Selected publications

    Preprints:


  1. Qi H*, Chen C*, Zhang H, Long JJ, Chung WK, Guan Y, Shen Y. (2018) MVP: predicting pathogenicity of missense variants by deep learning. bioRxiv, 259390
  2. Na Zhu*, Michael W Pauciulo*, Carrie L Welch*, Katie A Lutz, Anna W Coleman, Claudia Gonzaga-Jauregui, Jiayao Wang, Joseph M Grimes, Lisa J Martin, Hua He, PAH Biobank, Yufeng Shen#, Wendy K Chung#, Wlliam C Nichols#, (2019) Novel risk genes and mechanisms implicated by exome sequencing of 2,572 individuals with pulmonary arterial hypertension. bioRxiv, 550327
  3. Peer-reviewed:


  4. Ma W, Lee J, Backenroth D, Zhou YJ, Bush E, Sims P, Liu K, Shen Y, (2019) Single cell RNA-Seq reveals pre-cDCs fate determined by transcription factor combinatorial dose, BMC Mol Cell Biol, PMID: 31253076
  5. Qi H*, Yu L*, Zhou X*, Kitaygorodsky A, Wynn J, Zhu N, Aspelund G, Lim YF, Crombleholme T, Cusick R, Azarow K, Danko ME, Chung D, Warner BW, Mychaliska GB, Potoka D, Wagner AJ, ElFiky M, Nickerson DA, Bamshad MJ, Wilson JM, High FA, Longoni M, Donahoe P, Chung WK#, Shen Y#, (2018) De novo variants in congenital diaphragmatic hernia identify MYRF as a new syndrome and reveal genetic overlaps with other developmental disorders, PLOS Genetics, doi: 10.1371/journal.pgen.1007822
  6. Han X*, Chen S*, Flynn E, Wu S, Wintner D, Shen Y, (2018) Distinct epigenomic patterns are associated with haploinsufficiency and predict risk genes of developmental disorders. Nature Communications, doi: 10.1038/s41467-018-04552-7
  7. DeWolf S*, Grinshpun B*, Savage T, Lau SP, Obradovic A, Shonts B, Yang S, Morris H, Zuber J, Winchester R, Sykes M, Shen Y (2018) Quantifying size and diversity of the human T cell alloresponse, JCI Insight, doi: 10.1172/jci.insight.121256
  8. Zhu N, Welch CL, Wang J, Allen PM, Gonzaga-Jauregui C, Ma L, King AK, Krishnan U, Rosenzweig EB, Ivy DD, Austin ED, Hamid R, Pauciulo MW, Lutz KA, Nichols WC, Reid JG, Overton JD, Baras A, Dewey FE, Shen Y, Chung WK, (2018) Rare variants in SOX17 are associated with pulmonary arterial hypertension with congenital heart disease. Genome Medicine, doi: 10.1186/s13073-018-0566-x
  9. SPARK Consortium &, (2018) SPARK: A US Cohort of 50,000 Families to Accelerate Autism Research, Neuron, PMID: 29420931
  10. Zhu N*, Gonzaga-Jauregui C*, Welch CL*, Ma L, Qi H, King AK, Krishnan U, Rosenzweig EB, Ivy DD, Austin ED, Hamid R, Nichols WC, Pauciulo MW, Lutz KA, Sawle A, Reid JG, Overton JD, Baras A, Dewey F, Shen Y, Chung WK. (2018) Exome Sequencing in Children With Pulmonary Arterial Hypertension Demonstrates Differences Compared With Adults. Circulation: Genomic and Precision Medicine, PMID: 29631995
  11. 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
  12. Chen C, Qi H, Shen Y, Pickrell J, Przeworski M, (2017) Contrasting Determinants of Mutation Rates in Germline and Soma. Genetics. PMID: 28733365
  13. Zhang C #, Shen Y #, (2017) A cell type-specific expression signature predicts haploinsufficient autism-susceptibility genes. Human Mutation, PMID: 27860035
  14. Kumar BV*, Ma W*, Miron M, Granot T, Guyer RS, Carpenter DJ, Senda T, Sun X, Ho SH, Lerner H, Friedman AL, Shen Y #, Farber DL #, (2017) Human Tissue-Resident Memory T Cells Are Defined by Core Transcriptional and Functional Signatures in Lymphoid and Mucosal Sites, Cell Reports, PMID: 28930685
  15. Qi H, Dong C, Chung WK, Wang K, Shen Y, (2016) Deep Genetic Connection between Cancer and Developmental Disorders. Human Mutation, PMID: 27363847
  16. 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
  17. DeWolf S, Shen Y, Sykes M, (2016) A New Window into the Human Alloresponse. Transplantation, PMID: 26760572
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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.
  30. 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
  31. 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
  32. 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
  33. Sea Urchin Genome Sequencing Consortium &, The Genome of the Sea Urchin Strongylocentrotus purpuratus, Science 2006, 314(5801):941-952
  34. 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
# Joint corresponding author
* Joint first author
& Consortium member
Lab members marked as bold

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