, Kojima K, et al. A genomic and clinical prognostic index for hepatitis C-related early-stage cirrhosis that predicts clinical deterioration. Gut. 2015;64(8):1296-302. Epub 2014/08/20. doi: 10.1136/gutjnl-2014-307862. PubMed PMID: 25143343.
77. Joshi PK, Esko T, Mattsson H, Eklund N, Gandin I, Nutile T, et al. Directional dominance on stature and cognition in diverse human populations. Nature. 2015;523:459. doi: 10.1038/nature14618
https://www.nature.com/articles/nature14618 – supplementary-information.
78. Jiang P, Scarpa JR, Fitzpatrick K, Losic B, Gao VD, Hao K, et al. A systems approach identifies networks and genes linking sleep and stress: implications for neuropsychiatric disorders. Cell reports. 2015;11(5):835-48. Epub 2015/04/23. doi: 10.1016/j.celrep.2015.04.003. PubMed PMID: 25921536.
79. International G, Translational Research in Transplantation N. Design and Implementation of the International Genetics and Translational Research in Transplantation Network. Transplantation. 2015;99(11):2401-12. Epub 2015/11/04. doi: 10.1097/TP.0000000000000913. PubMed PMID: 26479416.
80. Huan T, Meng Q, Saleh MA, Norlander AE, Joehanes R, Zhu J, et al. Integrative network analysis reveals molecular mechanisms of blood pressure regulation. Molecular Systems Biology. 2015;11(4):799. doi: 10.15252/msb.20145399. PubMed PMID: PMC4422556.
81. Hodes GE, Pfau ML, Purushothaman I, Ahn HF, Golden SA, Christoffel DJ, et al. Sex Differences in Nucleus Accumbens Transcriptome Profiles Associated with Susceptibility versus Resilience to Subchronic Variable Stress. The Journal of Neuroscience. 2015;35(50):16362-76. doi: 10.1523/jneurosci.1392-15.2015.
82. Hayes JE, Trynka G, Vijai J, Offit K, Raychaudhuri S, Klein RJ. Tissue-Specific Enrichment of Lymphoma Risk Loci in Regulatory Elements. PLOS ONE. 2015;10(9):e0139360. doi: 10.1371/journal.pone.0139360.
83. Hartmann BM, Thakar J, Albrecht RA, Avey S, Zaslavsky E, Marjanovic N, et al. Human Dendritic Cell Response Signatures Distinguish 1918, Pandemic, and Seasonal H1N1 Influenza Viruses. Journal of Virology. 2015;89(20):10190-205. doi: 10.1128/JVI.01523-15. PubMed PMID: PMC4580178.
84. Hao K, Di Narzo AF, Ho L, Luo W, Li S, Chen R, et al. Shared genetic etiology underlying Alzheimer’s disease and type 2 diabetes. Molecular Aspects of Medicine. 2015;43-44:66-76. doi: https://doi.org/10.1016/j.mam.2015.06.006.
85. Gymrek M, Willems T, Guilmatre A, Zeng H, Markus B, Georgiev S, et al. Abundant contribution of short tandem repeats to gene expression variation in humans. Nature Genetics. 2015;48:22. doi: 10.1038/ng.3461
https://www.nature.com/articles/ng.3461 – supplementary-information.
86. Glicksberg BS, Li L, Cheng W-Y, Shameer K, Hakenberg J, Castellanos R, et al. AN INTEGRATIVE PIPELINE FOR MULTI-MODAL DISCOVERY OF DISEASE RELATIONSHIPS. Pacific Symposium on Biocomputing Pacific Symposium on Biocomputing. 2015;20:407-18. PubMed PMID: PMC4345399.
87. Gaulton KJ, Ferreira T, Lee Y, Raimondo A, Mägi R, Reschen ME, et al. Genetic fine-mapping and genomic annotation defines causal mechanisms at type 2 diabetes susceptibility loci. Nature genetics. 2015;47(12):1415-25. doi: 10.1038/ng.3437. PubMed PMID: PMC4666734.
88. Fulton BO, Sachs D, Beaty SM, Won ST, Lee B, Palese P, et al. Mutational analysis of measles virus suggests constraints on antigenic variation of the glycoproteins. Cell reports. 2015;11(9):1331-8. doi: 10.1016/j.celrep.2015.04.054. PubMed PMID: PMC4464907.
89. Finkin S, Yuan D, Stein I, Taniguchi K, Weber A, Unger K, et al. Ectopic lymphoid structures function as microniches for tumor progenitor cells in hepatocellular carcinoma. Nature immunology. 2015;16(12):1235-44. Epub 2015/10/26. doi: 10.1038/ni.3290. PubMed PMID: 26502405.
90. Ferguson D, Shao N, Heller E, Feng J, Neve R, Kim HD, et al. SIRT1-FOXO3a regulate cocaine actions in the nucleus accumbens. J Neurosci. 2015;35(7):3100-11. Epub 2015/02/24. doi: 10.1523/jneurosci.4012-14.2015. PubMed PMID: 25698746; PubMed Central PMCID: PMCPMC4331629.
91. Feng J, Shao N, Szulwach KE, Vialou V, Huynh J, Zhong C, et al. Role of Tet1 and 5-hydroxymethylcytosine in cocaine action. Nat Neurosci. 2015;18(4):536-44. Epub 2015/03/17. doi: 10.1038/nn.3976. PubMed PMID: 25774451; PubMed Central PMCID: PMCPMC4617315.
92. Fan Y, Xiao W, Li Z, Li X, Chuang PY, Jim B, et al. RTN1 mediates progression of kidney disease by inducing ER stress. Nature communications. 2015;6:7841-. doi: 10.1038/ncomms8841. PubMed PMID: 26227493.
93. El-Shamy A, Eng FJ, Doyle EH, Klepper AL, Sun X, Sangiovanni A, et al. A cell culture system for distinguishing hepatitis C viruses with and without liver cancer-related mutations in the viral core gene. Journal of hepatology. 2015;63(6):1323-33. Epub 2015/07/26. doi: 10.1016/j.jhep.2015.07.024. PubMed PMID: 26220749.
94. Ding J, Huang X, Shao N, Zhou H, Lee DF, Faiola F, et al. Tex10 Coordinates Epigenetic Control of Super-Enhancer Activity in Pluripotency and Reprogramming. Cell Stem Cell. 2015;16(6):653-68. Epub 2015/05/06. doi: 10.1016/j.stem.2015.04.001. PubMed PMID: 25936917; PubMed Central PMCID: PMCPMC4458159.
95. Dincer A, Gavin DP, Xu K, Zhang B, Dudley JT, Schadt EE, et al. Deciphering H3K4me3 broad domains associated with gene-regulatory networks and conserved epigenomic landscapes in the human brain. Translational Psychiatry. 2015;5(11):e679. doi: 10.1038/tp.2015.169. PubMed PMID: PMC5068762.
96. Deng Y, Wang L, Tan S, Kim GP, Dou R, Chen D, et al. KRAS as a predictor of poor prognosis and benefit from postoperative FOLFOX chemotherapy in patients with stage II and III colorectal cancer. Molecular Oncology. 2015;9(7):1341-7. doi: 10.1016/j.molonc.2015.03.006. PubMed PMID: PMC5528807.
97. Davidson A, Bethunaickan R, Berthier C, Sahu R, Zhang W, Kretzler M. Molecular studies of lupus nephritis kidneys. Immunologic Research. 2015;63(1):187-96. doi: 10.1007/s12026-015-8693-6.
98. Das SK, Sharma NK, Zhang B. Integrative network analysis reveals different pathophysiological mechanisms of insulin resistance among Caucasians and African Americans. BMC Medical Genomics. 2015;8:4. doi: 10.1186/s12920-015-0078-0. PubMed PMID: PMC4351975.
99. Cornella H, Alsinet C, Sayols S, Zhang Z, Hao K, Cabellos L, et al. Unique genomic profile of fibrolamellar hepatocellular carcinoma. Gastroenterology. 2015;148(4):806-18.e10. Epub 2014/12/31. doi: 10.1053/j.gastro.2014.12.028. PubMed PMID: 25557953.
100. Clemente JC, Pehrsson EC, Blaser MJ, Sandhu K, Gao Z, Wang B, et al. The microbiome of uncontacted Amerindians. Science Advances. 2015;1(3).
101. Chikina MD, Gerald CP, Li X, Ge Y, Pincas H, Nair VD, et al. Low variance RNAs identify Parkinson’s disease molecular signature in blood. Movement disorders : official journal of the Movement Disorder Society. 2015;30(6):813-21. doi: 10.1002/mds.26205. PubMed PMID: PMC4439364.
102. Chikina M, Zaslavsky E, Sealfon SC. CellCODE: a robust latent variable approach to differential expression analysis for heterogeneous cell populations. Bioinformatics. 2015;31(10):1584-91. doi: 10.1093/bioinformatics/btv015. PubMed PMID: PMC4426841.
103. Chapouly C, Tadesse Argaw A, Horng S, Castro K, Zhang J, Asp L, et al. Astrocytic TYMP and VEGFA drive blood–brain barrier opening in inflammatory central nervous system lesions. Brain. 2015;138(6):1548-67. doi: 10.1093/brain/awv077. PubMed PMID: PMC4614128.
104. Carithers LJ, Ardlie K, Barcus M, Branton PA, Britton A, Buia SA, et al. A Novel Approach to High-Quality Postmortem Tissue Procurement: The GTEx Project. Biopreservation and Biobanking. 2015;13(5):311-9. doi: 10.1089/bio.2015.0032. PubMed PMID: PMC4675181.
105. Burford NT, Livingston KE, Canals M, Ryan MR, Budenholzer LML, Han Y, et al. Discovery, Synthesis, and Molecular Pharmacology of Selective Positive Allosteric Modulators of the δ-Opioid Receptor. Journal of Medicinal Chemistry. 2015;58(10):4220-9. doi: 10.1021/acs.jmedchem.5b00007.
106. Burford NT, Livingston KE, Canals M, Ryan MR, Budenholzer LML, Han Y, et al. Discovery, synthesis, and molecular pharmacology of selective positive allosteric modulators of the δ-opioid receptor. Journal of medicinal chemistry. 2015;58(10):4220-9. Epub 2015/05/07. doi: 10.1021/acs.jmedchem.5b00007. PubMed PMID: 25901762.
107. Buitrago L, Rendon A, Liang Y, Simeoni I, Negri A, ThromboGenomics C, et al. αIIbβ3 variants defined by next-generation sequencing: Predicting variants likely to cause Glanzmann thrombasthenia. Proceedings of the National Academy of Sciences of the United States of America. 2015;112(15):E1898-E907. doi: 10.1073/pnas.1422238112. PubMed PMID: PMC4403182.
108. Buitrago L, Rendon A, Liang Y, Simeoni I, Negri A, ThromboGenomics C, et al. αIIbβ3 variants defined by next-generation sequencing: predicting variants likely to cause Glanzmann thrombasthenia. Proceedings of the National Academy of Sciences of the United States of America. 2015;112(15):E1898-E907. Epub 2015/03/31. doi: 10.1073/pnas.1422238112. PubMed PMID: 25827233.
109. Brohl AS, Li L, Andikyan V, Običan SG, Cioffi A, Hao K, et al. Age-Stratified Risk of Unexpected Uterine Sarcoma Following Surgery for Presumed Benign Leiomyoma. The Oncologist. 2015;20(4):433-9. doi: 10.1634/theoncologist.2014-0361. PubMed PMID: PMC4391766.
110. Bisignano P, Burford NT, Shang Y, Marlow B, Livingston KE, Fenton AM, et al. Ligand-Based Discovery of a New Scaffold for Allosteric Modulation of the μ-Opioid Receptor. Journal of Chemical Information and Modeling. 2015;55(9):1836-43. doi: 10.1021/acs.jcim.5b00388.
111. Berg D, Clemente JC, Colombel J-F. Can inflammatory bowel disease be permanently treated with short-term interventions on the microbiome? Expert Review of Gastroenterology & Hepatology. 2015;9(6):781-95. doi: 10.1586/17474124.2015.1013031.
112. Benitez AA, Spanko LA, Bouhaddou M, Sachs D, tenOever BR. Engineered mammalian RNAi can elicit antiviral protection that negates the requirement for the interferon response. Cell reports. 2015;13(7):1456-66. doi: 10.1016/j.celrep.2015.10.020. PubMed PMID: PMC4654977.
113. Benitez AA, Panis M, Xue J, Varble A, Shim JV, Frick AL, et al. In vivo RNAi screening identifies MDA5 as a significant contributor to the cellular defense against influenza A virus. Cell reports. 2015;11(11):1714-26. doi: 10.1016/j.celrep.2015.05.032. PubMed PMID: PMC4586153.
114. Bansal N, Petrie K, Christova R, Chung C-Y, Leibovitch BA, Howell L, et al. Targeting the SIN3A-PF1 interaction inhibits epithelial to mesenchymal transition and maintenance of a stem cell phenotype in triple negative breast cancer. Oncotarget. 2015;6(33):34087-105. PubMed PMID: PMC4741438.
115. Badgeley MA, Sealfon SC, Chikina MD. Hybrid Bayesian-rank integration approach improves the predictive power of genomic dataset aggregation. Bioinformatics. 2015;31(2):209-15. doi: 10.1093/bioinformatics/btu518. PubMed PMID: PMC4287939.
116. Ali MR, Latif R, Davies TF, Mezei M. Monte Carlo loop refinement and virtual screening of the thyroid-stimulating hormone receptor transmembrane domain. Journal of biomolecular structure & dynamics. 2015;33(5):1140-52. doi: 10.1080/07391102.2014.932310. PubMed PMID: PMC4484770.
117. Akbarian S, Liu C, Knowles JA, Vaccarino FM, Farnham PJ, Crawford GE, et al. The PsychENCODE project. Nature Neuroscience. 2015;18:1707. doi: 10.1038/nn.4156.
118. Aguilo F, Zhang F, Sancho A, Fidalgo M, Di Cecilia S, Vashisht A, et al. Coordination of m(6)A mRNA Methylation and Gene Transcription by ZFP217 Regulates Pluripotency and Reprogramming. Cell stem cell. 2015;17(6):689-704. Epub 2015/10/29. doi: 10.1016/j.stem.2015.09.005. PubMed PMID: 26526723.
119. Aguado LC, Schmid S, Sachs D, Shim JV, Lim JK, tenOever BR. microRNA function is limited to cytokine control in the acute response to virus infection. Cell host & microbe. 2015;18(6):714-22. doi: 10.1016/j.chom.2015.11.003. PubMed PMID: PMC4683400.
120. The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans. Science. 2015;348(6235):648.

2014

1. Zhang XY, Birtwistle MR, Gallo JM. A General Network Pharmacodynamic Model-Based Design Pipeline for Customized Cancer Therapy Applied to the VEGFR Pathway. CPT: pharmacometrics & systems pharmacology. 2014;3(1):e92-e. doi: 10.1038/psp.2013.65. PubMed PMID: 24429593.
2. Yoo S, Huang T, Campbell JD, Lee E, Tu Z, Geraci MW, et al. MODMatcher: Multi-Omics Data Matcher for Integrative Genomic Analysis. PLOS Computational Biology. 2014;10(8):e1003790. doi: 10.1371/journal.pcbi.1003790.
3. Ye F, Wang L, Castillo-Martin M, McBride R, Galsky MD, Zhu J, et al. Biomarkers for bladder cancer management: present and future. American Journal of Clinical and Experimental Urology. 2014;2(1):1-14. PubMed PMID: PMC4219291.
4. Wu M, Peng S, Yang J, Tu Z, Cai X, Cai C-L, et al. Baf250a orchestrates an epigenetic pathway to repress the Nkx2.5-directed contractile cardiomyocyte program in the sinoatrial node. Cell Research. 2014;24(10):1201-13. doi: 10.1038/cr.2014.113. PubMed PMID: PMC4185344.
5. Wood AR, Esko T, Yang J, Vedantam S, Pers TH, Gustafsson S, et al. Defining the role of common variation in the genomic and biological architecture of adult human height. Nature genetics. 2014;46(11):1173-86. doi: 10.1038/ng.3097. PubMed PMID: PMC4250049.
6. Wei Y, Peng S, Wu M, Sachidanandam R, Tu Z, Zhang S, et al. Multifaceted roles of miR-1s in repressing the fetal gene program in the heart. Cell Research. 2014;24:278. doi: 10.1038/cr.2014.12
https://www.nature.com/articles/cr201412 – supplementary-information.
7. Wang Q, Chikina MD, Pincas H, Sealfon SC. Homer1 Alternative Splicing Is Regulated by Gonadotropin-Releasing Hormone and Modulates Gonadotropin Gene Expression. Molecular and Cellular Biology. 2014;34(10):1747-56. doi: 10.1128/MCB.01401-13. PubMed PMID: PMC4019030.
8. Varble A, Albrecht RA, Backes S, Crumiller M, Bouvier NM, Sachs D, et al. Influenza A virus transmission bottlenecks are defined by infection route and recipient host. Cell host & microbe. 2014;16(5):691-700. doi: 10.1016/j.chom.2014.09.020. PubMed PMID: PMC4272616.
9. Toki D, Zhang W, Hor KLM, Liuwantara D, Alexander SI, Yi Z, et al. The Role of Macrophages in the Development of Human Renal Allograft Fibrosis in the First Year After Transplantation. American Journal of Transplantation. 2014;14(9):2126-36. doi: 10.1111/ajt.12803.
10. Stoesser N, Giess A, Batty EM, Sheppard AE, Walker AS, Wilson DJ, et al. Genome Sequencing of an Extended Series of NDM-Producing Klebsiella pneumoniae Isolates from Neonatal Infections in a Nepali Hospital Characterizes the Extent of Community- versus Hospital-Associated Transmission in an Endemic Setting. Antimicrobial Agents and Chemotherapy. 2014;58(12):7347-57. doi: 10.1128/AAC.03900-14. PubMed PMID: PMC4249533.
11. Skinner MK, Savenkova MI, Zhang B, Gore AC, Crews D. Gene bionetworks involved in the epigenetic transgenerational inheritance of altered mate preference: environmental epigenetics and evolutionary biology. BMC Genomics. 2014;15(1):377. doi: 10.1186/1471-2164-15-377. PubMed PMID: PMC4073506.
12. Shi J, Wang Y, Zeng L, Wu Y, Deng J, Zhang Q, et al. Disrupting the Interaction of BRD4 with Di-acetylated Twist Suppresses Tumorigenesis in Basal-like Breast Cancer. Cancer cell. 2014;25(2):210-25. doi: 10.1016/j.ccr.2014.01.028. PubMed PMID: PMC4004960.
13. Shen L, Shao N, Liu X, Nestler E. ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases. BMC Genomics. 2014;15:284. Epub 2014/04/17. doi: 10.1186/1471-2164-15-284. PubMed PMID: 24735413; PubMed Central PMCID: PMCPMC4028082.
14. Shapiro JS, Schmid S, Aguado LC, Sabin LR, Yasunaga A, Shim JV, et al. Drosha as an interferon-independent antiviral factor. Proceedings of the National Academy of Sciences of the United States of America. 2014;111(19):7108-13. doi: 10.1073/pnas.1319635111. PubMed PMID: PMC4024876.
15. Shang Y, LeRouzic V, Schneider S, Bisignano P, Pasternak GW, Filizola M. Mechanistic Insights into the Allosteric Modulation of Opioid Receptors by Sodium Ions. Biochemistry. 2014;53(31):5140-9. doi: 10.1021/bi5006915.
16. Shabman RS, Jabado OJ, Mire CE, Stockwell TB, Edwards M, Mahajan M, et al. Deep Sequencing Identifies Noncanonical Editing of Ebola and Marburg Virus RNAs in Infected Cells. mBio. 2014;5(6):e02011-14. doi: 10.1128/mBio.02011-14.
17. Scobie KN, Damez-Werno D, Sun H, Shao N, Gancarz A, Panganiban CH, et al. Essential role of poly(ADP-ribosyl)ation in cocaine action. Proc Natl Acad Sci U S A. 2014;111(5):2005-10. Epub 2014/01/23. doi: 10.1073/pnas.1319703111. PubMed PMID: 24449909; PubMed Central PMCID: PMCPMC3918779.
18. Schmid S, Sachs D, tenOever BR. Mitogen-activated Protein Kinase-mediated Licensing of Interferon Regulatory Factor 3/7 Reinforces the Cell Response to Virus. The Journal of Biological Chemistry. 2014;289(1):299-311. doi: 10.1074/jbc.M113.519934. PubMed PMID: PMC3879553.
19. Scarabelli G, Provasi D, Negri A, Filizola M. Bioactive Conformations of Two Seminal Delta Opioid Receptor Penta-peptides Inferred from Free-Energy Profiles. Biopolymers. 2014;101(1):10.1002/bip.22251. doi: 10.1002/bip.22251. PubMed PMID: PMC3812360.
20. Rideout JR, He Y, Navas-Molina JA, Walters WA, Ursell LK, Gibbons SM, et al. Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences. PeerJ. 2014;2:e545. doi: 10.7717/peerj.545.
21. Purcell SM, Moran JL, Fromer M, Ruderfer D, Solovieff N, Roussos P, et al. A polygenic burden of rare disruptive mutations in schizophrenia. Nature. 2014;506:185. doi: 10.1038/nature12975
https://www.nature.com/articles/nature12975 – supplementary-information.
22. Provasi D, Negri A, Coller BS, Filizola M. Talin-driven inside-out activation mechanism of platelet αIIbβ3 integrin probed by multimicrosecond, all-atom molecular dynamics simulations. Proteins. 2014;82(12):3231-40. doi: 10.1002/prot.24540. PubMed PMID: PMC5156318.
23. Pinto D, Delaby E, Merico D, Barbosa M, Merikangas A, Klei L, et al. Convergence of Genes and Cellular Pathways Dysregulated in Autism Spectrum Disorders. The American Journal of Human Genetics. 2014;94(5):677-94. doi: 10.1016/j.ajhg.2014.03.018.
24. Peloso Gina M, Auer Paul L, Bis Joshua C, Voorman A, Morrison Alanna C, Stitziel Nathan O, et al. Association of Low-Frequency and Rare Coding-Sequence Variants with Blood Lipids and Coronary Heart Disease in 56,000 Whites and Blacks. American Journal of Human Genetics. 2014;94(2):223-32. doi: 10.1016/j.ajhg.2014.01.009. PubMed PMID: PMC3928662.
25. Parfrey LW, Walters WA, Lauber CL, Clemente JC, Berg-Lyons D, Teiling C, et al. Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity. Frontiers in Microbiology. 2014;5:298. doi: 10.3389/fmicb.2014.00298. PubMed PMID: PMC4063188.
26. Pandey G, Arora S, Manocha S, Whalen S. Enhancing the Functional Content of Eukaryotic Protein Interaction Networks. PLOS ONE. 2014;9(10):e109130. doi: 10.1371/journal.pone.0109130.
27. Ng MCY, Shriner D, Chen BH, Li J, Chen W-M, Guo X, et al. Meta-Analysis of Genome-Wide Association Studies in African Americans Provides Insights into the Genetic Architecture of Type 2 Diabetes. PLoS Genetics. 2014;10(8):e1004517. doi: 10.1371/journal.pgen.1004517. PubMed PMID: PMC4125087.
28. Narayanan M, Huynh JL, Wang K, Yang X, Yoo S, McElwee J, et al. Common dysregulation network in the human prefrontal cortex underlies two neurodegenerative diseases. Molecular Systems Biology. 2014;10(7):743-. doi: 10.15252/msb.20145304. PubMed PMID: PMC4299500.
29. Maze I, Shen L, Zhang B, Garcia BA, Shao N, Mitchell A, et al. Analytical tools and current challenges in the modern era of neuroepigenomics. Nat Neurosci. 2014;17(11):1476-90. Epub 2014/10/29. doi: 10.1038/nn.3816. PubMed PMID: 25349914; PubMed Central PMCID: PMCPMC4262187.
30. Maze I, Chaudhury D, Dietz DM, Von Schimmelmann M, Kennedy PJ, Lobo MK, et al. G9a influences neuronal subtype specification in striatum. Nat Neurosci. 2014;17(4):533-9. Epub 2014/03/04. doi: 10.1038/nn.3670. PubMed PMID: 24584053; PubMed Central PMCID: PMCPMC3972624.
31. Manichanh C, Eck A, Varela E, Roca J, Clemente JC, González A, et al. Anal gas evacuation and colonic microbiota in patients with flatulence: effect of diet. Gut. 2014;63(3):401-8. doi: 10.1136/gutjnl-2012-303013. PubMed PMID: PMC3933177.
32. Mäkinen V-P, Civelek M, Meng Q, Zhang B, Zhu J, Levian C, et al. Integrative Genomics Reveals Novel Molecular Pathways and Gene Networks for Coronary Artery Disease. PLOS Genetics. 2014;10(7):e1004502. doi: 10.1371/journal.pgen.1004502.
33. Linderman MD, Brandt T, Edelmann L, Jabado O, Kasai Y, Kornreich R, et al. Analytical validation of whole exome and whole genome sequencing for clinical applications. BMC Medical Genomics. 2014;7:20-. doi: 10.1186/1755-8794-7-20. PubMed PMID: PMC4022392.
34. Li L, Ruau DJ, Patel CJ, Weber SC, Chen R, Tatonetti NP, et al. Disease Risk Factors Identified through Shared Genetic Architecture and Electronic Medical Records. Science translational medicine. 2014;6(234):234ra57-ra57. doi: 10.1126/scitranslmed.3007191. PubMed PMID: PMC4323098.
35. Li J, Vootukuri S, Shang Y, Negri A, Jiang J-K, Nedelman M, et al. RUC-4: a novel αIIbβ3 antagonist for prehospital therapy of myocardial infarction. Arteriosclerosis, thrombosis, and vascular biology. 2014;34(10):2321-9. Epub 2014/08/21. doi: 10.1161/ATVBAHA.114.303724. PubMed PMID: 25147334.
36. Li J, Vootukuri S, Shang Y, Negri A, Jiang J-k, Nedelman M, et al. RUC-4: A Novel αIIbβ3 Antagonist for Pre-hospital Therapy of Myocardial Infarction. Arteriosclerosis, thrombosis, and vascular biology. 2014;34(10):2321-9. doi: 10.1161/ATVBAHA.114.303724. PubMed PMID: PMC4180209.
37. Lange LA, Hu Y, Zhang H, Xue C, Schmidt EM, Tang Z-Z, et al. Whole-exome sequencing identifies rare and low-frequency coding variants associated with LDL cholesterol. American journal of human genetics. 2014;94(2):233-45. doi: 10.1016/j.ajhg.2014.01.010. PubMed PMID: 24507775.
38. Kozlenkov A, Roussos P, Timashpolsky A, Barbu M, Rudchenko S, Bibikova M, et al. Differences in DNA methylation between human neuronal and glial cells are concentrated in enhancers and non-CpG sites. Nucleic Acids Research. 2014;42(1):109-27. doi: 10.1093/nar/gkt838. PubMed PMID: PMC3874157.
39. Johnston JM, Filizola M. Differential Stability of the Crystallographic Interfaces of Mu- and Kappa-Opioid Receptors. PLOS ONE. 2014;9(2):e90694. doi: 10.1371/journal.pone.0090694.
40. Johnston JM, Filizola M. Beyond Standard Molecular Dynamics: Investigating the Molecular Mechanisms of G Protein-Coupled Receptors with Enhanced Molecular Dynamics Methods. Advances in experimental medicine and biology. 2014;796:95-125. doi: 10.1007/978-94-007-7423-0_6. PubMed PMID: PMC4074508.
41. Jiang J-k, McCoy JG, Shen M, LeClair CA, Huang W, Negri A, et al. A novel class of ion displacement ligands as antagonists of the αIIbβ3 receptor that limit conformational reorganization of the receptor. Bioorganic & medicinal chemistry letters. 2014;24(4):1148-53. doi: 10.1016/j.bmcl.2013.12.122. PubMed PMID: PMC3951875.
42. Huttenhower C, Knight R, Brown CT, Caporaso JG, Clemente JC, Gevers D, et al. Advancing the Microbiome Research Community. Cell. 2014;159(2):227-30. doi: 10.1016/j.cell.2014.09.022. PubMed PMID: PMC4221798.
43. Hoffman GE, Mezey JG, Schadt EE. lrgpr: interactive linear mixed model analysis of genome-wide association studies with composite hypothesis testing and regression diagnostics in R. Bioinformatics. 2014;30(21):3134-5. doi: 10.1093/bioinformatics/btu435.
44. Heller EA, Cates HM, Pena CJ, Sun H, Shao N, Feng J, et al. Locus-specific epigenetic remodeling controls addiction- and depression-related behaviors. Nat Neurosci. 2014;17(12):1720-7. Epub 2014/10/28. doi: 10.1038/nn.3871. PubMed PMID: 25347353; PubMed Central PMCID: PMCPMC4241193.
45. Heaton NS, Langlois RA, Sachs D, Lim JK, Palese P, tenOever BR. Long-term survival of influenza virus infected club cells drives immunopathology. The Journal of Experimental Medicine. 2014;211(9):1707-14. doi: 10.1084/jem.20140488. PubMed PMID: PMC4144728.
46. Gaugler T, Klei L, Sanders SJ, Bodea CA, Goldberg AP, Lee AB, et al. Most genetic risk for autism resides with common variation. Nature Genetics. 2014;46:881. doi: 10.1038/ng.3039
https://www.nature.com/articles/ng.3039 – supplementary-information.
47. Gacias M, Gerona-Navarro G, Plotnikov AN, Zhang G, Zeng L, Kaur J, et al. Selective Chemical Modulation of Gene Transcription Favors Oligodendrocyte Lineage Progression. Chemistry & biology. 2014;21(7):841-54. doi: 10.1016/j.chembiol.2014.05.009. PubMed PMID: PMC4104156.
48. Fromer M, Pocklington AJ, Kavanagh DH, Williams HJ, Dwyer S, Gormley P, et al. De novo mutations in schizophrenia implicate synaptic networks. Nature. 2014;506:179. doi: 10.1038/nature12929
https://www.nature.com/articles/nature12929 – supplementary-information.
49. Ferré S, Casadó V, Devi LA, Filizola M, Jockers R, Lohse MJ, et al. G Protein–Coupled Receptor Oligomerization Revisited: Functional and Pharmacological Perspectives. Pharmacological Reviews. 2014;66(2):413-34. doi: 10.1124/pr.113.008052. PubMed PMID: PMC3973609.
50. Feng J, Wilkinson M, Liu X, Purushothaman I, Ferguson D, Vialou V, et al. Chronic cocaine-regulated epigenomic changes in mouse nucleus accumbens. Genome Biol. 2014;15(4):R65. Epub 2014/04/25. doi: 10.1186/gb-2014-15-4-r65. PubMed PMID: 24758366; PubMed Central PMCID: PMCPMC4073058.
51. Enns GM, Shashi V, Bainbridge M, Gambello MJ, Zahir FR, Bast T, et al. Mutations in NGLY1 Cause an Inherited Disorder of the Endoplasmic Reticulum-Associated Degradation (ERAD) Pathway. Genetics in medicine : official journal of the American College of Medical Genetics. 2014;16(10):751-8. doi: 10.1038/gim.2014.22. PubMed PMID: PMC4243708.
52. Dias C, Feng J, Sun H, Shao NY, Mazei-Robison MS, Damez-Werno D, et al. beta-catenin mediates stress resilience through Dicer1/microRNA regulation. Nature. 2014;516(7529):51-5. Epub 2014/11/11. doi: 10.1038/nature13976. PubMed PMID: 25383518; PubMed Central PMCID: PMCPMC4257892.
53. Di Narzo AF, Kozlenkov A, Roussos P, Hao K, Hurd Y, Lewis DA, et al. A unique gene expression signature associated with serotonin 2C receptor RNA editing in the prefrontal cortex and altered in suicide. Human Molecular Genetics. 2014;23(18):4801-13. doi: 10.1093/hmg/ddu195. PubMed PMID: PMC4140462.
54. De Rubeis S, He X, Goldberg AP, Poultney CS, Samocha K, Ercument Cicek A, et al. Synaptic, transcriptional and chromatin genes disrupted in autism. Nature. 2014;515:209. doi: 10.1038/nature13772
https://www.nature.com/articles/nature13772 – supplementary-information.
55. De Rubeis S, He X, Goldberg AP, Poultney CS, Samocha K, Cicek AE, et al. Synaptic, transcriptional, and chromatin genes disrupted in autism. Nature. 2014;515(7526):209-15. doi: 10.1038/nature13772. PubMed PMID: PMC4402723.
56. Consortium S. A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control consortium. Nature biotechnology. 2014;32(9):903-14. doi: 10.1038/nbt.2957. PubMed PMID: PMC4321899.
57. Chikina MD, Sealfon SC. Increasing Consistency of Disease Biomarker Prediction Across Datasets. PLOS ONE. 2014;9(4):e91272. doi: 10.1371/journal.pone.0091272.
58. Bunyavanich S, Schadt EE, Himes BE, Lasky-Su J, Qiu W, Lazarus R, et al. Integrated genome-wide association, coexpression network, and expression single nucleotide polymorphism analysis identifies novel pathway in allergic rhinitis. BMC Medical Genomics. 2014;7(1):48. doi: 10.1186/1755-8794-7-48.
59. Brennand K, Savas JN, Kim Y, Tran N, Simone A, Hashimoto-Torii K, et al. Phenotypic differences in hiPSC NPCs derived from patients with schizophrenia. Molecular Psychiatry. 2014;20:361. doi: 10.1038/mp.2014.22
https://www.nature.com/articles/mp201422 – supplementary-information.
60. Bongers G, Pacer ME, Geraldino TH, Chen L, He Z, Hashimoto D, et al. Interplay of host microbiota, genetic perturbations, and inflammation promotes local development of intestinal neoplasms in mice. The Journal of Experimental Medicine. 2014;211(3):457.
61. Bichoupan K, Martel-Laferriere V, Sachs D, Ng M, Schonfeld EA, Pappas A, et al. Costs of Telaprevir-based Triple Therapy for Hepatitis C: $189,000 per Sustained Virologic Response. Hepatology (Baltimore, Md). 2014;60(4):1187-95. doi: 10.1002/hep.27340. PubMed PMID: PMC4190678.
62. Backes S, Langlois RA, Schmid S, Varble A, Shim JV, Sachs D, et al. The mammalian response to virus infection is independent of small RNA silencing. Cell reports. 2014;8(1):114-25. doi: 10.1016/j.celrep.2014.05.038. PubMed PMID: PMC4096324.
63. Altman DR, Sebra R, Hand J, Attie O, Deikus G, Carpini KWD, et al. Transmission of Methicillin-Resistant Staphylococcus aureus via Deceased Donor Liver Transplantation Confirmed by Whole Genome Sequencing. American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons. 2014;14(11):2640-4. doi: 10.1111/ajt.12897. PubMed PMID: PMC4651443.
64. Loss-of-Function Mutations in APOC3, Triglycerides, and Coronary Disease. New England Journal of Medicine. 2014;371(1):22-31. doi: 10.1056/NEJMoa1307095.

2013

1. Zhang B, Gaiteri C, Bodea L-G, Wang Z, McElwee J, Podtelezhnikov AA, et al. Integrated systems approach identifies genetic nodes and networks in late-onset Alzheimer’s disease. Cell. 2013;153(3):707-20. doi: 10.1016/j.cell.2013.03.030. PubMed PMID: PMC3677161.
2. Zaslavsky E, Nudelman G, Marquez S, Hershberg U, Hartmann BM, Thakar J, et al. Reconstruction of regulatory networks through temporal enrichment profiling and its application to H1N1 influenza viral infection. BMC Bioinformatics. 2013;14(Suppl 6):S1-S. doi: 10.1186/1471-2105-14-S6-S1. PubMed PMID: PMC3633009.
3. Wu C, Zhu J, Zhang X. Network-based differential gene expression analysis suggests cell cycle related genes regulated by E2F1 underlie the molecular difference between smoker and non-smoker lung adenocarcinoma. BMC Bioinformatics. 2013;14(1):365. doi: 10.1186/1471-2105-14-365.
4. Whalen S, Pandey G. A Comparative Analysis of Ensemble Classifiers: Case Studies in Genomics. eprint arXiv:13095047. 2013:arXiv:1309.5047.
5. Warren BL, Vialou VF, Iniguez SD, Alcantara LF, Wright KN, Feng J, et al. Neurobiological sequelae of witnessing stressful events in adult mice. Biol Psychiatry. 2013;73(1):7-14. Epub 2012/07/17. doi: 10.1016/j.biopsych.2012.06.006. PubMed PMID: 22795644; PubMed Central PMCID: PMCPMC3498570.
6. Wang T, Liu J, Shen L, Tonti-Filippini J, Zhu Y, Jia H, et al. STAR: an integrated solution to management and visualization of sequencing data. Bioinformatics. 2013;29(24):3204-10. Epub 2013/10/01. doi: 10.1093/bioinformatics/btt558. PubMed PMID: 24078702; PubMed Central PMCID: PMCPMC3842760.
7. Wang Q, Chikina M, Zaslavsky E, Pincas H, Sealfon SC. β-Catenin Regulates GnRH-Induced FSHβ Gene Expression. Molecular Endocrinology. 2013;27(2):224-37. doi: 10.1210/me.2012-1310. PubMed PMID: PMC3683805.
8. Vimaleswaran KS, Berry DJ, Lu C, Tikkanen E, Pilz S, Hiraki LT, et al. Causal Relationship between Obesity and Vitamin D Status: Bi-Directional Mendelian Randomization Analysis of Multiple Cohorts. PLOS Medicine. 2013;10(2):e1001383. doi: 10.1371/journal.pmed.1001383.
9. Varble A, Benitez Asiel A, Schmid S, Sachs D, Shim Jaehee V, Rodriguez-Barrueco R, et al. An In Vivo RNAi Screening Approach to Identify Host Determinants of Virus Replication. Cell Host & Microbe. 2013;14(3):346-56. doi: https://doi.org/10.1016/j.chom.2013.08.007.
10. van Bakel H, Tsui K, Gebbia M, Mnaimneh S, Hughes TR, Nislow C. A Compendium of Nucleosome and Transcript Profiles Reveals Determinants of Chromatin Architecture and Transcription. PLOS Genetics. 2013;9(5):e1003479. doi: 10.1371/journal.pgen.1003479.
11. The GC. The Genotype-Tissue Expression (GTEx) project. Nature genetics. 2013;45(6):580-5. doi: 10.1038/ng.2653. PubMed PMID: PMC4010069.
12. Song SJ, Lauber C, Costello EK, Lozupone CA, Humphrey G, Berg-Lyons D, et al. Cohabiting family members share microbiota with one another and with their dogs. eLife. 2013;2:e00458. doi: 10.7554/eLife.00458. PubMed PMID: PMC3628085.
13. Sigdel TK, Shoemaker LD, Chen R, Li L, Butte AJ, Sarwal MM, et al. Immune response profiling identifies autoantibodies specific to Moyamoya patients. Orphanet Journal of Rare Diseases. 2013;8:45-. doi: 10.1186/1750-1172-8-45. PubMed PMID: PMC3648437.
14. Shen L, Shao NY, Liu X, Maze I, Feng J, Nestler EJ. diffReps: detecting differential chromatin modification sites from ChIP-seq data with biological replicates. PLoS One. 2013;8(6):e65598. Epub 2013/06/14. doi: 10.1371/journal.pone.0065598. PubMed PMID: 23762400; PubMed Central PMCID: PMCPMC3677880.
15. Shen L, Choi I, Nestler EJ, Won K-J. Human Transcriptome and Chromatin Modifications: An ENCODE Perspective. Genomics & Informatics. 2013;11(2):60-7. doi: 10.5808/GI.2013.11.2.60. PubMed PMID: PMC3704928.
16. Schadt EE, Banerjee O, Fang G, Feng Z, Wong WH, Zhang X, et al. Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases. Genome Research. 2013;23(1):129-41. doi: 10.1101/gr.136739.111. PubMed PMID: PMC3530673.
17. Sanderson SC, Linderman MD, Kasarskis A, Bashir A, Diaz GA, Mahajan MC, et al. Informed decision-making among students analyzing their personal genomes on a whole genome sequencing course: a longitudinal cohort study. Genome Medicine. 2013;5(12):113. doi: 10.1186/gm518.
18. Ridaura VK, Faith JJ, Rey FE, Cheng J, Duncan AE, Kau AL, et al. Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in Mice. Science. 2013;341(6150).
19. Poultney Christopher S, Goldberg Arthur P, Drapeau E, Kou Y, Harony-Nicolas H, Kajiwara Y, et al. Identification of Small Exonic CNV from Whole-Exome Sequence Data and Application to Autism Spectrum Disorder. American Journal of Human Genetics. 2013;93(4):607-19. doi: 10.1016/j.ajhg.2013.09.001. PubMed PMID: PMC3791269.
20. Patel CJ, Sivadas A, Tabassum R, Preeprem T, Zhao J, Arafat D, et al. Whole genome sequencing in support of wellness and health maintenance. Genome Medicine. 2013;5(6):58-. doi: 10.1186/gm462. PubMed PMID: PMC3967117.
21. Patel CJ, Chen R, Kodama K, Ioannidis JPA, Butte AJ. Systematic identification of interaction effects between genome- and environment-wide associations in type 2 diabetes mellitus. Human Genetics. 2013;132(5):495-508. doi: 10.1007/s00439-012-1258-z. PubMed PMID: PMC3625410.
22. Pantoja-Feliciano IG, Clemente JC, Costello EK, Perez ME, Blaser MJ, Knight R, et al. Biphasic assembly of the murine intestinal microbiota during early development. The ISME Journal. 2013;7(6):1112-5. doi: 10.1038/ismej.2013.15. PubMed PMID: PMC3660675.
23. Pandey G, Zhang B, Jian L. Predicting submicron air pollution indicators: a machine learning approach. Environmental Science: Processes & Impacts. 2013;15(5):996-1005. doi: 10.1039/C3EM30890A.
24. Nilsson E, Zhang B, Skinner MK. Gene bionetworks that regulate ovarian primordial follicle assembly. BMC Genomics. 2013;14(1):496. doi: 10.1186/1471-2164-14-496.
25. Neto EC, Broman AT, Keller MP, Attie AD, Zhang B, Zhu J, et al. Modeling Causality for Pairs of Phenotypes in System Genetics. Genetics. 2013;193(3):1003-13. doi: 10.1534/genetics.112.147124. PubMed PMID: PMC3583988.
26. Negri A, Rives M-L, Caspers MJ, Prisinzano TE, Javitch JA, Filizola M. Discovery of a Novel Selective Kappa-Opioid Receptor Agonist Using Crystal Structure-Based Virtual Screening. Journal of Chemical Information and Modeling. 2013;53(3):521-6. doi: 10.1021/ci400019t.
27. Mondal S, Johnston JM, Wang H, Khelashvili G, Filizola M, Weinstein H. Membrane Driven Spatial Organization of GPCRs. Scientific Reports. 2013;3:2909. doi: 10.1038/srep02909
https://www.nature.com/articles/srep02909 – supplementary-information.
28. Monda KL, Chen GK, Taylor KC, Palmer C, Edwards TL, Lange LA, et al. A Meta-Analysis Identifies New Loci Associated with Body Mass index in Individuals of African Ancestry. Nature genetics. 2013;45(6):690-6. doi: 10.1038/ng.2608. PubMed PMID: PMC3694490.
29. Miller CL, Anderson DR, Kundu RK, Raiesdana A, Nürnberg ST, Diaz R, et al. Disease-Related Growth Factor and Embryonic Signaling Pathways Modulate an Enhancer of TCF21 Expression at the 6q23.2 Coronary Heart Disease Locus. PLOS Genetics. 2013;9(7):e1003652. doi: 10.1371/journal.pgen.1003652.
30. Luo M, Liu L, Peter I, Zhu J, Scott SA, Zhao G, et al. An Ashkenazi Jewish SMN1 haplotype specific to duplication alleles improves pan-ethnic carrier screening for spinal muscular atrophy. Genetics In Medicine. 2013;16:149. doi: 10.1038/gim.2013.84
https://www.nature.com/articles/gim201384 – supplementary-information.
31. Lluch-Senar M, Luong K, Lloréns-Rico V, Delgado J, Fang G, Spittle K, et al. Comprehensive Methylome Characterization of Mycoplasma genitalium and Mycoplasma pneumoniae at Single-Base Resolution. PLOS Genetics. 2013;9(1):e1003191. doi: 10.1371/journal.pgen.1003191.
32. Leeper Nicholas J, Raiesdana A, Kojima Y, Kundu Ramendra K, Cheng H, Maegdefessel L, et al. Loss of CDKN2B Promotes p53-Dependent Smooth Muscle Cell Apoptosis and Aneurysm Formation. Arteriosclerosis, Thrombosis, and Vascular Biology. 2013;33(1):e1-e10. doi: 10.1161/ATVBAHA.112.300399.
33. Langille MGI, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, et al. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nature Biotechnology. 2013;31:814. doi: 10.1038/nbt.2676
https://www.nature.com/articles/nbt.2676 – supplementary-information.
34. Kittelmann S, Seedorf H, Walters WA, Clemente JC, Knight R, Gordon JI, et al. Simultaneous Amplicon Sequencing to Explore Co-Occurrence Patterns of Bacterial, Archaeal and Eukaryotic Microorganisms in Rumen Microbial Communities. PLoS ONE. 2013;8(2):e47879. doi: 10.1371/journal.pone.0047879. PubMed PMID: PMC3568148.
35. Karkheiran S, Krebs CE, Makarov V, Nilipour Y, Hubert B, Darvish H, et al. Identification of COL6A2 mutations in progressive myoclonus epilepsy syndrome. Human Genetics. 2013;132(3):275-83. doi: 10.1007/s00439-012-1248-1.
36. Karczewski KJ, Dudley JT, Kukurba KR, Chen R, Butte AJ, Montgomery SB, et al. Systematic functional regulatory assessment of disease-associated variants. Proceedings of the National Academy of Sciences of the United States of America. 2013;110(23):9607-12. doi: 10.1073/pnas.1219099110. PubMed PMID: PMC3677437.
37. Jin Y-J, Cai CY, Mezei M, Ohlmeyer M, Sanchez R, Burakoff SJ. Identification of a Novel Binding Site Between HIV Type 1 Nef C-Terminal Flexible Loop and AP2 Required for Nef-Mediated CD4 Downregulation. AIDS Research and Human Retroviruses. 2013;29(4):725-31. doi: 10.1089/aid.2012.0286. PubMed PMID: PMC3903168.
38. Huynh JL, Garg P, Thin TH, Yoo S, Dutta R, Trapp BD, et al. Epigenome-wide differences in pathology-free regions of multiple sclerosis–affected brains. Nature Neuroscience. 2013;17:121. doi: 10.1038/nn.3588
https://www.nature.com/articles/nn.3588 – supplementary-information.
39. Huan T, Zhang B, Wang Z, Joehanes R, Zhu J, Johnson AD, et al. A Systems Biology Framework Identifies Molecular Underpinnings of Coronary Heart Disease. Arteriosclerosis, thrombosis, and vascular biology. 2013;33(6):1427-34. doi: 10.1161/ATVBAHA.112.300112. PubMed PMID: PMC3752786.
40. Hu Y-J, Berndt Sonja I, Gustafsson S, Ganna A, Berndt Sonja I, Gustafsson S, et al. Meta-analysis of Gene-Level Associations for Rare Variants Based on Single-Variant Statistics. The American Journal of Human Genetics. 2013;93(2):236-48. doi: https://doi.org/10.1016/j.ajhg.2013.06.011.
41. Hsu I, Chen R, Ramesh A, Corona E, Kang HP, Ruau D, et al. Systematic identification of DNA variants associated with ultraviolet radiation using a novel Geographic-Wide Association Study (GeoWAS). BMC Medical Genetics. 2013;14:62-. doi: 10.1186/1471-2350-14-62. PubMed PMID: PMC3699381.
42. Heaton NS, Sachs D, Chen C-J, Hai R, Palese P. Genome-wide mutagenesis of influenza virus reveals unique plasticity of the hemagglutinin and NS1 proteins. Proceedings of the National Academy of Sciences of the United States of America. 2013;110(50):20248-53. doi: 10.1073/pnas.1320524110. PubMed PMID: PMC3864309.
43. Gomes I, Fujita W, Gupta A, Saldanha SA, Negri A, Pinello CE, et al. Identification of a μ-δ opioid receptor heteromer-biased agonist with antinociceptive activity. Proceedings of the National Academy of Sciences of the United States of America. 2013;110(29):12072-7. doi: 10.1073/pnas.1222044110. PubMed PMID: PMC3718106.
44. Ganesh SK, Tragante V, Guo W, Guo Y, Lanktree MB, Smith EN, et al. Loci influencing blood pressure identified using a cardiovascular gene-centric array. Human Molecular Genetics. 2013;22(8):1663-78. doi: 10.1093/hmg/dds555.
45. Gandy S, Haroutunian V, DeKosky ST, Sano M, Schadt EE. CR1 and the “Vanishing Amyloid” Hypothesis of Alzheimer’s Disease. Biological Psychiatry. 2013;73(5):393-5. doi: https://doi.org/10.1016/j.biopsych.2013.01.013.
46. Filizola M, Devi LA. Grand Opening of Structure-Guided Design for Novel Opioids. Trends in pharmacological sciences. 2013;34(1):6-12. doi: 10.1016/j.tips.2012.10.002. PubMed PMID: PMC3534797.
47. Fierer N, Ladau J, Clemente JC, Leff JW, Owens SM, Pollard KS, et al. Reconstructing the Microbial Diversity and Function of Pre-Agricultural Tallgrass Prairie Soils in the United States. Science. 2013;342(6158):621.
48. Ferguson D, Koo JW, Feng J, Heller E, Rabkin J, Heshmati M, et al. Essential role of SIRT1 signaling in the nucleus accumbens in cocaine and morphine action. J Neurosci. 2013;33(41):16088-98. Epub 2013/10/11. doi: 10.1523/jneurosci.1284-13.2013. PubMed PMID: 24107942; PubMed Central PMCID: PMCPMC3792451.
49. Feng Z, Fang G, Korlach J, Clark T, Luong K, Zhang X, et al. Detecting DNA Modifications from SMRT Sequencing Data by Modeling Sequence Context Dependence of Polymerase Kinetic. PLOS Computational Biology. 2013;9(3):e1002935. doi: 10.1371/journal.pcbi.1002935.
50. Faith JJ, Guruge JL, Charbonneau M, Subramanian S, Seedorf H, Goodman AL, et al. The long-term stability of the human gut microbiota. Science (New York, NY). 2013;341(6141):1237439-. doi: 10.1126/science.1237439. PubMed PMID: PMC3791589.
51. Ding Y, Hubert CG, Herman J, Corrin P, Toledo CM, Skutt-Kakaria K, et al. Cancer-specific requirement for BUB1B/BubR1 in human brain tumor isolates and genetically transformed cells. Cancer discovery. 2013;3(2):198-211. doi: 10.1158/2159-8290.CD-12-0353. PubMed PMID: PMC3632446.
52. Coudray N, Valvo S, Hu M, Lasala R, Kim C, Vink M, et al. Inward-facing conformation of the zinc transporter YiiP revealed by cryoelectron microscopy. Proceedings of the National Academy of Sciences of the United States of America. 2013;110(6):2140-5. doi: 10.1073/pnas.1215455110. PubMed PMID: PMC3568326.
53. Corona E, Chen R, Sikora M, Morgan AA, Patel CJ, Ramesh A, et al. Analysis of the Genetic Basis of Disease in the Context of Worldwide Human Relationships and Migration. PLoS Genetics. 2013;9(5):e1003447. doi: 10.1371/journal.pgen.1003447. PubMed PMID: PMC3662561.
54. Chen Z, Tang H, Qayyum R, Schick UM, Nalls MA, Handsaker R, et al. Genome-wide association analysis of red blood cell traits in African Americans: the COGENT Network. Human Molecular Genetics. 2013;22(12):2529-38. doi: 10.1093/hmg/ddt087. PubMed PMID: PMC3658166.
55. Blaser MJ, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Estrada I, et al. Distinct cutaneous bacterial assemblages in a sampling of South American Amerindians and US residents. The ISME Journal. 2013;7(1):85-95. doi: 10.1038/ismej.2012.81. PubMed PMID: PMC3526177.
56. Bilal E, Dutkowski J, Guinney J, Jang IS, Logsdon BA, Pandey G, et al. Improving Breast Cancer Survival Analysis through Competition-Based Multidimensional Modeling. PLOS Computational Biology. 2013;9(5):e1003047. doi: 10.1371/journal.pcbi.1003047.
57. Berndt SI, Gustafsson S, Mägi R, Ganna A, Wheeler E, Feitosa MF, et al. Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture. Nature Genetics. 2013;45:501. doi: 10.1038/ng.2606
https://www.nature.com/articles/ng.2606 – supplementary-information.
58. Bates ST, Clemente JC, Flores GE, Walters WA, Parfrey LW, Knight R, et al. Global biogeography of highly diverse protistan communities in soil. The ISME Journal. 2013;7(3):652-9. doi: 10.1038/ismej.2012.147. PubMed PMID: PMC3578557.
59. Au KF, Sebastiano V, Afshar PT, Durruthy JD, Lee L, Williams BA, et al. Characterization of the human ESC transcriptome by hybrid sequencing. Proceedings of the National Academy of Sciences of the United States of America. 2013;110(50):E4821-E30. doi: 10.1073/pnas.1320101110. PubMed PMID: PMC3864310.

2012

1. Zhu J, Sova P, Xu Q, Dombek KM, Xu EY, Vu H, et al. Stitching together Multiple Data Dimensions Reveals Interacting Metabolomic and Transcriptomic Networks That Modulate Cell Regulation. PLoS Biology. 2012;10(4):e1001301. doi: 10.1371/journal.pbio.1001301. PubMed PMID: PMC3317911.
2. Zhu J, Choi W-S, McCoy JG, Negri A, Zhu J, Naini S, et al. Structure-Guided Design of a High-Affinity Platelet Integrin α(IIb)β(3) Receptor Antagonist That Disrupts Mg(2+) Binding to the MIDAS. Science Translational Medicine. 2012;4(125):125ra32-ra32. doi: 10.1126/scitranslmed.3003576. PubMed PMID: PMC3390238.
3. Zhang G, Sanchez R, Zhou M-M. Scaling the Druggability Landscape of Human Bromodomains, a New Class of Drug Targets. Journal of Medicinal Chemistry. 2012;55(17):7342-5. doi: 10.1021/jm3011977.
4. Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, et al. Human gut microbiome viewed across age and geography. Nature. 2012;486(7402):222-7. doi: 10.1038/nature11053. PubMed PMID: PMC3376388.
5. Xia Y, Bin Z, Jun Z. Functional Genomics- and Network-driven Systems Biology Approaches for Pharmacogenomics and Toxicogenomics. Current Drug Metabolism. 2012;13(7):952-67. doi: http://dx.doi.org/10.2174/138920012802138633.
6. Wu H, Moshkina N, Min J, Zeng H, Joshua J, Zhou M-M, et al. Structural basis for substrate specificity and catalysis of human histone acetyltransferase 1. Proceedings of the National Academy of Sciences of the United States of America. 2012;109(23):8925-30. doi: 10.1073/pnas.1114117109. PubMed PMID: PMC3384170.
7. Wu C, Zhu J, Zhang X. Integrating gene expression and protein-protein interaction network to prioritize cancer-associated genes. BMC Bioinformatics. 2012;13(1):182. doi: 10.1186/1471-2105-13-182.
8. Wang IM, Zhang B, Yang X, Zhu J, Stepaniants S, Zhang C, et al. Systems analysis of eleven rodent disease models reveals an inflammatome signature and key drivers. Molecular Systems Biology. 2012;8:594-. doi: 10.1038/msb.2012.24. PubMed PMID: PMC3421440.
9. van der Harst P, Zhang W, Mateo Leach I, Rendon A, Verweij N, Sehmi J, et al. Seventy-five genetic loci influencing the human red blood cell. Nature. 2012;492:369. doi: 10.1038/nature11677
https://www.nature.com/articles/nature11677 – supplementary-information.
10. Ursell LK, Clemente JC, Rideout JR, Gevers D, Caporaso JG, Knight R. The interpersonal and intrapersonal diversity of human-associated microbiota in key body sites. The Journal of allergy and clinical immunology. 2012;129(5):1204-8. doi: 10.1016/j.jaci.2012.03.010. PubMed PMID: PMC3342686.
11. Tu Z, Keller MP, Zhang C, Rabaglia ME, Greenawalt DM, Yang X, et al. Integrative Analysis of a Cross-Loci Regulation Network Identifies App as a Gene Regulating Insulin Secretion from Pancreatic Islets. PLOS Genetics. 2012;8(12):e1003107. doi: 10.1371/journal.pgen.1003107.
12. The Human Microbiome Project C. Structure, Function and Diversity of the Healthy Human Microbiome. Nature. 2012;486(7402):207-14. doi: 10.1038/nature11234. PubMed PMID: PMC3564958.
13. The CDC, Deloukas P, Kanoni S, Willenborg C, Farrall M, Assimes TL, et al. Large-scale association analysis identifies new risk loci for coronary artery disease. Nature Genetics. 2012;45:25. doi: 10.1038/ng.2480
https://www.nature.com/articles/ng.2480 – supplementary-information.
14. Stahringer SS, Clemente JC, Corley RP, Hewitt J, Knights D, Walters WA, et al. Nurture trumps nature in a longitudinal survey of salivary bacterial communities in twins from early adolescence to early adulthood. Genome Research. 2012;22(11):2146-52. doi: 10.1101/gr.140608.112. PubMed PMID: PMC3483544.
15. Smith CC, Wang Q, Chin C-S, Salerno S, Damon LE, Levis MJ, et al. Validation of ITD mutations in FLT3 as a therapeutic target in human acute myeloid leukaemia. Nature. 2012;485:260. doi: 10.1038/nature11016
https://www.nature.com/articles/nature11016 – supplementary-information.
16. Skinner MK, Manikkam M, Haque MM, Zhang B, Savenkova MI. Epigenetic transgenerational inheritance of somatic transcriptomes and epigenetic control regions. Genome Biology. 2012;13(10):R91. doi: 10.1186/gb-2012-13-10-r91.
17. Ruau D, Dudley JT, Chen R, Phillips NG, Swan GE, Lazzeroni LC, et al. Integrative Approach to Pain Genetics Identifies Pain Sensitivity Loci across Diseases. PLoS Computational Biology. 2012;8(6):e1002538. doi: 10.1371/journal.pcbi.1002538. PubMed PMID: PMC3369906.
18. Rothbard JB, Kurnellas MP, Brownell S, Adams CM, Su L, Axtell RC, et al. Therapeutic Effects of Systemic Administration of Chaperone αB-Crystallin Associated with Binding Proinflammatory Plasma Proteins. The Journal of Biological Chemistry. 2012;287(13):9708-21. doi: 10.1074/jbc.M111.337691. PubMed PMID: PMC3322989.
19. Patel CJ, Chen R, Butte AJ. Data-driven integration of epidemiological and toxicological data to select candidate interacting genes and environmental factors in association with disease. Bioinformatics. 2012;28(12):i121-i6. doi: 10.1093/bioinformatics/bts229. PubMed PMID: PMC3371861.
20. Negri A, Li J, Naini S, Coller BS, Filizola M. Structure-based virtual screening of small-molecule antagonists of platelet integrin αIIbβ3 that do not prime the receptor to bind ligand. Journal of computer-aided molecular design. 2012;26(9):1005-15. doi: 10.1007/s10822-012-9594-6. PubMed PMID: PMC3496400.
21. Neale BM, Kou Y, Liu L, Ma’ayan A, Samocha KE, Sabo A, et al. Patterns and rates of exonic de novo mutations in autism spectrum disorders. Nature. 2012;485:242. doi: 10.1038/nature11011
https://www.nature.com/articles/nature11011 – supplementary-information.
22. Morgan AA, Chen R, Butte AJ. Clinical utility of sequence-based genotype compared with that derivable from genotyping arrays. Journal of the American Medical Informatics Association : JAMIA. 2012;19(e1):e21-e7. doi: 10.1136/amiajnl-2011-000737. PubMed PMID: PMC3392859.
23. Methé BA, Nelson KE, Pop M, Creasy HH, Giglio MG, Huttenhower C, et al. A framework for human microbiome research. Nature. 2012;486(7402):215-21. doi: 10.1038/nature11209. PubMed PMID: PMC3377744.
24. McDonald D, Clemente JC, Kuczynski J, Rideout JR, Stombaugh J, Wendel D, et al. The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome. GigaScience. 2012;1:7-. doi: 10.1186/2047-217X-1-7. PubMed PMID: PMC3626512.
25. Makarov V, O’Grady T, Cai G, Lihm J, Buxbaum JD, Yoon S. AnnTools: a comprehensive and versatile annotation toolkit for genomic variants. Bioinformatics. 2012;28(5):724-5. doi: 10.1093/bioinformatics/bts032.
26. Luo MJ, Thieringer R, Springer MS, Wright SD, Hermanowski-Vosatka A, Plump A, et al. 11β-HSD1 inhibition reduces atherosclerosis in mice by altering proinflammatory gene expression in the vasculature. Physiological Genomics. 2012;45(1):47-57. doi: 10.1152/physiolgenomics.00109.2012.
27. Lo K, Raftery AE, Dombek KM, Zhu J, Schadt EE, Bumgarner RE, et al. Integrating external biological knowledge in the construction of regulatory networks from time-series expression data. BMC Systems Biology. 2012;6(1):101. doi: 10.1186/1752-0509-6-101.
28. Li LI, Ruau D, Chen R, Weber S, Butte AJ. SYSTEMATIC IDENTIFICATION OF RISK FACTORS FOR ALZHEIMER’S DISEASE THROUGH SHARED GENETIC ARCHITECTURE AND ELECTRONIC MEDICAL RECORDS. Biocomputing 2013: WORLD SCIENTIFIC; 2012. p. 224-35.
29. Li L, Wozniak LJ, Rodder S, Heish S, Talisetti A, Wang Q, et al. A Common Peripheral Blood Gene Set for Diagnosis of Operational Tolerance in Pediatric and Adult Liver Transplantation. American Journal of Transplantation. 2012;12(5):1218-28. doi: 10.1111/j.1600-6143.2011.03928.x.
30. Li L, Khatri P, Sigdel TK, Tran T, Ying L, Vitalone M, et al. A Five-Gene Peripheral Blood Diagnostic Test for Acute Rejection in Renal Transplantation. American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons. 2012;12(10):2710-8. doi: 10.1111/j.1600-6143.2012.04253.x. PubMed PMID: PMC4148014.
31. Lam HYK, Clark MJ, Chen R, Chen R, Natsoulis G, O’Huallachain M, et al. Performance comparison of whole-genome sequencing platforms. Nature biotechnology. 2012;30(1):78-82. doi: 10.1038/nbt.2065. PubMed PMID: PMC4076012.
32. Kou Y, Betancur C, Xu H, Buxbaum JD, Ma’ayan A. Network- and attribute-based classifiers can prioritize genes and pathways for autism spectrum disorders and intellectual disability. American Journal of Medical Genetics Part C: Seminars in Medical Genetics. 2012;160C(2):130-42. doi: 10.1002/ajmg.c.31330.
33. Kodama K, Horikoshi M, Toda K, Yamada S, Hara K, Irie J, et al. Expression-based genome-wide association study links the receptor CD44 in adipose tissue with type 2 diabetes. Proceedings of the National Academy of Sciences of the United States of America. 2012;109(18):7049-54. doi: 10.1073/pnas.1114513109. PubMed PMID: PMC3344989.
34. Kidd Jeffrey M, Gravel S, Byrnes J, Moreno-Estrada A, Musharoff S, Bryc K, et al. Population Genetic Inference from Personal Genome Data: Impact of Ancestry and Admixture on Human Genomic Variation. American Journal of Human Genetics. 2012;91(4):660-71. doi: 10.1016/j.ajhg.2012.08.025. PubMed PMID: PMC3484644.
35. Kang HP, Yang X, Chen R, Zhang B, Corona E, Schadt EE, et al. Integration of disease-specific single nucleotide polymorphisms, expression quantitative trait loci and coexpression networks reveal novel candidate genes for type 2 diabetes. Diabetologia. 2012;55(8):2205-13. doi: 10.1007/s00125-012-2568-3. PubMed PMID: PMC3390705.
36. Kang HP, Morgan AA, Chen R, Schadt EE, Butte AJ. Coanalysis of GWAS with eQTLs reveals disease-tissue associations. AMIA Summits on Translational Science Proceedings. 2012;2012:35-41. PubMed PMID: PMC3392070.
37. Jostins L, Ripke S, Weersma RK, Duerr RH, McGovern DP, Hui KY, et al. Host–microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature. 2012;491:119. doi: 10.1038/nature11582
https://www.nature.com/articles/nature11582 – supplementary-information.
38. Johnston JM, Wang H, Provasi D, Filizola M. Assessing the Relative Stability of Dimer Interfaces in G Protein-Coupled Receptors. PLOS Computational Biology. 2012;8(8):e1002649. doi: 10.1371/journal.pcbi.1002649.
39. Ionita-Laza I, Makarov V, Buxbaum Joseph D. Scan-Statistic Approach Identifies Clusters of Rare Disease Variants in LRP2, a Gene Linked and Associated with Autism Spectrum Disorders, in Three Datasets. The American Journal of Human Genetics. 2012;90(6):1002-13. doi: https://doi.org/10.1016/j.ajhg.2012.04.010.
40. Gupta R, Ratan A, Rajesh C, Chen R, Kim HL, Burhans R, et al. Sequencing and analysis of a South Asian-Indian personal genome. BMC Genomics. 2012;13:440-. doi: 10.1186/1471-2164-13-440. PubMed PMID: PMC3534380.
41. Gargis AS, Kalman L, Berry MW, Bick DP, Dimmock DP, Hambuch T, et al. Assuring the quality of next-generation sequencing in clinical laboratory practice. Nature biotechnology. 2012;30(11):10.1038/nbt.2403. doi: 10.1038/nbt.2403. PubMed PMID: PMC3827024.
42. Fromer M, Moran Jennifer L, Chambert K, Banks E, Bergen Sarah E, Ruderfer Douglas M, et al. Discovery and Statistical Genotyping of Copy-Number Variation from Whole-Exome Sequencing Depth. The American Journal of Human Genetics. 2012;91(4):597-607. doi: https://doi.org/10.1016/j.ajhg.2012.08.005.
43. Fitzpatrick K, Winrow CJ, Gotter AL, Millstein J, Arbuzova J, Brunner J, et al. Altered Sleep and Affect in the Neurotensin Receptor 1 Knockout Mouse. Sleep. 2012;35(7):949-56. doi: 10.5665/sleep.1958. PubMed PMID: PMC3369230.
44. Fang G, Munera D, Friedman DI, Mandlik A, Chao MC, Banerjee O, et al. Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing. Nature Biotechnology. 2012;30:1232. doi: 10.1038/nbt.2432
https://www.nature.com/articles/nbt.2432 – supplementary-information.
45. Dudley JT, Kim Y, Liu L, Markov GJ, Gerold K, Chen R, et al. Human genomic disease variants: A neutral evolutionary explanation. Genome Research. 2012;22(8):1383-94. doi: 10.1101/gr.133702.111. PubMed PMID: PMC3409252.
46. Dudley JT, Chen R, Sanderford M, Butte AJ, Kumar S. Evolutionary Meta-Analysis of Association Studies Reveals Ancient Constraints Affecting Disease Marker Discovery. Molecular Biology and Evolution. 2012;29(9):2087-94. doi: 10.1093/molbev/mss079. PubMed PMID: PMC3424407.
47. Clemente JC, Ursell LK, Parfrey LW, Knight R. The Impact of the Gut Microbiota on Human Health: An Integrative View. Cell. 2012;148(6):1258-70. doi: 10.1016/j.cell.2012.01.035. PubMed PMID: PMC5050011.
48. Chen R, Mias GI, Li-Pook-Than J, Jiang L, Lam HYK, Chen R, et al. Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes. Cell. 2012;148(6):1293-307. doi: 10.1016/j.cell.2012.02.009. PubMed PMID: PMC3341616.
49. Chen R, Dudley JT, Ruau D, Butte AJ. Quantifying multi-ethnic representation in genetic studies of high mortality diseases. AMIA Summits on Translational Science Proceedings. 2012;2012:11-8. PubMed PMID: PMC3392055.
50. Chen R, Corona E, Sikora M, Dudley JT, Morgan AA, Moreno-Estrada A, et al. Type 2 Diabetes Risk Alleles Demonstrate Extreme Directional Differentiation among Human Populations, Compared to Other Diseases. PLoS Genetics. 2012;8(4):e1002621. doi: 10.1371/journal.pgen.1002621. PubMed PMID: PMC3325177.
51. Carvalho FA, Koren O, Goodrich JK, Johansson MEV, Nalbantoglu I, Aitken JD, et al. Transient Inability to manage Proteobacteria promotes chronic gut inflammation in TLR5-deficient mice. Cell host & microbe. 2012;12(2):139-52. doi: 10.1016/j.chom.2012.07.004. PubMed PMID: PMC4310462.
52. Buxbaum Joseph D, Daly Mark J, Devlin B, Lehner T, Roeder K, State Matthew W. The Autism Sequencing Consortium: Large-Scale, High-Throughput Sequencing in Autism Spectrum Disorders. Neuron. 2012;76(6):1052-6. doi: https://doi.org/10.1016/j.neuron.2012.12.008.
53. Bashir A, Klammer A, Robins WP, Chin C-S, Webster D, Paxinos E, et al. A Hybrid Approach for the Automated Finishing of Bacterial Genomes. Nature biotechnology. 2012;30(7):701-7. doi: 10.1038/nbt.2288. PubMed PMID: PMC3731737.
54. Anh Tran V, Carlos Clemente J, Nguyen Duc T, Li J, Dang X, Tu T, et al. IMPACT: A novel clustering algorithm based on attraction2012.

BODE

2018/07/2019/07 : 83 in total

1. 1. Yang X, Yuan T, Ma R, Chacko KI, Smith M, Deikus G, et al. Mce3R Stress-Resistance Pathway Is Vulnerable to Small-Molecule Targeting That Improves Tuberculosis Drug Activities. ACS Infectious Diseases. 2019. doi: 10.1021/acsinfecdis.9b00099.
 2. Wetherill L, Lai D, Johnson EC, Anokhin A, Bauer L, Bucholz KK, et al. Genome-wide association study identifies loci associated with liability to alcohol and drug dependence that is associated with variability in reward-related ventral striatum activity in African- and European-Americans. Genes, Brain and Behavior. 2019;0(0):e12580. doi: 10.1111/gbb.12580. PubMed PMID: 31099175.
 3. Vishnu A, Belbin GM, Wojcik GL, Bottinger EP, Gignoux CR, Kenny EE, et al. The role of country of birth, and genetic and self-identified ancestry, in obesity susceptibility among African and Hispanic Americans. The American Journal of Clinical Nutrition. 2019. doi: 10.1093/ajcn/nqz098.
 4. Verheije R, Kupchik GS, Isidor B, Kroes HY, Lynch SA, Hawkes L, et al. Heterozygous loss-of-function variants of MEIS2 cause a triad of palatal defects, congenital heart defects, and intellectual disability. European Journal of Human Genetics. 2019;27(2):278-90. doi: 10.1038/s41431-018-0281-5.
 5. Urreizti R, Mayer K, Evrony GD, Said E, Castilla-Vallmanya L, Cody NAL, et al. DPH1 syndrome: two novel variants and structural and functional analyses of seven missense variants identified in syndromic patients. European Journal of Human Genetics. 2019. doi: 10.1038/s41431-019-0374-9.
 6. Torres J, Hu J, Seki A, Eisele C, Nair N, Huang R, et al. Infants born to mothers with IBD present with altered gut microbiome that transfers abnormalities of the adaptive immune system to germ-free mice. Gut. 2019:gutjnl-2018-317855. doi: 10.1136/gutjnl-2018-317855. PubMed PMID: 31036757.
 7. Tejero R, Huang Y, Katsyv I, Kluge M, Lin J-Y, Tome-Garcia J, et al. Gene signatures of quiescent glioblastoma cells reveal mesenchymal shift and interactions with niche microenvironment. EBioMedicine. 2019;42:252-69. doi: 10.1016/j.ebiom.2019.03.064. PubMed PMID: 30952620.
 8. Steinbach N, Hasson D, Mathur D, Stratikopoulos EE, Sachidanandam R, Bernstein E, et al. PTEN interacts with the transcription machinery on chromatin and regulates RNA polymerase II-mediated transcription. Nucleic Acids Research. 2019. doi: 10.1093/nar/gkz272.
 9. Stefan-Lifshitz M, Karakose E, Cui L, Ettela A, Yi Z, Zhang W, et al. Epigenetic modulation of β cells by interferon-α via PNPT1/mir-26a/TET2 triggers autoimmune diabetes. JCI Insight. 2019;4(5):e126663. doi: 10.1172/jci.insight.126663. PubMed PMID: 30721151.
 10. Srinivasan S, Stephens C, Wilson E, Panchadsaram J, DeVoss K, Koistinen H, et al. Prostate Cancer Risk-Associated Single-Nucleotide Polymorphism Affects Prostate-Specific Antigen Glycosylation and Its Function. Clinical Chemistry. 2019;65(1):e1. doi: 10.1373/clinchem.2018.295790.
 11. Sewda A, White SR, Erazo M, Hao K, García-Fructuoso G, Fernández-Rodriguez I, et al. Nonsyndromic craniosynostosis: novel coding variants. Pediatric Research. 2019;85(4):463-8. doi: 10.1038/s41390-019-0274-2. PubMed PMID: 30651579.
 12. Ruf-Zamojski F, Ge Y, Pincas H, Shan J, Song Y, Hines N, et al. Cytogenetic, Genomic, and Functional Characterization of Pituitary Gonadotrope Cell Lines. Journal of the Endocrine Society. 2019;3(5):902-20. doi: 10.1210/js.2019-00064.
 13. Richter F, Hoffman GE, Manheimer KB, Patel N, Sharp AJ, McKean D, et al. ORE identifies extreme expression effects enriched for rare variants. Bioinformatics. 2019. doi: 10.1093/bioinformatics/btz202.
 14. Pertesi M, Vallée M, Wei X, Revuelta MV, Galia P, Demangel D, et al. Exome sequencing identifies germline variants in DIS3 in familial multiple myeloma. Leukemia. 2019. doi: 10.1038/s41375-019-0452-6.
 15. Ntranos A, Ntranos V, Bonnefil V, Liu J, Kim-Schulze S, He Y, et al. Fumarates target the metabolic-epigenetic interplay of brain-homing T cells in multiple sclerosis. Brain. 2019;142(3):647-61. doi: 10.1093/brain/awy344.
 16. Motch Perrine SM, Wu M, Stephens NB, Kriti D, van Bakel H, Jabs EW, et al. Mandibular dysmorphology due to abnormal embryonic osteogenesis in FGFR2-related craniosynostosis mice. Disease Models &amp; Mechanisms. 2019;12(5):dmm038513. doi: 10.1242/dmm.038513.
 17. Li Z, Chen H, Zhong F, Zhang W, Lee K, He JC. Expression of Glutamate Receptor Subtype 3 Is Epigenetically Regulated in Podocytes under Diabetic Conditions. Kidney Diseases. 2019;5(1):34-42. doi: 10.1159/000492933.
 18. Li YI, Wong G, Humphrey J, Raj T. Prioritizing Parkinson’s disease genes using population-scale transcriptomic data. Nat Commun. 2019;10(1):994-. doi: 10.1038/s41467-019-08912-9. PubMed PMID: 30824768.
 19. Laverty KU, Stout JM, Sullivan MJ, Shah H, Gill N, Holbrook L, et al. A physical and genetic map of Cannabis sativa identifies extensive rearrangements at the THC/CBD acid synthase loci. Genome Res. 2019;29(1):146-56. doi: 10.1101/gr.242594.118. PubMed PMID: 30409771.
 20. Lamim Ribeiro JM, Filizola M. Allostery in G protein-coupled receptors investigated by molecular dynamics simulations. Current Opinion in Structural Biology. 2019;55:121-8. doi: https://doi.org/10.1016/j.sbi.2019.03.016.
 21. Lai D, Wetherill L, Bertelsen S, Carey CE, Kamarajan C, Kapoor M, et al. Genome-wide association studies of alcohol dependence, DSM-IV criterion count and individual criteria. Genes, Brain and Behavior. 2019;0(0). doi: 10.1111/gbb.12579. PubMed PMID: 31090166.
 22. Kapoor M, Wang J-C, Farris SP, Liu Y, McClintick J, Gupta I, et al. Analysis of whole genome-transcriptomic organization in brain to identify genes associated with alcoholism. Transl Psychiatry. 2019;9(1):89-. doi: 10.1038/s41398-019-0384-y. PubMed PMID: 30765688.
 23. Jiang P, Scarpa JR, Gao VD, Vitaterna MH, Kasarskis A, Turek FW. Parkinson’s Disease is Associated with Dysregulations of a Dopamine-Modulated Gene Network Relevant to Sleep and Affective Neurobehaviors in the Striatum. Scientific Reports. 2019;9(1):4808. doi: 10.1038/s41598-019-41248-4.
 24. Huang F, Wang M, Liu R, Wang J-Z, Schadt E, Haroutunian V, et al. CDT2-controlled cell cycle reentry regulates the pathogenesis of Alzheimer’s disease. Alzheimer’s & Dementia. 2019;15(2):217-31. doi: https://doi.org/10.1016/j.jalz.2018.08.013.
 25. Hu X, Wang Y, Hunkele A, Provasi D, Pasternak GW, Filizola M. Kinetic and thermodynamic insights into sodium ion translocation through the μ-opioid receptor from molecular dynamics and machine learning analysis. PLOS Computational Biology. 2019;15(1):e1006689. doi: 10.1371/journal.pcbi.1006689.
 26. Hu J, Ly J, Zhang W, Huang Y, Glover V, Peter I, et al. Microbiota of newborn meconium is associated with maternal anxiety experienced during pregnancy. Developmental Psychobiology. 2019;0(0). doi: 10.1002/dev.21837. PubMed PMID: 30908632.
 27. Hirten RP, Grinspan A, Fu S-C, Luo Y, Suarez-Farinas M, Rowland J, et al. Microbial Engraftment and Efficacy of Fecal Microbiota Transplant for Clostridium Difficile in Patients With and Without Inflammatory Bowel Disease. Inflammatory Bowel Diseases. 2019;25(6):969-79. doi: 10.1093/ibd/izy398. PubMed PMID: 30852592.
 28. Garg P, Sharp AJ. Screening for rare epigenetic variations in autism and schizophrenia. Human Mutation. 2019;0(0). doi: 10.1002/humu.23740.
 29. Fu J, Akat KM, Sun Z, Zhang W, Schlondorff D, Liu Z, et al. Single-Cell RNA Profiling of Glomerular Cells Shows Dynamic Changes in Experimental Diabetic Kidney Disease. Journal of the American Society of Nephrology. 2019;30(4):533. doi: 10.1681/ASN.2018090896.
 30. Frades I RB, Amadori L, Koplev S, Talukdar HA, Crane HM, Crane PK,, Kovacic JC DJ, Giannarelli C, Björkegren JLM, Peter I. Systems Pharmacology Identifies an Arterial Wall Regulatory Gene Network Mediating Coronary Artery Disease Side Effects of Antiretroviral Therapy. Circ Genom Precis Med. 2019. Epub 2019 May 6. doi: doi: 10.1161/CIRCGEN.118.002390. PubMed Central PMCID: PMCPMID: 31059280
 31. Filizola M. Insights from molecular dynamics simulations to exploit new trends for the development of improved opioid drugs. Neuroscience Letters. 2019;700:50-5. doi: https://doi.org/10.1016/j.neulet.2018.02.037.
 32. Fernandez-Jimenez R, Jaslow R, Bansilal S, Santana M, Diaz-Munoz R, Latina J, et al. Child Health Promotion in Underserved Communities. Journal of the American College of Cardiology. 2019;73(16):2011. doi: 10.1016/j.jacc.2019.01.057.
 33. Edwards TL, Giri A, Hellwege JN, Hartmann KE, Stewart EA, Jeff JM, et al. A Trans-Ethnic Genome-Wide Association Study of Uterine Fibroids. Frontiers in Genetics. 2019;10:511.
 34. Di Narzo AF, Brodmerkel C, Telesco SE, Argmann C, Peters LA, Li K, et al. High-Throughput Identification of the Plasma Proteomic Signature of Inflammatory Bowel Disease. J Crohns Colitis. 2019;13(4):462-71. Epub 2018/11/15. doi: 10.1093/ecco-jcc/jjy190. PubMed PMID: 30445421.
 35. Daya M, Rafaels N, Brunetti TM, Chavan S, Levin AM, Shetty A, et al. Association study in African-admixed populations across the Americas recapitulates asthma risk loci in non-African populations. Nat Commun. 2019;10(1):880. doi: 10.1038/s41467-019-08469-7.
 36. Davenport B, Eberlein J, van der Heide V, Jhun K, Nguyen TT, Victorino F, et al. Aging of Antiviral CD8+ Memory T Cells Fosters Increased Survival, Metabolic Adaptations, and Lymphoid Tissue Homing. The Journal of Immunology. 2019;202(2):460. doi: 10.4049/jimmunol.1801277.
 37. Copin R, Sause WE, Fulmer Y, Balasubramanian D, Dyzenhaus S, Ahmed JM, et al. Sequential evolution of virulence and resistance during clonal spread of community-acquired methicillin-resistant Staphylococcus aureus</em&gt. Proceedings of the National Academy of Sciences. 2019;116(5):1745. doi: 10.1073/pnas.1814265116.
 38. Contijoch EJ, Britton GJ, Yang C, Mogno I, Li Z, Ng R, et al. Gut microbiota density influences host physiology and is shaped by host and microbial factors. Elife. 2019;8:e40553. doi: 10.7554/eLife.40553. PubMed PMID: 30666957.
 39. Choi H, Song W-m, Wang M, Sram RJ, Zhang B. Benzo[a]pyrene is associated with dysregulated myelo-lymphoid hematopoiesis in asthmatic children. Environment International. 2019;128:218-32. doi: https://doi.org/10.1016/j.envint.2019.04.052.
 40. Chen B, Wang M, Gan L, Zhang B, Desnick RJ, Yasuda M. Characterization of the hepatic transcriptome following phenobarbital induction in mice with AIP. Molecular Genetics and Metabolism. 2019. doi: https://doi.org/10.1016/j.ymgme.2018.12.010.
 41. Bowles KR, Tcw J, Qian L, Jadow BM, Goate AM. Reduced variability of neural progenitor cells and improved purity of neuronal cultures using magnetic activated cell sorting. PLoS One. 2019;14(3):e0213374-e. doi: 10.1371/journal.pone.0213374. PubMed PMID: 30917153.
 42. Zhao N, Sebastiano V, Moshkina N, Mena N, Hultquist J, Jimenez-Morales D, et al. Influenza virus infection causes global RNAPII termination defects. Nature Structural & Molecular Biology. 2018;25(9):885-93. doi: 10.1038/s41594-018-0124-7.
 43. Wei C, Banu K, Garzon F, Basgen JM, Philippe N, Yi Z, et al. SHROOM3-FYN Interaction Regulates Nephrin Phosphorylation and Affects Albuminuria in Allografts. Journal of the American Society of Nephrology. 2018;29(11):2641. doi: 10.1681/ASN.2018060573.
 44. Wang M, Beckmann ND, Roussos P, Wang E, Zhou X, Wang Q, et al. The Mount Sinai cohort of large-scale genomic, transcriptomic and proteomic data in Alzheimer’s disease. Scientific Data. 2018;5:180185. doi: 10.1038/sdata.2018.185

https://www.nature.com/articles/sdata2018185 – supplementary-information.

1. 1. Wang L, Law J, Kale SD, Murali TM, Pandey G. Large-scale protein function prediction using heterogeneous ensembles. F1000Res. 2018;7:ISCB Comm J-1577. doi: 10.12688/f1000research.16415.1. PubMed PMID: 30450194.
 2. Wang J-C, Alinaghi S, Tafakhori A, Sikora E, Azcona LJ, Karkheiran S, et al. Genetic screening in two Iranian families with early-onset Alzheimer’s disease identified a novel PSEN1 mutation. Neurobiol Aging. 2018;62:244.e15-.e17. Epub 2017/10/23. doi: 10.1016/j.neurobiolaging.2017.10.011. PubMed PMID: 29175279.
 3. Voorhees IEH, Dalziel BD, Glaser A, Dubovi EJ, Murcia PR, Newbury S, et al. Multiple Incursions and Recurrent Epidemic Fade-Out of H3N2 Canine Influenza A Virus in the United States. J Virol. 2018;92(16):e00323-18. doi: 10.1128/JVI.00323-18. PubMed PMID: 29875234.
 4. Verghese DA, Chun N, Paz K, Fribourg M, Woodruff TM, Flynn R, et al. C5aR1 regulates T follicular helper differentiation and chronic graft-versus-host disease bronchiolitis obliterans. JCI Insight. 2018;3(24):e124646. doi: 10.1172/jci.insight.124646. PubMed PMID: 30568034.
 5. Venkatesh D, Poen MJ, Bestebroer TM, Scheuer RD, Vuong O, Chkhaidze M, et al. Avian Influenza Viruses in Wild Birds: Virus Evolution in a Multihost Ecosystem. J Virol. 2018;92(15):e00433-18. doi: 10.1128/JVI.00433-18. PubMed PMID: 29769347.
 6. Tome-Garcia J, Erfani P, Nudelman G, Tsankov AM, Katsyv I, Tejero R, et al. Analysis of chromatin accessibility uncovers TEAD1 as a regulator of migration in human glioblastoma. Nat Commun. 2018;9(1):4020. doi: 10.1038/s41467-018-06258-2.
 7. Sun Z, Filipescu D, Andrade J, Gaspar-Maia A, Ueberheide B, Bernstein E. Transcription-associated histone pruning demarcates macroH2A chromatin domains. Nature Structural & Molecular Biology. 2018;25(10):958-70. doi: 10.1038/s41594-018-0134-5.
 8. Strub T, Ghiraldini FG, Carcamo S, Li M, Wroblewska A, Singh R, et al. SIRT6 haploinsufficiency induces BRAFV600E melanoma cell resistance to MAPK inhibitors via IGF signalling. Nat Commun. 2018;9(1):3440. doi: 10.1038/s41467-018-05966-z.
 9. Shameer K, Perez-Rodriguez MM, Bachar R, Li L, Johnson A, Johnson KW, et al. Pharmacological risk factors associated with hospital readmission rates in a psychiatric cohort identified using prescriptome data mining. BMC Medical Informatics and Decision Making. 2018;18(3):79. doi: 10.1186/s12911-018-0653-3.
 10. Scarpa JR, Jiang P, Gao VD, Fitzpatrick K, Millstein J, Olker C, et al. Cross-species systems analysis identifies gene networks differentially altered by sleep loss and depression. Science Advances. 2018;4(7):eaat1294. doi: 10.1126/sciadv.aat1294.
 11. Ruf-Zamojski F, Ge Y, Nair V, Zamojski M, Pincas H, Toufaily C, et al. Single-cell stabilization method identifies gonadotrope transcriptional dynamics and pituitary cell type heterogeneity. Nucleic acids research. 2018;46(21):11370-80. Epub 2018/10/24. doi: 10.1093/nar/gky991. PubMed PMID: 30357357.
 12. Ribeiro EA, Salery M, Scarpa JR, Calipari ES, Hamilton PJ, Ku SM, et al. Transcriptional and physiological adaptations in nucleus accumbens somatostatin interneurons that regulate behavioral responses to cocaine. Nat Commun. 2018;9(1):3149-. doi: 10.1038/s41467-018-05657-9. PubMed PMID: 30089879.
 13. Ren C, Zhang G, Han F, Fu S, Cao Y, Zhang F, et al. Spatially constrained tandem bromodomain inhibition bolsters sustained repression of BRD4 transcriptional activity for TNBC cell growth. Proceedings of the National Academy of Sciences. 2018;115(31):7949. doi: 10.1073/pnas.1720000115.
 14. Readhead B, Hartley BJ, Eastwood BJ, Collier DA, Evans D, Farias R, et al. Expression-based drug screening of neural progenitor cells from individuals with schizophrenia. Nat Commun. 2018;9(1):4412. doi: 10.1038/s41467-018-06515-4.
 15. Rathore N, Ramani SR, Pantua H, Payandeh J, Bhangale T, Wuster A, et al. Paired Immunoglobulin-like Type 2 Receptor Alpha G78R variant alters ligand binding and confers protection to Alzheimer’s disease. PLoS Genet. 2018;14(11):e1007427-e. doi: 10.1371/journal.pgen.1007427. PubMed PMID: 30388101.
 16. Ramdhani S, Navarro E, Udine E, Schilder BM, Parks M, Raj T. Tensor Decomposition of Stimulated Monocyte and Macrophage Gene Expression Profiles Identifies Neurodegenerative Disease-specific Trans-eQTLs. bioRxiv. 2018:499509. doi: 10.1101/499509.
 17. Rajarajan P, Borrman T, Liao W, Schrode N, Flaherty E, Casiño C, et al. Neuron-specific signatures in the chromosomal connectome associated with schizophrenia risk. Science. 2018;362(6420):eaat4311. doi: 10.1126/science.aat4311.
 18. Raj T, Li YI, Wong G, Humphrey J, Wang M, Ramdhani S, et al. Integrative transcriptome analyses of the aging brain implicate altered splicing in Alzheimer’s disease susceptibility. Nat Genet. 2018;50(11):1584-92. Epub 2018/10/08. doi: 10.1038/s41588-018-0238-1. PubMed PMID: 30297968.
 19. Peter I, Dubinsky M, Bressman S, Park A, Lu C, Chen N, et al. Anti–Tumor Necrosis Factor Therapy and Incidence of Parkinson Disease Among Patients With Inflammatory Bowel DiseaseAnti-TNF Therapy and Incidence of Parkinson Disease Among Patients With Inflammatory Bowel DiseaseAnti-TNF Therapy and Incidence of Parkinson Disease Among Patients With Inflammatory Bowel Disease. JAMA Neurology. 2018;75(8):939-46. doi: 10.1001/jamaneurol.2018.0605. PubMed PMID: 29710331.
 20. Peng S, Deyssenroth MA, Di Narzo AF, Cheng H, Zhang Z, Lambertini L, et al. Genetic regulation of the placental transcriptome underlies birth weight and risk of childhood obesity. PLoS Genet. 2018;14(12):e1007799-e. doi: 10.1371/journal.pgen.1007799. PubMed PMID: 30596636.
 21. Papa L, Zimran E, Djedaini M, Ge Y, Ozbek U, Sebra R, et al. Ex vivo human HSC expansion requires coordination of cellular reprogramming with mitochondrial remodeling and p53 activation. Blood Adv. 2018;2(20):2766-79. doi: 10.1182/bloodadvances.2018024273. PubMed PMID: 30348672.
 22. Nadkarni GN, Gignoux CR, Sorokin EP, Daya M, Rahman R, Barnes KC, et al. Worldwide Frequencies of APOL1 Renal Risk Variants. N Engl J Med. 2018;379(26):2571-2. doi: 10.1056/NEJMc1800748. PubMed PMID: 30586505.
 23. Michlmayr D, Pak TR, Rahman AH, Amir E-AD, Kim E-Y, Kim-Schulze S, et al. Comprehensive innate immune profiling of chikungunya virus infection in pediatric cases. Mol Syst Biol. 2018;14(8):e7862-e. doi: 10.15252/msb.20177862. PubMed PMID: 30150281.
 24. Meral D, Provasi D, Filizola M. An efficient strategy to estimate thermodynamics and kinetics of G protein-coupled receptor activation using metadynamics and maximum caliber. The Journal of Chemical Physics. 2018;149(22):224101. doi: 10.1063/1.5060960.
 25. Mena J, Brito B, Moreira R, Tadich T, González I, Cruces J, et al. Reemergence of H3N8 Equine Influenza A virus in Chile, 2018. Transboundary and Emerging Diseases. 2018;65(6):1408-15. doi: 10.1111/tbed.12984.
 26. Litvinchuk A, Wan Y-W, Swartzlander DB, Chen F, Cole A, Propson NE, et al. Complement C3aR Inactivation Attenuates Tau Pathology and Reverses an Immune Network Deregulated in Tauopathy Models and Alzheimer’s Disease. Neuron. 2018;100(6):1337-53.e5. doi: https://doi.org/10.1016/j.neuron.2018.10.031.
 27. Li W, Middha M, Bicak M, Sjoberg DD, Vertosick E, Dahlin A, et al. Genome-wide Scan Identifies Role for AOX1 in Prostate Cancer Survival. European Urology. 2018;74(6):710-9. doi: 10.1016/j.eururo.2018.06.021.
 28. Li H, Zhang W, Zhong F, Das GC, Xie Y, Li Z, et al. Epigenetic regulation of RCAN1 expression in kidney disease and its role in podocyte injury. Kidney International. 2018;94(6):1160-76. doi: 10.1016/j.kint.2018.07.023.
 29. Laganà A, Beno I, Melnekoff D, Leshchenko V, Madduri D, Ramdas D, et al. Precision Medicine for Relapsed Multiple Myeloma on the Basis of an Integrative Multiomics Approach. JCO Precision Oncology. 2018(2):1-17. doi: 10.1200/PO.18.00019.
 30. Kajiwara Y, Wang E, Wang M, Sin WC, Brennand KJ, Schadt E, et al. GJA1 (connexin43) is a key regulator of Alzheimer’s disease pathogenesis. Acta Neuropathol Commun. 2018;6(1):144-. doi: 10.1186/s40478-018-0642-x. PubMed PMID: 30577786.
 31. Granot-Hershkovitz E, Karasik D, Friedlander Y, Rodriguez-Murillo L, Dorajoo R, Liu J, et al. A study of Kibbutzim in Israel reveals risk factors for cardiometabolic traits and subtle population structure. European Journal of Human Genetics. 2018;26(12):1848-58. doi: 10.1038/s41431-018-0230-3. PubMed PMID: 30108283.
 32. Garg P, Joshi RS, Watson C, Sharp AJ. A survey of inter-individual variation in DNA methylation identifies environmentally responsive co-regulated networks of epigenetic variation in the human genome. PLoS Genet. 2018;14(10):e1007707. doi: 10.1371/journal.pgen.1007707.
 33. Gandal MJ, Zhang P, Hadjimichael E, Walker RL, Chen C, Liu S, et al. Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder. Science. 2018;362(6420):eaat8127. doi: 10.1126/science.aat8127.
 34. Dong L, Wu N, Wang S, Cheng Y, Han L, Zhao J, et al. Detection of novel germline mutations in six breast cancer predisposition genes by targeted next-generation sequencing. Human Mutation. 2018;39(10):1442-55. doi: 10.1002/humu.23597.
 35. Deming Y, Dumitrescu L, Barnes LL, Thambisetty M, Kunkle B, Gifford KA, et al. Sex-specific genetic predictors of Alzheimer’s disease biomarkers. Acta Neuropathologica. 2018;136(6):857-72. doi: 10.1007/s00401-018-1881-4.
 36. Bonnemaijer PWM, Iglesias AI, Nadkarni GN, Sanyiwa AJ, Hassan HG, Cook C, et al. Genome-wide association study of primary open-angle glaucoma in continental and admixed African populations. Human Genetics. 2018;137(10):847-62. doi: 10.1007/s00439-018-1943-7. PubMed PMID: 30317457.
 37. Bis JC, Jian X, Kunkle BW, Chen Y, Hamilton-Nelson KL, Bush WS, et al. Whole exome sequencing study identifies novel rare and common Alzheimer’s-Associated variants involved in immune response and transcriptional regulation. Molecular Psychiatry. 2018. doi: 10.1038/s41380-018-0112-7. PubMed PMID: 30108311
 38. Altman DR, Sullivan MJ, Chacko KI, Balasubramanian D, Pak TR, Sause WE, et al. Genome Plasticity of agr-Defective Staphylococcus aureus during Clinical Infection. Infect Immun. 2018;86(10):e00331-18. doi: 10.1128/IAI.00331-18. PubMed PMID: 30061376.
 39. Alonso A, Bernstein E, Hasson D. Histone Native Chromatin Immunoprecipitation. In: Orsi GA, Almouzni G, editors. Histone Variants: Methods and Protocols. New York, NY: Springer New York; 2018. p. 77-104.

2017/07 – 2018/07: 73 in total

1. Turcot V, Lu Y, Highland HM, Schurmann C, Justice AE, Fine RS, et al. Protein-altering variants associated with body mass index implicate pathways that control energy intake and expenditure in obesity. Nature Genetics. 2018;50(1):26-41. doi: 10.1038/s41588-017-0011-x.

2. Marino KA, Filizola M. Investigating Small-Molecule Ligand Binding to G Protein-Coupled Receptors with Biased or Unbiased Molecular Dynamics Simulations. Methods in molecular biology (Clifton, NJ). 2018;1705:351-64. doi: 10.1007/978-1-4939-7465-8_17. PubMed PMID: PMC5745006.

3. Manasson J, Shen N, Garcia Ferrer Helga R, Ubeda C, Iraheta I, Heguy A, et al. Gut Microbiota Perturbations in Reactive Arthritis and Postinfectious Spondyloarthritis. Arthritis & Rheumatology. 2018;70(2):242-54. doi: 10.1002/art.40359.

4. Linde N, Casanova-Acebes M, Sosa MS, Mortha A, Rahman A, Farias E, et al. Macrophages orchestrate breast cancer early dissemination and metastasis. Nature Communications. 2018;9(1):21. doi: 10.1038/s41467-017-02481-5.

5. Hughes TET, Lodowski DT, Huynh KW, Yazici A, Del Rosario J, Kapoor A, et al. Structural basis of TRPV5 channel inhibition by econazole revealed by cryo-EM. Nature Structural & Molecular Biology. 2018;25(1):53-60. doi: 10.1038/s41594-017-0009-1.

6. Hong J, Hatchell KE, Bradfield JP, Andrew B, Alessandra C, Chao-Qiang L, et al. Trans-ethnic Evaluation Identifies Novel Low Frequency Loci Associated with 25-Hydroxyvitamin D Concentrations. The Journal of Clinical Endocrinology & Metabolism. 2018:jc.2017-01802-jc.2017-. doi: 10.1210/jc.2017-01802.

7. Fazlollahi M, Chun Y, Grishin A, Wood RA, Burks AW, Dawson P, et al. Early‐life gut microbiome and egg allergy. Allergy. 2018;. doi: 10.1111/all.13389.

8. Cruchaga C, Del-Aguila JL, Saef B, Black K, Fernandez MV, Budde J, et al. Polygenic risk score of sporadic late-onset Alzheimer’s disease reveals a shared architecture with the familial and early-onset forms. Alzheimer’s & Dementia. 2018;14(2):205-14. doi: https://doi.org/10.1016/j.jalz.2017.08.013.

9. Clemente JC, Manasson J, Scher JU. The role of the gut microbiome in systemic inflammatory disease. BMJ. 2018;360.

11. Barbosa M, Joshi RS, Garg P, Martin-Trujillo A, Patel N, Jadhav B, Watson CT, Gibson W, Chetnik K, Tessereau C, Mei H, De Rubeis S, Reichert J, Lopes F, Vissers LELM, Kleefstra T, Grice DE, Edelmann L, Soares G, Maciel P, Brunner HG, Buxbaum JD, Gelb BD, Sharp AJ. Identification of rare de novo epigenetic variations in congenital disorders. Nature Communications. 2018;9(1):2064. doi: 10.1038/s41467-018-04540-x. PubMed Central PMCID: PMC5970273; PMID: 29802345

12. Aushev VN, Lee E, Zhu J, Gopalakrishnan K, Li Q, Teitelbaum SL, et al. Novel Predictors of Breast Cancer Survival Derived from miRNA Activity Analysis. Clinical Cancer Research. 2018;24(3):581.

13. Zhao W, Rasheed A, Tikkanen E, Lee J-J, Butterworth AS, Howson JMM, et al. Identification of new susceptibility loci for type 2 diabetes and shared etiological pathways with coronary heart disease. Nature genetics. 2017;49(10):1450-7. doi: 10.1038/ng.3943. PubMed PMID: PMC5844224.

14. Dole NS, Mazur CM, Acevedo C, Lopez JP, Monteiro DA, Fowler TW, et al. Osteocyte-Intrinsic TGFβ Signaling Regulates Bone Quality through Perilacunar/Canalicular Remodeling. Cell Reports.21(9):2585-96. doi: 10.1016/j.celrep.2017.10.115

15. Yoo S, Wang W, Wang Q, Fiel MI, Lee E, Hiotis SP, et al. A pilot systematic genomic comparison of recurrence risks of hepatitis B virus-associated hepatocellular carcinoma with low- and high-degree liver fibrosis. BMC Medicine. 2017;15(1):214. doi: 10.1186/s12916-017-0973-7.

16. Yano H, Provasi D, Cai NS, Filizola M, Ferré S, Javitch JA. Development of novel biosensors to study receptor-mediated activation of the G-protein α subunits Gs and Golf. Journal of Biological Chemistry. 2017;292(49):19989-98.

17. Wheeler E, Leong A, Liu C-T, Hivert M-F, Strawbridge RJ, Podmore C, et al. Impact of common genetic determinants of Hemoglobin A1c on type 2 diabetes risk and diagnosis in ancestrally diverse populations: A transethnic genome-wide meta-analysis. PLoS Medicine. 2017;14(9):e1002383. doi: 10.1371/journal.pmed.1002383. PubMed PMID: PMC5595282.

18. Wain LV, Vaez A, Jansen R, Joehanes R, van der Most PJ, Erzurumluoglu AM, et al. Novel Blood Pressure Locus and Gene Discovery Using Genome-Wide Association Study and Expression Data Sets From Blood and the Kidney. Hypertension. 2017;70(3):e4.

19. Tcw J, Wang M, Pimenova AA, Bowles KR, Hartley BJ, Lacin E, et al. An Efficient Platform for Astrocyte Differentiation from Human Induced Pluripotent Stem Cells. Stem Cell Reports. 2017;9(2):600-14. doi: 10.1016/j.stemcr.2017.06.018. PubMed PMID: PMC5550034.

20. Shen L, Zhu J, Robert Li S-Y, Fan X. Detect differentially methylated regions using non-homogeneous hidden Markov model for methylation array data. Bioinformatics. 2017;33(23):3701-8. doi: 10.1093/bioinformatics/btx467.

21. Scott SA, Owusu Obeng A, Botton MR, Yang Y, Scott ER, Ellis SB, et al. Institutional profile: translational pharmacogenomics at the Icahn School of Medicine at Mount Sinai. Pharmacogenomics. 2017;18(15):1381-6. doi: 10.2217/pgs-2017-0137.

22. Romero Navarro JA, Phillips-Mora W, Arciniegas-Leal A, Mata-Quirós A, Haiminen N, Mustiga G, et al. Application of Genome Wide Association and Genomic Prediction for Improvement of Cacao Productivity and Resistance to Black and Frosty Pod Diseases. Frontiers in Plant Science. 2017;8:1905. doi: 10.3389/fpls.2017.01905. PubMed PMID: PMC5694496.

23. Ridge PG, Karch CM, Hsu S, Arano I, Teerlink CC, Ebbert MTW, et al. Linkage, whole genome sequence, and biological data implicate variants in RAB10 in Alzheimer’s disease resilience. Genome Medicine. 2017;9(1):100. doi: 10.1186/s13073-017-0486-1.

24. Ribeiro EA, Scarpa JR, Garamszegi SP, Kasarskis A, Mash DC, Nestler EJ. Gene Network Dysregulation in Dorsolateral Prefrontal Cortex Neurons of Humans with Cocaine Use Disorder. Scientific Reports. 2017;7:5412. doi: 10.1038/s41598-017-05720-3. PubMed PMID: PMC5511210.

25. Rengasamy M, Zhang F, Vashisht A, Song W-M, Aguilo F, Sun Y, et al. The PRMT5/WDR77 complex regulates alternative splicing through ZNF326 in breast cancer. Nucleic Acids Research. 2017;45(19):11106-20. doi: 10.1093/nar/gkx727. PubMed PMID: PMC5737218.

26. Rahman Adeeb H, Lavin Y, Kobayashi S, Leader A, Merad M. High‐dimensional single cell mapping of cerium distribution in the lung immune microenvironment of an active smoker. Cytometry Part B: Clinical Cytometry. 2017;0(0). doi: 10.1002/cyto.b.21545.

27. Petralia F, Aushev VN, Gopalakrishnan K, Kappil M, W. Khin N, Chen J, et al. A new method to study the change of miRNA–mRNA interactions due to environmental exposures. Bioinformatics. 2017;33(14):i199-i207. doi: 10.1093/bioinformatics/btx256.

28. Peters LA, Perrigoue J, Mortha A, Iuga A, Song W-m, Neiman EM, et al. A functional genomics predictive network model identifies regulators of inflammatory bowel disease. Nature Genetics. 2017;49:1437. doi: 10.1038/ng.3947
https://www.nature.com/articles/ng.3947 – supplementary-information.

29. Hartmann BM, Albrecht RA, Zaslavsky E, Nudelman G, Pincas H, Marjanovic N,
Schotsaert M, Martínez-Romero C, Fenutria R, Ingram JP, Ramos I, Fernandez-Sesma A, Balachandran S, García-Sastre A, Sealfon SC. Pandemic H1N1 influenza A viruses suppress immunogenic RIPK3-driven dendritic cell death. Nat Commun. 2017 Dec5;8(1):1931. doi: 10.1038/s41467-017-02035-9. PubMed PMID: 29203926; PubMedCentral PMCID: PMC5715119

30. Pak TR, Chacko KI, O’Donnell T, Huprikar SS, van Bakel H, Kasarskis A, et al. Estimating Local Costs Associated With Clostridium difficile Infection Using Machine Learning and Electronic Medical Records. Infection Control & Hospital Epidemiology. 2017;38(12):1478-86. Epub 2017/11/06. doi: 10.1017/ice.2017.214.
31. Ortiz-Virumbrales M, Moreno CL, Kruglikov I, Marazuela P, Sproul A, Jacob S, et al. CRISPR/Cas9-Correctable mutation-related molecular and physiological phenotypes in iPSC-derived Alzheimer’s PSEN2(N141I) neurons. Acta Neuropathologica Communications. 2017;5:77. doi: 10.1186/s40478-017-0475-z. PubMed PMID: PMC5660456.

32. Nelson CP, Goel A, Butterworth AS, Kanoni S, Webb TR, Marouli E, et al. Association analyses based on false discovery rate implicate new loci for coronary artery disease. Nature Genetics. 2017;49:1385. doi: 10.1038/ng.3913
https://www.nature.com/articles/ng.3913 – supplementary-information.

33. Moser DA, Doucet GE, Ing A, Dima D, Schumann G, Bilder RM, et al. An integrated brain–behavior model for working memory. Molecular Psychiatry. 2017. doi: 10.1038/mp.2017.247
https://www.nature.com/articles/mp2017247 – supplementary-information.

34. McKenzie AT, Moyon S, Wang M, Katsyv I, Song W-M, Zhou X, et al. Multiscale network modeling of oligodendrocytes reveals molecular components of myelin dysregulation in Alzheimer’s disease. Molecular Neurodegeneration. 2017;12(1):82. doi: 10.1186/s13024-017-0219-3.

35. Macé A, Tuke MA, Deelen P, Kristiansson K, Mattsson H, Nõukas M, et al. CNV-association meta-analysis in 191,161 European adults reveals new loci associated with anthropometric traits. Nature Communications. 2017;8:744. doi: 10.1038/s41467-017-00556-x. PubMed PMID: PMC5622064.

36. Eisfeld AJ, Halfmann PJ, Wendler JP, Kyle JE, Burnum-Johnson KE, Peralta Z, et al. Multi-platform Omics Analysis of Human Ebola Virus Disease Pathogenesis. Cell Host & Microbe.22(6):817-29.e8. doi: 10.1016/j.chom.2017.10.011.

37. Liu DJ, Peloso GM, Yu H, Butterworth AS, Wang X, Mahajan A, et al. Exome-wide association study of plasma lipids in >300,000 individuals. Nature Genetics. 2017;49:1758. doi: 10.1038/ng.3977
https://www.nature.com/articles/ng.3977 – supplementary-information.

38. Lee E, Pain M, Wang H, Herman JA, Toledo CM, DeLuca JG, et al. Sensitivity to BUB1B Inhibition Defines an Alternative Classification of Glioblastoma. Cancer Research. 2017;77(20):5518.

39. Labonté B, Engmann O, Purushothaman I, Menard C, Wang J, Tan C, et al. Sex-specific transcriptional signatures in human depression. Nature Medicine. 2017;23:1102. doi: 10.1038/nm.4386
https://www.nature.com/articles/nm.4386 – supplementary-information.

40. Kapoor A, Martinez-Rosell G, Provasi D, de Fabritiis G, Filizola M. Dynamic and Kinetic Elements of µ-Opioid Receptor Functional Selectivity. Scientific Reports. 2017;7(1):11255. doi: 10.1038/s41598-017-11483-8.

41. Jiang Y, Loh Y-HE, Rajarajan P, Hirayama T, Liao W, Kassim BS, et al. Kmt1e regulates a large neuron-specific topological chromatin domain. Nature genetics. 2017;49(8):1239-50. doi: 10.1038/ng.3906. PubMed PMID: PMC5560095.

42. Jason F, Fuchsberger C, Mahajan A, Teslovich TM, Agarwala V, Gaulton KJ, et al. Sequence data and association statistics from 12,940 type 2 diabetes cases and controls. Scientific Data. 2017;4:170179. doi: 10.1038/sdata.2017.179. PubMed PMID: PMC5735917.

43. Ito K, Park SH, Katsyv I, Zhang W, De Angelis C, Schiff R, et al. PTK6 regulates growth and survival of endocrine therapy-resistant ER+ breast cancer cells. npj Breast Cancer. 2017;3(1):45. doi: 10.1038/s41523-017-0047-1.

44. Hogstad B, Berres M-L, Chakraborty R, Tang J, Bigenwald C, Serasinghe M, et al. RAF/MEK/extracellular signal–related kinase pathway suppresses dendritic cell migration and traps dendritic cells in Langerhans cell histiocytosis lesions. The Journal of Experimental Medicine. 2017.

45. Hellwege JN, Jeff JM, Wise LA, Gallagher CS, Wellons M, Hartmann KE, et al. A multi-stage genome-wide association study of uterine fibroids in African Americans. Human Genetics. 2017;136(10):1363-73. doi: 10.1007/s00439-017-1836-1. PubMed PMID: PMC5628188.

46. Haure-Mirande J-V, Audrain M, Fanutza T, Kim SH, Klein WL, Glabe C, et al. Deficiency of TYROBP, an adapter protein for TREM2 and CR3 receptors, is neuroprotective in a mouse model of early Alzheimer’s pathology. Acta Neuropathologica. 2017;134(5):769-88. doi: 10.1007/s00401-017-1737-3. PubMed PMID: PMC5645450.

47. Haro C, García‐Carpintero S, Rangel‐Zúñiga Oriol A, Alcalá‐Díaz Juan F, Landa Blanca B, Clemente José C, et al. Consumption of Two Healthy Dietary Patterns Restored Microbiota Dysbiosis in Obese Patients with Metabolic Dysfunction. Molecular Nutrition & Food Research. 2017;61(12):1700300. doi: 10.1002/mnfr.201700300.

48. Hamlin RE, Rahman A, Pak TR, Maringer K, Mena I, Bernal-Rubio D, et al. High-dimensional CyTOF analysis of dengue virus–infected human DCs reveals distinct viral signatures. JCI Insight. 2017;2(13):e92424. doi: 10.1172/jci.insight.92424. PubMed PMID: PMC5499363.

49. Graff M, Emery LS, Justice AE, Parra E, Below JE, Palmer ND, et al. Genetic architecture of lipid traits in the Hispanic community health study/study of Latinos. Lipids in Health and Disease. 2017;16:200. doi: 10.1186/s12944-017-0591-6. PubMed PMID: PMC5639746.

50. Gong J, Nishimura KK, Fernandez-Rhodes L, Haessler J, Bien S, Graff M, et al. Trans-ethnic analysis of metabochip data identifies two new loci associated with BMI. International Journal Of Obesity. 2017. doi: 10.1038/ijo.2017.304
https://www.nature.com/articles/ijo2017304 – supplementary-information.

51. Forst CV, Zhou B, Wang M, Chou T-W, Mason G, Song W-m, et al. Integrative gene network analysis identifies key signatures, intrinsic networks and host factors for influenza virus A infections. npj Systems Biology and Applications. 2017;3(1):35. doi: 10.1038/s41540-017-0036-x.

52. Fernández MV, Kim JH, Budde JP, Black K, Medvedeva A, Saef B, et al. Analysis of neurodegenerative Mendelian genes in clinically diagnosed Alzheimer Disease. PLOS Genetics. 2017;13(11):e1007045. doi: 10.1371/journal.pgen.1007045.

53. Dong L, Meng F, Wu L, Mitchell AV, Block CJ, Zhang B, et al. Cooperative oncogenic effect and cell signaling crosstalk of co-occurring HER2 and mutant PIK3CA in mammary epithelial cells. International Journal of Oncology. 2017;51(4):1320-30. doi: 10.3892/ijo.2017.4108. PubMed PMID: PMC5592866.

54. Degli Esposti D, Aushev VN, Lee E, Cros M-P, Zhu J, Herceg Z, et al. miR-500a-5p regulates oxidative stress response genes in breast cancer and predicts cancer survival. Scientific Reports. 2017;7(1):15966. doi: 10.1038/s41598-017-16226-3.

55. Dahl C, Stanislawski M, Iszatt N, Mandal S, Lozupone C, Clemente JC, et al. Gut microbiome of mothers delivering prematurely shows reduced diversity and lower relative abundance of Bifidobacterium and Streptococcus. PLOS ONE. 2017;12(10):e0184336. doi: 10.1371/journal.pone.0184336.

56. Cates HM, Heller EA, Lardner CK, Purushothaman I, Peña CJ, Walker DM, et al. Transcription Factor E2F3a in Nucleus Accumbens Affects Cocaine Action via Transcription and Alternative Splicing. Biological Psychiatry. 2017. doi: https://doi.org/10.1016/j.biopsych.2017.11.027.

57. Belbin GM, Odgis J, Sorokin EP, Yee M-C, Kohli S, Glicksberg BS, et al. Genetic identification of a common collagen disease in Puerto Ricans via identity-by-descent mapping in a health system. eLife. 2017;6:e25060. doi: 10.7554/eLife.25060. PubMed PMID: PMC5595434.

58. Watson C, Cohain A, Griffin R, Beckmann N, Grishin A, Haczynska H, et al. Analysis of Serial Peripheral Blood Transcriptomes from Peanut Allergic Children Undergoing Double-blind, Placebo-controlled Oral Food Challenges Reveals Key Drivers of the Acute Allergic Response to Peanut. Journal of Allergy and Clinical Immunology.139(2):AB189. doi: 10.1016/j.jaci.2016.12.615.

59. Nielsen JB, Fritsche LG, Zhou W, Teslovich TM, Holmen OL, Gustafsson S, et al. Genome-wide Study of Atrial Fibrillation Identifies Seven Risk Loci and Highlights Biological Pathways and Regulatory Elements Involved in Cardiac Development. The American Journal of Human Genetics.102(1):103-15. doi: 10.1016/j.ajhg.2017.12.003.

60. Fu J, Wang Z, Lee K, Wei C, Liu Z, Zhang M, et al. Transcriptomic analysis uncovers novel synergistic mechanisms in combination therapy for lupus nephritis. Kidney International.93(2):416-29. doi: 10.1016/j.kint.2017.08.031.

61. Fontanals-Cirera B, Hasson D, Vardabasso C, Di Micco R, Agrawal P, Chowdhury A, et al. Harnessing BET Inhibitor Sensitivity Reveals AMIGO2 as a Melanoma Survival Gene. Molecular Cell. 2017;68(4):731-44.e9. doi: https://doi.org/10.1016/j.molcel.2017.11.004.

62. Galatioto J, Caescu CI, Hansen J, Cook JR, Miramontes I, Iyengar R, et al. Cell Type-Specific Contributions of the Angiotensin II Type 1a Receptor to Aorta Homeostasis and Aneurysmal Disease-Brief Report. Arteriosclerosis, Thrombosis, and Vascular Biology. 2018;38(3):588.

63. Gilsbach R, Schwaderer M, Preissl S, Grüning BA, Kranzhöfer D, Schneider P, et al. Distinct epigenetic programs regulate cardiac myocyte development and disease in the human heart in vivo. Nature Communications. 2018;9(1):391. doi: 10.1038/s41467-017-02762-z.

64. Jin SC, Homsy J, Zaidi S, Lu Q, Morton S, DePalma SR, et al. Contribution of rare inherited and de novo variants in 2,871 congenital heart disease probands. Nature Genetics. 2017;49:1593. doi: 10.1038/ng.3970
https://www.nature.com/articles/ng.3970 – supplementary-information.

65. Keenan AB, Jenkins SL, Jagodnik KM, Koplev S, He E, Torre D, et al. The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations. Cell Systems. 2018;6(1):13-24. doi: https://doi.org/10.1016/j.cels.2017.11.001.

67. Manheimer KB, Richter F, Edelmann LJ, D’Souza SL, Shi L, Shen Y, et al. Robust identification of mosaic variants in congenital heart disease. Human Genetics. 2018;137(2):183-93. doi: 10.1007/s00439-018-1871-6.

68. Pandey G, Pandey OP, Rogers AJ, Hoffman GE, Raby BA, Weiss ST, et al. A Novel Nasal Brush-based Classifier of Asthma Identified by Machine Learning Analysis of Nasal RNA Sequence Data. bioRxiv. 2017.

69. Peña CJ, Kronman HG, Walker DM, Cates HM, Bagot RC, Purushothaman I, et al. Early life stress confers lifelong stress susceptibility in mice via ventral tegmental area OTX2. Science. 2017;356(6343):1185.

70. Xiong Y, Soumillon M, Wu J, Hansen J, Hu B, van Hasselt JGC, et al. A Comparison of mRNA Sequencing with Random Primed and 3′-Directed Libraries. Scientific Reports. 2017;7(1):14626. doi: 10.1038/s41598-017-14892-x.

71. Wei X, Calvo-Vidal MN, Chen S, Wu G, Revuelta MV, Sun J, Zhang J, Walsh MF, Nichols KE, Joseph V, Snyder C, Vachon CM, McKay JD, Wang S-P, Jayabalan DS, Jacobs LM, Becirovic D, Waller RG, Artomov M, Viale A, Patel J, Phillip JM, Chen-Kiang S, Curtin K, Salama M, Atanackovic D, Niesvizky R, Landgren O, Slager SL, Godley LA, Churpek J, Garber JE, Anderson KC, Daly MJ, Roeder RG, Dumontet C, Lynch HT, Mullighan CG, Camp NJ, Offit K, Klein RJ, Yu H, Cerchietti L, Lipkin SM. Germline mutations in lysine specific demethylase 1 (LSD1/KDM1A) confer susceptibility to multiple myeloma. Cancer Research. 2018. PubMed Central PMCID: PMC5955848; PMID: 29559475
DOI:10.1158/0008-5472.CAN-17-1900

72. Lim ET, Uddin M, De Rubeis S, Chan Y, Kamumbu AS, Zhang X, D’Gama AM, Kim SN, Hill RS, Goldberg AP, Poultney C, Minshew NJ, Kushima I, Aleksic B, Ozaki N, Parellada M, Arango C, Penzol MJ, Carracedo A, Kolevzon A, Hultman CM, Weiss LA, Fromer M, Chiocchetti AG, Freitag CM, Autism Sequencing C, Church GM, Scherer SW, Buxbaum JD, Walsh CA. Rates, distribution and implications of postzygotic mosaic mutations in autism spectrum disorder. Nature Neuroscience. 2017;20:1217. doi: 10.1038/nn.4598
https://http://www.nature.com/articles/nn.4598 – supplementary-information. PubMed Central PMCID: PMC5672813; PMID: 28714951

73. Ibi D, de la Fuente Revenga M, Kezunovic N, Muguruza C, Saunders JM, Gaitonde SA, Moreno JL, Ijaz MK, Santosh V, Kozlenkov A, Holloway T, Seto J, García-Bea A, Kurita M, Mosley GE, Jiang Y, Christoffel DJ, Callado LF, Russo SJ, Dracheva S, López-Giménez JF, Ge Y, Escalante CR, Meana JJ, Akbarian S, Huntley GW, González-Maeso J. Antipsychotic-induced Hdac2 transcription via NF-κB leads to synaptic and cognitive side effects. Nature Neuroscience. 2017;20:1247. doi: 10.1038/nn.4616
https://http://www.nature.com/articles/nn.4616 – supplementary-information. PubMed Central PMCID: PMC5675106; PMID: 28783139

1. - 07/2016-07/2017: 85 in total

Hauberg ME, Zhang W, Giambartolomei C, Franzén O, Morris DL, Vyse TJ, Ruusalepp A; CommonMind Consortium, Sklar P, Schadt EE, Björkegren JLM, Roussos P. Large-Scale Identification of Common Trait and Disease Variants Affecting Gene Expression. Am J Hum Genet. 2017 Jun 1;100(6):885-894. doi: 10.1016/j.ajhg.2017.04.016. Epub 2017 May 25. PubMed PMID: 28552197.

Fullard JF, Giambartolomei C, Hauberg ME, Xu K, Voloudakis G, Shao Z, Bare C, Dudley JT, Mattheisen M, Robakis NK, Haroutunian V, Roussos P. Open chromatin profiling of human postmortem brain infers functional roles for non-coding schizophrenia loci. Hum Mol Genet. 2017 May 15;26(10):1942-1951. doi: 10.1093/hmg/ddx103. PubMed PMID: 28335009.

Carcamo-Orive I, Hoffman GE, Cundiff P, Beckmann ND, D’Souza SL, Knowles JW, Patel A, Papatsenko D, Abbasi F, Reaven GM, Whalen S, Lee P, Shahbazi M, Henrion MY, Zhu K, Wang S, Roussos P, Schadt EE, Pandey G, Chang R, Quertermous T, Lemischka I. Analysis of Transcriptional Variability in a Large Human iPSC Library Reveals Genetic and Non-genetic Determinants of Heterogeneity. Cell Stem Cell. 2017 Apr 6;20(4):518-532.e9. doi: 10.1016/j.stem.2016.11.005. Epub 2016 Dec 22. PubMed PMID: 28017796; PubMed Central PMCID: PMC5384872.

Egervari G, Landry J, Callens J, Fullard JF, Roussos P, Keller E, Hurd YL. Striatal H3K27 Acetylation Linked to Glutamatergic Gene Dysregulation in Human Heroin Abusers Holds Promise as Therapeutic Target. Biol Psychiatry. 2017 Apr 1;81(7):585-594. doi: 10.1016/j.biopsych.2016.09.015. Epub 2016 Sep 28. PubMed PMID: 27863698; PubMed Central PMCID: PMC5346335.

Roussos P, Guennewig B, Kaczorowski DC, Barry G, Brennand KJ. Activity-Dependent Changes in Gene Expression in Schizophrenia Human-Induced Pluripotent Stem Cell Neurons. JAMA Psychiatry. 2016 Nov 1;73(11):1180-1188. doi: 10.1001/jamapsychiatry.2016.2575. PubMed PMID: 27732689; PubMed Central PMCID: PMC5437975.

Wang M, Roussos P, McKenzie A, Zhou X, Kajiwara Y, Brennand KJ, De Luca GC, Crary JF, Casaccia P, Buxbaum JD, Ehrlich M, Gandy S, Goate A, Katsel P, Schadt E, Haroutunian V, Zhang B. Integrative network analysis of nineteen brain regions identifies molecular signatures and networks underlying selective regional vulnerability to Alzheimer’s disease. Genome Med. 2016 Nov 1;8(1):104. PubMed PMID: 27799057; PubMed Central PMCID: PMC5088659.

Franzén O, Ermel R, Cohain A, Akers NK, Di Narzo A, Talukdar HA, Foroughi-Asl H, Giambartolomei C, Fullard JF, Sukhavasi K, Köks S, Gan LM, Giannarelli C, Kovacic JC, Betsholtz C, Losic B, Michoel T, Hao K, Roussos P, Skogsberg J, Ruusalepp A, Schadt EE, Björkegren JL. Cardiometabolic risk loci share downstream cis- and trans-gene regulation across tissues and diseases. Science. 2016 Aug 19;353(6301):827-30. doi: 10.1126/science.aad6970. PubMed PMID: 27540175.

Rialdi A, Hultquist J, Jimenez-Morales D, Peralta Z, Campisi L, Fenouil R, Moshkina N, Wang ZZ, Laffleur B, Kaake RM, McGregor MJ, Haas K, Pefanis E, Albrecht RA, Pache L, Chanda S, Jen J, Ochando J, Byun M, Basu U, García-Sastre A, Krogan N, van Bakel H, Marazzi I. The RNA Exosome Syncs IAV-RNAPII Transcription to Promote Viral Ribogenesis and Infectivity. Cell. 2017 May 4;169(4):679-692.e14. PMID:28475896; DOI: 10.1016/j.cell.2017.04.021

Crowley, R.S., Riley, A.P., Sherwood, A.M., Groer, C.E., Shivaperumal, N., Biscaia, M., Paton, K., Schneider, S., Provasi, D., Kivell, B.M., Filizola, M., and Prisinzano, T.E. “Synthetic Studies of Neoclerodane Diterpenes from Salvia divinorum: Identification of a Potent and Centrally Acting μ Opioid Analgesic with Reduced Abuse Liability” Journal of Medicinal Chemistry, 59(24):11027-11038 [PMID:27958743]

Marino, K., Prada-Gracia, D., Provasi, D., Filizola, M. “Impact of Lipid Composition and Receptor Conformation on the Spatio-Temporal Organization of mu-Opioid Receptors in a Multi-component Plasma Membrane Model” (2016) PLOS Computational Biology 12(12):e1005240 [PMID: 27959924].

Schneider, S., Provasi, D., Filizola, M. “How Oliceridine (TRV-130) Binds and Stabilizes a μ-Opioid Receptor Conformational State that Selectively Triggers G Protein-Signaling Pathways.” (2016) Biochemistry 55(46):6456-6466 [PMID: 27778501]

Li Y, Lucas-Osma AM, Black S, Bandet MV, Stephens MJ, Vavrek R, Sanelli L, Fenrich KK, Di Narzo AF, Dracheva S, Winship IR, Fouad K, Bennett DJ. Pericytes impair capillary blood flow and motor function after chronic spinal cord injury. Nat Med. 2017 May 1. doi: 10.1038/nm.4331. [Epub ahead of print] PubMed PMID: 28459438.

Kozlenkov A, Jaffe AE, Timashpolsky A, Apontes P, Rudchenko S, Barbu M, Byne W, Hurd YL, Horvath S, Dracheva S. DNA Methylation Profiling of Human Prefrontal Cortex Neurons in Heroin Users Shows Significant Difference between Genomic Contexts of Hyper- and Hypomethylation and a Younger Epigenetic Age. Genes (Basel). 2017 May 30;8(6). pii: E152. doi: 10.3390/genes8060152. PubMed PMID: 28556790.

Miller ML, Ren Y, Szutorisz H, Warren NA, Tessereau C, Egervari G, Mlodnicka A, Kapoor M, Chaarani B, Morris CV, Schumann G, Garavan H, Goate AM, Bannon MJ; IMAGEN Consortium, Halperin JM, Hurd YL. Ventral striatal regulation of CREM mediates impulsive action and drug addiction vulnerability. Mol Psychiatry. 2017 Apr 25. doi: 10.1038/mp.2017.80. [Epub ahead of print] PMID: 28439100

Deming Y, Li Z, Kapoor M, Harari O, Del-Aguila JL, Black K, Carrell D, Cai Y, Fernandez MV, Budde J, Ma S, Saef B, Howells B, Huang KL, Bertelsen S, Fagan AM, Holtzman DM, Morris JC, Kim S, Saykin AJ, De Jager PL, Albert M, Moghekar A, O’Brien R, Riemenschneider M, Petersen RC, Blennow K, Zetterberg H, Minthon L, Van Deerlin VM, Lee VM, Shaw LM, Trojanowski JQ, Schellenberg G, Haines JL, Mayeux R, Pericak-Vance MA, Farrer LA, Peskind ER, Li G, Di Narzo AF; Alzheimer’s Disease Neuroimaging Initiative (ADNI); Alzheimer Disease Genetic Consortium (ADGC), Kauwe JS, Goate AM, Cruchaga C. Genome-wide association study identifies four novel loci associated with Alzheimer’s endophenotypes and disease modifiers. Acta Neuropathol. 2017 May;133(5):839-856. doi: 10.1007/s00401-017-1685-y. Epub 2017 Feb 28. PMID: 28247064

Tosto G, Bird TD, Tsuang D, Bennett DA, Boeve BF, Cruchaga C, Faber K, Foroud TM, Farlow M, Goate AM, Bertlesen S, Graff-Radford NR, Medrano M, Lantigua R, Manly J, Ottman R, Rosenberg R, Schaid DJ, Schupf N, Stern Y, Sweet RA, Mayeux R. Polygenic risk scores in familial Alzheimer disease. Neurology. 2017 Mar 21;88(12):1180-1186. doi: 10.1212/WNL.0000000000003734. Epub 2017 Feb 17. PMID: 28213371

Meyers JL, Zhang J, Wang JC, Su J, Kuo SI, Kapoor M, Wetherill L, Bertelsen S, Lai D, Salvatore JE, Kamarajan C, Chorlian D, Agrawal A, Almasy L, Bauer L, Bucholz KK, Chan G, Hesselbrock V, Koganti L, Kramer J, Kuperman S, Manz N, Pandey A, Seay M, Scott D, Taylor RE, Dick DM, Edenberg HJ, Goate A, Foroud T, Porjesz B. An endophenotype approach to the genetics of alcohol dependence: a genome wide association study of fast beta EEG in families of African ancestry. Mol Psychiatry. 2017 Jan 10. doi: 10.1038/mp.2016.239. [Epub ahead of print] PMID: 28070124

Meyers JL, Zhang J, Manz N, Rangaswamy M, Kamarajan C, Wetherill L, Chorlian DB, Kang SJ, Bauer L, Hesselbrock V, Kramer J, Kuperman S, Nurnberger JI Jr, Tischfield J, Wang JC, Edenberg HJ, Goate A, Foroud T, Porjesz B. A genome wide association study of fast beta EEG in families of European ancestry. Int J Psychophysiol. 2017 May;115:74-85. doi: 10.1016/j.ijpsycho.2016.12.008. Epub 2016 Dec 28. PMID: 28040410

Monsell SE, Mock C, Fardo DW, Bertelsen S, Cairns NJ, Roe CM, Ellingson SR, Morris JC, Goate AM, Kukull WA. ] Genetic Comparison of Symptomatic and Asymptomatic Persons With Alzheimer Disease Neuropathology. Ventral striatal regulation of CREM mediates impulsive action and drug addiction vulnerability. Alzheimer Dis Assoc Disord. 2016 Nov 15. [Epub ahead of print PMID: 27849641

Tosto G, Bird TD, Bennett DA, Boeve BF, Brickman AM, Cruchaga C, Faber K, Foroud TM, Farlow M, Goate AM, Graff-Radford NR, Lantigua R, Manly J, Ottman R, Rosenberg R, Schaid DJ, Schupf N, Stern Y, Sweet RA, Mayeux R; National Institute on Aging Late-Onset Alzheimer Disease/National Cell Repository for Alzheimer Disease (NIA-LOAD/NCRAD) Family Study Group. The Role of Cardiovascular Risk Factors and Stroke in Familial Alzheimer Disease. JAMA Neurol. 2016 Oct 1;73(10):1231-1237. doi: 10.1001/jamaneurol.2016.2539. PMID: 27533593

Integrative Network Analysis Identifies Novel Drivers of Pathogenesis and Progression in Newly Diagnosed Multiple Myeloma.” Lagana A, Perumal D, Melnekoff D, Readhead B, Kidd B, Leshchenko V, Kuo PY, Keats J, DeRome M, Yesil J, Auclair D, Lonial S, Chari A, Cho HJ, Barlogie B, Jagannath S, Dudley J, Parekh S.Leukemia, Leukemia. 2017 Jun 23. doi: 10.1038/leu.2017.197. PMID: 2864259

Hammerstad SS, Stefan M, Blackard J, Owen RP, Lee HJ, Concepcion E, Yi Z, Zhang W, Tomer Y. HEPATITIS C VIRUS E2 PROTEIN INDUCES UPREGULATION OF IL-8 PATHWAYS AND PRODUCTION OF HEAT SHOCK PROTEINS IN HUMAN THYROID CELLS. J Clin Endocrinol Metab. 2016 Nov 18:jc20163403. [Epub ahead of print] PubMed PMID: 27860532.

Di Cecilia S, Zhang F, Sancho-Medina A, Li S, Aguilo F, Sun Y, Rengasamy M, Zhang W, Del Vecchio L, Salvatore F, Walsh MJ. RBM-AS1 is critical for self-renewal of colon cancer stem-like cells. Cancer Res. 2016 Aug 12. pii: canres.1824.2015. [Epub ahead of print] PMID:27520449; PMCID:PMC5050123; DOI:10.1158/0008-5472.CAN-15-1824

Bardot E, Calderon D, Santoriello F, Han S, Cheung K, Jadhav B, Burtscher I, Artap S, Jain R, Epstein J, Lickert H, Gouon-Evans V, Sharp AJ, Dubois NC. Foxa2 identifies a cardiac progenitor population with ventricular differentiation potential. Nat Commun. 2017 Feb 14;8:14428. PMID:28195173; PMCID:PMC5316866; DOI:10.1038/ncomms14428

Peter CJ, Fischer LK, Kundakovic M, Garg P, Jakovcevski M, Dincer A, Amaral AC, Ginns EI, Galdzicka M, Bryce CP, Ratner C, Waber DP, Mokler D, Medford G, Champagne FA, Rosene DL, McGaughy JA, Sharp AJ, Galler JR, Akbarian S. DNA Methylation Signatures of Early Childhood Malnutrition Associated With Impairments in Attention and Cognition. Biol Psychiatry. 2016 Nov 15;80(10):765-774.
PMID: 27184921; PMCID:PMC5036982[Available on 2017-11-15]; DOI:10.1016/j.biopsych.2016.03.2100

Joshi RS, Garg P, Zaitlen N, Lappalainen T, Watson CT, Azam N, Ho D, Li X, Antonarakis SE, Brunner HG, Buiting K, Cheung SW, Coffee B, Eggermann T, Francis D, Geraedts JP, Gimelli G, Jacobson SG, Le Caignec C, de Leeuw N, Liehr T, Mackay DJ, Montgomery SB, Pagnamenta AT, Papenhausen P, Robinson DO, Ruivenkamp C, Schwartz C, Steiner B, Stevenson DA, Surti U, Wassink T, Sharp AJ. DNA Methylation Profiling of Uniparental Disomy Subjects Provides a Map of Parental Epigenetic Bias in the Human Genome. Am J Hum Genet. 2016 Sep 1;99(3):555-66. PMID:27569549; PMCID: PMC5011056 [Available on 2017-03-01]; DOI: 10.1016/j.ajhg.2016.06.032

Graff M, Scott RA, Justice AE, Young KL, Feitosa MF, Barata L, Winkler TW, Chu AY, Mahajan A, Hadley D, Xue L, Workalemahu T, Heard-Costa NL, den Hoed M, Ahluwalia TS, Qi Q, Ngwa JS, Renström F, Quaye L, Eicher JD, Hayes JE, Cornelis M, Kutalik Z, Lim E, Luan J, Huffman JE, Zhang W, Zhao W, Griffin PJ, Haller T, Ahmad S, Marques-Vidal PM, Bien S, Yengo L, Teumer A, Smith AV, Kumari M, Harder MN, Justesen JM, Kleber ME, Hollensted M, Lohman K, Rivera NV, Whitfield JB, Zhao JH, Stringham HM, Lyytikäinen LP, Huppertz C, Willemsen G, Peyrot WJ, Wu Y, Kristiansson K, Demirkan A, Fornage M, Hassinen M, Bielak LF, Cadby G, Tanaka T, Mägi R, van der Most PJ, Jackson AU, Bragg-Gresham JL, Vitart V, Marten J, Navarro P, Bellis C, Pasko D, Johansson Å, Snitker S, Cheng YC, Eriksson J, Lim U, Aadahl M, Adair LS, Amin N, Balkau B, Auvinen J, Beilby J, Bergman RN, Bergmann S, Bertoni AG, Blangero J, Bonnefond A, Bonnycastle LL, Borja JB, Brage S, Busonero F, Buyske S, Campbell H, Chines PS, Collins FS, Corre T, Smith GD, Delgado GE, Dueker N, Dörr M, Ebeling T, Eiriksdottir G, Esko T, Faul JD, Fu M, Færch K, Gieger C, Gläser S, Gong J, Gordon-Larsen P, Grallert H, Grammer TB, Grarup N, van Grootheest G, Harald K, Hastie ND, Havulinna AS, Hernandez D, Hindorff L, Hocking LJ, Holmens OL, Holzapfel C, Hottenga JJ, Huang J, Huang T, Hui J, Huth C, Hutri-Kähönen N, James AL, Jansson JO, Jhun MA, Juonala M, Kinnunen L, Koistinen HA, Kolcic I, Komulainen P, Kuusisto J, Kvaløy K, Kähönen M, Lakka TA, Launer LJ, Lehne B, Lindgren CM, Lorentzon M, Luben R, Marre M, Milaneschi Y, Monda KL, Montgomery GW, De Moor MHM, Mulas A, Müller-Nurasyid M, Musk AW, Männikkö R, Männistö S, Narisu N, Nauck M, Nettleton JA, Nolte IM, Oldehinkel AJ, Olden M, Ong KK, Padmanabhan S, Paternoster L, Perez J, Perola M, Peters A, Peters U, Peyser PA, Prokopenko I, Puolijoki H, Raitakari OT, Rankinen T, Rasmussen-Torvik LJ, Rawal R, Ridker PM, Rose LM, Rudan I, Sarti C, Sarzynski MA, Savonen K, Scott WR, Sanna S, Shuldiner AR, Sidney S, Silbernagel G, Smith BH, Smith JA, Snieder H, Stančáková A, Sternfeld B, Swift AJ, Tammelin T, Tan ST, Thorand B, Thuillier D, Vandenput L, Vestergaard H, van Vliet-Ostaptchouk JV, Vohl MC, Völker U, Waeber G, Walker M, Wild S, Wong A, Wright AF, Zillikens MC, Zubair N, Haiman CA, Lemarchand L, Gyllensten U, Ohlsson C, Hofman A, Rivadeneira F, Uitterlinden AG, Pérusse L, Wilson JF, Hayward C, Polasek O, Cucca F, Hveem K, Hartman CA, Tönjes A, Bandinelli S, Palmer LJ, Kardia SLR, Rauramaa R, Sørensen TIA, Tuomilehto J, Salomaa V, Penninx BWJH, de Geus EJC, Boomsma DI, Lehtimäki T, Mangino M, Laakso M, Bouchard C, Martin NG, Kuh D, Liu Y, Linneberg A, März W, Strauch K, Kivimäki M, Harris TB, Gudnason V, Völzke H, Qi L, Järvelin MR, Chambers JC, Kooner JS, Froguel P, Kooperberg C, Vollenweider P, Hallmans G, Hansen T, Pedersen O, Metspalu A, Wareham NJ, Langenberg C, Weir DR, Porteous DJ, Boerwinkle E, Chasman DI; CHARGE Consortium; EPIC-InterAct Consortium; PAGE Consortium, Abecasis GR, Barroso I, McCarthy MI, Frayling TM, O’Connell JR, van Duijn CM, Boehnke M, Heid IM, Mohlke KL, Strachan DP, Fox CS, Liu CT, Hirschhorn JN, Klein RJ, Johnson AD, Borecki IB, Franks PW, North KE, Cupples LA, Loos RJF, Kilpeläinen TO. Genome-wide physical activity interactions in adiposity – A meta-analysis of 200,452 adults. PLoS Genet. 2017 Apr 27;13(4):e1006528. doi: 10.1371/journal.pgen.1006528. eCollection 2017 Apr. PubMed PMID: 28448500; PubMed Central PMCID: PMC5407576.

Hoffmann TJ, Passarelli MN, Graff RE, Emami NC, Sakoda LC, Jorgenson E, Habel LA, Shan J, Ranatunga DK, Quesenberry CP, Chao CR, Ghai NR, Aaronson D, Presti J, Nordström T, Wang Z, Berndt SI, Chanock SJ, Mosley JD, Klein RJ, Middha M, Lilja H, Melander O, Kvale MN, Kwok PY, Schaefer C, Risch N, Van Den Eeden SK, Witte JS. Genome-wide association study of prostate-specific antigen levels identifies novel loci independent of prostate cancer. Nat Commun. 2017 Jan 31;8:14248. doi: 10.1038/ncomms14248. PubMed PMID: 28139693; PubMed Central PMCID: PMC5290311.

van Rooij FJ, Qayyum R, Smith AV, Zhou Y, Trompet S, Tanaka T, Keller MF, Chang LC, Schmidt H, Yang ML, Chen MH, Hayes J, Johnson AD, Yanek LR, Mueller C, Lange L, Floyd JS, Ghanbari M, Zonderman AB, Jukema JW, Hofman A, van Duijn CM, Desch KC, Saba Y, Ozel AB, Snively BM, Wu JY, Schmidt R, Fornage M, Klein RJ, Fox CS, Matsuda K, Kamatani N, Wild PS, Stott DJ, Ford I, Slagboom PE, Yang J, Chu AY, Lambert AJ, Uitterlinden AG, Franco OH, Hofer E, Ginsburg D, Hu B, Keating B, Schick UM, Brody JA, Li JZ, Chen Z, Zeller T, Guralnik JM, Chasman DI, Peters LL, Kubo M, Becker DM, Li J, Eiriksdottir G, Rotter JI, Levy D, Grossmann V, Patel KV, Chen CH; BioBank Japan Project, Ridker PM, Tang H, Launer LJ, Rice KM, Li-Gao R, Ferrucci L, Evans MK, Choudhuri A, Trompouki E, Abraham BJ, Yang S, Takahashi A, Kamatani Y, Kooperberg C, Harris TB, Jee SH, Coresh J, Tsai FJ, Longo DL, Chen YT, Felix JF, Yang Q, Psaty BM, Boerwinkle E, Becker LC, Mook-Kanamori DO, Wilson JG, Gudnason V, O’Donnell CJ, Dehghan A, Cupples LA, Nalls MA, Morris AP, Okada Y, Reiner AP, Zon LI, Ganesh SK. Genome-wide Trans-ethnic Meta-analysis Identifies Seven Genetic Loci Influencing Erythrocyte Traits and a Role for RBPMS in Erythropoiesis. Am J Hum Genet. 2017 Jan 5;100(1):51-63. doi: 10.1016/j.ajhg.2016.11.016. Epub 2016 Dec 22. PubMed PMID: 28017375; PubMed Central PMCID: PMC5223059.

Douvaras P, Sun B, Wang M, Kruglikov I, Lallos G, Zimmer M, Terrenoire C, Zhang B, Gandy S, Schadt E, Freytes DO, Noggle S, Fossati V. Directed Differentiation of Human Pluripotent Stem Cells to Microglia. Stem Cell Reports. 2017 May 18. pii: S2213-6711(17) 30177-7. doi: 10.1016/j.stemcr.2017.04.023. [Epub ahead of print] PMID: 28528700; PMCID:PMC5470097; DOI:10.1016/j.stemcr.2017.04.023

Shigeki Nakagawa1, Lan Wei, Won Min Song, Takaaki Higashi, Sarani Ghoshal, Rosa S. Kim, C. Billie Bian, Suguru Yamada, Xiaochen Sun, Anu Venkatesh, Nicolas Goossens, Gretchen Bain, Gregory Y. Lauwers, Anna P. Koh, Mohamed El-Abtah1, Noor B. Ahmad, Hiroki Hoshida, Derek J. Erstad, Ganesh Gunasekaran, Youngmin Lee, Ming-Lung Yu, Wan-Long Chuang, Chia-Yen Dai, Masahiro Kobayashi, Hiromitsu Kumada, Toru Beppu, Hideo Baba, Milind Mahajan, Venugopalan D. Nair, Michael Lanuti1, Augusto Villanueva, Angelo Sangiovanni, Massimo Iavarone, Massimo Colombo, Josep M. Llovet, Aravind Subramanian, Andrew M. Tager, Scott L. Friedman, Thomas F. Baumert, Myron E. Schwarz, Raymond T. Chung, Kenneth K. Tanabe, Bin Zhang, Bryan C. Fuchs, Yujin Hoshida. (2016) Molecular liver cancer prevention in cirrhosis by organ transcriptome analysis and lysophosphatidic acid pathway inhibition. Cancer Cell 30 (6). PMID: 27960085; PMCID:PMC5161110 [Available on 2017-12-12];DOI:10.1016/j.ccell.2016.11.004

Andrew T. McKenzie, Igor Katsyv, Won-Min Song, Minghui Wang, and Bin Zhang§. (2016) DGCA: A Comprehensive R Package for Differential Gene Correlation Analysis. BMC Systems Biology 10:106. PMID: 27846853; PMCID: PMC5111277; DOI:10.1186/s12918-016-0349-1

Hectors SJ, Wagner M, Bane O, Besa C, Lewis S, Remark R, Chen N, Fiel MI, Zhu H, Gnjatic S, Merad M, Hoshida Y, Taouli B. Quantification of hepatocellular carcinoma heterogeneity with multiparametric magnetic resonance imaging. Sci Rep. 2017 May 26;7(1):2452. doi: 10.1038/s41598-017-02706-z. PubMed PMID: 28550313; PubMed Central PMCID: PMC5446396.

Taouli B, Hoshida Y, Kakite S, Chen X, Tan PS, Sun X, Kihira S, Kojima K, Toffanin S, Fiel MI, Hirschfield H, Wagner M, Llovet JM. Imaging-based surrogate markers of transcriptome subclasses and signatures in hepatocellular carcinoma: preliminary results. Eur Radiol. 2017 Apr 24. doi: 10.1007/s00330-017-4844-6. [Epub ahead of print] PubMed PMID: 28439654.

Ono A, Goossens N, Finn RS, Schmidt WN, Thung SN, Im GY, Hoshida Y. Persisting risk of hepatocellular carcinoma after HCV cure monitored by a liver transcriptome signature. Hepatology. 2017 Apr 8. doi: 10.1002/hep.29203. [Epub ahead of print] PubMed PMID: 28390144.

Hicks DF, Goossens N, Blas-García A, Tsuchida T, Wooden B, Wallace MC, Nieto N, Lade A, Redhead B, Cederbaum AI, Dudley JT, Fuchs BC, Lee YA, Hoshida Y, Friedman SL. Transcriptome-based repurposing of apigenin as a potential anti-fibrotic agent targeting hepatic stellate cells. Sci Rep. 2017 Mar 3;7:42563. doi: 10.1038/srep42563. PubMed PMID: 28256512; PubMed Central PMCID: PMC5335661.

Van Renne N, Roca Suarez AA, Duong FH, Gondeau C, Calabrese D, Fontaine N, Ababsa A, Bandiera S, Croonenborghs T, Pochet N, De Blasi V, Pessaux P, Piardi T, Sommacale D, Ono A, Chayama K, Fujita M, Nakagawa H, Hoshida Y, Zeisel MB, Heim MH, Baumert TF, Lupberger J. miR-135a-5p-mediated downregulation of protein tyrosine phosphatase receptor delta is a candidate driver of HCV-associated hepatocarcinogenesis. Gut. 2017 Feb 3. pii: gutjnl-2016-312270. doi:10.1136/gutjnl-2016-312270. [Epub ahead of print] PubMed PMID: 28159835.

Kim RS, Hasegawa D, Goossens N, Tsuchida T, Athwal V, Sun X, Robinson CL, Bhattacharya D, Chou HI, Zhang DY, Fuchs BC, Lee Y, Hoshida Y, Friedman SL. The XBP1 Arm of the Unfolded Protein Response Induces Fibrogenic Activity in Hepatic Stellate Cells Through Autophagy. Sci Rep. 2016 Dec 20;6:39342. doi:10.1038/srep39342. PubMed PMID: 27996033; PubMed Central PMCID: PMC5172197.

Bollard J, Miguela V, Ruiz de Galarreta M, Venkatesh A, Bian CB, Roberto MP, Tovar V, Sia D, Molina-Sánchez P, Nguyen CB, Nakagawa S, Llovet JM, Hoshida Y, Lujambio A. Palbociclib (PD-0332991), a selective CDK4/6 inhibitor, restricts tumour growth in preclinical models of hepatocellular carcinoma. Gut. 2017 Jul;66(7):1286-1296. doi: 10.1136/gutjnl-2016-312268. Epub 2016 Nov 14. PubMed PMID: 27849562.

Lu H, Rogowskyj J, Yu W, Venkatesh A, Khan N, Nakagawa S, Goossens N, Koh AP, Higashi T, Gunasekaran G, Schwarz ME, Hiotis SP, Xu X, Kinney W, Hoshida Y, Block T, Cuconati A, Du Y. Novel substituted aminothiazoles as potent and selective anti-hepatocellular carcinoma agents. Bioorg Med Chem Lett. 2016 Dec1;26(23):5819-5824. doi:10.1016/j.bmcl.2016.10.015. Epub 2016 Oct 10. PubMed PMID: 27793566.

Verrier ER, Colpitts CC, Bach C, Heydmann L, Zona L, Xiao F, Thumann C, Crouchet E, Gaudin R, Sureau C, Cosset FL, McKeating JA, Pessaux P, Hoshida Y, Schuster C, Zeisel MB, Baumert TF. Solute Carrier NTCP Regulates Innate Antiviral Immune Responses Targeting Hepatitis C Virus Infection of Hepatocytes. Cell Rep. 2016 Oct 25;17(5):1357-1368. doi: 10.1016/j.celrep.2016.09.084. PubMed PMID: 27783949; PubMed Central PMCID: PMC5098118.

Goossens N, Hoshida Y, Song WM, Jung M, Morel P, Nakagawa S, Zhang B, Frossard JL, Spahr L, Friedman SL, Negro F, Rubbia-Brandt L, Giostra E. Nonalcoholic Steatohepatitis Is Associated With Increased Mortality in Obese Patients Undergoing Bariatric Surgery. Clin Gastroenterol Hepatol. 2016 Nov;14(11):1619-1628. doi: 10.1016/j.cgh.2015.10.010. Epub 2015 Oct 20. PubMed PMID: 26492845; PubMed Central PMCID: PMC4838546.

Zhang C, Hoshida Y, Sadler KC. Comparative Epigenomic Profiling of the DNA Methylome in Mouse and Zebrafish Uncovers High Interspecies Divergence. Front Genet. 2016 Jun 17;7:110. doi: 10.3389/fgene.2016.00110. eCollection 2016. PubMed PMID: 27379160; PubMed Central PMCID: PMC4911366.

Asgharpour A, Cazanave SC, Pacana T, Seneshaw M, Vincent R, Banini BA, Kumar DP, Daita K, Min HK, Mirshahi F, Bedossa P, Sun X, Hoshida Y, Koduru SV, Contaifer D Jr, Warncke UO, Wijesinghe DS, Sanyal AJ. A diet-induced animal model of non-alcoholic fatty liver disease and hepatocellular cancer. J Hepatol. 2016 Sep;65(3):579-88. doi: 10.1016/j.jhep.2016.05.005. Epub 2016 May 31. PubMed PMID: 27261415; PubMed Central PMCID: PMC5012902.

Jiao J, Ooka K, Fey H, Fiel MI, Rahmman AH, Kojima K, Hoshida Y, Chen X, de Paula T, Vetter D, Sastre D, Lee KH, Lee YA, Bansal M, Friedman SL, Merad M, Aloman C. Interleukin-15 receptor α on hepatic stellate cells regulates hepatic fibrogenesis in mice. J Hepatol. 2016 Aug;65(2):344-53. doi: 10.1016/j.jhep.2016.04.020. Epub 2016 May 3. PubMed PMID: 27154062; PubMed Central PMCID: PMC5048472.

Zhang DY, Goossens N, Guo J, Tsai MC, Chou HI, Altunkaynak C, Sangiovanni A, Iavarone M, Colombo M, Kobayashi M, Kumada H, Villanueva A, Llovet JM, Hoshida Y, Friedman SL. A hepatic stellate cell gene expression signature associated with outcomes in hepatitis C cirrhosis and hepatocellular carcinoma after curative resection. Gut. 2016 Oct;65(10):1754-64. doi: 10.1136/gutjnl-2015-309655. Epub 2015 Jun 4. PubMed PMID: 26045137; PubMed Central PMCID: PMC4848165.

Kenny T, Schmidt H, Adelson K, Hoshida Y, Koh AP, Shah N, Mandeli JP, Ting J, Germain D. Patient-derived interstitial fluids and predisposition to aggressive sporadic breast cancer through collagen remodeling and inactivation of p53. Clin Cancer Res. 2017 Jun 19. pii: clincanres.0342.2017. doi: 10.1158/1078-0432.CCR-17-0342. [Epub ahead of print] PMID: 28630214

Goossens N, Singal AG, King LY, Andersson KL, Fuchs BC, Besa C, Taouli B, Chung RT, Hoshida Y. Cost-effectiveness of risk score-stratified hepatocellular carcinoma screening in patients with cirrhosis. Clin Transl Gastroenterol. 2017 PMID: 28640287; DOI: 10.1038/ctg.2017.26

Robert A Scott, Laura J Scott, Reedik Mägi, Letizia Marullo, Kyle J Gaulton, Marika Kaakinen, Natalia Pervjakova, Tune H Pers, Andrew D Johnson, John D Eicher, Anne U Jackson, Teresa Ferreira, Yeji Lee, Clement Ma, Valgerdur Steinthorsdottir, Gudmar Thorleifsson, Lu Qi, Natalie R Van Zuydam, Anubha Mahajan, Han Chen, Peter Almgren, Ben F Voight, Harald Grallert, Martina Müller-Nurasyid, Janina S Ried, William N Rayner, Neil Robertson, Lennart C Karssen, Elisabeth M van Leeuwen, Sara M Willems, Christian Fuchsberger, Phoenix Kwan, Tanya M Teslovich, Pritam Chanda, Man Li, Yingchang Lu, Christian Dina, Dorothee Thuillier, Loic Yengo, Longda Jiang, Thomas Sparso, Hans A Kestler, Himanshu Chheda, Lewin Eisele, Stefan Gustafsson, Mattias Frånberg, Rona J Strawbridge, Rafn Benediktsson, Astradur B Hreidarsson, Augustine Kong, Gunnar Sigurðsson, Nicola D Kerrison, Jian’an Luan, Liming Liang, Thomas Meitinger, Michael Roden, Barbara Thorand, Tõnu Esko, Evelin Mihailov, Caroline Fox, Ching-Ti Liu, Denis Rybin, Bo Isomaa, Valeriya Lyssenko, Tiinamaija Tuomi, David J Couper, James S Pankow, Niels Grarup, Christian T Have, Marit E Jørgensen, Torben Jørgensen, Allan Linneberg, Marilyn C Cornelis, Rob M van Dam, David J Hunter, Peter Kraft, Qi Sun, Sarah Edkins, Katharine R Owen, John RB Perry, Andrew R Wood, Eleftheria Zeggini, Juan Tajes-Fernandes, Goncalo R Abecasis, Lori L Bonnycastle, Peter S Chines, Heather M Stringham, Heikki A Koistinen, Leena Kinnunen, Bengt Sennblad, Thomas W Mühleisen, Markus M Nöthen, Sonali Pechlivanis, Damiano Baldassarre, Karl Gertow, Steve E Humphries, Elena Tremoli, Norman Klopp, Julia Meyer, Gerald Steinbach, Roman Wennauer, Johan G Eriksson, Satu Mӓnnistö, Leena Peltonen, Emmi Tikkanen, Guillaume Charpentier, Elodie Eury, Stéphane Lobbens, Bruna Gigante, Karin Leander, Olga McLeod, Erwin P Bottinger, Omri Gottesman, Douglas Ruderfer, Matthias Blüher, Peter Kovacs, Anke Tonjes, Nisa M Maruthur, Chiara Scapoli, Raimund Erbel, Karl-Heinz Jöckel, Susanne Moebus, Ulf de Faire, Anders Hamsten, Michael Stumvoll, Panagiotis Deloukas, Peter J Donnelly, Timothy M Frayling, Andrew T Hattersley, Samuli Ripatti, Veikko Salomaa, Nancy L Pedersen, Bernhard O Boehm, Richard N Bergman, Francis S Collins, Karen L Mohlke, Jaakko Tuomilehto, Torben Hansen, Oluf Pedersen, Inês Barroso, Lars Lannfelt, Erik Ingelsson, Lars Lind, Cecilia M Lindgren, Stephane Cauchi, Philippe Froguel, Ruth JF Loos, Beverley Balkau, Heiner Boeing, Paul W Franks. An Expanded Genome-Wide Association Study of Type 2 Diabetes in Europeans. Diabetes. 2017 May 31. pii: db161253. doi: 10.2337/db16-1253. PMID: 28566273

Mathias Gorski, Peter J Van Der Most, Alexander Teumer, Audrey Y Chu, Man Li, Vladan Mijatovic, Ilja M Nolte, Massimiliano Cocca, Daniel Taliun, Felicia Gomez, Yong Li, Bamidele Tayo, Adrienne Tin, Mary F Feitosa, Thor Aspelund, John Attia, Reiner Biffar, Murielle Bochud, Eric Boerwinkle, Ingrid Borecki, Erwin P Bottinger, Ming-Huei Chen, Vincent Chouraki, Marina Ciullo, Josef Coresh, Marilyn C Cornelis, Gary C Curhan, Adamo Pio d’Adamo, Abbas Dehghan, Laura Dengler, Jingzhong Ding, Gudny Eiriksdottir, Karlhans Endlich, Stefan Enroth, Tõnu Esko, Oscar H Franco, Paolo Gasparini, Christian Gieger, Giorgia Girotto, Omri Gottesman, Vilmundur Gudnason, Ulf Gyllensten, Stephen J Hancock, Tamara B Harris, Catherine Helmer, Simon Höllerer, Edith Hofer, Albert Hofman, Elizabeth G Holliday, Georg Homuth, Frank B Hu, Cornelia Huth, Nina Hutri-Kähönen, Shih-Jen Hwang, Medea Imboden, Åsa Johansson, Mika Kähönen, Wolfgang König, Holly Kramer, Bernhard K Krämer, Ashish Kumar, Zoltan Kutalik, Jean-Charles Lambert, Lenore J Launer, Terho Lehtimäki, Martin H De Borst, Gerjan Navis, Morris Swertz, Yongmei Liu, Kurt Lohman, Ruth JF Loos, Yingchang Lu, Leo-Pekka Lyytikäinen, Mark A McEvoy, Christa Meisinger, Thomas Meitinger, Andres Metspalu, Marie Metzger, Evelin Mihailov, Paul Mitchell, Matthias Nauck, Albertine J Oldehinkel, Matthias Olden, Brenda WJH Penninx, Giorgio Pistis, Peter P Pramstaller, Nicole Probst-Hensch, Olli T Raitakari, Rainer Rettig, Paul M Ridker, Fernando Rivadeneira, Antonietta Robino, Sylvia E Rosas, Douglas Ruderfer, Daniela Ruggiero, Yasaman Saba, Cinzia Sala, Helena Schmidt, Reinhold Schmidt, Rodney J Scott, Sanaz Sedaghat, Albert V Smith, Rossella Sorice, Benedicte Stengel, Sylvia Stracke, Konstantin Strauch, Daniela Toniolo, Andre G Uitterlinden, Sheila Ulivi, Jorma S Viikari, Uwe Völker, Peter Vollenweider, Henry Völzke, Dragana Vuckovic, Melanie Waldenberger, Jie Jin Wang, Qiong Yang, Daniel I Chasman, Gerard Tromp, Harold Snieder, Iris M Heid, Caroline S Fox, Anna Köttgen, Cristian Pattaro, Carsten A Böger, Christian Fuchsberger. Corrigendum: 1000 Genomes-based meta-analysis identifies 10 novel loci for kidney function. Sci Rep. 2017 May 26;7:46835. doi: 10.1038/srep46835. PMID: 28548086 PMCID: PMC5445557

Bo Yang, Wei Zhou, Jiao Jiao, Jonas B Nielsen, Michael R Mathis, Mahyar Heydarpour, Guillaume Lettre, Lasse Folkersen, Siddharth Prakash, Claudia Schurmann, Lars Fritsche, Gregory A Farnum, Maoxuan Lin, Mohammad Othman, Whitney Hornsby, Anisa Driscoll, Alexandra Levasseur, Marc Thomas, Linda Farhat, Marie-Pierre Dubé, Eric M Isselbacher, Anders Franco-Cereceda, Dong-Chuan Guo, Erwin P Bottinger, G Michael Deeb, Anna Booher, Sachin Kheterpal, Y Eugene Chen, Hyun Min Kang, Jacob Kitzman, Heather J Cordell, Bernard D Keavney, Judith A Goodship, Santhi K Ganesh, Gonçalo Abecasis, Kim A Eagle, Alan P Boyle, Ruth JF Loos, Per Eriksson, Jean-Claude Tardif, Chad M Brummett, Dianna M Milewicz, Simon C Body, Cristen J Willer. Protein-altering and regulatory genetic variants near GATA4 implicated in bicuspid aortic valve. Nat Commun. 2017 May 25;8:15481. doi: 10.1038/ncomms15481. PMID:28541271

Nancy L Saccone, Leslie S Emery, Tamar Sofer, Stephanie M Gogarten, Diane M Becker, Erwin P Bottinger, Li-Shiun Chen, Robert C Culverhouse, Weimin Duan, Dana B Hancock, H Dean Hosgood, Eric O Johnson, Ruth JF Loos, Tin Louie, George Papanicolaou, Krista M Perreira, Erik J Rodriquez, Claudia Schurmann, Adrienne M Stilp, Adam A Szpiro, Gregory A Talavera, Kent D Taylor, James F Thrasher, Lisa R Yanek, Cathy C Laurie, Eliseo J Pérez-Stable, Laura J Bierut, Robert C Kaplan. Genome-wide association study of heavy smoking and daily/nondaily smoking in the Hispanic Community Health Study / Study of Latinos (HCHS/SOL). Nicotine Tob Res. 2017 May 17. doi: 10.1093/ntr/ntx107. [Epub ahead of print] PMID: 28520984

Jingjing Liang, Thu H Le, Digna R Velez Edwards, Bamidele O Tayo, Kyle J Gaulton, Jennifer A Smith, Yingchang Lu, Richard A Jensen, Guanjie Chen, Lisa R Yanek, Karen Schwander, Salman M Tajuddin, Tamar Sofer, Wonji Kim, James Kayima, Colin A McKenzie, Ervin Fox, Michael A Nalls, J Hunter Young, Yan V Sun, Jacqueline M Lane, Sylvia Cechova, Jie Zhou, Hua Tang, Myriam Fornage, Solomon K Musani, Heming Wang, Juyoung Lee, Adebowale Adeyemo, Albert W Dreisbach, Terrence Forrester, Pei-Lun Chu, Anne Cappola, Michele K Evans, Alanna C Morrison, Lisa W Martin, Kerri L Wiggins, Qin Hui, Wei Zhao, Rebecca D Jackson, Erin B Ware, Jessica D Faul, Alex P Reiner, Michael Bray, Joshua C Denny, Thomas H Mosley, Walter Palmas, Xiuqing Guo, George J Papanicolaou, Alan D Penman, Joseph F Polak, Kenneth Rice, Ken D Taylor, Eric Boerwinkle, Erwin P Bottinger, Kiang Liu, Neil Risch, Steven C Hunt, Charles Kooperberg, Alan B Zonderman, Cathy C Laurie, Diane M Becker, Jianwen Cai, Ruth JF Loos, Bruce M Psaty, David R Weir, Sharon LR Kardia, Donna K Arnett, Sungho Won, Todd L Edwards, Susan Redline, Richard S Cooper, DC Rao, Jerome I Rotter, Charles Rotimi, Daniel Levy, Aravinda Chakravarti, Xiaofeng Zhu, Nora Franceschini. Single-trait and multi-trait genome-wide association analyses identify novel loci for blood pressure in African-ancestry populations. PLoS Genet. 2017 May 12;13(5):e1006728. doi: 10.1371/journal.pgen.1006728. eCollection 2017 May. PMID: 28498854; PMCID: PMC5446189

Mathias Gorski, Peter J Van der Most, Alexander Teumer, Audrey Y Chu, Man Li, Vladan Mijatovic, Ilja M Nolte, Massimiliano Cocca, Daniel Taliun, Felicia Gomez, Yong Li, Bamidele Tayo, Adrienne Tin, Mary F Feitosa, Thor Aspelund, John Attia, Reiner Biffar, Murielle Bochud, Eric Boerwinkle, Ingrid Borecki, Erwin P Bottinger, Ming-Huei Chen, Vincent Chouraki, Marina Ciullo, Josef Coresh, Marilyn C Cornelis, Gary C Curhan, Adamo Pio d’Adamo, Abbas Dehghan, Laura Dengler, Jingzhong Ding, Gudny Eiriksdottir, Karlhans Endlich, Stefan Enroth, Tõnu Esko, Oscar H Franco, Paolo Gasparini, Christian Gieger, Giorgia Girotto, Omri Gottesman, Vilmundur Gudnason, Ulf Gyllensten, Stephen J Hancock, Tamara B Harris, Catherine Helmer, Simon Höllerer, Edith Hofer, Albert Hofman, Elizabeth G Holliday, Georg Homuth, Frank B Hu, Cornelia Huth, Nina Hutri-Kähönen, Shih-Jen Hwang, Medea Imboden, Åsa Johansson, Mika Kähönen, Wolfgang König, Holly Kramer, Bernhard K Krämer, Ashish Kumar, Zoltan Kutalik, Jean-Charles Lambert, Lenore J Launer, Terho Lehtimäki, Martin De Borst, Gerjan Navis, Morris Swertz, Yongmei Liu, Kurt Lohman, Ruth JF Loos, Yingchang Lu, Leo-Pekka Lyytikäinen, Mark A McEvoy, Christa Meisinger, Thomas Meitinger, Andres Metspalu, Marie Metzger, Evelin Mihailov, Paul Mitchell, Matthias Nauck, Albertine J Oldehinkel, Matthias Olden, Brenda WJH Penninx, Giorgio Pistis, Peter P Pramstaller, Nicole Probst-Hensch, Olli T Raitakari, Rainer Rettig, Paul M Ridker, Fernando Rivadeneira, Antonietta Robino, Sylvia E Rosas, Douglas Ruderfer, Daniela Ruggiero, Yasaman Saba, Cinzia Sala, Helena Schmidt, Reinhold Schmidt, Rodney J Scott, Sanaz Sedaghat, Albert V Smith, Rossella Sorice, Benedicte Stengel, Sylvia Stracke, Konstantin Strauch, Daniela Toniolo, Andre G Uitterlinden, Sheila Ulivi, Jorma S Viikari, Uwe Völker, Peter Vollenweider, Henry Völzke, Dragana Vuckovic, Melanie Waldenberger, Jie Jin Wang, Qiong Yang, Daniel I Chasman, Gerard Tromp, Harold Snieder, Iris M Heid, Caroline S Fox, Anna Köttgen, Cristian Pattaro, Carsten A Böger, Christian Fuchsberger. 1000 Genomes-based meta-analysis identifies 10 novel loci for kidney function. Sci Rep. 2017 Apr 28;7:45040. doi: 10.1038/srep45040.
PMID: 28452372; PMCID:PMC5408227

Anne E Justice, Thomas W Winkler, Mary F Feitosa, Misa Graff, Virginia A Fisher, Kristin Young, Llilda Barata, Xuan Deng, Jacek Czajkowski, David Hadley, Julius S Ngwa, Tarunveer S Ahluwalia, Audrey Y Chu, Nancy L Heard-Costa, Elise Lim, Jeremiah Perez, John D Eicher, Zoltán Kutalik, Luting Xue, Anubha Mahajan, Frida Renström, Joseph Wu, Qibin Qi, Shafqat Ahmad, Tamuno Alfred, Najaf Amin, Lawrence F Bielak, Amelie Bonnefond, Jennifer Bragg, Gemma Cadby, Martina Chittani, Scott Coggeshall, Tanguy Corre, Nese Direk, Joel Eriksson, Krista Fischer, Mathias Gorski, Marie Neergaard Harder, Momoko Horikoshi, Tao Huang, Jennifer E Huffman, Anne U Jackson, Johanne Marie Justesen, Stavroula Kanoni, Leena Kinnunen, Marcus E Kleber, Pirjo Komulainen, Meena Kumari, Unhee Lim, Jian’an Luan, Leo-Pekka Lyytikäinen, Massimo Mangino, Ani Manichaikul, Jonathan Marten, Rita PS Middelberg, Martina Müller-Nurasyid, Pau Navarro, Louis Pérusse, Natalia Pervjakova, Cinzia Sarti, Albert Vernon Smith, Jennifer A Smith, Alena Stančáková, Rona J Strawbridge, Heather M Stringham, Yun Ju Sung, Toshiko Tanaka, Alexander Teumer, Stella Trompet, Sander W van der Laan, Peter J van der Most, Jana V Van Vliet-Ostaptchouk, Sailaja L Vedantam, Niek Verweij, Jacqueline M Vink, Veronique Vitart, Ying Wu, Loic Yengo, Weihua Zhang, Jing Hua Zhao, Martina E Zimmermann, Niha Zubair, Gonçalo R Abecasis, Linda S Adair, Saima Afaq, Uzma Afzal, Stephan JL Bakker, Traci M Bartz, John Beilby, Richard N Bergman, Sven Bergmann, Reiner Biffar, John Blangero, Eric Boerwinkle, Lori L Bonnycastle, Erwin Bottinger, Daniele Braga, Brendan M Buckley, Steve Buyske, Harry Campbell, John C Chambers, Francis S Collins, Joanne E Curran, Gert J de Borst, Anton JM De Craen, Eco JC de Geus, George Dedoussis, Graciela E Delgado, Hester M den Ruijter, Gudny Eiriksdottir, Anna L Eriksson, Tõnu Esko, Jessica D Faul, Ian Ford, Terrence Forrester, Karl Gertow, Bruna Gigante, Nicola Glorioso, Jian Gong, Harald Grallert, Tanja B Grammer, Niels Grarup, Saskia Haitjema, Göran Hallmans, Anders Hamsten, Torben Hansen, Tamara B Harris, Catharina A Hartman, Maija Hassinen, Nicholas D Hastie, Andrew C Heath, Dena Hernandez, Lucia Hindorff, Lynne J Hocking, Mette Hollensted, Oddgeir L Holmen, Georg Homuth, Jouke Jan Hottenga, Jie Huang, Joseph Hung, Nina Hutri-Kähönen, Erik Ingelsson, Alan L James, John-Olov Jansson, Marjo-Riitta Jarvelin, Min A Jhun, Marit E Jørgensen, Markus Juonala, Mika Kähönen, Magnus Karlsson. Genome-wide meta-analysis of 241,258 adults accounting for smoking behaviour identifies novel loci for obesity traits. Nat Commun. 2017 Apr 26;8:14977. doi: 10.1038/ncomms14977. PMID: 28443625 PMCID:PMC5414044

Maggie CY Ng, Mariaelisa Graff, Yingchang Lu, Anne E Justice, Poorva Mudgal, Ching-Ti Liu, Kristin Young, Lisa R Yanek, Mary F Feitosa, Mary K Wojczynski, Kristin Rand, Jennifer A Brody, Brian E Cade, Latchezar Dimitrov, Qing Duan, Xiuqing Guo, Leslie A Lange, Michael A Nalls, Hayrettin Okut, Salman M Tajuddin, Bamidele O Tayo, Sailaja Vedantam, Jonathan P Bradfield, Guanjie Chen, Wei-Min Chen, Alessandra Chesi, Marguerite R Irvin, Badri Padhukasahasram, Jennifer A Smith, Wei Zheng, Matthew A Allison, Christine B Ambrosone, Elisa V Bandera, Traci M Bartz, Sonja I Berndt, Leslie Bernstein, William J Blot, Erwin P Bottinger, John Carpten, Stephen J Chanock, Yii-Der Ida Chen, David V Conti, Richard S Cooper, Myriam Fornage, Barry I Freedman, Melissa Garcia, Phyllis J Goodman, Yu-Han H Hsu, Jennifer Hu, Chad D Huff, Sue A Ingles, Esther M John, Rick Kittles, Eric Klein, Jin Li, Barbara McKnight, Uma Nayak, Barbara Nemesure, Adesola Ogunniyi, Andrew Olshan, Michael F Press, Rebecca Rohde, Benjamin A Rybicki, Babatunde Salako, Maureen Sanderson, Yaming Shao, David S Siscovick, Janet L Stanford, Victoria L Stevens, Alex Stram, Sara S Strom, Dhananjay Vaidya, John S Witte, Jie Yao, Xiaofeng Zhu, Regina G Ziegler, Alan B Zonderman, Adebowale Adeyemo, Stefan Ambs, Mary Cushman, Jessica D Faul, Hakon Hakonarson, Albert M Levin, Katherine L Nathanson, Erin B Ware, David R Weir, Wei Zhao, Degui Zhi, Donna K Arnett, Struan FA Grant, Sharon LR Kardia, Olufunmilayo I Oloapde, DC Rao, Charles N Rotimi, Michele M Sale, L Keoki Williams, Babette S Zemel, Diane M Becker, Ingrid B Borecki, Michele K Evans, Tamara B Harris, Joel N Hirschhorn, Yun Li, Sanjay R Patel, Bruce M Psaty, Jerome I Rotter, James G Wilson, Donald W Bowden, L Adrienne Cupples, Christopher A Haiman, Ruth JF Loos, Kari E North. Discovery and fine-mapping of adiposity loci using high density imputation of genome-wide association studies in individuals of African ancestry: African Ancestry Anthropometry Genetics Consortium. PLoS Genet. 2017 Apr 21;13(4):e1006719. doi: 10.1371/journal.pgen.1006719. eCollection 2017 Apr. PMID:28430825; PMCID:PMC5419579

Niha Zubair, Mariaelisa Graff, Jose Luis Ambite, William S Bush, Gleb Kichaev, Yingchang Lu, Ani Manichaikul, Wayne HH Sheu, Devin Absher, Themistocles L Assimes, Suzette J Bielinski, Erwin P Bottinger, Petra Buzkova, Lee-Ming Chuang, Ren-Hua Chung, Barbara Cochran, Logan Dumitrescu, Omri Gottesman, Jeffrey W Haessler, Christopher Haiman, Gerardo Heiss, Chao A Hsiung, Yi-Jen Hung, Chii-Min Hwu, Jyh-Ming J Juang, Loic Le Marchand, I-Te Lee, Wen-Jane Lee, Li-An Lin, Danyu Lin, Shih-Yi Lin, Rachel H Mackey, Lisa W Martin, Bogdan Pasaniuc, Ulrike Peters, Irene Predazzi, Thomas Quertermous, Alex P Reiner, Jennifer Robinson, Jerome I Rotter, Kelli K Ryckman, Pamela J Schreiner, Eli Stahl, Ran Tao, Michael Y Tsai, Lindsay L Waite, Tzung-Dau Wang, Steven Buyske, Yii-Der Ida Chen, Iona Cheng, Dana C Crawford, Ruth JF Loos, Stephen S Rich, Myriam Fornage, Kari E North, Charles Kooperberg, Cara L Carty. Fine-mapping of lipid regions in global populations discovers ethnic-specific signals and refines previously identified lipid loci. Hum Mol Genet. 2016 Dec 15;25(24):5500-5512. doi: 10.1093/hmg/ddw358. PMID: 28426890

Ingrid E Christophersen, Michiel Rienstra, Carolina Roselli, Xiaoyan Yin, Bastiaan Geelhoed, John Barnard, Honghuang Lin, Dan E Arking, Albert V Smith, Christine M Albert, Mark Chaffin, Nathan R Tucker, Molong Li, Derek Klarin, Nathan A Bihlmeyer, Siew-Kee Low, Peter E Weeke, Martina Müller-Nurasyid, J Gustav Smith, Jennifer A Brody, Maartje N Niemeijer, Marcus Dörr, Stella Trompet, Jennifer Huffman, Stefan Gustafsson, Claudia Schurmann, Marcus E Kleber, Leo-Pekka Lyytikäinen, Ilkka Seppälä, Rainer Malik, Andrea RVR Horimoto, Marco Perez, Juha Sinisalo, Stefanie Aeschbacher, Sébastien Thériault, Jie Yao, Farid Radmanesh, Stefan Weiss, Alexander Teumer, Seung Hoan Choi, Lu-Chen Weng, Sebastian Clauss, Rajat Deo, Daniel J Rader, Svati H Shah, Albert Sun, Jemma C Hopewell, Stephanie Debette, Ganesh Chauhan, Qiong Yang, Bradford B Worrall, Guillaume Paré, Yoichiro Kamatani, Yanick P Hagemeijer, Niek Verweij, Joylene E Siland, Michiaki Kubo, Jonathan D Smith, David R Van Wagoner, Joshua C Bis, Siegfried Perz, Bruce M Psaty, Paul M Ridker, Jared W Magnani, Tamara B Harris, Lenore J Launer, M Benjamin Shoemaker, Sandosh Padmanabhan, Jeffrey Haessler, Traci M Bartz, Melanie Waldenberger, Peter Lichtner, Marina Arendt, Jose E Krieger, Mika Kähönen, Lorenz Risch, Alfredo J Mansur, Annette Peters, Blair H Smith, Lars Lind, Stuart A Scott, Yingchang Lu, Erwin B Bottinger, Jussi Hernesniemi, Cecilia M Lindgren, Jorge A Wong, Jie Huang, Markku Eskola, Andrew P Morris, Ian Ford, Alex P Reiner, Graciela Delgado, Lin Y Chen, Yii-Der Ida Chen, Roopinder K Sandhu, Man Li, Eric Boerwinkle, Lewin Eisele, Lars Lannfelt, Natalia Rost, Christopher D Anderson, Kent D Taylor, Archie Campbell, Patrik K Magnusson, David Porteous, Lynne J Hocking, Efthymia Vlachopoulou, Nancy L Pedersen, Kjell Nikus, Marju Orho-Melander, Anders Hamsten, Jan Heeringa, Joshua C Denny, Jennifer Kriebel, Dawood Darbar, Christopher Newton-Cheh, Christian Shaffer, Peter W Macfarlane, Stefanie Heilmann-Heimbach, Peter Almgren, Paul L Huang, Nona Sotoodehnia, Elsayed Z Soliman, Andre G Uitterlinden, Albert Hofman, Oscar H Franco, Uwe Völker, Karl-Heinz Jöckel, Moritz F Sinner, Henry J Lin, Xiuqing Guo, Martin Dichgans, Erik Ingelsson, Charles Kooperberg, Olle Melander, Ruth JF Loos, Jari Laurikka, David Conen, Jonathan Rosand, Pim van der Harst, Marja-Liisa Lokki, Sekar Kathiresan, Alexandre Pereira, J Wouter Jukema, Caroline Hayward, Jerome I Rotter, Winfried März, Terho Lehtimäki, Bruno H Stricker, Mina K Chung. Large-scale analyses of common and rare variants identify 12 new loci associated with atrial fibrillation. Nat Genet. 2017 Jun;49(6):946-952. doi: 10.1038/ng.3843. Epub 2017 Apr 17. PMID: 28416818

Fernández Rhodes L, Gong J, Haessler J, Franceschini, N, Graff M, Nishimura KK, Wang Y, Highland, HM, Yoneyama S, Bush WS, Goodloe R, Ritchie MD, Crawford D, Gross M, Fornage M, Buzkova P, Tao R, Isasi C, Avilés Santa L, Daviglus M, Mackey RH, Houston D, Gu CC, Ehret G, Nguyen KH, Lewis CE, Leppert M, Irvin MR, Lim U, Haiman CA, Le Marchand L, Schumacher F, Wilkens L, Lu Y, Bottinger EP, Loos RJL, Sheu WH, Guo X, Lee WJ, Hai Y, Hung YJ, Absher D, Wu IC, Taylor KD, Lee IT, Liu Y, Wang TD, Quertermous T, Juang, Rotter JI, Assimes T, Hsiung, CA, Chen YI, Prentice R, Kuller LH, Manson JE, Kooperberg C, Smokowski P, Robinson, WR, Gordon Larsen P, Li R, Hindorff L, Buyske S · Matise TC, Peters U, North KE.Trans-ethnic fine-mapping of genetic loci for body mass index in the diverse ancestral populations of the Population Architecture using Genomics and Epidemiology (PAGE) Study reveals evidence for multiple signals at established loci. Hum Genet. 2017 Jun;136(6):771-800. doi: 10.1007/s00439-017-1787-6. Epub 2017 Apr 8. PMID: 28391526

Thomas R Webb, Jeanette Erdmann, Kathleen E Stirrups, Nathan O Stitziel, Nicholas GD Masca, Henning Jansen, Stavroula Kanoni, Christopher P Nelson, Paola G Ferrario, Inke R König, John D Eicher, Andrew D Johnson, Stephen E Hamby, Christer Betsholtz, Arno Ruusalepp, Oscar Franzén, Eric E Schadt, Johan LM Björkegren, Peter E Weeke, Paul L Auer, Ursula M Schick, Yingchang Lu, He Zhang, Marie-Pierre Dube, Anuj Goel, Martin Farrall, Gina M Peloso, Hong-Hee Won, Ron Do, Erik van Iperen, Jochen Kruppa, Anubha Mahajan, Robert A Scott, Christina Willenborg, Peter S Braund, Julian C Van Capelleveen, Alex SF Doney, Louise A Donnelly, Rosanna Asselta, Pier A Merlini, Stefano Duga, Nicola Marziliano, Josh C Denny, Christian Shaffer, Nour Eddine El-Mokhtari, Andre Franke, Stefanie Heilmann, Christian Hengstenberg, Per Hoffmann, Oddgeir L Holmen, Kristian Hveem, Jan-Håkan Jansson, Karl-Heinz Jöckel, Thorsten Kessler, Jennifer Kriebel, Karl L Laugwitz, Eirini Marouli, Nicola Martinelli, Mark I McCarthy, Natalie R Van Zuydam, Christa Meisinger, Tõnu Esko, Evelin Mihailov, Stefan A Escher, Maris Alver, Susanne Moebus, Andrew D Morris, Jarma Virtamo, Majid Nikpay, Oliviero Olivieri, Sylvie Provost, Alaa AlQarawi, Neil R Robertson, Karen O Akinsansya, Dermot F Reilly, Thomas F Vogt, Wu Yin, Folkert W Asselbergs, Charles Kooperberg, Rebecca D Jackson, Eli Stahl, Martina Müller-Nurasyid, Konstantin Strauch, Tibor V Varga, Melanie Waldenberger, Lingyao Zeng, Rajiv Chowdhury, Veikko Salomaa, Ian Ford, J Wouter Jukema, Philippe Amouyel, Jukka Kontto, Børge G Nordestgaard, Jean Ferrières, Danish Saleheen, Naveed Sattar, Praveen Surendran, Aline Wagner, Robin Young, Joanna MM Howson, Adam S Butterworth, John Danesh, Diego Ardissino, Erwin P Bottinger, Raimund Erbel, Paul W Franks, Domenico Girelli, Alistair S Hall, G Kees Hovingh, Adnan Kastrati, Wolfgang Lieb, Thomas Meitinger, William E Kraus, Svati H Shah, Ruth McPherson, Marju Orho-Melander, Olle Melander, Andres Metspalu, Colin NA Palmer, Annette Peters, Daniel J Rader, Muredach P Reilly, Ruth JF Loos, Alex P Reiner, Dan M Roden, Jean-Claude Tardif, John R Thompson, Nicholas J Wareham, Hugh Watkins, Cristen J Willer, Nilesh J Samani, Heribert Schunkert, Panos Deloukas, Sekar Kathiresan, Myocardial Infarction Genetics, Wellcome Trust Case Control Consortium, MORGAM Investigators, CARDIoGRAM Exome Consortia Investigators. Systematic Evaluation of Pleiotropy Identifies 6 Further Loci Associated With Coronary Artery Disease. J Am Coll Cardiol. 2017 Feb 21;69(7):823-836. doi: 10.1016/j.jacc.2016.11.056. PMID: 28209224; PMCID:PMC5314135

Louise V Wain, Nick Shrine, María Soler Artigas, A Mesut Erzurumluoglu, Boris Noyvert, Lara Bossini-Castillo, Ma’en Obeidat, Amanda P Henry, Michael A Portelli, Robert J Hall, Charlotte K Billington, Tracy L Rimington, Anthony G Fenech, Catherine John, Tineka Blake, Victoria E Jackson, Richard J Allen, Bram P Prins, Archie Campbell, David J Porteous, Marjo-Riitta Jarvelin, Matthias Wielscher, Alan L James, Jennie Hui, Nicholas J Wareham, Jing Hua Zhao, James F Wilson, Peter K Joshi, Beate Stubbe, Rajesh Rawal, Holger Schulz, Medea Imboden, Nicole M Probst-Hensch, Stefan Karrasch, Christian Gieger, Ian J Deary, Sarah E Harris, Jonathan Marten, Igor Rudan, Stefan Enroth, Ulf Gyllensten, Shona M Kerr, Ozren Polasek, Mika Kähönen, Ida Surakka, Veronique Vitart, Caroline Hayward, Terho Lehtimäki, Olli T Raitakari, David M Evans, A John Henderson, Craig E Pennell, Carol A Wang, Peter D Sly, Emily S Wan, Robert Busch, Brian D Hobbs, Augusto A Litonjua, David W Sparrow, Amund Gulsvik, Per S Bakke, James D Crapo, Terri H Beaty, Nadia N Hansel, Rasika A Mathias, Ingo Ruczinski, Kathleen C Barnes, Yohan Bossé, Philippe Joubert, Maarten Van Den Berge, Corry-Anke Brandsma, Peter D Paré, Don D Sin, David C Nickle, Ke Hao, Omri Gottesman, Frederick E Dewey, Shannon E Bruse, David J Carey, H Lester Kirchner, Stefan Jonsson, Gudmar Thorleifsson, Ingileif Jonsdottir, Thorarinn Gislason, Kari Stefansson, Claudia Schurmann, Girish Nadkarni, Erwin P Bottinger, Ruth JF Loos, Robin G Walters, Zhengming Chen, Iona Y Millwood, Julien Vaucher, Om P Kurmi, Liming Li, Anna L Hansell, Chris Brightling, Eleftheria Zeggini, Michael H Cho, Edwin K Silverman, Ian Sayers, Gosia Trynka, Andrew P Morris, David P Strachan, Ian P Hall, Martin D Tobin, Understanding Society Scientific Group, Geisinger-Regeneron DiscovEHR Collaboration. Genome-wide association analyses for lung function and chronic obstructive pulmonary disease identify new loci and potential druggable targets. Nat Genet. 2017 Mar;49(3):416-425. doi: 10.1038/ng.3787. Epub 2017 Feb 6. PMID: 28166213; PMCID: PMC5326681 [Available on 2017-08-06]

Eirini Marouli, Mariaelisa Graff, Carolina Medina-Gomez, Ken Sin Lo, Andrew R Wood, Troels R Kjaer, Rebecca S Fine, Yingchang Lu, Claudia Schurmann, Heather M Highland, Sina Rüeger, Gudmar Thorleifsson, Anne E Justice, David Lamparter, Kathleen E Stirrups, Valérie Turcot, Kristin L Young, Thomas W Winkler, Tõnu Esko, Tugce Karaderi, Adam E Locke, Nicholas GD Masca, Maggie CY Ng, Poorva Mudgal, Manuel A Rivas, Sailaja Vedantam, Anubha Mahajan, Xiuqing Guo, Goncalo Abecasis, Katja K Aben, Linda S Adair, Dewan S Alam, Eva Albrecht, Kristine H Allin, Matthew Allison, Philippe Amouyel, Emil V Appel, Dominique Arveiler, Folkert W Asselbergs, Paul L Auer, Beverley Balkau, Bernhard Banas, Lia E Bang, Marianne Benn, Sven Bergmann, Lawrence F Bielak, Matthias Blüher, Heiner Boeing, Eric Boerwinkle, Carsten A Böger, Lori L Bonnycastle, Jette Bork-Jensen, Michiel L Bots, Erwin P Bottinger, Donald W Bowden, Ivan Brandslund, Gerome Breen, Murray H Brilliant, Linda Broer, Amber A Burt, Adam S Butterworth, David J Carey, Mark J Caulfield, John C Chambers, Daniel I Chasman, Yii-Der Ida Chen, Rajiv Chowdhury, Cramer Christensen, Audrey Y Chu, Massimiliano Cocca, Francis S Collins, James P Cook, Janie Corley, Jordi Corominas Galbany, Amanda J Cox, Gabriel Cuellar-Partida, John Danesh, Gail Davies, Paul IW De Bakker, Gert J De Borst, Simon De Denus, Mark CH De Groot, Renée De Mutsert, Ian J Deary, George Dedoussis, Ellen W Demerath, Anneke I Den Hollander, Joe G Dennis, Emanuele Di Angelantonio, Fotios Drenos, Mengmeng Du, Alison M Dunning, Douglas F Easton, Tapani Ebeling, Todd L Edwards, Patrick T Ellinor, Paul Elliott, Evangelos Evangelou, Aliki-Eleni Farmaki, Jessica D Faul, Mary F Feitosa, Shuang Feng, Ele Ferrannini, Marco M Ferrario, Jean Ferrieres, Jose C Florez, Ian Ford, Myriam Fornage, Paul W Franks, Ruth Frikke-Schmidt, Tessel E Galesloot, Wei Gan, Ilaria Gandin, Paolo Gasparini, Vilmantas Giedraitis, Ayush Giri, Giorgia Girotto, Scott D Gordon, Penny Gordon-Larsen, Mathias Gorski, Niels Grarup, Megan L Grove, Vilmundur Gudnason, Stefan Gustafsson, Torben Hansen, Kathleen Mullan Harris, Tamara B Harris, Andrew T Hattersley, Caroline Hayward, Liang He, Iris M Heid, Kauko Heikkilä, Øyvind Helgeland, Jussi Hernesniemi, Alex W Hewitt, Lynne J Hocking, Mette Hollensted, Oddgeir L Holmen, G Kees Hovingh, Joanna MM Howson, Carel B Hoyng, Paul L Huang, Kristian Hveem, M Arfan Ikram, Erik Ingelsson, Anne U Jackson, Jan-Håkan Jansson, Gail P Jarvik, Gorm B Jensen, Min A Jhun. Rare and low-frequency coding variants alter human adult height. Nature. 2017 Feb 9;542(7640):186-190. doi: 10.1038/nature21039. Epub 2017 Feb 1. PMID: 28146470; PMCID:PMC5302847 [Available on 2017-08-01]

Li M, Li Y, Weeks O, Mijatovic V, Teumer A, Huffman JE, Tromp G, Fuchsberger C, Gorski M, Lyytikäinen LP, Nutile T, Sedaghat S, Sorice R, Tin A, Yang Q, Ahluwalia TS, Arking DE, Bihlmeyer NA, Böger CA, Carroll RJ, Chasman DI, Cornelis MC, Dehghan A, Faul JD, Feitosa MF, Gambaro G, Gasparini P, Giulianini F, Heid I, Huang J, Imboden M, Jackson AU, Jeff J, Jhun MA, Katz R, Kifley A, Kilpeläinen TO, Kumar A, Laakso M, Li-Gao R, Lohman K, Lu Y, Mägi R, Malerba G, Mihailov E, Mohlke KL, Mook-Kanamori DO, Robino A, Ruderfer D, Salvi E, Schick UM, Schulz CA, Smith AV, Smith JA, Traglia M, Yerges-Armstrong LM, Zhao W, Goodarzi MO, Kraja AT, Liu C, Wessel J; CHARGE Glycemic-T2D Working Group,.; CHARGE Blood Pressure Working Group,., Boerwinkle E, Borecki IB, Bork-Jensen J, Bottinger EP, Braga D, Brandslund I, Brody JA, Campbell A, Carey DJ, Christensen C, Coresh J, Crook E, Curhan GC, Cusi D, de Boer IH, de Vries AP, Denny JC, Devuyst O, Dreisbach AW, Endlich K, Esko T, Franco OH, Fulop T, Gerhard GS, Glümer C, Gottesman O, Grarup N, Gudnason V, Harris TB, Hayward C, Hocking L, Hofman A, Hu FB, Husemoen LL, Jackson RD, Jørgensen T, Jørgensen ME, Kähönen M, Kardia SL, König W, Kooperberg C, Kriebel J, Launer LJ, Lauritzen T, Lehtimäki T, Levy D, Linksted P, Linneberg A, Liu Y, Loos RJ, Lupo A, Meisinger C, Melander O, Metspalu A, Mitchell P, Nauck M, Nürnberg P, Orho-Melander M, Parsa A, Pedersen O, Peters A, Peters U, Polasek O, Porteous D, Probst-Hensch NM, Psaty BM, Qi L, Raitakari OT, Reiner AP, Rettig R, Ridker PM, Rivadeneira F, Rossouw JE, Schmidt F, Siscovick D, Soranzo N, Strauch K, Toniolo D, Turner ST, Uitterlinden AG, Ulivi S, Velayutham D, Völker U, Völzke H, Waldenberger M, Wang JJ, Weir DR, Witte D, Kuivaniemi H, Fox CS, Franceschini N, Goessling W, Köttgen A, Chu AY. SOS2 and ACP1 Loci Identified through Large-Scale Exome Chip Analysis Regulate Kidney Development and Function. J Am Soc Nephrol. 2016 Dec 5. pii: ASN.2016020131. PMID: 27920155; PMCID: PMC5328154 [Available on 2018-03-01]

Christina Loley, Maris Alver, Themistocles L Assimes, Andrew Bjonnes, Anuj Goel, Stefan Gustafsson, Jussi Hernesniemi, Jemma C Hopewell, Stavroula Kanoni, Marcus E Kleber, King Wai Lau, Yingchang Lu, Leo-Pekka Lyytikäinen, Christopher P Nelson, Majid Nikpay, Liming Qu, Elias Salfati, Markus Scholz, Taru Tukiainen, Christina Willenborg, Hong-Hee Won, Lingyao Zeng, Weihua Zhang, Sonia S Anand, Frank Beutner, Erwin P Bottinger, Robert Clarke, George Dedoussis, Ron Do, Tõnu Esko, Markku Eskola, Martin Farrall, Dominique Gauguier, Vilmantas Giedraitis, Christopher B Granger, Alistair S Hall, Anders Hamsten, Stanley L Hazen, Jie Huang, Mika Kähönen, Theodosios Kyriakou, Reijo Laaksonen, Lars Lind, Cecilia Lindgren, Patrik KE Magnusson, Eirini Marouli, Evelin Mihailov, Andrew P Morris, Kjell Nikus, Nancy Pedersen, Loukianos Rallidis, Veikko Salomaa, Svati H Shah, Alexandre FR Stewart, John R Thompson, Pierre A Zalloua, John C Chambers, Rory Collins, Erik Ingelsson, Carlos Iribarren, Pekka J Karhunen, Jaspal S Kooner, Terho Lehtimäki, Ruth JF Loos, Winfried März, Ruth McPherson, Andres Metspalu, Muredach P Reilly, Samuli Ripatti, Dharambir K Sanghera, Joachim Thiery, Hugh Watkins, Panos Deloukas, Sekar Kathiresan, Nilesh J Samani, Heribert Schunkert, Jeanette Erdmann, Inke R König. No Association of Coronary Artery Disease with X-Chromosomal Variants in Comprehensive International Meta-Analysis. Sci Rep. 2016 Oct 12;6:35278. doi: 10.1038/srep35278. PMID: 27731410; PMCID:PMC5059659

Chunyu Liu, Aldi T Kraja, Jennifer A Smith, Jennifer A Brody, Nora Franceschini, Joshua C Bis, Kenneth Rice, Alanna C Morrison, Yingchang Lu, Stefan Weiss, Xiuqing Guo, Walter Palmas, Lisa W Martin, Yii-Der Ida Chen, Praveen Surendran, Fotios Drenos, James P Cook, Paul L Auer, Audrey Y Chu, Ayush Giri, Wei Zhao, Johanna Jakobsdottir, Li-An Lin, Jeanette M Stafford, Najaf Amin, Hao Mei, Jie Yao, Arend Voorman, Martin G Larson, Megan L Grove, Albert V Smith, Shih-Jen Hwang, Han Chen, Tianxiao Huan, Gulum Kosova, Nathan O Stitziel, Sekar Kathiresan, Nilesh Samani, Heribert Schunkert, Panos Deloukas, Myocardial Infarction Genetics, CARDIoGRAM Exome Consortia, Man Li, Christian Fuchsberger, Cristian Pattaro, Mathias Gorski, Charles Kooperberg, George J Papanicolaou, Jacques E Rossouw, Jessica D Faul, Sharon LR Kardia, Claude Bouchard, Leslie J Raffel, André G Uitterlinden, Oscar H Franco, Ramachandran S Vasan, Christopher J O’Donnell, Kent D Taylor, Kiang Liu, Erwin P Bottinger, Omri Gottesman, E Warwick Daw, Franco Giulianini, Santhi Ganesh, Elias Salfati, Tamara B Harris, Lenore J Launer, Marcus Dörr, Stephan B Felix, Rainer Rettig, Henry Völzke, Eric Kim, Wen-Jane Lee, I-Te Lee, Wayne HH Sheu, Krystal S Tsosie, Digna R Velez Edwards, Yongmei Liu, Adolfo Correa, David R Weir, Uwe Völker, Paul M Ridker, Eric Boerwinkle, Vilmundur Gudnason, Alexander P Reiner, Cornelia M van Duijn, Ingrid B Borecki, Todd L Edwards, Aravinda Chakravarti, Jerome I Rotter, Bruce M Psaty, Ruth JF Loos, Myriam Fornage, Georg B Ehret, Christopher Newton-Cheh, Daniel Levy, Daniel I Chasman, CHD Exome+ Consortium, ExomeBP Consortium, GoT2DGenes Consortium, T2D-GENES Consortium, CKDGen Consortium. Meta-analysis identifies common and rare variants influencing blood pressure and overlapping with metabolic trait loci. Nat Genet. 2016 Oct;48(10):1162-70. doi: 10.1038/ng.3660. Epub 2016 Sep 12. PMID: 27618448; PMCID: PMC5320952

Christian Fuchsberger, Jason Flannick, Tanya M Teslovich, Anubha Mahajan, Vineeta Agarwala, Kyle J Gaulton, Clement Ma, Pierre Fontanillas, Loukas Moutsianas, Davis J McCarthy, Manuel A Rivas, John RB Perry, Xueling Sim, Thomas W Blackwell, Neil R Robertson, N William Rayner, Pablo Cingolani, Adam E Locke, Juan Fernandez Tajes, Heather M Highland, Josee Dupuis, Peter S Chines, Cecilia M Lindgren, Christopher Hartl, Anne U Jackson, Han Chen, Jeroen R Huyghe, Martijn van de Bunt, Richard D Pearson, Ashish Kumar, Martina Müller-Nurasyid, Niels Grarup, Heather M Stringham, Eric R Gamazon, Jaehoon Lee, Yuhui Chen, Robert A Scott, Jennifer E Below, Peng Chen, Jinyan Huang, Min Jin Go, Michael L Stitzel, Dorota Pasko, Stephen CJ Parker, Tibor V Varga, Todd Green, Nicola L Beer, Aaron G Day-Williams, Teresa Ferreira, Tasha Fingerlin, Momoko Horikoshi, Cheng Hu, Iksoo Huh, Mohammad Kamran Ikram, Bong-Jo Kim, Yongkang Kim, Young Jin Kim, Min-Seok Kwon, Juyoung Lee, Selyeong Lee, Keng-Han Lin, Taylor J Maxwell, Yoshihiko Nagai, Xu Wang, Ryan P Welch, Joon Yoon, Weihua Zhang, Nir Barzilai, Benjamin F Voight, Bok-Ghee Han, Christopher P Jenkinson, Teemu Kuulasmaa, Johanna Kuusisto, Alisa Manning, Maggie CY Ng, Nicholette D Palmer, Beverley Balkau, Alena Stančáková, Hanna E Abboud, Heiner Boeing, Vilmantas Giedraitis, Dorairaj Prabhakaran, Omri Gottesman, James Scott, Jason Carey, Phoenix Kwan, George Grant, Joshua D Smith, Benjamin M Neale, Shaun Purcell, Adam S Butterworth, Joanna MM Howson, Heung Man Lee, Yingchang Lu, Soo-Heon Kwak, Wei Zhao, John Danesh, Vincent KL Lam, Kyong Soo Park, Danish Saleheen, Wing Yee So, Claudia HT Tam, Uzma Afzal, David Aguilar, Rector Arya, Tin Aung, Edmund Chan, Carmen Navarro, Ching-Yu Cheng, Domenico Palli, Adolfo Correa, Joanne E Curran, Denis Rybin, Vidya S Farook, Sharon P Fowler, Barry I Freedman, Michael Griswold, Daniel Esten Hale, Pamela J Hicks, Chiea-Chuen Khor, Satish Kumar, Benjamin Lehne, Dorothée Thuillier, Wei Yen Lim, Jianjun Liu, Yvonne T van der Schouw, Marie Loh, Solomon K Musani, Sobha Puppala, William R Scott, Loïc Yengo, Sian-Tsung Tan, Herman A Taylor Jr, Farook Thameem, Gregory Wilson, Tien Yin Wong, Pål Rasmus Njølstad, Jonathan C Levy, Massimo Mangino, Lori L Bonnycastle, Thomas Schwarzmayr, João Fadista, Gabriela L Surdulescu, Christian Herder, Christopher J Groves, Thomas Wieland, Jette Bork-Jensen, Ivan Brandslund, Cramer Christensen, Heikki A Koistinen. The genetic architecture of type 2 diabetes. Nature. 2016 Aug 4;536(7614):41-7. Epub 2016 Jul 11.
PMID:27398621 PMCID:PMC5034897 DOI:10.1038/nature18642

Salman M Tajuddin, Ursula M Schick, John D Eicher, Nathalie Chami, Ayush Giri, Jennifer A Brody, W David Hill, Tim Kacprowski, Jin Li, Leo-Pekka Lyytikäinen, Ani Manichaikul, Evelin Mihailov, Michelle L O’Donoghue, Nathan Pankratz, Raha Pazoki, Linda M Polfus, Albert Vernon Smith, Claudia Schurmann, Caterina Vacchi-Suzzi, Dawn M Waterworth, Evangelos Evangelou, Lisa R Yanek, Amber Burt, Ming-Huei Chen, Frank JA van Rooij, James S Floyd, Andreas Greinacher, Tamara B Harris, Heather M Highland, Leslie A Lange, Yongmei Liu, Reedik Mägi, Mike A Nalls, Rasika A Mathias, Deborah A Nickerson, Kjell Nikus, John M Starr, Jean-Claude Tardif, Ioanna Tzoulaki, Digna R Velez Edwards, Lars Wallentin, Traci M Bartz, Lewis C Becker, Joshua C Denny, Laura M Raffield, John D Rioux, Nele Friedrich, Myriam Fornage, He Gao, Joel N Hirschhorn, David CM Liewald, Stephen S Rich, Andre Uitterlinden, Lisa Bastarache, Diane M Becker, Eric Boerwinkle, Simon de Denus, Erwin P Bottinger, Caroline Hayward, Albert Hofman, Georg Homuth, Ethan Lange, Lenore J Launer, Terho Lehtimäki, Yingchang Lu, Andres Metspalu, Chris J O’Donnell, Rakale C Quarells, Melissa Richard, Eric S Torstenson, Kent D Taylor, Anne-Claire Vergnaud, Alan B Zonderman, David R Crosslin, Ian J Deary, Marcus Dörr, Paul Elliott, Michele K Evans, Vilmundur Gudnason, Mika Kähönen, Bruce M Psaty, Jerome I Rotter, Andrew J Slater, Abbas Dehghan, Harvey D White, Santhi K Ganesh, Ruth JF Loos, Tõnu Esko, Nauder Faraday, James G Wilson, Mary Cushman, Andrew D Johnson, Todd L Edwards, Neil A Zakai, Guillaume Lettre, Alex P Reiner, Paul L Auer. Large-Scale Exome-wide Association Analysis Identifies Loci for White Blood Cell Traits and Pleiotropy with Immune-Mediated Diseases. Am J Hum Genet. 2016 Jul 7;99(1):22-39. doi: 10.1016/j.ajhg.2016.05.003. Epub 2016 Jun 23. PMID:27346689; PMCID:PMC5005433

John D Eicher, Nathalie Chami, Tim Kacprowski, Akihiro Nomura, Ming-Huei Chen, Lisa R Yanek, Salman M Tajuddin, Ursula M Schick, Andrew J Slater, Nathan Pankratz, Linda Polfus, Claudia Schurmann, Ayush Giri, Jennifer A Brody, Leslie A Lange, Ani Manichaikul, W David Hill, Raha Pazoki, Paul Elliot, Evangelos Evangelou, Ioanna Tzoulaki, He Gao, Anne-Claire Vergnaud, Rasika A Mathias, Diane M Becker, Lewis C Becker, Amber Burt, David R Crosslin, Leo-Pekka Lyytikäinen, Kjell Nikus, Jussi Hernesniemi, Mika Kähönen, Emma Raitoharju, Nina Mononen, Olli T Raitakari, Terho Lehtimäki, Mary Cushman, Neil A Zakai, Deborah A Nickerson, Laura M Raffield, Rakale Quarells, Cristen J Willer, Gina M Peloso, Goncalo R Abecasis, Dajiang J Liu, Panos Deloukas, Nilesh J Samani, Heribert Schunkert, Jeanette Erdmann, Myriam Fornage, Melissa Richard, Jean-Claude Tardif, John D Rioux, Marie-Pierre Dube, Simon de Denus, Yingchang Lu, Erwin P Bottinger, Ruth JF Loos, Albert Vernon Smith, Tamara B Harris, Lenore J Launer, Vilmundur Gudnason, Digna R Velez Edwards, Eric S Torstenson, Yongmei Liu, Russell P Tracy, Jerome I Rotter, Stephen S Rich, Heather M Highland, Eric Boerwinkle, Jin Li, Ethan Lange, James G Wilson, Evelin Mihailov, Reedik Mägi, Joel Hirschhorn, Andres Metspalu, Tõnu Esko, Caterina Vacchi-Suzzi, Mike A Nalls, Alan B Zonderman, Michele K Evans, Gunnar Engström, Marju Orho-Melander, Olle Melander, Michelle L O’Donoghue, Dawn M Waterworth, Lars Wallentin, Harvey D White, James S Floyd, Traci M Bartz, Kenneth M Rice, Bruce M Psaty, JM Starr, David CM Liewald, Caroline Hayward, Ian J Deary, Andreas Greinacher, Uwe Völker, Thomas Thiele, Henry Völzke, Frank JA van Rooij, André G Uitterlinden, Oscar H Franco, Abbas Dehghan, Todd L Edwards, Santhi K Ganesh, Sekar Kathiresan, Nauder Faraday, Paul L Auer, Alex P Reiner, Guillaume Lettre, Andrew D Johnson, Global Lipids Genetics Consortium, CARDIoGRAM Exome Consortium, Myocardial Infarction Genetics Consortium. Platelet-Related Variants Identified by Exomechip Meta-analysis in 157,293 Individuals. Am J Hum Genet. 2016 Jul 7;99(1):40-55. doi: 10.1016/j.ajhg.2016.05.005. Epub 2016 Jun 23. PMID: 27346686; PMCID: PMC5005441

Nathalie Chami, Ming-Huei Chen, Andrew J Slater, John D Eicher, Evangelos Evangelou, Salman M Tajuddin, Latisha Love-Gregory, Tim Kacprowski, Ursula M Schick, Akihiro Nomura, Ayush Giri, Samuel Lessard, Jennifer A Brody, Claudia Schurmann, Nathan Pankratz, Lisa R Yanek, Ani Manichaikul, Raha Pazoki, Evelin Mihailov, W David Hill, Laura M Raffield, Amber Burt, Traci M Bartz, Diane M Becker, Lewis C Becker, Eric Boerwinkle, Jette Bork-Jensen, Erwin P Bottinger, Michelle L O’Donoghue, David R Crosslin, Simon de Denus, Marie-Pierre Dubé, Paul Elliott, Gunnar Engström, Michele K Evans, James S Floyd, Myriam Fornage, He Gao, Andreas Greinacher, Vilmundur Gudnason, Torben Hansen, Tamara B Harris, Caroline Hayward, Jussi Hernesniemi, Heather M Highland, Joel N Hirschhorn, Albert Hofman, Marguerite R Irvin, Mika Kähönen, Ethan Lange, Lenore J Launer, Terho Lehtimäki, Jin Li, David CM Liewald, Allan Linneberg, Yongmei Liu, Yingchang Lu, Leo-Pekka Lyytikäinen, Reedik Mägi, Rasika A Mathias, Olle Melander, Andres Metspalu, Nina Mononen, Mike A Nalls, Deborah A Nickerson, Kjell Nikus, Chris J O’Donnell, Marju Orho-Melander, Oluf Pedersen, Astrid Petersmann, Linda Polfus, Bruce M Psaty, Olli T Raitakari, Emma Raitoharju, Melissa Richard, Kenneth M Rice, Fernando Rivadeneira, Jerome I Rotter, Frank Schmidt, Albert Vernon Smith, John M Starr, Kent D Taylor, Alexander Teumer, Betina H Thuesen, Eric S Torstenson, Russell P Tracy, Ioanna Tzoulaki, Neil A Zakai, Caterina Vacchi-Suzzi, Cornelia M van Duijn, Frank JA van Rooij, Mary Cushman, Ian J Deary, Digna R Velez Edwards, Anne-Claire Vergnaud, Lars Wallentin, Dawn M Waterworth, Harvey D White, James G Wilson, Alan B Zonderman, Sekar Kathiresan, Niels Grarup, Tõnu Esko, Ruth JF Loos, Leslie A Lange, Nauder Faraday, Nada A Abumrad, Todd L Edwards, Santhi K Ganesh, Paul L Auer, Andrew D Johnson, Alexander P Reiner, Guillaume Lettre. Exome Genotyping Identifies Pleiotropic Variants Associated with Red Blood Cell Traits. Am J Hum Genet. 2016 Jul 7;99(1):8-21. doi: 10.1016/j.ajhg.2016.05.007. Epub 2016 Jun 23. PMID:27346685; PMCID:PMC5005438

Ching-Ti Liu, Sridharan Raghavan, Nisa Maruthur, Edmond Kato Kabagambe, Jaeyoung Hong, Maggie CY Ng, Marie-France Hivert, Yingchang Lu, Ping An, Amy R Bentley, Anne M Drolet, Kyle J Gaulton, Xiuqing Guo, Loren L Armstrong, Marguerite R Irvin, Man Li, Leonard Lipovich, Denis V Rybin, Kent D Taylor, Charles Agyemang, Nicholette D Palmer, Brian E Cade, Wei-Min Chen, Marco Dauriz, Joseph AC Delaney, Todd L Edwards, Daniel S Evans, Michele K Evans, Leslie A Lange, Aaron Leong, Jingmin Liu, Yongmei Liu, Uma Nayak, Sanjay R Patel, Bianca C Porneala, Laura J Rasmussen-Torvik, Marieke B Snijder, Sarah C Stallings, Toshiko Tanaka, Lisa R Yanek, Wei Zhao, Diane M Becker, Lawrence F Bielak, Mary L Biggs, Erwin P Bottinger, Donald W Bowden, Guanjie Chen, Adolfo Correa, David J Couper, Dana C Crawford, Mary Cushman, John D Eicher, Myriam Fornage, Nora Franceschini, Yi-Ping Fu, Mark O Goodarzi, Omri Gottesman, Kazuo Hara, Tamara B Harris, Richard A Jensen, Andrew D Johnson, Min A Jhun, Andrew J Karter, Margaux F Keller, Abel N Kho, Jorge R Kizer, Ronald M Krauss, Carl D Langefeld, Xiaohui Li, Jingling Liang, Simin Liu, William L Lowe, Thomas H Mosley, Kari E North, Jennifer A Pacheco, Patricia A Peyser, Alan L Patrick, Kenneth M Rice, Elizabeth Selvin, Mario Sims, Jennifer A Smith, Salman M Tajuddin, Dhananjay Vaidya, Mary P Wren, Jie Yao, Xiaofeng Zhu, Julie T Ziegler, Joseph M Zmuda, Alan B Zonderman, Aeilko H Zwinderman, Adebowale Adeyemo, Eric Boerwinkle, Luigi Ferrucci, M Geoffrey Hayes, Sharon LR Kardia, Iva Miljkovic, James S Pankow, Charles N Rotimi, Michele M Sale, Lynne E Wagenknecht, Donna K Arnett, Yii-Der Ida Chen, Michael A Nalls, Michael A Province, WH Linda Kao, David S Siscovick, Bruce M Psaty, James G Wilson, Ruth JF Loos, Josée Dupuis, Stephen S Rich, Jose C Florez, Jerome I Rotter, Andrew P Morris, James B Meigs, AAAG Consortium, CARe Consortium, COGENT-BP Consortium, eMERGE Consortium, MEDIA Consortium, MAGIC Consortium. Trans-ethnic Meta-analysis and Functional Annotation Illuminates the Genetic Architecture of Fasting Glucose and Insulin. Am J Hum Genet. 2016 Jul 7;99(1):56-75. doi: 10.1016/j.ajhg.2016.05.006. Epub 2016 Jun 16. PMID:27321945; PMCID:PMC5005440

Yun Ju Sung, Thomas W Winkler, Alisa K Manning, Hugues Aschard, Vilmundur Gudnason, Tamara B Harris, Albert V Smith, Eric Boerwinkle, Michael R Brown, Alanna C Morrison, Myriam Fornage, Li‐An Lin, Melissa Richard, Traci M Bartz, Bruce M Psaty, Caroline Hayward, Ozren Polasek, Jonathan Marten, Igor Rudan, Mary F Feitosa, Aldi T Kraja, Michael A Province, Xuan Deng, Virginia A Fisher, Yanhua Zhou, Lawrence F Bielak, Jennifer Smith, Jennifer E Huffman, Sandosh Padmanabhan, Blair H Smith, Jingzhong Ding, Yongmei Liu, Kurt Lohman, Claude Bouchard, Tuomo Rankinen, Treva K Rice, Donna Arnett, Karen Schwander, Xiuqing Guo, Walter Palmas, Jerome I Rotter, Tamuno Alfred, Erwin P Bottinger, Ruth JF Loos, Najaf Amin, Oscar H Franco, Cornelia M Duijn, Dina Vojinovic, Daniel I Chasman, Paul M Ridker, Lynda M Rose, Sharon Kardia, Xiaofeng Zhu, Kenneth Rice, Ingrid B Borecki, Dabeeru C Rao, W James Gauderman, L Adrienne Cupples. An Empirical Comparison of Joint and Stratified Frameworks for Studying G × E Interactions: Systolic Blood Pressure and Smoking in the CHARGE Gene-Lifestyle Interactions Working Group. Genet Epidemiol. 2016 Jul;40(5):404-15. doi: 10.1002/gepi.21978. Epub 2016 May 27. PMID:27230302; PMCID:PMC4911246

Lim E, Uddin M, De Rubeis S, Chan Y, Kamumbu A, Zhang X, D’Gama A, Kim S, Hill S, Goldberg A, Poultney C, Minshew N, Kushima I, Aleksic B, Ozaki N, Parellada M, Arando C, Penzo M, Carracedo A, Kolevzon A, Hultman C, Weiss L, Fromer M, Chiocchetti AG, Freitag C, Church G, Scherer S, Buxbaum JD, Walsh C. (In press) Rates, Distribution, and Implications of Post-zygotic Mutations in Autism Spectrum Disorder. Nature Neuroscience.

Pollak, J., Rai, K. G., Funk, C. C., Arora, S., Lee, E., Zhu, J., Price, N. D., Paddison, P. J., Ramirez, J. M., and Rostomily, R. C., ‘Ion Channel Expression Patterns in Glioblastoma Stem Cells with Functional and Therapeutic Implications for Malignancy’, PLoS One, 12 (2017), e0172884. PMID: 28264064; PMCID:PMC5338779; DOI:10.1371/journal.pone.0172884

Cohain, A., Divaraniya, A. A., Zhu, K., Scarpa, J. R., Kasarskis, A., Zhu, J., Chang, R., Dudley, J. T., and Schadt, E. E., ‘Exploring the Reproducibility of Probabilistic Causal Molecular Network Models’, Pac Symp Biocomput, 22 (2016), 120-31. PMID:27896968;PMCID:PMC5161348

Gong, Y., Wang, L., Chippada-Venkata, U., Dai, X., Oh, W. K., and Zhu, J.*, ‘Constructing Bayesian Networks by Integrating Gene Expression and Copy Number Data Identifies Nlgn4y as a Novel Regulator of Prostate Cancer Progression’, Oncotarget (2016). PMID: 27626693; PMCID:PMC5356583; DOI:10.18632/oncotarget.11925

Wang, L., Oh, W. K., and Zhu, J.*, ‘Disease-Specific Classification Using Deconvoluted Whole Blood Gene Expression’, Sci Rep, 6 (2016), 32976. PMID:27596246; PMCID:PMC5011717; DOI:10.1038/srep32976

Yang, J., Huang, T., Song, W. M., Petralia, F., Mobbs, C. V., Zhang, B., Zhao, Y., Schadt, E. E., Zhu, J., and Tu, Z., ‘Discover the Network Mechanisms Underlying the Connections between Aging and Age-Related Diseases’, Sci Rep, 6 (2016), 32566. PMID: 27582315; PMCID:PMC5007654; DOI:10.1038/srep32566

Epel, E. S., Puterman, E., Lin, J., Blackburn, E. H., Lum, P. Y., Beckmann, N. D., Zhu, J., Lee, E., Gilbert, A., Rissman, R. A., Tanzi, R. E., and Schadt, E. E., ‘Meditation and Vacation Effects Have an Impact on Disease-Associated Molecular Phenotypes’, Transl Psychiatry, 6 (2016), e880. PMID: 27576169; PMCID:PMC5022094; DOI:10.1038/tp.2016.164

Fromer, M., Roussos, P., Sieberts, S. K., Johnson, J. S., Kavanagh, D. H., Perumal, T. M., Ruderfer, D. M., Oh, E. C., Topol, A., Shah, H. R., Klei, L. L., Kramer, R., Pinto, D., Gumus, Z. H., Cicek, A. E., Dang, K. K., Browne, A., Lu, C., Xie, L., Readhead, B., Stahl, E. A., Xiao, J., Parvizi, M., Hamamsy, T., Fullard, J. F., Wang, Y. C., Mahajan, M. C., Derry, J. M., Dudley, J. T., Hemby, S. E., Logsdon, B. A., Talbot, K., Raj, T., Bennett, D. A., De Jager, P. L., Zhu, J., Zhang, B., Sullivan, P. F., Chess, A., Purcell, S. M., Shinobu, L. A., Mangravite, L. M., Toyoshiba, H., Gur, R. E., Hahn, C. G., Lewis, D. A., Haroutunian, V., Peters, M. A., Lipska, B. K., Buxbaum, J. D., Schadt, E. E., Hirai, K., Roeder, K., Brennand, K. J., Katsanis, N., Domenici, E., Devlin, B., and Sklar, P., ‘Gene Expression Elucidates Functional Impact of Polygenic Risk for Schizophrenia’, Nat Neurosci (2016). PMID:27668389; PMCID:PMC5083142;DOI:10.1038/nn.4399

Katsyv, I., Wang, M., Song, W. M., Zhou, X., Zhao, Y., Park, S., Zhu, J., Zhang, B., and Irie, H. Y., ‘Eprs Is a Critical Regulator of Cell Proliferation and Estrogen Signaling in Er+ Breast Cancer’, Oncotarget (2016). PMID:27612429; PMCID:PMC5342500; DOI:10.18632/oncotarget.11870

Wang, Q., Lin, L., Yoo, S., Wang, W., Blank, S., Fiel, M. I., Kadri, H., Luan, W., Warren, L., Zhu, J., and Hiotis, S. P., ‘Impact of Non-Neoplastic Vs Intratumoural Hepatitis B Viral DNA and Replication on Hepatocellular Carcinoma Recurrence’, Br J Cancer, 115 (2016), 841-7. PMID:27537392; PMCID:PMC5046201 [Available on 2017-09-27] DOI:10.1038/bjc.2016.239

Collazo-Lorduy, A., Castillo-Martin, M., Wang, L., Patel, V., Iyer, G., Jordan, E., Al-Ahmadie, H., Leonard, I., Oh, W. K., Zhu, J., McBride, R. B., Cordon-Cardo, C., Solit, D. B., Sfakianos, J. P., and Galsky, M. D., ‘Urachal Carcinoma Shares Genomic Alterations with Colorectal Carcinoma and May Respond to Epidermal Growth Factor Inhibition’, Eur Urol (2016). Eur Urol. 2016 Nov;70(5):771-775. doi: 10.1016/j.eururo.2016.04.037. Epub 2016 May 10. PMID:27178450; PMCID:PMC5489411 [Available on 2017-11-01] DOI:10.1016/j.eururo.2016.04.037

Akerman I, Tu Z, Beucher A, Rolando DM, Sauty-Colace C, Benazra M, Nakic N, Yang J, Wang H, Pasquali L, Moran I, Garcia-Hurtado J, Castro N, Gonzalez-Franco R, Stewart AF, Bonner C, Piemonti L, Berney T, Groop L, Kerr-Conte J, Pattou F, Argmann C, Schadt E, Ravassard P, Ferrer J. Human Pancreatic β Cell lncRNAs Control Cell-Specific Regulatory Networks. Cell Metab. 2017 Feb 7;25(2):400-411. doi: 10.1016/j.cmet.2016.11.016. Epub 2016 Dec 29. PubMed PMID: 28041957; PubMed Central PMCID: PMC5300904.

Yang J, Huang T, Song WM, Petralia F, Mobbs CV, Zhang B, Zhao Y, Schadt EE, Zhu J, Tu Z. Discover the network mechanisms underlying the connections between aging and age-related diseases. Sci Rep. 2016 Sep 1;6:32566. doi: 10.1038/srep32566. PubMed PMID: 27582315; PubMed Central PMCID: PMC5007654.

Uzilov AV, Ding W, Fink MY, Antipin Y, Brohl AS, Davis C, Lau CY, Pandya C, Shah H, Kasai Y, Powell J, Micchelli M, Castellanos R, Zhang Z, Linderman M, Kinoshita Y, Zweig M, Raustad K, Cheung K, Castillo D, Wooten M, Bourzgui I, Newman LC, Deikus G, Mathew B, Zhu J, Glicksberg BS, Moe AS, Liao J, Edelmann L, Dudley JT, Maki RG, Kasarskis A, Holcombe RF, Mahajan M, Hao K, Reva B, Longtine J, Starcevic D, Sebra R, Donovan MJ, Li S, Schadt EE, Chen R. Development and clinical application of an integrative genomic approach to personalized cancer therapy. Genome Med. 2016 Jun 1;8(1):62. doi: 10.1186/ s13073-016-0313-0. PubMed PMID: 27245685; PubMed Central PMCID: PMC4888213.

1. - 07/2015-07/2016: 7 in total

1. Valle-García D, Qadeer ZA, McHugh DS, Ghiraldini FG, Chowdhury AH, Hasson D, Dyer MA, Recillas-Targa F, Bernstein E. ATRX binds to atypical chromatin domains at the 3′ exons of zinc finger genes to preserve H3K9me3 enrichment. Epigenetics. (2016 Mar 30);11(6):398-414. http://www.ncbi.nlm.nih.gov/pubmed/27029610

2. Rialdi A, Campisi L, Zhao N, Lagda AC, Pietzsch C, Ho JS, Martinez-Gil L, Fenouil R, Chen X, Edwards M, Metreveli G, Jordan S, Peralta Z, Munoz-Fontela C, Bouvier N, Merad M, Jin J, Weirauch M, Heinz S, Benner C, van Bakel H, Basler C, García-Sastre A, Bukreyev A, Marazzi I. Topoisomerase 1 inhibition suppresses inflammatory genes and protects from death by inflammation. Science. (2016 Apr 28); 352(6289).http://www.ncbi.nlm.nih.gov/pubmed/27127234

3. Heaton NS, Moshkina N, Fenouil R, Gardner TJ, Aguirre S, Shah PS, Zhao N, Manganaro L, Hultquist JF, Noel J, Sachs DH, Hamilton J, Leon PE, Chawdury A, Tripathi S, Melegari C, Campisi L, Hai R, Metreveli G, Gamarnik AV, García-Sastre A, Greenbaum B, Simon V, Fernandez-Sesma A, Krogan NJ, Mulder LC, van Bakel H, Tortorella D, Taunton J, Palese P, Marazzi I. Targeting Viral Proteostasis Limits Influenza Virus, HIV, and Dengue Virus Infection. Immunity. (2016 Jan 19); 44(1):46-58. http://www.ncbi.nlm.nih.gov/pubmed/26789921

4. Pak TR, Altman DR, Attie O, Sebra R, Hamula CL, Lewis M, Deikus G, Newman LC, Fang G, Hand J, Patel G, Wallach F, Schadt EE, Huprikar S, van Bakel H, Kasarskis A, Bashir A.
Whole-genome sequencing identifies emergence of a quinolone resistance mutation in a case of Stenotrophomonas maltophilia bacteremia. Antimicrob Agents Chemother. (2015 Aug 31); 59(11):7117-20.http://www.ncbi.nlm.nih.gov/pubmed/26324280

5. Chung C-Y., Sun Z., Mullokandov G., Bosch-Gutierrez A., Qadeer Z.A., Cihan E., Rapp Z., Parsons R., Aguirre-Ghiso J.A., Farias E.F., Brown B.,Gaspar-Maia A., Bernstein E. Cbx8 acts non-canonically with Wdr5 to promote mammary tumorigenesis. Cell Reports(2016 Jun 22 ). http://www.ncbi.nlm.nih.gov/pubmed/27346354

6. Sanders SJ, He X, Willsey AJ, Ercan-Sencicek AG, Samocha KE, Cicek AE, et al. Insights into Autism Spectrum Disorder Genomic Architecture and Biology from 71 Risk Loci. Neuron. (2015 Sep 23);87(6):1215–33.http://www.ncbi.nlm.nih.gov/pubmed/26402605

7. Quilez J, Guilmatre A, Garg P, Highnam G, Mittelman D, Sharp AJ. Polymorphic tandem repeats within gene promoters act as modifiers of gene expression and DNA methylation in humans. Nucleic Acids. (2016 Apr 7); 44(8):3750-62.http://www.ncbi.nlm.nih.gov/pubmed/27060133

8. Watson CT, Roussos P, Garg P, Ho D, Azam N, Haroutunian V, Sharp AJ. Genome-wide DNA methylation profiling in the superior temporal gyrus reveals epigenetic signatures associated with Alzheimer’s disease. Genome Med. (2016 Jan 19); 8(1):5.http://www.ncbi.nlm.nih.gov/pubmed/26803900

9. Gymrek M, Willems T, Guilmatre A, Zeng H, Markus B, Georgiev S, Daly MJ, Price AL, Pritchard J, Sharp AJ, Erlich Y. Abundant contribution of short tandem repeats to gene expression variation in humans. Nature Genet. (2015 Dec 7); 48(1):22-9.http://www.ncbi.nlm.nih.gov/pubmed/26642241

10. Li, C. W., Menconi, F., Osman, R., Mezei, M., Jacobson, E. M., Concepcion, E., David, C. S., Kastrinsky, D. B., Ohlmeyer, M., and Tomer, Y. Identifying a Small Molecule Blocking Antigen Presentation in Autoimmune Thyroiditis, J Biol Chem. (2015 Dec 24); 291(8): 4079-4090. http://www.ncbi.nlm.nih.gov/pubmed/26703475

11. Osman, R., Mezei, M., and Engel, S. The Role of Protein “Stability Patches” in Molecular Recognition: A Case Study of the Human Growth Hormone-Receptor Complex, J Comput Chem. (2015 Dec 21); 37(10): 913-919.http://www.ncbi.nlm.nih.gov/pubmed/26691434

12. Long, Q., Argmann, C., Houten, S. M., Huang, T., Peng, S., Zhao, Y., Tu, Z., and Zhu, J. *, ‘Inter-Tissue Coexpression Network Analysis Reveals Dpp4 as an Important Gene in Heart to Blood Communication’, Genome Med. (2016 Feb 9);8(1):15. http://www.ncbi.nlm.nih.gov/pubmed/26856537

13. Lee, E., Ito, K., Zhao, Y., Schadt, E. E., Irie, H. Y., and Zhu, J.*, Inferred miRNA activity identifies miRNA-mediated regulatory networks underlying multiple cancers, Bioinformatics (2015 Sep 10);32(1):96-105. http://www.ncbi.nlm.nih.gov/pubmed/26358730

14. Wang, L., Gong, Y., Chippada-Venkata, U., Heck, M. M., Retz, M., Nawroth, R., Galsky, M., Tsao, C. K., Schadt, E., de Bono, J., Olmos, D., Zhu, J.*, and Oh, W. K.*, A Robust Blood Gene Expression-Based Prognostic Model for Castration-Resistant Prostate Cancer, BMC Med. (2015 Aug 21);13:20.http://www.ncbi.nlm.nih.gov/pubmed/26297150

15. Kovatch, P., Costa, A., Giles, Z., Fluder, E., Cho, H., Mazurkova, S. (2015). Big Omics Data Experience. Supercomputing 2015. PMID: 30788464 PMCID: PMC6379072 DOI: 10.1145/2807591.2807595. http://dl.acm.org/citation.cfm?id=2807595