Yufeng "Joshua" Shen, PhD

Center for Computational Biology and Bioinformatics
and Pe'er Computational Genetics and Genomics Lab
Columbia University

Research

Education

2007 Ph.D., Computational Biology, SCBMB program, Baylor College of Medicine
    Advisor: George Weinstock

2000 B.S., Biochemistry and Molecular Biology, Peking University

1999 The Honor Science Program, Peking University

Publication

Selected

* Joint first authorship status

Complete

Journal Articles

  1. Daly AK, Donaldson PT, Bhatnagar P, Shen Y, Pe'er I, Floratos A, Daly MJ, Goldstein DB, John S, Nelson MR, Graham J, Park BK, Dillon JF, Bernal W, Cordell HJ, Pirmohamed M, Aithal GP, Day CP; for the DILIGEN study; International SAE Consortium., (2009) HLA-B*5701 genotype is a major determinant of drug-induced liver injury due to flucloxacillin. Nature Genetics [Epub ahead of print]

  2. Bovine Genome Sequencing and Analysis Consortium, (2009) The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science, 324(5926):522-8
  3. Liu Y, Qin X, Song XZ, Jiang H, Shen Y, Durbin KJ, Lien S, Kent MP, Sodeland M, Ren Y, Zhang L, Sodergren E, Havlak P, Worley KC, Weinstock GM, Gibbs RA. (2009) Bos taurus genome assembly. BMC Genomics, 10(1):180.
  4. Yufeng Shen, Sarin S, Liu Y, Hobert O, Pe'er I (2008) Comparing Platforms for C. elegans Mutant Identification Using High-Throughput Whole-Genome Sequencing. PLoS ONE 3(12): e4012 doi:10.1371/journal.pone.0004012
  5. Xiaohu Wang, Haichun Gao, Yufeng Shen, George M. Weinstock, Jizhong Zhou and Timothy Palzkill (2008) A high-throughput percentage-of-binding strategy to measure binding energies in DNA-protein interactions: application to genome-scale site discovery Nucleic Acids Res. 36(15):4863-71
  6. David A. Wheeler *, Maithreyan Srinivasan *, Michael Egholm *, Yufeng Shen *, Lei Chen, Amy McGuire, Wen He, Yi-Ju Chen, Vinod Makhijani, G. Thomas Roth, Xavier Gomes, Karrie Tartaro, Faheem Niazi, Cynthia L. Turcotte, Gerard P. Irzyk, James R. Lupski, Craig Chinault, Xing-zhi Song, Yue Liu, Ye Yuan, Lynne Nazareth, Xiang Qin, Donna M. Muzny, Marcel Margulies, George M. Weinstock, Richard A. Gibbs & Jonathan M. Rothberg, (2008) The complete genome of an individual by massively parallel DNA sequencing, Nature 452:872-876 Abstract
  7. Rhesus Macaque Genome Sequencing and Analysis Consortium, (2007), Evolutionary and biomedical insights from the rhesus macaque genome, Science 13;316(5822):222-34 abstract
  8. Sea Urchin Genome Sequencing Consortium, (2006) The Genome of the Sea Urchin Strongylocentrotus purpuratus, Science 314(5801):941-952 abstract
  9. Erica Sodergren, Yufeng Shen, Xingzhi Song, Lan Zhang, Richard A. Gibbs and George M. Weinstock, (2006) Shedding genomic light on Aristotle's lantern, Developmental Biology, 300(1):2-8 abstract
  10. Yufeng Shen, Yifei Kong and Jianpeng Ma, (2002), Intrinsic flexibility and gating mechanism of the potassium channel KcsA, Proc. Natl. Acad. Sci. USA. 99:1949-1953
  11. Yifei Kong, Yufeng Shen, Tiffany E. Warth and Jianpeng Ma, (2002), Conformational Pathways in the Gating of E.coli Mechanosensitive Channel, Proc. Natl. Acad. Sci. USA. 99: 5999-6004