Selected publications

# Joint corresponding author
* Joint first author
& Consortium member
Lab members marked as bold
  1. Lee J*, Zhou YJ*, Ma W*, Zhang W, Aljoufi A, Luh T, Lucero K, Liang D, Thomsen M, Bhagat G, Shen Y #, Liu K #, (2017) Lineage specification of human dendritic cells is marked by IRF8 expression in hematopoietic stem cells and multipotent progenitors. Nature Immunology, PMID: 28650480
  2. Chen C, Qi H, Shen Y, Pickrell J, Przeworski M, (2017) Contrasting Determinants of Mutation Rates in Germline and Soma. Genetics. PMID: 28733365
  3. Zhang C #, Shen Y #, (2017) A cell type-specific expression signature predicts haploinsufficient autism-susceptibility genes. Human Mutation, PMID: 27860035
  4. Qi H, Dong C, Chung WK, Wang K, Shen Y, (2016) Deep Genetic Connection between Cancer and Developmental Disorders. Human Mutation, PMID: 27363847
  5. Sims JS, Grinshpun B, Feng Y, Ung TH, Neira JA, Samanamud JL, Canoll P, Shen Y #, Sims PA #, Bruce JN#, (2016) Diversity and divergence of the glioma-infiltrating T-cell receptor repertoire. PNAS, PMID: 27261081
  6. DeWolf S, Shen Y, Sykes M, (2016) A New Window into the Human Alloresponse. Transplantation, PMID: 26760572
  7. Homsy J*, Zaidi S*, Shen Y*, Ware JS, Samocha KE, Karczewski KJ, DePalma SR, McKean D, Wakimoto H, Gorham J, Jin SC, Deanfield J, Giardini A, Porter GA Jr, Kim R, Bilguvar K, López-Giráldez F, Tikhonova I, Mane S, Romano-Adesman A, Qi H, Vardarajan B, Ma L, Daly M, Roberts AE, Russell MW, Mital S, Newburger JW, Gaynor JW, Breitbart RE, Iossifov I, Ronemus M, Sanders SJ, Kaltman JR, Seidman JG, Brueckner M, Gelb BD, Goldmuntz E, Lifton RP, Seidman CE, Chung WK. (2015) De novo mutations in congenital heart disease with neurodevelopmental and other congenital anomalies. Science, PMID: 26785492
  8. Morris H, DeWolf S, Robins H, Sprangers B, LoCascio SA, Shonts BA, Kawai T, Wong W, Yang S, Zuber J, Shen Y #, Sykes M #, (2015) Tracking donor-reactive T cells: Evidence for clonal deletion in tolerant kidney transplant patients, Science Translational Medicine, PMID: 25632034
  9. Yu L, Sawle AD, Wynn J, Aspelund G, Stolar CJ, Arkovitz MS, Potoka D, Azarow KS, Mychaliska GB, Shen Y #, Chung WK #, (2015) Increased burden of de novo predicted deleterious variants in complex congenital diaphragmatic hernia, Human Molecular Genetics, PMID: 26034137
  10. Nelson MR, Tipney H, Painter JL, Shen J, Nicoletti P, Shen Y, Floratos A, Sham PC, Li MJ, Wang J, Cardon LR, Whittaker JC, Sanseau P. (2015) The support of human genetic evidence for approved drug indications. Nature Genetics, PMID: 26121088
  11. Thome JJC, Yudanin N, Ohmura Y, Kubota M, Grinshpun B, Sathaliyawala T, Kat T, Lerner H, Shen Y, Farber DL, (2014) Spatial Map of Human T Cell Compartmentalization and Maintenance over Decades of Life, Cell, DOI: http://dx.doi.org/10.1016/j.cell.2014.10.026
  12. Backenroth D, Homsy J, Murillo LR, Glessner J, Lin E, Brueckner M, Lifton R, Goldmuntz E, Chung WK, Shen Y, (2014) CANOES: Detecting rare copy number variants from whole exome sequencing data, Nucleic Acids Research doi: 10.1093/nar/gku345 PMID: 24771342
  13. Overby CL, Hripcsak G, Shen Y, (2014) Estimating heritability of drug-induced liver injury from common variants and implications for future study designs, Scientific Reports, doi: 10.1038/srep05762, PMID: 25042059
  14. Grinshpun B, Sims J, Canoll P, Bruce JN, Sims P, Shen Y, (2013) Analyzing T cell repertoire diversity by high-throughput sequencing, Global Conference on Signal and Information Processing (GlobalSIP), 2013 IEEE, doi: 10.1109/GlobalSIP.2013.6736810
  15. Yufeng Shen#, Ruijie Song, and Itsik Pe'er, Coverage Tradeoffs and Power Estimation in the Design of Whole-Genome Sequencing Experiments for Detecting Association,Bioinformatics, 2011
  16. M. Isabel Lucena*, Mariam Molokhia*, Yufeng Shen*, Thomas J. Urban, et al., (2011) Susceptibility to amoxicillin-clavulanate-induced liver injury is influenced by multiple HLA class I and class II alleles, Gastroenterology doi: 10.1053/j.gastro.2011.04.001. PMID: 21570397
  17. Yufeng Shen#, Yiwei Gu and Itsik Pe'er, A Hidden Markov Model for Copy Number Variant Prediction from Whole Genome Resequencing Data, BMC Bioinformatics 2011
  18. Yufeng Shen, Paola Nicoletti, Aris Floratos, Munir Pirmohamed, et al., (2012) Genome-Wide Association Study of Serious Blistering Skin Rash Caused by Drugs,Pharmacogenomics J. doi: 10.1038/tpj.2010.84. Epub 2011 Jan 11. PMID: 21221126
  19. Yufeng Shen#, Zhengzheng Wan, Cristian Coarfa, Rafal Drabek, Lei Chen, Elizabeth A. Ostrowski, Yue Liu, George M. Weinstock, David A. Wheeler, Richard A. Gibbs, and Fuli Yu, A SNP discovery method to assess variant allele probability from next generation resequencing data. Genome Research 2010, 20(2):273-80. Epub 2009 Dec 17.
  20. Ann K Daly, Peter T Donaldson, Pallav Bhatnagar, Yufeng Shen, Itsik Pe'er, Aris Floratos, Mark J Daly, David B Goldstein, Sally John, Matthew R Nelson, Julia Graham, B Kevin Park, John F Dillon, William Bernal, Heather J Cordell, Munir Pirmohamed, Guruprasad P Aithal, Christopher P Day, for the DILIGEN study & International SAE Consortium, HLA-B*5701 genotype is a major determinant of drug-induced liver injury due to flucloxacillin. Nature Genetics 2009, 41(7):816-9. PMID: 19483685
  21. Yufeng Shen, Sumeet Sarin, Ye Liu, Oliver Hobert, Itsik Pe'er, Comparing Platforms for C. elegans Mutant Identification Using High-Throughput Whole-Genome Sequencing. PLoS ONE 2008, 3(12): e4012
  22. 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, The complete genome of an individual by massively parallel DNA sequencing, Nature 2008, 452:872-876
  23. Sea Urchin Genome Sequencing Consortium &, The Genome of the Sea Urchin Strongylocentrotus purpuratus, Science 2006, 314(5801):941-952
  24. Yufeng Shen, Yifei Kong and Jianpeng Ma, Intrinsic flexibility and gating mechanism of the potassium channel KcsA, Proc. Natl. Acad. Sci. USA. 2002, 99:1949-1953

All publications on pubmed