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BODE2-Publication

Dec 10, 2020 | Research Services

Year 2020: 61

  1. 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
  2. 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
  3. 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
  4. Andrews SJ, Goate A. 2019. Mendelian randomization indicates that TNF is not causally associated with Alzheimer’s disease. Neurobiology of aging 84:241 e1- e3
  5. Andrews SJ, Goate A, Anstey KJ. 2020. Association between alcohol consumption and Alzheimer’s disease: A Mendelian randomization study. Alzheimer’s & dementia : the journal of the Alzheimer’s Association 16:345-53
  6. 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
  7. 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
  8. 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
  9. 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. The Journal of allergy and clinical immunology 145:1219-30
  10. 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. Nat Commun 11:4634-
  11. 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-
  12. 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
  13. 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
  14. 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:eabc1917
  15. 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
  16. Han L, Zhao X, Benton ML, Perumal T, Collins RL, et al. 2020. Functional annotation of rare structural variation in the human brain. Nat Commun 11:2990-
  17. Hoffman GE, Bendl J, Girdhar K, Roussos P. 2020. decorate: differential epigenetic correlation test. Bioinformatics 36:2856-61
  18. Hoffman GE, Roussos P. 2020. dream: Powerful differential expression analysis for repeated measures designs. Bioinformatics
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. Kapoor A, Provasi D, Filizola M. 2020. Atomic-Level Characterization of the Methadone-Stabilized Active Conformation of µ-Opioid Receptor. Molecular Pharmacology:mol.119.119339
  26. Kapoor A, Provasi D, Filizola M. 2020. Atomic-Level Characterization of the Methadone-Stabilized Active Conformation of <em>µ</em>-Opioid Receptor. Molecular Pharmacology 98:475
  27. 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
  28. 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:
  29. 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-
  30. 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 <em>TP53</em> mutations. bioRxiv:2020.07.16.207605
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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
  37. Nešić D, Zhang Y, Spasic A, Li J, Provasi D, et al. 2020. Cryo-Electron Microscopy Structure of the αIIbβ3-Abciximab Complex. Arterioscler Thromb Vasc Biol 40:624-37
  38. 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
  39. 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<sup>+</sup> B cells. bioRxiv:2020.05.05.077362
  40. Perumal D, Imai N, Laganà A, Finnigan J, Melnekoff D, et al. 2020. Mutation-derived Neoantigen-specific T-cell Responses in Multiple Myeloma. Clin Cancer Res 26:450-64
  41. 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
  42. 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
  43. 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. Frontiers in Immunology 11
  44. 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
  45. 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
  46. 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
  47. 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
  48. 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
  49. 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
  50. 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
  51. 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
  52. Wang H-Y, MacDonald ML, Borgmann-Winter KE, Banerjee A, Sleiman P, et al. 2020. mGluR5 hypofunction is integral to glutamatergic dysregulation in schizophrenia. Mol Psychiatry 25:750-60
  53. 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-
  54. 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
  55. 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
  56. 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
  57. 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-
  58. 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. Nat Commun 11:1600
  59. 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
  60. 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
  61. 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. Nat Commun 11:4799