Publications

Selected Journal Papers/Book Chapters (*co-first author, § corresponding author, † co-senior author)

  1. Qian Wang, Yuanxi Zhang, Minghui Wang, Won-Min Song, Qi,Shen, Andrew McKenzie, Insup Choi, Xianxiao Zhou, Ping-Yue Pan, Zhenyu Yue§ and Bin Zhang§. (2019) The Landscape of Multiscale Transcriptomic Networks and Key Regulators in Parkinson’s Disease. Nature Communications 10, Article number: 5234 (2019). 10.1038/s41467-019-13144-y.
  2. Chang Wang, Christian V. Forst, Tsui-wen Chou, Adam Geber, Minghui Wang, Wissam Hamou, Melissa Smith, Robert Sebra, Bin Zhang, Bin Zhou, and Elodie Ghedin. (2019) Cell-to-cell variation in defective virus expression and effects on host responses during influenza virus infection. mBio (in press)
  3. Won-Min Song, Xiandong Lin, Xuehong Liao, Dan Hu, Jieqiong Lin, Umut Sarpel, Yunbin Ye, Yael Feferman, Daniel M. Labow, Martin J. Walsh, Xiongwei Zheng, and Bin Zhang. (2019) Multiscale Network Analysis Reveals Molecular Mechanisms and Key Regulators of the Tumor Microenvironment in Gastric Cancer. International Journal of Cancer doi: 10.1002/ijc.32643. PMID: 31463974
  4. Qi Shen, Goayu Xiao, Yingwei Zheng, Jie Wang, Yue Liu, Xutao Zhu, Fan Jia, Peng Su,Binbin Nie, Fuqiang Xu, Bin Zhang. (2019) ARMBIS: Accurate and Robust Matching of Brain Image Sequences from Multiple Modal Imaging Techniques. Bioinformatics pii: btz404. doi: 10.1093/bioinformatics/btz404. PMID: 31114841
  5. Hyunok Choi, Won-min Song, Minghui Wang, Radim J. Sram and Bin Zhang. (2019) Benzo[a]pyrene is associated with dysregulated myelo-lymphoid hematopoiesis in asthmatic children. Environment International 128 . PMID: 31059917
  6. Fanyan Meng, Ling Wu, Lun Dong, Allison V. Mitchell, C. James Block, Jenney Liu, Haijun Zhang, Qing Lu, Won-min Song, Bin Zhang, Wei Chen, Jiani Hu, Jian Wang, Qifeng Yang, Maik Hüttemann and Guojun Wu. (2019) EGFL9 promotes breast cancer metastasis by inducing cMET activation and metabolic reprogramming. Nature Communications 10, 5033 (2019) doi:10.1038/s41467-019-13034-3. PMID: 31695034
  7. Véronik Lachance, Qian Wang, Eric Sweet, Insup Choi, Cui-Zan Cai, Xu-Xu Zhuang, Yuanxi Zhang, Jessica Li Jiang, Robert D. Blitzer, Ozlem Bozdagi-Gunal, Bin Zhang, Jia-Hong Lu and Zhenyu Yue. (2019) Autophagy protein NRBF2 has reduced expression in Alzheimer’s brains and modulates memory and amyloid-beta homeostasis in mice. Molecular Neurodegeneration doi: 10.1186/s13024-019-0342-4.
  8. Jialiang Yang, Shouneng Peng, Bin Zhang, Sander Houten, Eric Schadt, Jun Zhu, Yousin Suh, Zhidong Tu. (2019) Human geroprotector discovery by targeting the converging subnetworks of aging and age-related diseases. Geroscience. doi: 10.1007/s11357-019-00106-x.
  9. Yiyuan Liu, Minghui Wang, Edoardo M. Marcora, Bin Zhang and Alison M. Goate. (2019) Promoter DNA hypermethylation – Implications for Alzheimer’s disease. Neuroscience Letters 711:134403. PMID: 31351091
  10. Rut Tejero, Yong Huang, Igor Katsyv, Michael Kluge, Jung-Yi Lin, Jessica Tome-Garcia, Nicolas Daviaud, Bin Zhang, Caroline Friedel, Nadejda Tsankova, Hongyan Zou and Roland Horst Friedel. (2019) Gene signatures of quiescent glioblastoma cells reveal mesenchymal shift and interactions with niche microenvironment. EBioMedicine vol 42: 252-269. https://doi.org/10.1016/j.ebiom.2019.03.064. PMID: 30952620
  11. Eduardo J. Contijoch, Graham J. Britton1, Chao Yang, Ilaria Mogno, Zhihua Li, Ruby Ng, Sean R. Llewellyn, Sheela Hira, Crystal Johnson, Keren Rabinowitz, Revital Barkan, Iris Dotan, Robert P. Hirten, Shih-Chen Fu, Nancy Yang, Tramy Luong, Philippe R. Labrias, Sergio Lira, Inga Peter, Ari Grinspan, Jose Clemente, Roman Kosoy, Seunghee Kim-Schulze, Xiaochen Qin, Anabella Castillo, Amanda Hurley, Ashish Atreja, Jason Rogers, Farah Fasihuddin, Merjona Saliaj, Amy Nolan, Pamela Reyes-Mercedes, Carina Rodriguez, Sarah Aly, Kenneth Santa-Cruz, Lauren Peters, Mayte Suárez-Fariñas, Ruiqui Huang, Ke Hao, Jun Zhu, Bin Zhang, Bojan Losic, Aritz Irizar, Won-Min Song, Antonio Di Narzo, Wenhui Wang, Benjamin Cohen, Christopher DiMaio, David Greenwald, Steven Itzkowitz, Aimee Lucas, James Marion, Elana Maser, Ryan Ungaro, Steven Naymagon, Joshua Novak, Ionnis Oikonomous, Brijen Shah, Thomas Ullman, Peter Rubin, Asher Kornbluth, James George, Peter Legnani, Shannon Telesco, Jacqueline Perrigoue, Joshua R. Friedman, Judy Cho, Jean-Frederic Colombel, Carrie Brodmerke, Scott Plevy, Eric Schadt, Carmen Argmann, Marla Dubinsky, Andrew Kasarskis, Bruce Sands, Jeremiah J. Faith. (2019) Gut microbiota density influences host physiology and is shaped by host and microbial factors. eLife pii: e40553. doi: 10.7554/eLife.40553. PMID: 30666957
  12. Litvinchuk A, Wan YW, Swartzlander DB, Chen F, Cole A, Propson NE, Wang Q, Zhang B, Liu Z, Zheng H. (2018) Complement C3aR Inactivation Attenuates Tau Pathology and Reverses an Immune Network Deregulated in Tauopathy Models and Alzheimer’s Disease. Neuron 100(6):1337-1353.e5. doi: 10.1016/j.neuron.2018.10.031. PMID: 30415998
  13. Min Qin, Hong-Lian Li, Jian Bao, Yiyuan Xia, Dan Ke, Qun Wang, Rong Liu, Jian-Zhi Wang, Bin Zhang, Xiji Shu and Xiaochuan Wang. SET SUMOylation promotes its cytoplasmic retention and induces tau pathology and cognitive impairments. Acta Neuropathologica Communications 7(1):21. doi: 10.1186/s40478-019-0663-0. PMID: 30767764
  14. Brenden Chen, Minghui Wang, Lin Gan, Bin Zhang, Robert J Desnick and Makiko Yasuda. (2019) Characterization of the Hepatic Transcriptome Following Phenobarbital Induction in the AIP Mice. Molecular Genetics and Metabolism doi:10.1016/j.ymgme.2018.12.010. PMID: 30777612
  15. Yuji Kajiwara, Erming Wang, Minghui Wang, Wun Chey Sin, Kristen Brenand, Eric Schadt, Christian C. Naus, Joseph Buxbaum and Bin Zhang. (2018) GJA1 (connexin43) is a Key Regulator of Alzheimer’s Disease Pathogenesis. Acta Neuropathologica Communications 6:144. PMID: 30577786
  16. Fang Huang, Minghui Wang, Rong Liu, Jian-Zhi Wang, Eric Schadt, Vahram Haroutunian, Pavel Katsel, Bin Zhang and Xiaochuan Wang§. (2018) CDT2 Controlled Cell Cycle Reentry Regulates the Pathogenesis of Alzheimer’s Disease. Alzheimer’s & Dementia pii: S1552-5260(18)33522-2. doi: 10.1016/j.jalz.2018.08.013. PMID: 30321504
  17. Cheng Lin, Jingfeng Zong, Wansong Lin, Minghui Wang, Yuanji Xu, Rui Zhou, Shaojun Lin, Qiaojuan Guo, Honglin Chen, Yunbin Ye, Bin Zhang and Jianji Pan§. (2018) EBV-miR-BART8-3p induces epithelial-mesenchymal transition and promotes metastasis of nasopharyngeal carcinoma cells through activating NF-κB and Erk1/2 pathways. Journal of Experimental & Clinical Cancer Research 37:283. doi: 10.1186/s13046-018-0953-6. PMID: 30477559
  18. Prashanth Rajarajan, Tyler Borrman, Will Liao, Nadine Schrode, Erin Flaherty, Charlize Casiño, Samuel Powell, Chittampalli Yashaswini, Elizabeth LaMarca, Bibi Kassim, Behnam Javidfar, Sergio Espeso-Gil, Aiqun Li, Hyejung Won, Daniel H Geschwind, Seok-Man Ho, Matthew MacDonald, Gabriel E. Hoffman, Panos Roussos, Bin Zhang, Chang-Gyu Hahn, Zhiping Weng, Kristen J. Brennand and Schahram Akbarian. Neuron-specific Signatures in the Chromosomal Connectome Are Associated with Schizophrenia Risk. Science 362(6420). pii: eaat4311. doi: 10.1126/science.aat4311. PMID: 30545851
  19. Qing Zhang, Yiyuan Xia, Hongbin Luo, Sheng Huang, Yongjun Wang, Yangping Shentu, Yacoubou Abdoul Razak Mahaman, Fang Huang, Dan Ke, Qun Wang, Rong Liu, Jian-Zhi Wang, Bin Zhang and Xiaochuan Wang. (2018) Codonopsis pilosula Polysaccharide Attenuates Tau Hyperphosphorylation and Cognitive Impairments in hTau Infected Mice. Frontiers in Molecular Neuroscience. doi: 10.3389/fnmol.2018.00437. PMID: 30542264
  20. Maibouge Tanko Mahamane Salissou, Yacoubou Abdoul Razak Mahaman, Feiqi Zhu, Fang Huang, Yuman Wang, Zhendong Xu, Dan Ke, Qun Wang, Rong Liu, Jian-Zhi Wang, Bin Zhang and Xiaochuan Wang. Methanolic extract of Tamarix Gallica attenuates hyperhomocysteinemia induced AD-like pathology and cognitive impairments in rats. Ageing 10(11):3229-3248. doi: 10.18632/aging.101627. PMID: 30425189
  21. Emilsson V, llkov M, Lamb JR, Horman SR, Aspelund T, Trifonov V, Gudmundsson EF, Jakobsdottir J, Manolescu A, Knuth, MW, Klock HE, Lesley HA, To J, Zhang J, Harris TB,  Launer LJ, Eiriksdottir G, Zhu J, Zhang B, Smith AV, Jennings LL, Orth AP, Gudnason V. (2018) Co-regulatory networks of human serum proteins link genetics to disease. Science 361(6404):769-773. doi: 10.1126/science.aaq1327. PMID: 30072576
  22. Towfique Raj, Yang I. Li, Garrett Wong, Jack Humphrey, Minghui Wang, Satesh Ramdhani, Ying-chih Wang, Bernard Ng, Ishaan Gupta, Vahram Haroutunian, Eric E. Schadt, Tracy Young-Pearse, Sara Mostafavi, Bin Zhang, Pamela Sklar, David Bennett, and Philip L. De Jager. (2018) Integrative transcriptome analyses of the aging brain implicate altered splicing in Alzheimer’s disease susceptibility. Nature Genetics 50(11):1584-1592. doi: 10.1038/s41588-018-0238-1. PMID: 30297968
  23. Jessica Tome Garcia, Parsa Erfani, German Nudelman, Alexander Tsankov, Igor Katsyv, Rut Tejero-Villalba, Bin Zhang, Martin Walsh, Roland Friedel, Elena Zaslavsky, and Nadejda Tsankova. (2018) Analysis of chromatin accessibility uncovers TEAD1 as a regulator of migration in human glioblastoma. Nature Communications 9(1):4020. doi: 10.1038/s41467-018-06258-2. PMID: 30275445
  24. Jean-Vianney Haure-Mirande, Minghui Wang, Mickael Audrain, Tomas Fanutza, Soong Ho Kim, Szilvia Heja, Ben Readhead, Joel Dudley, Robert Blitzer, Eric Schadt, Bin Zhang§, Michelle. Ehrlich§ and Samuel Gandy§. (2018) 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 24(3):431-446. doi: 10.1038/s41380-018-0255-6. PMID:30283032. PMID: 30283032
  25. Mickael Audrain, Jean-Vianney Haure-Mirande, Minghui Wang, Soong Ho Kim, Tomas Fanutza, Paramita Chakrabarty, Paul Fraser, Peter H St George-Hyslop, Todd E. Golde, Robert D. Blitzer, Eric E. Schadt, Bin Zhang†, Michelle E. Ehrlich† and Sam Gandy†. (2018) 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 doi: 10.1038/s41380-018-0258-3. PMID:30283031
  26. Xianxiao Zhou, Minghui Wang, Igor Katsyv, Hanna Irie and Bin Zhang. (2018) EMUDRA: Ensemble of Multiple Drug Repositioning Approaches to Improve Prediction Accuracy. Bioinformatics 34(18):3151-3159. doi: 10.1093/bioinformatics/bty325.
  27. Hui-Ming Chen, William van der Touw, Yuan Shuo Wang, Kyeongah Kang, Sunny Mai, Jilu Zhang, Dayanira Alsina-Beauchamp, J. Andrew Duty, Sathish Kumar Mungamuri, Bin Zhang, Thomas Moran, Richard Flavell, Stuart Aaronson, Suresh Ramanathan, Raja Flores, Ping-Ying Pan1, Shu-Hsia Chen. (2018) Blocking immunoinhibitory receptor LILRB2 reprograms tumor-associated myeloid cells and promotes antitumor immunity. Journal of Clinical Investigation 128(12):5647-5662. doi: 10.1172/JCI97570. PMID: 30352428
  28. Minghui Wang, Noam Beckmann, Panos Roussos, Erming Wang, Xianxiao Zhou, Qian Wang, Chen Ming, Ryan Neff, Weiping Ma, John F. Fullard, Mads E. Hauberg, Jaroslav Bendl, Mette A. Peters, Ben Logsdon, Pei Wang, Milind Mahajan, Lara Mangravite, Eric B. Dammer, Duc M. Duong, James J. Lah, Nicholas T. Seyfried, Allan I. Levey, Joseph Buxbaum, Michelle Ehrlich, Sam Gandy, Pavel Katsel, Vahram Haroutunian, Eric Schadt, and Bin Zhang. (2018) The Mount Sinai cohort of large-scale genomic, transcriptomic and proteomic data in Alzheimer’s disease. Nature Scientific Data 5:180185. doi: 10.1038/sdata.2018.185. PMID: 30204156
  29. Andrew T. McKenzie, Minghui Wang, Mads E. Hauberg, John F. Fullard, Alexey Kozlenkov, Alexandra Keenan, Stella Dracheva, Patrizia Casaccia, Panos Roussos, Bin Zhang. (2018) Brain Cell Type Specific Gene Expression and Co-expression Network Architectures. Scientific Reports 8(1):8868. doi: 10.1038/s41598-018-27293-5. [one of the top 100 read neuroscience papers for Scientific Reports in 2018]. PMID: 29892006
  30. Cesar L. Moreno, Lucio Della Guardia, Valeria Shnyder, Maitane Ortiz-Virumbrales, Ilya Kruglikov, Bin Zhang, Eric E. Schadt, Rudolph E. Tanzi, Scott Noggle, Christoph Buettner and Sam Gandy. (2018) iPSC-derived familial Alzheimer’s PSEN2N141I cholinergic neurons exhibit mutation-dependent molecular pathology corrected by insulin signaling. Molecular Neurodegeneration 13(1):33. doi: 10.1186/s13024-018-0265-5. PMID: 29945658
  31. Michiko Sekiya, Minghui Wang, Naoki Fujisaki, Yasufumi Sakakibara, Xiuming Quan, Michelle E. Ehrlich, Philip L. De Jager, David A. Bennett, Eric E. Schadt, Sam Gandy, Kanae Andom, Bin Zhang and Koichi M. Iijima§. (2018) Molecular and Pathological Interactions among Aβ42, Tau, TREM2, and TYROBP in Drosophila Models. Genome Medicine 10(1):26. doi: 10.1186/s13073-018-0530-9. PMID: 29598827
  32. Jian Bao, Min Qin, Yacoubou Abdoul Razak Mahaman, Bin Zhang, Fang Huang, Kuan Zeng, Yiyuan Xia, Dan Ke, Qun Wang, Rong Liu, Jian-Zhi Wang, Keqiang Ye and Xiaochuan Wang. (2018) BACE1 SUMOylation increases its stability and escalates the protease activity in Alzheimer’s disease. Proc Natl Acad Sci USA. 115(15):3954-3959. doi: 10.1073/pnas.1800498115. PMID: 29581300
  33. Marnix Lameijer, Tina Binderup, Mandy M. T. van Leent1, Max L. Senders, Francois Fay, Joost Malkus, Brenda L. Sanchez-Gaytan, Abraham J. P. Teunissen, Nicolas Karakatsanis, Philip Robson, Xianxiao Zhou, Yuxiang Ye, Gregory Wojtkiewicz, Jun Tang, Tom T. P. Seijkens, Jeffrey Kroon, Erik S. G. Stroes, Andreas Kjaer, Jordi Ochando, Thomas Reiner, Carlos Pérez-Medina, Claudia Calcagno, Edward A. Fischer, Bin Zhang, Ryan E. Temel, Filip K. Swirski, Matthias Nahrendorf, Zahi A. Fayad, Esther Lutgens, Willem J. M. Mulder, and Raphaël Duivenvoorden. (2018) Efficacy and safety assessment of a TRAF6-targeted nanoimmunotherapy in atherosclerotic mice and non-human primates. Nature Biomedical Engineering. doi:10.1038/s41551-018-0221-2. PMID: 30936448
  34. Jian Bao, Yacoubou A. R. Mahaman, Rong Liu, Jian-Zhi Wang, Zhiguo Zhang, Bin Zhang and Xiaochuan Wang. (2017) Sex Differences in the Cognitive and Hippocampal Effects of Streptozotocin in an Animal Model of Sporadic AD. Frontiers in Aging Neuroscience 9: 347. doi: 10.3389/fnagi.2017.00347. PMID: 29163130
  35. Guo CP, Wei Z, Huang F, Qin M, Li X, Wang YM, Wang Q, Wang JZ, Liu R, Zhang B, Li HL, Wang XC. (2017) High salt induced hypertension leads to cognitive defect. Oncotarget 8(56):95780-95790. doi: 10.18632/oncotarget.21326. PMID: 29221166
  36. Liu X, Zeng K, Li M, Wang Q, Liu R, Zhang B, Wang JZ, Shu X, Wang X. (2017) Expression of P301L-hTau in mouse MEC induces hippocampus-dependent memory deficit. Scientific Reports 7(1):3914. doi: 10.1038/s41598-017-04305-4. PMID:28634382
  37. Andrew T. McKenzie, Sarah Moyon, Minghui Wang, Igor Katsyv, Won-Min Song, Xianxiao Zhou, Eric B. Dammer, Duc M. Duong, Joshua Aaker, Yongzhong Zhao, Noam Beckmann, Pei Wang, Jun Zhu, James J. Lah, Nicholas T. Seyfried, Allan I. Levey, Pavel Katsel, Vahram Haroutunian, Eric E. Schadt, Brian Popko, Patrizia Casaccia and Bin Zhang. (2017) Multiscale Network Modeling of Oligodendrocytes Reveals Molecular Components of Myelin Dysregulation in Alzheimer’s Disease. Molecular Neurodegeneration 12:82 doi: 10.1186/s13024-017-0219-3. PMID: 29110684
  38. Christian V. Forst, Bin Zhou, Minghui Wang, Tsui-Wen Chou, Guy Mason, Won-min Song, Eric Schat, Elodie Ghedin and Bin Zhang. (2017) Integrative Gene Network Analysis Identifies Key Signatures, Intrinsic Networks and Host Factors for Influenza Virus A Infections. NPJ Systems Biology and Applications 3:35. doi: 10.1038/s41540-017-0036-x. PMID: 29214055
  39. Benoit Labonté, Olivia Engmann, Immanuel Purushothaman, Caroline Menard, Junshi Wang, Chunfeng Tan, Joseph R Scarpa, Gregory Moy, Yong-Hwee E Loh, Michael Cahill, Zachary S Lorsch, Peter J. Hamilton, Erin S Calipari, Georgia E. Hodes, Orna Issler, Hope Kronman, Madeline Pfau, Aleksander Obradovic, Yan Dong, Rachel Neve, Scott Russo, Andrew Kazarskis, Carol Tamminga, Naguib Mechawar, Gustavo Turecki, Bin Zhang†, Li Shen†, Eric J Nestler†. (2017) Sex-Specific Transcriptional Signatures in Human Depression. Nature Medicine 23(9):1102-1111 doi:10.1038/nm.4386. PMID 28825715
  40. Neha S. Dole, Courtney M. Mazur, Claire Acevedo, Justin P. Lopez, David A. Monteiro, Tristan W. Fowler, Bernd Gludovatz, Flynn Walsh, Jenna N. Regan, Sara Messina, Daniel S. Evans, Thomas F. Lang, Bin Zhang, Robert O. Ritchie, Khalid S. Mohammad and Tamara Alliston. Osteocyte intrinsic TGFβ signaling regulates bone quality through perilacunar/canalicular remodeling. Cell Reports 21(9):2585-2596. doi: 10.1016/j.celrep.2017.10.115. PMID 29186693.
  41. Maitane Ortiz-Virumbrales, Cesar L Moreno, Ilya Kruglikov, Paula Marazuela, Andrew Sproul, Samson Jacob, Matthew Zimmer, Daniel Paull, Bin Zhang, Eric E Schadt, Michelle E Ehrlich, Rudolph E Tanzi, Ottavio Arancio, Scott Noggle and Sam Gandy. CRISPR/Cas9-Correctable Mutation-Related Molecular and Physiological Phenotypes in iPSC-Derived Alzheimer’s PSEN2N141I Neurons. Acta Neuropathologica Communications 5(1):77. doi: 10.1186/s40478-017-0475-z. PMID: 29078805.
  42. Julia TCW, Minghui Wang, Anna A. Pimenova, Kathryn Bowles, Brigham J. Hartley, Emre Lacin, Saima Machlovi, Rawan Abdelaa, Celeste M. Karch, Hemali Phetnani5, Paul A. Slesinger, Bin Zhang, Alison M. Goate, Kristen J. Brennand. (2017) An efficient platform for astrocyte differentiation from human induced pluripotent stem cells. Stem Cell Reports 9(2):600-614. doi: 10.1016/j.stemcr.2017.06.018. PMID: 28757165.
  43. Lauren A. Peters, Jacqueline Perrigoue, Arthur Mortha, Alina Iuga, Won-min Song, Eric M. Neiman, Sean Llewyllan, Brian A. Kidd, Shannon Telesco, Aleksandar Stojmirovic, Jocelyn Sendecki, Khader Shameer, Riccardo Miotto, Ke Hao, Bojan Losic, Hardik Shah, Yongzhong Zhao, Antonio Di Narzo, Minghui Wang, Jeremiah Faith, Andrew Kasarskis, Carrie Brodmerkel, Mark Curran, Anuk Das, Joshua R. Friedman, Yoshinori Fukui, Mary Beth Humphrey, Brian Iritani, Nicholas Sibinga, Teresa K. Tarrant, Carmen Argmann, Panos Roussos, Jun Zhu, Bin Zhang, Radu Dobrin, Lloyd F. Mayer, Eric E. Schadt. (2017) A functional genomics predictive network model identifies regulators of inflammatory bowel disease. Nature Genetics 49(10):1437-1449. doi: 10.1038/ng.3947. PMID: 28892060.
  44. Lun Dong, Fangyan Meng, Ling Wu, Alliso n V. Mitchell, C. James Block, Bin Zhang, Douglas B. Craig, Hyejeong Jang, Wei Chen, Qifeng Yang and Guojun Wu. (2017) Cooperative oncogenic effect and cell signaling crosstalk of co‑occurring HER2 and mutant PIK3CA in mammary epithelial cells. International Journal of Oncology 51(4):1320-1330. PMID: 28902361 doi: 10.3892/ijo.2017.4108. PMID: 28902361
  45. Madhumitha Rengasamy, Fan Zhang, Ajay Vashisht, Won-min Song, Francesca Aguilo, Yifei Sun, SiDe Li, Weijia Zhang, Bin Zhang, James Wohlschlegel, Martin Walsh. (2017) The PRMT5/WDR77 complex regulates alternative splicing through ZNF326 in breast cancer. Nucleic Acids Research 45(19):11106-11120. doi: 10.1093/nar/gkx727. PMID: 28977470
  46. Hyunok Choi, Won-Min Song and Bin Zhang. (2017) Linking childhood allergic asthma phenotypes with endotype through integrated systems biology: current evidence and research needs. Rev Environ Health 32(1-2):55-63. doi: 10.1515/reveh-2016-0054. PMID: 28170342
  47. Jean-Vianney Haure-Mirande, Mickael Audrain, Tomas Fanutza, Soong Ho Kim, William L. Klein, Charles Glabe, Ben Readhead, Joel T. Dudley, Robert D. Blitzer, Minghui Wang, Bin Zhang, Eric E. Schadt, Sam Gandy, and Michelle E. Ehrlich. (2017) Deficiency of TYROBP, an adapter protein for TREM2 and CR3 receptors, is neuroprotective in a mouse model of early Alzheimer’s pathology. Acta Neuropathologica doi: 10.1007/s00401-017-1737-3. PMID: 28612290
  48. Kuan-lin Huang, Edoardo Marcora, Anna A Pimenova, Antonio F Di Narzo, Manav Kapoor, Sheng Chih Jin, Oscar Harari, Sarah Bertelsen, Benjamin P Fairfax, Jake Czajkowski, Vincent Chouraki, Benjamin Grenier-Boley, Céline Bellenguez, Yuetiva Deming, Andrew McKenzie, Towfique Raj, Alan E Renton, John Budde, Albert Smith, Annette Fitzpatrick, Joshua C Bis, Anita DeStefano, Hieab HH Adams, M Arfan Ikram, Sven van der Lee, Jorge L. Del-Aguila, Maria Victoria Fernandez, Laura Ibañez, The International Genomics of Alzheimer’s Project, The Alzheimer’s Disease Neuroimaging Initiative, Rebecca Sims, Valentina Escott-Price, Richard Mayeux, Jonathan L Haines, Lindsay A Farrer, Margaret A. Pericak-Vance, Jean Charles Lambert, Cornelia van Duijn, Lenore Launer, Sudha Seshadri, Julie Williams, Philippe Amouye, Gerard D Schellenberg, Bin Zhang, Ingrid Borecki, John S K Kauwe, Carlos Cruchaga, Ke Hao, Alison M Goate. (2017) A common haplotype lowers PU.1 expression in myeloid cells and delays onset of Alzheimer’s disease. Nature Neuroscience 20(8):1052-1061. doi:10.1038/nn.4587. PMID: 28628103
  49. 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. (2017) Directed Differentiation of Human Pluripotent Stem Cells to Microglia. Stem Cell Reports. pii: S2213-6711(17) 30177-7. doi: 10.1016/j.stemcr.2017.04.023. PMID: 28528700
  50. Axelsson AS, Mahdi T, Nenonen HA, Singh T, Hänzelmann S, Wendt A, Bagge A, Reinbothe TM1, Millstein J, Yang X, Zhang B, Gusmao EG, Shu L, Szabat M, Tang Y, Wang J, Salö S, Eliasson L, Artner I, Fex M, Johnson JD, Wollheim CB, Derry JMJ, Mecham B, Spégel P, Mulder H, Gesteira Costa Filho I, Zhang E, Rosengren AH. (2017) Sox5 regulates beta-cell phenotype and is reduced in type 2 diabetes. Nature Communications 8:15652. doi: 10.1038/ncomms15652. PMID: 28585545
  51. 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
  52. Minghui Wang, Panos Roussos, Andrew McKenzie, Xianxiao Zhou, Yuji Kajiwara, Kristen Brennand, Gabriele C DeLuca, John F. Crary, Patrizia Casaccia, Joseph Buxbaum, Michelle Ehrlich, Sam Gandy, Alison Goate, Pavel Katsel, Eric Schadt, Vahram Haroutunian, and Bin Zhang§. (2016) Integrative Network Analysis of Nineteen Brain Regions Identifies Molecular Signatures and Networks Underlying Selective Regional Vulnerability to Alzheimer’s Disease. Genome Medicine 8:104 DOI 10.1186/s13073-016-0355-3. PMID: 27799057
  53. 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
  54. Menachem Fromer, Panos Roussos, Solveig K Sieberts, Jessica S Johnson, David H Kavanagh, Thanneer M Perumal, Douglas M Ruderfer, Edwin C Oh, Aaron Topol, Hardik R Shah, Lambertus L Klei, Robin Kramer, Dalila Pinto, Zeynep H Gümüş, A Ercument Cicek, Kristen K Dang, Andrew Browne, Cong Lu, Lu Xie, Ben Readhead, Eli A Stahl, Jianqiu Xiao, Mahsa Parvizi, Tymor Hamamsy, John F Fullard, Ying-Chih Wang, Milind C Mahajan, Jonathan M J Derry, Joel T Dudley, Scott E Hemby, Benjamin A Logsdon, Konrad Talbot, Towfique Raj, David A Bennett, Philip L De Jager, Jun Zhu, Bin Zhang, Patrick F Sullivan, Andrew Chess, Shaun M Purcell, Leslie A Shinobu, Lara M Mangravite, Hiroyoshi Toyoshiba, Raquel E Gur, Chang-Gyu Hahn, David A Lewis, Vahram Haroutunian, Mette A Peters, Barbara K Lipska, Joseph D Buxbaum, Eric E Schadt, Keisuke Hirai, Kathryn Roeder, Kristen J Brennand, Nicholas Katsanis, Enrico Domenici, Bernie Devlin and Pamela Sklar. (2016) Gene expression elucidates functional impact of polygenic risk for schizophrenia. Nature Neuroscience 19(11): 1442–1453. doi:10.1038/nn.4399. PMID: 27668389
  55. Le Shu, Yuqi Zhao, Zeyneb Kurt, Sean Geoffrey Byars, Taru Tukiainen, Johannes Kettunen, Luz D Orozco, Matteo Pellegrini, Aldons J Lusis, Samuli Ripatti, Bin Zhang, Michael Inouye, Ville-Petteri Mäkinen, Xia Yang. Mergeomics: Multidimensional data integration to identify pathogenic perturbations to biological systems. BMC Genomics 17:874 DOI: 10.1186/s12864-016-3198-9. PMID: 27814671
  56. Igor Katsyv, Minghui Wang, Won Min Song, Xianxiao Zhou, Yongzhong Zhao, Sun Park, Jun Zhu, Bin Zhang, and Hanna Y. Irie§. (2016) EPRS is a Critical Regulator of Cell Proliferation and Estrogen Signaling in ER+ Breast Cancer. Oncotarget 7(43):69592-69605 doi: 10.18632/oncotarget.11870. PMID: 27612429
  57. Yuji Kajiwara, Andrew McKenzie, Nate Dorr, Miguel A Gama Sosa, Gregory Elder, James Schmeidler, Dara L Dickstein, Ozlem Bozdagi, Bin Zhang, and Joseph D Buxbaum. (2016) The human-specific CASP4 gene contributes to Alzheimer-related synaptic and behavioral deficits. Human Molecular Genetics, 25(19):4315-4327. doi: 10.1093/hmg/ddw265. PMID: 27516385
  58. Fan Zhang, Chunyan Ren, Kwun Kit Lau, Zihan Zheng, Geming Lu,Zhengzi Yi, Yongzhong Zhao, Fei Su, Shaojun Zhang, Bin Zhang, Eric A. Sobie, Weijia Zhang, and Martin J. Walsh. (2016) A network approach to build a comprehensive atlas for the prognosis of human cancer. Bioinformatics Briefings 17(6):1044-1059 doi: 10.1093/bib/bbw076. PMID: 27559151
  59. Jialiang Yang, Tao Huang, Won-min Song, Francesca Petralia, Charles V. Mobbs, Bin Zhang, Yong Zhao, Eric E. Schadt, Jun Zhu and Zhidong Tu. (2016) Discover the network mechanisms underlying the connections between aging and age-related diseases. Scientific Reports 6, 32566; doi: 10.1038/srep32566. PMID: 27582315
  60. Rosemary C. Bagot, Hannah M. Cates, Immanuel Purushothaman, Zachary S. Lorsch, Deena M. Walker, Junshi Wang, Xiaojie Huang, Oliver M. Schlüter, Ian Maze1, Catherine J. Peña, Elizabeth A. Heller, Orna Issler, Minghui Wang, Won-min Song, Jason. L. Stein, Xiaochuan Liu, Marie A. Doyle, Kimberly N. Scobie, Hao Sheng Sun, Rachael L. Neve, Daniel Geschwind, Yan Dong, Li Shen, Bin Zhang§, & Eric J. Nestler§. (2016) Circuit-wide transcriptional profiling reveals brain region-specific gene networks regulating depression susceptibility. Neuron 90(5):969-83．PMID:27181059
  61. Yongzhong Zhao, Won-min Song, Fan Zhang, Ming-Ming Zhou, Weijia Zhang, Martin J. Walsh and Bin Zhang. (2016) Distinct Distributions of Genomic Features of the 5′ (N-terminal) and 3′ (C-terminal) Partners of Coding Somatic Cancer Gene Fusions. Oncotarget doi: 10.18632/oncotarget.10734. PMID: 28977995
  62. Yongzhong Zhao, Christian Forst, Camil E. Sayegh, I-Ming Wang, Xia Yang, and Bin Zhang. (2016) Molecular and Genetic Inflammation Networks in Major Human Diseases. Molecular BioSystems　12(8):2318-41. doi: 10.1039/c6mb00240d. PMID: 27303926
  63. Qingying Meng, Zhe Ying, Emily Noble, Yuqi Zhao, Rahul Agrawal, Andrew Mikhail, Yumei Zhuang, Ethika Tyagi, Qing Zhang, Jae-Hyung Lee, Marco Morselli, Luz Orozco, Weilong Guo, Tina M. Kilts, Jun Zhu, Bin Zhang, Matteo Pellegrini, Xinshu Xiao, Marian F. Young, Fernando Gomez-Pinilla, Xia Yang. (2016) Systems Nutrigenomics Reveals Brain Gene Networks Linking Metabolic and Brain Disorders. EBioMedicine 7 (2016) 157–166. PMID: 27322469
  64. Qi Li, Cheng Hiang Lee, Lauren A. Peters, Lucas A. Mastropaolo, Cornelia Thoeni, Abdul Elkadri, Tobias Schwerd, Jun Zhu, Bin Zhang, Yongzhong Zhao, Ke Hao, Antonio Dinarzo, Gabriel Hoffman, Brian A. Kidd, Ryan Murchie, Ziad Al Adham§, Conghui Guo, Daniel Kotlarz, Ernest Cutz, Thomas D. Walters, Dror S. Shouval, Mark Curran, Radu Dobrin, Carrie Brodmerkel, Scott B. Snapper, Christoph Klein, John H. Brumell, Mingjing Hu, Ralph Nanan, Brigitte Snanter-Nanan, Melanie Wong, Francoise Le Deist, Elie Haddad, Chaim M. Roifman, Colette Deslandres, Anne M. Griffiths, Kevin J. Gaskin, Holm H. Uhlig, Eric E. Schadt, Aleixo M. Muise. (2016) Variants in TRIM22 that Affect NOD2 Signaling Are Associated With Very Early Onset Inflammatory Bowel Disease. Gastroenterology 150(5):1196-1207. doi: 10.1053/j.gastro.2016.01.031. PMID: 26836588
  65. Minghui Wang, Yongzhong Zhao and Bin Zhang. (2015) Efficient Test and Visualization of Multi-Set Intersections. Scientific Reports 5:16923. doi: 10.1038/srep16923. PMID:26603754
  66. Won-min Song and Bin Zhang. (2015) Multiscale Embedded Gene Co-expression Network Analysis. PLoS Computational Biology 11(11): e1004574. doi:10.1371/. PMID:26618778
  67. Nicolas Goossens, Yujin Hoshida, Won Min Song, Minoa Jung, Philippe Morel, Shigeki Nakagawa, Bin Zhang, Jean-Louis Frossard, Laurent Spahr, Scott L Friedman, Francesco Negro, Laura Rubbia-Brandt and Emiliano Giostra. (2015) Nonalcoholic Steatohepatitis Is Associated With Increased Mortality in Obese Patients Undergoing Bariatric Surgery. Clinical Gastroenterology and Hepatology pii: S1542-3565(15)01406-8. doi: 10.1016/j.cgh.2015.10.010. PMID: 26492845
  68. Alexey Kozlenkov, Minghui Wang, Panos Roussos, Sergei Rudchenko, Mihaela Barbu, Marina Bibikova, Brandy Klotzle, Andrew J. Dwork, Bin Zhang, Yasmin L. Hurd, Eugene V Koonin, Michael Wegner and Stella Dracheva. (2015) Substantial DNA Methylation Differences between Two Major Neuronal Subtypes in Human Brain. Nucleic Acids Research doi:10.1093/nar/gkv1304. PMID: 26612861
  69. Georgia Hodes, Madeline Pfau, Immanuel Purushothaman, H. Ahn, Sam Golden, Daniel Christoffel, Jane Magida, Anna Brancato, Aki Takahashi, Meghan Flanigan, Caroline Menard, Hossein Aleyasin, Ja Wook Koo, Zachary Lorsch, Jian Feng, Mitra Heshmati, minghui wang, Gustavo Turecki, Rachael Neve, Bin Zhang, Li Shen, Eric Nestler, and Scott Russo. (2015) Sex differences in nucleus accumbens transcriptome profiles associated with susceptibility versus resilience to sub-chronic variable stress. Journal of Neuroscience 35: 16362-16376. PMID:26674863
  70. Zhidong Tu, Bin Zhang and Jun Zhu. (2015) Network integration of genetically regulated gene expression to study complex diseases. In (George C. Tseng, Debashis Ghosh, Xianghong Jasmine Zhou Eds). Integrating Omics Data. Cambridge University Press. Cambridge, CB2 8BS, United Kingdom. http://dx.doi.org/10.1017/CBO9781107706484.005
  71. Jialiang Yang, Tao Huang, Francesca Petralia, Quan Long, Bin Zhang, Carmen Argmann, Yong Zhao1,2, Charles V Mobbs3,4,5, GTEx Consortium#, Eric E Schadt, Jun Zhu and Zhidong Tu. (2015) Synchronized age-related gene expression changes across multiple tissues in human and the link to complex diseases. Scientific Reports 5:15145. PMID: 26477495
  72. Ben Readhead, Jean-Vianney Haure-mirande, Bin Zhang, Sam Gandy, Eric E. Schadt Joel T. Dudley, and Michelle E. Ehrlich. (2015). Molecular systems evaluation of transcriptional perturbations in oligomerogenic APPE693Q and fibrillogenic APPKM670/671NL/PSEN1Δexon9 mouse models in the context of human Alzheimer’s brain molecular pathology. Molecular Psychiatry doi:10.1038/mp.2015.167. PMID: 26552589
  73. Aslihan Dincer, Corey Xu, David P. Gavin, Bin Zhang, Joel Dudley, Eric E. Schadt, Schahram Akbarian. (2015) Deciphering H3K4me3 Broad Domains Associated With Gene Regulatory Networks and Conserved Epigenomic Landscapes in the Human Brain. Translational Psychiatry 5:e679. doi: 10.1038/tp.2015.169. PMID: 26575220
  74. Xiandong Lin, Yongzhong Zhao, Won-min Song and Bin Zhang. (2015) Molecular Classification and Prediction in Gastric Cancer. Computational and Structural Biotechnology Journal 13:448-58. doi: 10.1016/j.csbj.2015.08.001. PMID: 26380657
  75. The GTEx Consortium [I am a co-author]. (2015) The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans. Science 348(6235):648-60. doi: 10.1126/science.1262110. PMID: 25954001
  76. Tianxiao Huan, Qingying Meng, Mohamed A. Saleh, Allison E. Norlander, Roby Joehanes, Jun Zhu, Brian H. Chen, Bin Zhang, Zhi Wang, Andrew D. Johnson, Saixia Ying, Paul Courchesne, Nalini Raghavachari, Richard Wang, Poching Liu, International Consortium for Blood Pressure GWAS (ICBP), Christopher J. O’Donnell, Ramachandran Vasan, Peter J. Munson,　Meena S. Madhur, David G. Harrison, Xia Yang, and Daniel Levy. (2015) Integrative network analysis reveals molecular mechanisms of blood pressure regulation. Molecular Systems Biology 11 (4). PMID: 25882670
  77. Swapan Kumar Das, Neeraj Kumar Sharma, and Bin Zhang§. (2015) Integrative network analysis reveals different pathophysiological mechanisms of insulin resistance among Caucasians and African Americans. BMC Medical Genomics 8:4. DOI: 10.1186/s12920-015-0078-0. PMID: 25868721
  78. Peng Jiang, Joseph R. Scarpa, Karrie Fitzpatrick, Bojan Losic, Vance D. Gao, Ke Hao, Keith C. Summa, He S. Yang, Bin Zhang, Ravi Allada, Martha H. Vitaterna, Fred W. Turek, Andrew Kasarskis. (2015) A Systems Approach Identifies Networks and Genes Linking Sleep and Stress Implications for Neuropsychiatric Disorders. Cell Report 11(5):835-48. PMID: 25921536
  79. Tianxiao Huan, Jian Rong, Kahraman Tanriverdi, Qingying Meng, David McManus, Roby Joehanes, Themistocles Assimes, Ruth McPherson, Nilesh Samani, Jeanette Erdmann, Heribert Schunkert, Paul Courchesne, Peter Munson, Andrew Johnson, Christopher J. O’Donnell, Bin Zhang, Martin Larson, Jane E. Freedman, Daniel Levy, and Xia Yang. (2015) Dissecting the Roles of microRNAs in Coronary Heart Disease via Integrative Genomics Analyses. Arteriosclerosis, Thrombosis, and Vascular Biology 35(4):1011-21. PMID: 25657313
  80. Fanyan Meng, Cecilia Speyer, Bin Zhang, Yongzhong Zhao, Wei Chen, David Gorski, Fred R. Miller and Guojun Wu. (2014) PDGFRα and β Play Critical Roles in Mediating Foxq1-Driven Breast Cancer Stemness and Chemoresistance. Cancer Research 75(3):584-93. doi: 10.1158/0008-5472.CAN-13-3029. PMID: 25502837
  81. Ian Maze, Li Shen, Bin Zhang, Benjamin A. Garcia, Ningyi Shao, Amanda Mitchell, Schahram Akbarian, C. David Allis and Eric J. Nestler. (2014) Analytical Tools and Current Challenges in the Modern Era of Neuroepigenomics. Nature Neuroscience 17(11): 1476-1490. PMID: 25349914
  82. Manikandan Narayanan, Jimmy L. Huynh, Kai Wang, Xia Yang, Seungyeul Yoo, Joshua McElwee, Bin Zhang, Chunsheng Zhang, John R. Lamb, Tao Xie, Christine Suver, Cliona Molony, Stacey Melquist, Andrew D. Johnson, Guoping Fan, David J. Stone, Eric E. Schadt, Patrizia Casacci, Valur Emilsson, Jun Zhu. (2014) Common Dysregulation Network in the Human Prefrontal Cortex underlies Two Neurodegenerative Diseases. Molecular Systems Biology: 10:743. PMID: 25080494
  83. Zhidong Tu, Bin Zhang and Jun Zhu. (2014) Network integration of genetically regulated gene expression to study complex diseases. Integrating Omics Data edited by George Tseng, Debashis Ghosh, Xianghong Jasmine Zhou. Cambridge Press.
  84. Bin Zhang, Linh Tran, Valur Emilsson and Jun Zhu. (2014) Characterization of Genetic Networks Associated with Alzheimer’s Disease. Systems Biology of Alzheimer’s disease. In (Juan I. Castrillo and Stephen G. Oliver Eds). Systems Biology of Alzheimer’s disease: Methods and Protocols. MIMB Series Humana, Springer. New York. (http://www.springer.com/us/book/9781493926268). PMID: 26235085
  85. Ville-Petteri Mäkinen, Mete Civelek, Qingying Meng, Bin Zhang, Jun Zhu, Candace Levian, Tianxiao Huan, Ayellet V Segrè,7 Sujoy Ghosh, Juan Vivar, Majid Nikpay, Alexandre FR Stewart, Christopher P Nelson, Christina Willenborg, Jeanette Erdmann, Stefan Blakenberg, Christopher O’Donnell, Winfried März, Reijo Laaksonen, Stephen E Epstein, Sekar Kathiresan, Svati H Shah, Stanley L Hazen, Muredach P Reilly, the Coronary ARtery DIsease Genome-Wide Replication And Meta-Analysis (CARDIoGRAM) Consortium, Aldons J Lusis, Nilesh J Samani, Heribert Schunkert, Thomas Quertermous, Ruth McPherson, Xia Yang, Themistocles LAssimes. (2014) Integrative Genomics Reveals Novel Molecular Pathways and Gene Networks for Coronary Artery Disease. PLoS Genetics 10(7):e1004502. PMID: 25033284
  86. Supinda Bunyavanich, Eric E. Schadt, Blanca E. Himes, Jessica Lasky-Su, Wei-Liang Qui, Ross Lazarus, Ariella Cohain, Michael Linderman, Bin Zhang, Benjamin A. Raby, Scott T. Weiss. (2014) Integrated Genome-wide Association, Coexpression Network, and Expression Single Nucleotide Polymorphism Analysis Identifies Novel Pathway in Allergic Rhinitis. BMC Medical Genomics. BMC Medical Genomics:7(1):48 PMID: 25085501
  87. Kristen Brennand, Jeffrey Silvas, Yongsung Kim, Ngoc Tran, Anthony Simone, Ian Ladran, Kristin Beaumont, Hyung Joon Kim, Milan Mrksich, Gang Fang, Bin Zhang, John Yates, Fred H. Gage1. (2014) Phenotypic differences in hiPSC NPCs derived from patients with schizophrenia. Molecular Psychiatry doi: 10.1038/mp.2014.22. PMID: 24686136
  88. Michael K. Skinner, Marina I. Savenkova, Bin Zhang, Andrea C. Gore, David Crews. (2014) Gene bionetworks involved in the epigenetic transgenerational inheritance of altered mate preference: Environmental epigenetics and evolutionary biology. BMC Genomics 15:377. doi: 10.1186/1471-2164-15-377. PMID: 24885959
  89. Bin Zhang*, Chris Gaiteri*, Liviu-Gabriel Bodea*, Zhi Wang, Joshua McElwee, Alexei A. Podtelezhnikov, Chunsheng Zhang, Tao Xie, Linh Tran, Radu Dobrin, Eugene Fluder, Bruce Clurman, Stacey Melquist, Manikandan Narayanan, David A Bennett, Christine Suver, Hardik Shah, Milind Mahajan, John R. Lamb, Cliona Molony, David J. Stone, Vilmundur Gudnason, Amanda J. Myers, Eric E. Schadt, Harald Neumann, Jun Zhu & Valur Emilsson§. (2013) Integrated Systems Approach Identifies Genetic Nodes and Networks in Late-Onset Alzheimer’s Disease. Cell 153(3):707-720. PMID: 23622250
  90. Eric Nilsson, Bin Zhang and Michael K Skinner. (2013) Gene bionetworks that regulate ovarian primordial follicle assembly. BMC Genomics 14:496. PMID: 23875758
  91. Xin He, Chris K Fuller, Yi Song, Qingying Meng, Bin Zhang, Xia Yang and Hao Li. (2013) Sherlock: detecting gene-disease associations by matching patterns of expression QTL and GWAS. The American Journal of Human Genetics 92(5):667-680. PMID: 23643380
  92. Jong-Min Lee, Ekaterina I. Galkina, Rachel M. Levantovsky, Elisa Fossale, Mary Anne Anderson, Tammy Gillis, Jayalakshmi Srinidhi Mysore, Kathryn R. Coser, Toshi Shioda, Bin Zhang, Matthew D. Furia, Jonathan Derry, Isaac S. Kohane, Ihn Sik Seong, Vanessa C. Wheeler, James F. Gusella and Marcy E. MacDonald. (2013) Dominant effects of the Huntington’s disease HTT CAG repeat length are captured in gene expression datasets by a continuous analysis mathematical modeling strategy. Human Molecular Genetics: 22(16):3227-38. doi: 10.1093/hmg/ddt176. PMID: 23595883
  93. Tianxiao Huan, Bin Zhang, Zhi Wang, Roby Joehanes, Jun Zhu, Andrew D. Johnson, Saixia Ying, Peter J. Munson, Nalini Raghavachari, Richard Wang, Poching Liu, Paul Courchesne, Themistocles L. Assimes, Ruth McPherson, Nilesh J. Samani, Heribert Schunkert, Coronary ARteryDIsease Genome wide Replication and Meta-analysis (CARDIoGRAM) Consortium, Christine Suver, Christopher J. O’Donnell, Jonathan Derry, Xia Yang, and Daniel Levy. (2013) A systems biology framework identifies molecular underpinnings of coronary heart disease. Arteriosclerosis, Thrombosis, and Vascular Biology112.300112 [Epub ahead of print]. PMID: 23539213
  94. Gaurav Pandey, Bin Zhang and Le Jian. (2013) Predicting submicron air pollution indicators: A machine learning approach. Environmental Science: Processes Impacts 15 (5): 996 – 1005. PMID 23539213
  95. Elias Chaibub Neto, Aimee T. Broman, Mark P. Keller, Alan D. Attie, Bin Zhang, Jun Zhu and Brian S. Yandell. (2013) Modeling Causality for Pairs of Phenotypes in System Genetics. Genetics 193(3):1003-13. PMID: 23288936
  96. Yu Ding, Christopher G. Hubert, Philip Corrin, Julio Vazquez, Ryan Baysom, Bin Zhang, Jenni Risler, Jennifer DeLuca, Steven M. Pollard, Jeffery Delrow, Jun Zhu, James M. Olson, and Patrick J. Paddison. (2013) Cancer-specific requirement for BUB1B/BubR1 in human brain tumor isolates and genetically transformed cells. Cancer Discovery 3(2):198-211. PMID: 23154965
  97. Luke Jostins, Stephan Ripke, Rinse Weersma, Richard Duerr, Dermot McGovern, Ken Hui, James Lee, L Schumm, Yashoda Sharma, Carl Anderson, Jonah Essers, Mitja Mitrovic, Kaida Ning, Isabelle Cleynen, Emilie Theatre, Sarah Spain, Soumya Raychaudhuri, Philippe Goyette, Zhi Wei, Clara Abraham, Jean-Paul Achkar, Tariq Ahmad, Leila Amininejad, Ashwin Ananthakrishnan, Vibeke Andersen, Jane Andrews, Leonard Baidoo, Tobias Balschun, Peter Bampton, Alain Bitton, Gabrielle Boucher, Stephan Brand, Carsten Büning, Ariella Cohain, Sven Cichon, Mauro D’Amato, Dirk de Jong, Kathryn Devaney, Marla Dubinsky, Cathryn Edwards, David Ellinghaus, Lynnette Ferguson, Denis Franchimont, Karin Fransen, Richard Gearry, Christian Gieger, Jürgen Glas, Talin Haritunians, Ailsa Hart, Chris Hawkey, Matija Hedl, Xinli Hu, Tom Karlsen, Limas Kupcinskas, Subra Kugathasan, Anna Latiano, Debby Laukens, Ian Lawrance, Charlie Lees, Edouard Louis, Gillian Mahy, John Mansfield, Angharad Morgan, Craig Mowat, William Newman, Orazio Palmieri, Cyriel Ponsioen, Uros Potocnik, Natalie Prescott, Miguel Regueiro, Jerome Rotter, Richard Russell, Jeremy Sanderson, Miquel Sans, Jack Satsangi, Stefan Schreiber, Lisa Simms, Jurgita Sventoraityte, Stephan Targan, Kent D Taylor, Mark Tremelling, Hein Verspaget, Martine De Vos, Cisca Wijmenga, David Wilson, Juliane Winkelmann, Ramnik Xavier, Sebastian Zeissig, Bin Zhang, Clarence Zhang, Hongyu Zhao, The International IBD Genetics Consortium, Mark Silverberg, Vito Annese, Hakon Hakonarson, Steven Brant, Graham Radford-Smith, Christopher Mathew, John Rioux, Eric Schadt, Mark Daly, Andre Franke, Miles Parkes, Severine Vermeire, Jeffrey Barrett, Michel Georges and Judy H Cho. (2012) Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature 491(7422):119-24. doi: 10.1038/nature11582. PMID: 23128233
  98. Michael K. Skinner, Mohan Manikkam, Md. M. Haque, Bin Zhang and Marina I. Savenkova. (2012) Epigenetic Transgenerational Inheritance of Somatic Transcriptomes and Epigenetic Control Regions. Genome Biology 13:R91. PMID: 23034163
  99. I-Ming Wang, Bin Zhang*, Xia Yang, Jun Zhu, Serguei Stepaniants, Chunsheng Zhang, Qingying Meng, Mette Peters, Yudong He, Chester Ni, Deborah Slipetz, Michael A. Crackower, Hani Houshyar, Christopher M. Tan, Ernest Asante-Appiah, Gary O’Neill, Mingjuan Jane Luo, Rolf Thieringer, Jeffrey Yuan, Chi-Sung Chiu, Pek Yee Lum, John Lamb, Yves Boie, Hilary A. Wilkinson, Eric E. Schadt, Hongyue Dai and Christopher Roberts. (2012) Systems Analysis of Eleven Rodent Disease Models Reveals an Inflammatome Signature and Key Drivers. Molecular Systems Biology 8:594 (http://www.nature.com/doifinder/10.1038/msb.2012.24) PMID: 22806142
  100. Xia Yang, Bin Zhang, Jun Zhu. (2012) Functional Genomics- and Network-driven Systems Biology Approaches for Pharmacogenomics and Toxicogenomics. Curr Drug Metab. PMID: 22591344
  101. Peter Kang, Rong Chen, Erik Corona, Xia Yang, Bin Zhang, Eric E. Schadt, Atul J. Butte. (2012) Integration of disease-specific single nucleotide polymorphisms, expression quantitative trait loci and coexpression networks reveal novel candidate genes for type 2 diabetes. Diabetologia: 55(8), doi: 10.1007/s00125-012-2568-3. PMID: 22584726
  102. Linh Tran, Bin Zhang*, Zhan Zhang, Jun Zhu, Chunsheng Zhang, Tao Xie, John R. Lamb, Hongyue Dai, Eric E. Schadt. (2011) Inferring Causal Genomic Alterations in Breast Cancer Using Gene Expression Data. BMC Systems Biology 5(121), doi:1752-0509-5-121 [pii]10.1186/1752-0509-5-121. PMID: 21806811
  103. Joshua Millstein, Christopher J. Winrow, Andrew Kasarskis, Joseph R. Owens, Lili Zhou, Keith C. Summa, Karrie Fitzpatrick, Bin Zhang, Martha H. Vitaterna, Stephen Friend, Eric Schadt, John J. Renger, Fred W. Turek. (2011) Identification of Causal Genes, Networks and Transcriptional Regulators of REM Sleep and Wake. Sleep 34 (11), http://dx.doi.org/10.5665/sleep.1378. PMID: 22043117
  104. Ke Hao, John Lamb, Chunsheng Zhang, Tao Xie, Kai Wang, Bin Zhang, Eugene Chudin, Nikki P Lee, Mao Mao, Hua Zhong, Danielle Greenawalt, Mark D Ferguson, Irene O Ng, Pak C Sham, Ronnie T Poon, Cliona Molony, Eric E Schadt, Hongyue Dai and John M Luk. (2011) Clinicopathologic and gene expression parameters predict liver cancer prognosis. BMC Cancer 11(481), doi:10.1186/1471-2407-11-481. PMID: 22070665
  105. Danielle M Greenawalt, Radu Dobrin, Eugene Chudin, Ida J Hatoum, Christine Suver, John Beaulaurier, Bin Zhang, Victor Castro, Jun Zhu, Solveig K Sieberts, Susanna Wang, Cliona Molony, Steven B. Heymsfield, Daniel M Kemp, Marc L Reitman, Pek Yee Lum, Eric E Schadt, Lee M Kaplan. (2011) A survey of the genetics of stomach, liver, and adipose gene expression from a morbidly obese cohort. Genome Research 21, 1008-1016, doi:gr.112821.110 [pii] 10.1101/gr.112821.110. PMID: 21602305
  106. Hunter B. Fraser, Tomas Babak, John Tsang, Bin Zhang, Margarete Mehrabian, and Eric E. Schadt. (2011) Systematic Detection of Polygenic cis-Regulatory Evolution. PLoS Genetics 7(3): e1002023. doi:10.1371/journal.pgen.1002023. PMID: 21483757
  107. John R. Lamb, Chunsheng Zhang, Tao Xie, Kai Wang, Bin Zhang, Ke Hao, Eugene Chudin, Hunter B. Fraser,Joshua Millstein, Mark Ferguson, Christine Suver, Irena Ivanovska, Martin Scott, Ulrike Philippar, Dimple Bansal, Zhan Zhang, Julja Burchard, Ryan Smith, Danielle Greenawalt, Jonathan Derry, I-Ming Wang, Andrey Loboda, James Watters, Ronnie T.P. Poon, Chun Yeung, Nikki P.Y. Lee, Cliona Molony, Valur Emilsson, Carolyn Buser-Doepner, Jun Zhu, Stephen Friend, Mao Mao, Peter M. Shaw, Hongyue Dai, John M. Luk, Eric E. Schadt. (2011) Predictive Genes in Adjacent Normal Tissue Are Preferentially Altered by sCNV during Tumorigenesis in Liver Cancer and May Rate Limiting. PLoS ONE 6(7): e20090, doi:10.1371/journal.pone.0020090. PMID: 21750698
  108. Haijun Zhang, Fanyan Meng, Gang Liu, Bin Zhang, Jun Zhu, Feng Wu, Stephen P. Ethier, Fred Miller, Guojun Wu. (2011) Forkhead transcription factor foxq1 promotes epithelial-mesenchymal transition and breast cancer metastasis. Cancer Research 71(4): 1-10. PMID: 21285253
  109. Gaurav Pandey, Bin Zhang*, Aaron Chang, Jun Zhu, Vipin Kumar and Eric Schadt. (2010) Integrative Multi-Network Approach to Predict Synthetic Lethal Interactions. PLoS Computational Biology 6(9): e1000928. doi:10.1371/journal.pcbi.1000928. PMID: 20838583
  110. Eric E. Nilsson, Marina Savenkova, Ryan Schindler, Bin Zhang, Eric Schadt and Michael K. Skinner. (2010) Gene Bionetwork Analysis of Ovarian Primordial Follicle Development. PLoS ONE 5(7): e11637. doi:10.1371/journal.pone.0011637. PMID: 20661288
  111. Xia Yang, Bin Zhang*, Cliona Molony, Eugene Chudin, Ke Hao, Jun Zhu, Andrea Gaedigk, Christine Suver, Hua Zhong, J. Steven Leeder, F. Peter Guengerich, Stephen C. Strom, Erin Schuetz, Thomas H. Rushmore, Roger G. Ulrich, J. Greg Slatter, Eric E. Schadt, Andrew Kasarskis, Pek Yee Lum. (2010) Genetic and Genomic Analysis of Cytochrome P450 Enzyme Activities in Human Liver. Genome Research 20: 1020-1036. doi:10.1101/gr.103341.109. PMID: 20538623
  112. Jonathan M. J. Derry, Hua Zhong, Cliona Molony, Doug MacNeil, Debraj Guhathakurta, Bin Zhang, John Mudgett, Kersten Small, Lahcen El Fertak, Alain Guimond, Mohammed Selloum, Wenqing Zhao, Marie France Champy, Laurent Monassier, Tom Vogt, Doris Cully, Andrew Kasarskis, Eric E. Schadt. (2010) Identification of Genes and Networks Driving Cardiovascular and Metabolic Phenotypes in a Mouse F2 Intercross. PLoS ONE 5(12): e14319. doi:10.1371/journal.pone.0014319. PMID: 21179467
  113. Tao Xie, Chunsheng Zhang, Bin Zhang, Cliona Molony, Chris Roberts, Hongyue, Dai, Eric Schadt, Lamb John. (2010) A survey of cancer cell lines reveals highly structured and hierarchical relationships within and between DNA and mRNA that may be the result of selection. Omics: 14(1):91-7. PMID: 20141331
  114. Hua Zhong, John Beaulaurier, Pek Yee Lum, Cliona Molony, Xia Yang, Bin Zhang, Danielle Greenawalt, Hao Ke, Douglas J. MacNeil, Drew T Weingarth, Sangsoon Woo, Alan D. Attie, Mark P. Keller, Lee M. Kaplan, Eric E. Schadt. (2010) Liver and Adipose Expression Associated SNPs Are Enriched for Association to Type 2 Diabetes. PLoS Genetics 6(5): e1000932. doi:10.1371/journal.pgen.1000932. PMID: 20463879
  115. Joshua Millstein, Bin Zhang, Jun Zhu and Eric E. Schadt. (2009) Disentangling Molecular Relationships with a Causal Inference Test. BMC Genetics, 10:23doi:10.1186/1471-2156-10-23. PMID: 19473544
  116. Xia Yang, Joshua L. Deignan, Hongxiu Qi, Jun Zhu, Su Qian, Gevork Torosyan, Sana Majid, Brie Falkard, Robert R. Kleinhanz, Jenny Karlsson, Lawrence W. Castellani, Sheena Mumick, Kai Wang, John R. Lamb, Tao Xie, Michael Coon, Chunsheng Zhang, Daria Estrada-Smith, Charles R. Farber, Susanna S. Wang, Atila Van Nas, Anatole Ghazalpour, Bin Zhang, Douglas J. MacNeil, Marc L. Reitman, Katrina M. Dipple, Margarete Mehrabian, Pek Y. Lum, Eric E. Schadt, Aldons J. Lusis,, Thomas A. Drake. (2009) Validation of candidate causal genes for obesity that affect shared metabolic pathways and networks. Nature Genetics 41: 415 – 423. PMID: 19270708
  117. Eric E. Schadt, Bin Zhang and Jun Zhu. (2009) Advances in systems biology are enhancing our understanding of disease and moving us closer to novel disease treatments. Genetica, DOI 10.1007/s10709-009-9359-x. PMID: 19363597
  118. Jun Zhu, Bin Zhang, and Eric E. Schadt. (2008) A Systems Biology Approach to Drug Discovery. Genetic Dissection of Complex Traits, Second Edition, edited by D. C. Rao. Elsevier Inc., New York, NY. PMID: 18358334
  119. Atila van Nas, Debraj GuhaThakurta, Susanna S. Wang, Nadir Yehya, Steve Horvath, Bin Zhang, Leslie Ingram-Drake, Gautam Chaudhuri, Eric E. Schadt, Thomas A. Drake, Arthur P. Arnold, and Aldons J. Lusis. (2008) Elucidating the Role of Gonadal Hormones in Sexually Dimorphic Gene Co-Expression Networks. Endocrinology, doi:10.1210/en.2008-0563. PMID: 18974276
  120. Jun Zhu, Bin Zhang, Erin Smith, Becky Drees, Rachel Brem, Roger Bumgarner, Eric E. Schadt. (2008) Integrating Large-Scale Functional Genomic Data to Dissect the Complexity of Yeast Regulatory Networks. Nature Genetics 40: 854-861. PMID: 18552845
  121. Valur Emilsson, Gudmar Thorleifsson, Bin Zhang, Amy S Leonardson, Florian Zink, Sonia Carlson, Agnar Helgason, G. Bragi Walters, Steinunn Gunnarsdottir, Magali Mouy, Gudrun H. Eiriksdottir, Daniel Gudbjartsson, Anna Helgadottir, Inga Reynisdottir, Aslaug Jonasdottir, Adalbjorg Jonasdottir, Unnur Styrkarsdottir, Hreinn Stefansson, Ragnheidur Fossdal, Kristleifur Kristjansson, Hjortur G. Gislason, Tryggvi Stefansson, Bjorn G. Leifsson, Unnur Thorsteinsdottir, John R Lamb, Jeffrey R. Gulcher, Marc L. Reitman, Augustine Kong, Eric E. Schadt, and Kari Stefansson. (2008) Genetics of Gene Expression and Its Effect on Disease. Nature 452: 423-428. PMID: 18344981
  122. Yanqing Chen, Jun Zhu, Pek Yee Lum, Xia Yang, Shirly Pinto, Douglas J. MacNeil, Chunsheng Zhang, John Lamb, Stephen Edwards1, Solveig K. Sieberts, Amy Leonardson, Lawrence W. Castellini, Susanna Wang, Bin Zhang, Valur Emilsson, Sudheer Doss, Anatole Ghazalpour, Steve Horvath, Thomas A. Drake, Aldons J. Lusis, Eric E. Schadt. (2008) Variations in DNA elucidate molecular networks that cause disease. Nature: 452: 429-435. PMID: 18344982
  123. Eric E. Schadt, Cliona Molony, Eugene Chudin, Ke Hao, Xia Yang, Pek Y. Lum, Andrew Kasarskis, Bin Zhang, Susanna Wang, Christine Suver, Jun Zhu, Joshua Millstein, Solveig Sieberts, John Lamb, Debraj GuhaThakurta, Jonathan Derry, John D. Storey, Iliana Avila-Campillo, Mark J. Kruger, Jason M. Johnson, Carol A. Rohl, Atila van Nas, Margarete Mehrabian Thomas A. Drake, Aldons J. Lusis, Ryan C. Smith, F. Peter Guengerich Stephen C. Strom, Erin Schuetz, Thomas H. Rushmore, Roger Ulrich. (2008) Mapping the Genetic Architecture of Gene Expression in Human Liver. PLoS Biol 6(5): e107 doi:10.1371/journal.pbio.0060107. PMID: 18344982
  124. Peter Langfelder*, Bin Zhang* (co-first author), Steve Horvath. (2007) Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R. Bioinformatics 24(5):719-20 doi: 10.1093/bioinformatics/btm563. PMID: 18024473
  125. Horvath, B. Zhang, M. Carlson, K. V. Lu, S. Zhu, R. M. Felciano, M. F. Laurance, W. Zhao, S. Qi, Z. Chen, Y. Lee, A. C. Scheck, L. M. Liau, H. Wu, D. H. Geschwind, P. G. Febbo, H. I. Kornblum, T. F. Cloughesy, S. F. Nelson, and P. S. Mischel. (2006) Analysis of oncogenic signaling networks in glioblastoma identifies ASPM as a molecular target. Proc Natl Acad Sci U S A 103: 17402-17407. PMID: 17090670
  126. Peter S. Gargalovic, Minori Imura, Bin Zhang, Nima M. Gharavi, Michael J. Clark, Joanne Pagnon, Wen-Pin Yang, Aiqing He, Amy Truong, Shilpa Patel, Stanley F. Nelson, Steve Horvath, Judith A. Berliner, Todd G. Kirchgessner and Aldons J. Lusis. (2006) Identification of Inflammatory Gene Modules based on Variations of Human Endothelial Cell Responses to Oxidized Lipids. Proc Natl Acad Sci U S A. 103(34):12741-6. PMID: 16912112
  127. Anatole Ghazalpour, Sudheer Doss, Bin Zhang, Susanna Wang, Christopher Plaisier, Ruth Castellanos, Alec Brozell, Eric E. Schadt, Thomas A. Drake, Aldons J Lusis, Steve Horvath. (2006) Integrating Genetic and Network Analysis to Characterize Genes Related to Mouse Weight. PLoS Genet. DOI: 10.1371/journal.pgen.0020130.eor. PMID: 16934000
  128. Marc Carlson, Bin Zhang, Zhixing Fang, Paul Mischel, Steve Horvath, and Stan Nelson. (2006) Gene connectivity, function, and sequence conservation: predictions from modular yeast co-expression networks. BMC Genomics, 7:40. doi:10.1186/1471-2164-7-40. PMID: 16515682
  129. Scherise Mitchell, Asuka Ota, William Foster, Bin Zhang, Zixing Fang, Shilpa Patel, Stanley F. Nelson, Steve Horvath, Yibin Wang.(2006) Distinct Gene Expression Profiles in Adult Mouse Heart Following Targeted MAP Kinase Activation. Physiological Genomics, vol. 25, pp. 50-59. PMID: 16368875
  130. Jia Lin, Alex Halavais , and Bin Zhang. (2006) The Blog Network in America: Blogs as Indicators of Relationships among US Cities. CONNECTIONS 27(2): 15-23.
  131. Bin Zhang and Steve Horvath. (2005) A General Framework for Weighted Gene Co-expression Network Analysis. Statistical Applications in Genetics and Molecular Biology, 4, issue 1. PMID: 16646834
  132. Bin Zhang and Steve Horvath. (2005) Ridge Regression based Hybrid Genetic Algorithms for Multi-Locus Quantitative Trait Mapping. International Journal of Bioinformatics Research and Applications, vol. 1, no.3, pp. 261-272. PMID: 18048135
  133. Bin Zhang and Sargur N. Srihari. (2004) Fast k-nearest Neighbor Classification Using Cluster-based Trees. IEEE Transaction Pattern Analysis and Machine Intelligence, vol 26, no. 4, pp. 525-528. PMID: 15382657