Publications

Selected Publications ( co-first author, § co-corresponding author)


1. 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 and Valur Emilsson§. (2013) Integrated Systems Approach Identifies Genetic Nodes and Networks in Late-Onset Alzheimer's Disease. Cell 153(3):707-720.

2. 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.

3. 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.

(in press)

4. 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 Biology ATVBAHA.112.300112.

5. 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 (http://pubs.rsc.org/en/content/articlelanding/2013/EM/C3EM30890A).

6. 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.

7. 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 Buning, 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, Jurgen 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.

8. 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. (2012) Cancer-specific requirement for BUB1B/BubR1 in human brain tumor isolates and genetically transformed cells. Cancer Discovery CD-12-0353.

9. 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.

10. 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)

11. Xia Yang, Bin Zhang, Jun Zhu. (2012) Functional Genomics- and Network-driven Systems Biology Approaches for Pharmacogenomics and Toxicogenomics. Curr Drug Metab.

12. 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, doi: 10.1007/s00125-012-2568-3.

13. Linh Tran, Bin Zhang☆§, Zhan Zhang, Chunsheng Zhang, Tao Xie, John R. Lamb, Hongyue Dai, Eric E. Schadt§, Jun Zhu§. (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.

14. 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.

15. 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.

16. 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.

17. 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.

18. 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

19. 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.

20. 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. (identified as one of the breakthroughs in the field of computational biology in 2010, Nature Biotechnology 29, 45 (2011) | doi:10.1038/nbt.1747, http://www.nature.com/nbt/journal/v29/n1/full/nbt.1747.html)

21. 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.

22. 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 P0 Enzyme Activities in Human Liver. Genome Research 20: 1020-1036. doi:10.1101/gr.103341.109

23. 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

24. 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.

25. 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.

26. 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.

27. 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 Abdominal Obesity Which Affect Shared Metabolic Pathways and Networks. Nature Genetics 41: 415 - 423.

28. 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.

29. 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.

30. 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.

31. 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.

32. 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.

33. 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.

34. 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.

35. Peter Langfelder, Bin Zhang, Steve Horvath. (2007) Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut library for R. Bioinformatics doi: 10.1093/bioinformatics/btm563. (http://bioinformatics.oxfordjournals.org/cgi/reprint/btm563?ijkey=iRs3I4pFc6TEXdR&keytype=ref).

36. S. 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 103: 17402-17407.

37. 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. 103(34):12741-6.

38. 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

39. 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

40. 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.

41. 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.

42. Bin Zhang and Steve Horvath. (2005) A General Framework for Weighted Gene Co-expression Network Analysis. Statistical Applications in Genetics and Molecular Biology, vol. 4, issue 1.

43. 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.

44. 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.

45. Bin Zhang and Sargur N. Srihari. (2004) Handwriting Identification Using Multi-scale Features. Journal of Forensic Document Examination, vol 16.