All papers

Lab members marked as bold; * equal contribution; [+] Co-senior authors

    2024

  1. Hou C, Shen Y. (2024) SeqDance: A Protein Language Model for Representing Protein Dynamic Properties. bioRxiv. PDF
  2. Qiao L, Welch CL, Hernan R, Wynn J, Krishnan US, Khlevner J, De A, Farkouh-Karoleski C, Wagner AJ, Heydweiller A, et al, High FA, Sun X, Donahoe PK, Bendixen C, Brosens E, Shen Y [+], Chung WK [+]. (2024) Common variants increase risk for congenital diaphragmatic hernia within the context of de novo variants. AJHG. PMID: 39332409. PDF
  3. Prakash P, Street K, Narayanan S, Fernandez BA, Shen Y, Shu C.. (2024) Benchmarking Machine Learning Missing Data Imputation Methods in Large-Scale Mental Health Survey Databases. medRxiv.
  4. Sudnawa KK, Li W, Calamia S, Kanner CH, Bain JM, Abdelhakim AH, Geltzeiler A, Mebane CM, Provenzano FA, Sands TT, Fee RJ, Montes J, Shen Y, Chung WK.. (2024) Heterogeneity of comprehensive clinical phenotype and longitudinal adaptive function and correlation with computational predictions of severity of missense genotypes in KIF1A-associated neurological disorder. Genetics in Medicine. PMID: 38785164.
  5. Wright JR, Astrovskaya I, Barns SD, Goler A, Zhou X, Shu C, Snyder LG, Han B; SPARK Consortium; Shen Y, Volfovsky N, Hall JB, Feliciano P, Chung WK. (2024) Return of genetic research results in 21,532 individuals with autism. Genetics in Medicine. PMID: 38958063.
  6. G Zhong, Y Zhao, D Zhuang, WK Chung, Shen Y. (2024) PreMode predicts mode of action of missense variants by deep graph representation learning of protein sequence and structural context. bioRxiv.
  7. Xiao F, Zhang X, Morton SU, Kim SW, Fan Y, Gorham JM, Zhang H, Berkson PJ, Mazumdar N, Cao Y, Chen J, Hagen J, Liu X, Zhou P, Richter F, Shen Y, Ward T, Gelb BD, Seidman JG, Seidman CE, Pu WT. (2024) Functional dissection of human cardiac enhancers and noncoding de novo variants in congenital heart disease. Nature Genetics. PMID: 38378865.
  8. Watkins WS, Hernandez EJ, Miller TA, Blue NR, Zimmerman R, Griffiths ER, Frise E, Bernstein D, Boskovski MT, Brueckner M, Chung WK, Gaynor JW, Gelb BD, Goldmuntz E, Gruber PJ, Newburger JW, Roberts AE, Morton SU, Mayer JE, Seidman CE, Seidman JG, Shen Y, Wagner M, Yost HJ, Yandell M, Tristani-Firouzi M. (2024) Genome Sequencing is Critical for Forecasting Outcomes following Congenital Cardiac Surgery. medRxiv.
  9. Stokes G, Li Z, Talaba N, Genthe W, Brix MB, Pham B, Wienhold MD, Sandok G, Hernan R, Wynn J, Tang H, Tabima DM, Rodgers A, Hacker TA, Chesler NC, Zhang P, Murad R, Yuan JX, Shen Y, Chung WK, McCulley DJ.. (2024) Rescuing lung development through embryonic inhibition of histone acetylation. Science Translational Medicine. PMID: 38295182.

    10. 2023

  10. Zhao Y, Zhong G, Hagen J, Pan H, Chung WK, Shen Y. (2023) A probabilistic graphical model for estimating selection coefficient of nonsynonymous variants from human population sequence data. medRxiv. PDF
  11. Edwards NA, Kashyap A, Warren A, Agricola ZN, Kenny AP, Shen Y, Chung WK, Zorn AM. (2023) Disrupted endosomal trafficking of the Vangl-Celsr polarity complex underlies congenital anomalies in trachea-esophageal morphogenesis. bioRxiv.
  12. Wang Z, Shen Y. (2023) SABRE: Self-Attention Based model for predicting T-cell Receptor Epitope Specificity. bioRxiv. PDF
  13. Zhong G, Choi YA, Shen Y. (2023) VBASS enables integration of single cell gene expression data in Bayesian association analysis of rare variants. Communications Biology. PMID: 37491581. PDF
  14. Lewis MJ, Hsieh A, Qiao L, Tan R, Kazzi B, Channing A, Griffin EL, Jobanputra V, Su J, Shahryar C, Kochilas L, Gaynor JW, Lee T, Goldmuntz E, Russell M, Mital S, Tristani M, Brueckner M, Newburger J, Shen Y, Chung WK. (2023) Association of Predicted Damaging De Novo Variants on Ventricular Function in Individuals With Congenital Heart Disease. Circulation Genomic and Precision Medicine. PMID: 36866680.
  15. Poon MML, Caron DP, Wang Z, Wells SB, Chen D, Meng W, Szabo PA, Lam N, Kubota M, Matsumoto R, Rahman A, Luning Prak ET, Shen Y, Sims PA, Farber DL. (2023) Tissue adaptation and clonal segregation of human memory T cells in barrier sites. Nature Immunology. PMID: 36658238.
  16. Zhu N, LeDuc CA, Fennoy I, Laferrère B, Doege CA, Shen Y, Chung WK, Leibel RL. (2023) Rare predicted loss of function alleles in Bassoon (BSN) are associated with obesity. npj Genomic Medicine. PMID: 36865254. PDF
  17. Fan X, Pan H, Tian A, Chung WK, Shen Y. (2023) SHINE: Protein Language Model based Pathogenicity Prediction for Inframe Insertion and Deletion Variants. Briefings in Bioinformatics. PMID: 36575831. PDF

    18. 2022

  18. Zhang H, Xu MS, Fan X, Chung WK, Shen Y. (2022) Predicting functional effect of missense variants using graph attention neural networks. Nature Machine Intelligence. PDF
  19. Tan R, Shen Y. (2022) Accurate in silico confirmation of rare copy number variant calls from exome sequencing data using transfer learning. Nucleic acids research. PMID: 36124672. PDF
  20. Obiajulu J, Kuang R, Zhong G, Hagen J, Shu C, Chung WK, Shen Y. (2022) AlphaCluster: Coevolutionary driven residue-residue interaction models enable quantifiable clustering analysis of de novo variants to enhance predictions of pathogenicity. Research Square. PDF
  21. Zhou X *, Feliciano P *, Shu C *, Wang T *, Astrovskaya I *, Hall J, Obiajulu J, Wright J, Xu S, Marchenko O, Fleisch C, Barns SD, Green Synder L, Han B, Murali S, Harvey W, Brueggeman L, Chang TS, Turner TN, Nishida A, O'Roak BJ, Geschwind D, The SPARK Consortium, Michaelson J, Volfovsky N, Eichler EE, Shen Y [+], Chung WK [+]. (2022) Integrating de novo and inherited variants in over 42,607 autism cases identifies mutations in new moderate risk genes. Nature Genetics. PDF
  22. Zhong G, Shen Y. (2022) Statistical models of the genetic etiology of congenital heart disease. Current Opinion in Genetics & Development. PMID: 35939966. PDF
  23. Chung WK [+], Berg JS, Botkin JR, Brenner SE, Brosco JP, Brothers KB, Currier RJ, Gaviglio A, Kowtoniuk WE, Olson C, Lloyd-Puryear M, Saarinen A, Sahin M, Shen Y, Sherr EH, Watson MS, Hu Z.. (2022) Newborn screening for neurodevelopmental diseases: Are we there yet?. Am J Med Genet. PMID: 35838066.
  24. Zhong G *, Ahimaz P *, Edwards NA *, Hagen JJ, Faure C, Kingma P, Middlesworth W, Khlevner J, El Fiky M, Schindel D, Fialkowski E, Kashyap A, Forlenza S, Kenny AP, Zorn AM [+], Shen Y [+], Chung WK [+]. (2022) Identification and validation of novel candidate risk genes in endocytic vesicular trafficking associated with esophageal atresia and tracheoesophageal fistulas. HGG Advances. PMID: 35519826. PDF
  25. Ware SM, Bhatnagar S, Dexheimer PJ, Wilkinson JD, Sridhar A, Fan X, Shen Y, Tariq M, Schubert JA, Colan SD, Shi L, Canter CE, Hsu DT, Bansal N, Webber SA, Everitt MD, Kantor PF, Rossano JW, Pahl E, Rusconi P, Lee TM, Towbin JA, Lal AK, Chung WK, Miller EM, Aronow B, Martin LJ, Lipshultz SE; Pediatric Cardiomyopathy Registry Study Group. (2022) The genetic architecture of pediatric cardiomyopathy. AJHG. PMID: 35026164.
  26. Shu C, Snyder LG, Shen Y, Chung WK.. (2022) Imputing cognitive impairment in SPARK, a large autism cohort. Autism Research. PMID: 34636158. PDF

    27. 2021

  27. Qiao L, Xu L, Yu L, Wynn J, Hernan R, Zhou X, Farkouh-Karoleski C, Krishnan U, Khlevner J, De A, Zygmunt A, Crombleholme T, Lim F, Needelman H, Cusick R, Mychaliska G, Warner B, Wagner A, Danko M, Chung D, Potoka D, Kosinski P, McCulley D, Elfiky M, Azarow K, Fialkowski E, Schindel D, Soffer S, Lyon J, Zalieckas J, Vardarajan B, Aspelund G, Duron V, High F, Sun X, Donahoe P, Shen Y [+], Chung WK [+]. (2021) Rare and de novo variants in 827 congenital diaphragmatic hernia probands implicate LONP1 as candidate risk gene. AJHG. PMID: 34547244. PDF
  28. De Rosa MC, Glover HJ, Stratigopoulos G, LeDuc CA, Su Q, Shen Y, Sleeman MW, Chung WK, Leibel RL, Altarejos JY, Doege CA.. (2021) Gene expression atlas of energy balance brain regions. JCI Insight. PMID: 34283813.
  29. Kitaygorodsky A, Jin E, Shen Y. (2021) Predicting localized affinity of RNA binding proteins to transcripts with convolutional neural networks. bioRxiv. PDF
  30. Zhu N*, Swietlik EM *, Welch CL *, Pauciulo MW, Hagen JJ, Zhou X, et al, Morrell NW [+], Shen Y [+], Gräf S [+], Nichols WC [+], Chung WK [+]. (2021) Rare variant analysis of 4,241 pulmonary arterial hypertension cases from an international consortium implicate FBLN2, PDGFD and rare de novo variants in PAH. Genome Medicine. PMID: 33971972. PDF
  31. Fan X, Wynn J, Shang N, Liu C, Fedotov A, Hallquist MLG, Buchanan AH, Williams MS, Smith ME, Hoell C, Rasmussen-Torvik LJ, Peterson JF, Wiesner GL, Murad AM, Jarvik GP, Gordon AS, Rosenthal EA, Stanaway IB, Crosslin DR, Larson EB, Leppig KA, Henrikson NB, Williams JL, Li R, Hebbring S, Weng C, Shen Y [+], Crew KD [+], Chung W [+].. (2021) Penetrance of breast cancer genes from the eMERGE III Network. JNCI Cancer Spectrum. PDF
  32. Boyle L, Rao L, Kaur S, Fan X, Mebane C, Hamm L, Thornton A, Ahrendsen JT, Anderson MP, Christodoulou J, Gennerich A, Shen Y, Chung WK. (2021) Genotype and defects in microtubule-based motility correlate with clinical severity in KIF1A-associated neurological disorder. HGG Advances.
  33. Yun TJ, Igarashi S, Zhao H, Perez OA, Pereira MR, Zorn E, Shen Y, Goodrum F, Rahman A, Sims PA, Farber DL, Reizis B. (2021) Human plasmacytoid dendritic cells mount a distinct antiviral response to virus-infected cells. Science Immunology. PMID: 33811059.
  34. Morton SU, Shimamura A, Newburger PE, Opotowsky AR, Quiat D, Pereira AC, Jin SC, Gurvitz M, Brueckner M, Chung WK, Shen Y, Bernstein D, Gelb BD, Giardini A, Goldmuntz E, Kim RW, Lifton RP, Porter GA Jr, Srivastava D, Tristani-Firouzi M, Newburger JW, Seidman JG, Seidman CE.. (2021) Association of Damaging Variants in Genes With Increased Cancer Risk Among Patients With Congenital Heart Disease. JAMA Cardiology. PMID: 33084842.
  35. Fu J, Zuber J, Shonts B, Obradovic A, Wang Z, Frangaj K, Meng W, Rosenfeld AM, Waffarn EE, Liou P, Lau SP, Savage TM, Yang S, Rogers K, Danzl NM, Ravella S, Satwani P, Iuga A, Ho SH, Griesemer A, Shen Y, Prak ETL, Martinez M, Kato T, Sykes M. (2021) Lymphohematopoietic graft-versus-host responses promote mixed chimerism in patients receiving intestinal transplantation. JCI. PMID: 33630757.
  36. Cuella-Martin R, Hayward SB *, Fan X *, Chen X, Huang JW, Taglialatela A, Leuzzi G, Zhao J, Rabadan R, Lu C, Shen Y, Ciccia A.. (2021) Functional interrogation of DNA damage response variants with base editing screens. Cell. PMID: 33606978. PDF
  37. Qi H *, Zhang H *, Zhao Y *, Chen C *, Long JJ, Chung WK, Guan Y, Shen Y. (2021) MVP predicts pathogenicity of missense variants by deep learning. Nature Communications. PMID: 33479230. PDF

    38. 2020

  38. Zhang H, Shen Y. (2020) Template-based prediction of protein structure with deep learning. BMC Genomics. PMID: 33372607.
  39. Richter F *, Morton SU *, Kim SW *, Kitaygorodsky A *, Wasson L, Chen KM, Zhou J, Qi H, Patel N, DePalma S, et al, Srivastava D [+], Tristani-Firouzi M [+], Troyanskaya OG [+], Dickel DE [+], Shen Y [+], Seidman JG [+], Seidman CE [+], Gelb BD [+]. (2020) Genomic analyses implicate noncoding de novo variants in congenital heart disease. Nature Genetics. PMID: 32601476. PDF
  40. Qiao L *, Wynn J *, Yu L, Hernan R, Zhou X, Duron V, Aspelund G, et al, Wagner AJ, Soffer S, Schindel D, McCulley D, Shen Y [+], Chung WK [+]. (2020) Likely damaging de novo variants in congenital diaphragmatic hernia patients are associated with worse clinical outcomes. Genetics in Medicine. PDF
  41. Wang J *, Ahimaz PR *, Hashemifar S *, Khlevner J, Picoraro JA, Middlesworth W, Elfiky MM, Que J, Shen Y [+], Chung WK [+]. (2020) Novel Candidate Genes in Esophageal Atresia/Tracheoesophageal Fistula Identified by Exome Sequencing. EJHG. PDF
  42. Chen S, Zhou X, Byington E, Bruce S, Zhang H, Shen Y. (2020) Dissecting Autism Genetic Risk Using Single-cell RNA-seq Data. bioRxiv. PDF
  43. Hsieh A, Morton S, Willcox J, Gorham J, Tai A, Qi H, DePalma S, McKean D, Griffin E, Manheimer K, Bernstein D, Kim R, Newburger J, Porter G, Srivastava D, Tristani-Firouzi M, Brueckner M, Lifton R, Goldmuntz E, Gelb B, Chung W, Seidman C, Seidman J, Shen Y. (2020) EM-mosaic detects mosaic point mutations that contribute to congenital heart disease. Genome medicine. PMID: 32349777. PDF
  44. Richter F *, Morton SU *, Qi H *, Kitaygorodsky A *, Wang J, Homsy J, DePalma S, Patel N, Gelb BD, Seidman JG, Seidman CE, Shen Y. (2020) Whole Genome De Novo Variant Identification with FreeBayes and Neural Network Approaches. bioRxiv.
  45. Potus F, Pauciulo M, Cook E, Zhu N, Hsieh A, Welch C, Shen Y, Tian L, Lima P, Mewburn J, D'Arsigny C, Lutz K, Coleman A, Damico R, Snetsinger B, Martin A, Hassoun P, Nichols W, Chung W, Rauh M, Archer S. (2020) Novel Mutations and Decreased Expression of the Epigenetic Regulator TET2 in Pulmonary Arterial Hypertension. Circulation. PMID: 32192357.
  46. Dogra P, Rancan C, Ma W, Toth M, Senda T, Carpenter D, Kubota M, Matsumoto R, Thapa P, Szabo P, Li J, Arakawa-Hoyt J, Shen Y, Fong L, Lanier L, Farber D. (2020) Tissue Determinants of Human NK Cell Development, Function, and Residence. Cell. PMID: 32059780.

    47. 2019

  47. Zhu N, Pauciulo M, Welch C, Lutz K, Coleman A, Gonzaga-Jauregui C, Wang J, Grimes J, Martin L, He H, Shen Y [+], Chung W [+], Nichols W [+]. (2019) Novel risk genes and mechanisms implicated by exome sequencing of 2572 individuals with pulmonary arterial hypertension. Genome medicine. PMID: 31727138.
  48. Watkins W, Hernandez E, Wesolowski S, Bisgrove B, Sunderland R, Lin E, Lemmon G, Demarest B, Miller T, Bernstein D, Brueckner M, Chung W, Gelb B, Goldmuntz E, Newburger J, Seidman C, Shen Y, Yost H, Yandell M, Tristani-Firouzi M. (2019) De novo and recessive forms of congenital heart disease have distinct genetic and phenotypic landscapes. Nature communications. PMID: 31624253.
  49. Savage T, Shonts B, Lau S, Obradovic A, Robins H, Shaked A, Shen Y, Sykes M. (2019) Deletion of donor-reactive T cell clones after human liver transplant. American journal of transplantation. PMID: 31509321.
  50. Lyudovyk O, Shen Y, Tatonetti N, Hsiao S, Mansukhani M, Weng C. (2019) Pathway analysis of genomic pathology tests for prognostic cancer subtyping. Journal of biomedical informatics. PMID: 31499184.
  51. Feliciano P *, Zhou X *, Astrovskaya I, Turner T, Wang T, Brueggeman L, Barnard R, Hsieh A, Snyder L, Muzny D, Sabo A, Gibbs R, Eichler E, O'Roak B, Michaelson J, Volfovsky N, Shen Y, Chung W. (2019) Exome sequencing of 457 autism families recruited online provides evidence for autism risk genes. NPJ genomic medicine. PMID: 31452935. PDF
  52. Ma W, Lee J, Backenroth D, Zhou Y, Bush E, Sims P, Liu K, Shen Y. (2019) Single cell RNA-Seq reveals pre-cDCs fate determined by transcription factor combinatorial dose. BMC molecular and cell biology. PMID: 31253076. PDF
  53. Nicoletti P, Barrett S, McEvoy L, Daly A, Aithal G, Lucena M, Andrade R, Wadelius M, Hallberg P, Stephens C, Bjornsson E, Friedmann P, Kainu K, Laitinen T, Marson A, Molokhia M, Phillips E, Pichler W, Romano A, Shear N, Sills G, Tanno L, Swale A, Floratos A, Shen Y, Nelson M, Watkins P, Daly M, Morris A, Alfirevic A, Pirmohamed M. (2019) Shared Genetic Risk Factors Across Carbamazepine-Induced Hypersensitivity Reactions. Clinical pharmacology and therapeutics. PMID: 31066027.
  54. Khosravi-Maharlooei M, Obradovic A, Misra A, Motwani K, Holzl M, Seay H, DeWolf S, Nauman G, Danzl N, Li H, Ho S, Winchester R, Shen Y, Brusko T, Sykes M. (2019) Crossreactive public TCR sequences undergo positive selection in the human thymic repertoire. The Journal of clinical investigation. PMID: 30920391.
  55. Ganapathi M, Padgett L, Yamada K, Devinsky O, Willaert R, Person R, Au P, Tagoe J, McDonald M, Karlowicz D, Wolf B, Lee J, Shen Y, Okur V, Deng L, LeDuc C, Wang J, Hanner A, Mirmira R, Park M, Mastracci T, Chung W. (2019) Recessive Rare Variants in Deoxyhypusine Synthase, an Enzyme Involved in the Synthesis of Hypusine, Are Associated with a Neurodevelopmental Disorder. American journal of human genetics. PMID: 30661771.
  56. Nicoletti P, Aithal G, Chamberlain T, Coulthard S, Alshabeeb M, Grove J, Andrade R, Bjornsson E, Dillon J, Hallberg P, Lucena M, Martin J, Molokhia M, Pirmohamed M, Wadelius M, Shen Y, Nelson M, Daly A. (2019) Drug-Induced Liver Injury due to Flucloxacillin: Relevance of Multiple Human Leukocyte Antigen Alleles. Clinical pharmacology and therapeutics. PMID: 30661239.

    57. 2018

  57. Qi H *, Yu L *, Zhou X *, Wynn J, Zhao H, Guo Y, Zhu N, Kitaygorodsky A, Hernan R, Aspelund G, Lim F, Crombleholme T, Cusick R, Azarow K, Danko M, Chung D, Warner B, Mychaliska G, Potoka D, Wagner A, ElFiky M, Wilson J, Nickerson D, Bamshad M, High F, Longoni M, Donahoe P, Chung W, 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. PMID: 30532227. PDF
  58. Fu J, Zuber J, Martinez M, Shonts B, Obradovic A, Wang H, Lau S, Xia A, Waffarn E, Frangaj K, Savage T, Simpson M, Yang S, Guo X, Miron M, Senda T, Rogers K, Rahman A, Ho S, Shen Y, Griesemer A, Farber D, Kato T, Sykes M. (2018) Human Intestinal Allografts Contain Functional Hematopoietic Stem and Progenitor Cells that Are Maintained by a Circulating Pool. Cell stem cell. PMID: 30503142.
  59. Savage T, Shonts B, Obradovic A, Dewolf S, Lau S, Zuber J, Simpson M, Berglund E, Fu J, Yang S, Ho S, Tang Q, Turka L, Shen Y, Sykes M. (2018) Early expansion of donor-specific Tregs in tolerant kidney transplant recipients. JCI insight. PMID: 30429370.
  60. Youn A, Kim K, Rabadan R, Tycko B, Shen Y, Wang S. (2018) A pan-cancer analysis of driver gene mutations, DNA methylation and gene expressions reveals that chromatin remodeling is a major mechanism inducing global changes in cancer epigenomes. BMC medical genomics. PMID: 30400878.
  61. Bohnen M, Ma L, Zhu N, Qi H, McClenaghan C, Gonzaga-Jauregui C, Dewey F, Overton J, Reid J, Shuldiner A, Baras A, Sampson K, Bleda M, Hadinnapola C, Haimel M, Bogaard H, Church C, Coghlan G, Corris P, Eyries M, Gibbs J, Girerd B, Houweling A, Humbert M, Guignabert C, Kiely D, Lawrie A, Martin J, Montani D, Peacock A, Pepke-Zaba J, Soubrier F, Suntharalingam J, Toshner M, Treacy C, Trembath R, Wharton J, Wilkins M, Wort S, Yates K, Gräf S, Morrell N, Krishnan U, Rosenzweig E, Shen Y, Nichols C, Kass R, Chung W. (2018) Loss-of-Function ABCC8 Mutations in Pulmonary Arterial Hypertension. Circulation. Genomic and precision medicine. PMID: 30354297.
  62. Miron M, Kumar B, Meng W, Granot T, Carpenter D, Senda T, Chen D, Rosenfeld A, Zhang B, Lerner H, Friedman A, Hershberg U, Shen Y, Rahman A, Farber D. (2018) Human Lymph Nodes Maintain TCF-1(hi) Memory T Cells with High Functional Potential and Clonal Diversity throughout Life. Journal of immunology. PMID: 30111633.
  63. DeWolf S, Grinshpun B, Savage T, Lau S, 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. PMID: 30089728. PDF
  64. Zhu N, Welch C, Wang J, Allen P, Gonzaga-Jauregui C, Ma L, King A, Krishnan U, Rosenzweig E, Ivy D, Austin E, Hamid R, Pauciulo M, Lutz K, Nichols W, Reid J, Overton J, Baras A, Dewey F, Shen Y, Chung W. (2018) Rare variants in SOX17 are associated with pulmonary arterial hypertension with congenital heart disease. Genome medicine. PMID: 30029678. PDF
  65. 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. PMID: 29849042. PDF
  66. Zhu N, Gonzaga-Jauregui C, Welch C, Ma L, Qi H, King A, Krishnan U, Rosenzweig E, Ivy D, Austin E, Hamid R, Nichols W, Pauciulo M, Lutz K, Sawle A, Reid J, Overton J, Baras A, Dewey F, Shen Y, Chung W. (2018) Exome Sequencing in Children With Pulmonary Arterial Hypertension Demonstrates Differences Compared With Adults. Circulation. Genomic and precision medicine. PMID: 29631995.
  67. Manheimer K, Richter F, Edelmann L, D'Souza S, Shi L, Shen Y, Homsy J, Boskovski M, Tai A, Gorham J, Yasso C, Goldmuntz E, Brueckner M, Lifton R, Chung W, Seidman C, Seidman J, Gelb B. (2018) Robust identification of mosaic variants in congenital heart disease. Human genetics. PMID: 29417219.
  68. Feliciano P, Daniels A, Beaumont A, Camba A, Esler A, Gulsrud A, Mason A, Gutierrez A, Nicholson A, Paolicelli A, McKenzie A, Rachubinski A, Stephens A, Simon A, Stedman A, Shocklee A, Swanson A, Finucane B, Hilscher B, Hauf B, O'Roak B, McKenna B, Robertson B, Rodriguez B, Vernoia B, Bradley C, Cohen C, Erickson C, Harkins C, Hayes C, Lord C, Martin C, Ortiz C, Ochoa-Lubinoff C, Peura C, Rice C, Rosenberg C, Smith C, Thomas C, Taylor C, White L, Walston C, Amaral D, Coury D, Sarver D, Istephanous D, Li D, Nugyen D, Fox E, Butter E, Berry-Kravis E, Courchesne E, Fombonne E, Hofammann E, Lamarche E, Wodka E, Matthews E, O'Connor E, Palen E, Miller F, Dichter G, Marzano G, Stein G, Hutter H, Kaplan H, Li H, Lechniak H, Schneider H, Zaydens H, Arriaga I, Gerdts J, Cubells J, Cordova J, Gunderson J, Lillard J, Manoharan J, McCracken J, Michaelson J, Neely J, Orobio J, Pandey J, Piven J, Scherr J, Sutcliffe J, Tjernagel J, Wallace J, Callahan K, Dent K, Schweers K, Hamer K, Law J, Lowe K, O'Brien K, Smith K, Pawlowski K, Pierce K, Roeder K, Abbeduto L, Berry L, Cartner L, Coppola L, Carpenter L, Cordeiro L, DeMarco L, Grosvenor L, Higgins L, Huang-Storms L, Hosmer-Quint L, Herbert L, Kasparson L, Prock L, Pacheco L, Raymond L, Simon L, Soorya L, Wasserburg L, Lazar M, Alessandri M, Brown M, Currin M, Gwynette M, Heyman M, Hale M, Jones M, Jordy M, Morrier M, Sahin M, Siegel M, Verdi M, Parlade M, Yinger M, Bardett N, Hanna N, Harris N, Pottschmidt N, Russo-Ponsaran N, Takahashi N, Ousley O, Juarez A, Manning P, Annett R, Bernier R, Clark R, Landa R, Goin-Kochel R, Remington R, Schultz R, Brewster S, Booker S, Carpenter S, Eldred S, Francis S, Friedman S, Horner S, Hepburn S, Jacob S, Kanne S, Lee S, Mastel S, Plate S, Qiu S, Sandhu S, Thompson S, White S, Myers V, Singh V, Yang W, Warren Z, Amatya A, Ace A, Chatha A, Lash A, Negron B, Rigby C, Ridenour C, Stock C, Schmidt D, Fisk I, Acampado J, Nestle J, Nestle J, Layman K, Butler M, Kent M, Mallardi M, Carriero N, Lawson N, Volfovsky N, Edgar R, Marini R, Rana R, Ganesan S, Shah S, Ramsey T, Chin W, Jensen W, Krentz A, Gruber A, Sabo A, Salomatov A, Eng C, Muzny D, Astrovskaya I, Gibbs R, Han X, Shen Y, Reichardt L, Chung W. (2018) SPARK: A US Cohort of 50,000 Families to Accelerate Autism Research. Neuron. PMID: 29420931.

    69. 2017

  69. Jin S, Homsy J, Zaidi S, Lu Q, Morton S, DePalma S, Zeng X, Qi H, Chang W, Sierant M, Hung W, Haider S, Zhang J, Knight J, Bjornson R, Castaldi C, Tikhonoa I, Bilguvar K, Mane S, Sanders S, Mital S, Russell M, Gaynor J, Deanfield J, Giardini A, Porter G, Srivastava D, Lo C, Shen Y, Watkins W, Yandell M, Yost H, Tristani-Firouzi M, Newburger J, Roberts A, Kim R, Zhao H, Kaltman J, Goldmuntz E, Chung W, Seidman J, Gelb B, Seidman C, Lifton R, Brueckner M. (2017) Contribution of rare inherited and de novo variants in 2,871 congenital heart disease probands. Nature genetics. PMID: 28991257.
  70. Kumar B *, Ma W *, Miron M, Granot T, Guyer R, Carpenter D, Senda T, Sun X, Ho S, Lerner H, Friedman A, Shen Y [+], Farber D [+]. (2017) Human Tissue-Resident Memory T Cells Are Defined by Core Transcriptional and Functional Signatures in Lymphoid and Mucosal Sites. Cell reports. PMID: 28930685. PDF
  71. Kardon G, Ackerman K, McCulley D, Shen Y, Wynn J, Shang L, Bogenschutz E, Sun X, Chung W. (2017) Congenital diaphragmatic hernias: from genes to mechanisms to therapies. Disease models & mechanisms. PMID: 28768736.
  72. Chen C, Qi H, Shen Y, Pickrell J, Przeworski M. (2017) Contrasting Determinants of Mutation Rates in Germline and Soma. Genetics. PMID: 28733365.
  73. Lee J *, Zhou Y *, 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. PDF
  74. Thome J, Grinshpun B, Kumar B, Kubota M, Ohmura Y, Lerner H, Sempowski G, Shen Y, Farber D. (2017) Longterm maintenance of human naive T cells through in situ homeostasis in lymphoid tissue sites. Science immunology. PMID: 28361127.
  75. Longoni M, High F, Qi H, Joy M, Hila R, Coletti C, Wynn J, Loscertales M, Shan L, Bult C, Wilson J, Shen Y, Chung W, Donahoe P. (2017) Genome-wide enrichment of damaging de novo variants in patients with isolated and complex congenital diaphragmatic hernia. Human genetics. PMID: 28303347.
  76. Zuber J, Shonts B, Lau S, Obradovic A, Fu J, Yang S, Lambert M, Coley S, Weiner J, Thome J, DeWolf S, Farber D, Shen Y, Caillat-Zucman S, Bhagat G, Griesemer A, Martinez M, Kato T, Sykes M. (2017) Bidirectional intragraft alloreactivity drives the repopulation of human intestinal allografts and correlates with clinical outcome. Science immunology. PMID: 28239678.
  77. Nicoletti P, Aithal G, Bjornsson E, Andrade R, Sawle A, Arrese M, Barnhart H, Bondon-Guitton E, Hayashi P, Bessone F, Carvajal A, Cascorbi I, Cirulli E, Chalasani N, Conforti A, Coulthard S, Daly M, Day C, Dillon J, Fontana R, Grove J, Hallberg P, Hernández N, Ibáñez L, Kullak-Ublick G, Laitinen T, Larrey D, Lucena M, Martin J, Molokhia M, Pirmohamed M, Powell E, Qin S, Serrano J, Stephens C, Stolz A, Wadelius M, Watkins P, Floratos A, Shen Y, Nelson M, Urban T, Daly A. (2017) Association of Liver Injury From Specific Drugs, or Groups of Drugs, With Polymorphisms in HLA and Other Genes in a Genome-Wide Association Study. Gastroenterology. PMID: 28043905.

    78. 2016

  78. Zhang C [+], Shen Y [+]. (2016) A Cell Type-Specific Expression Signature Predicts Haploinsufficient Autism-Susceptibility Genes. Human mutation. PMID: 27860035. PDF
  79. McKean D, Homsy J, Wakimoto H, Patel N, Gorham J, DePalma S, Ware J, Zaidi S, Ma W, Patel N, Lifton R, Chung W, Kim R, Shen Y, Brueckner M, Goldmuntz E, Sharp A, Seidman C, Gelb B, Seidman J. (2016) Loss of RNA expression and allele-specific expression associated with congenital heart disease. Nature communications. PMID: 27670201.
  80. Castel S, Mohammadi P, Chung W, Shen Y, Lappalainen T. (2016) Rare variant phasing and haplotypic expression from RNA sequencing with phASER. Nature communications. PMID: 27605262.
  81. Bain J, Cho M, Telegrafi A, Wilson A, Brooks S, Botti C, Gowans G, Autullo L, Krishnamurthy V, Willing M, Toler T, Ben-Zev B, Elpeleg O, Shen Y, Retterer K, Monaghan K, Chung W. (2016) Variants in HNRNPH2 on the X Chromosome Are Associated with a Neurodevelopmental Disorder in Females. American journal of human genetics. PMID: 27545675.
  82. Berko E, Cho M, Eng C, Shao Y, Sweetser D, Waxler J, Robin N, Brewer F, Donkervoort S, Mohassel P, Bönnemann C, Bialer M, Moore C, Wolfe L, Tifft C, Shen Y, Retterer K, Millan F, Chung W. (2016) De novo missense variants in HECW2 are associated with neurodevelopmental delay and hypotonia. Journal of medical genetics. PMID: 27389779.
  83. Qi H, Dong C, Chung W, Wang K, Shen Y. (2016) Deep Genetic Connection Between Cancer and Developmental Disorders. Human mutation. PMID: 27363847. PDF
  84. Shi L, Guo Y, Dong C, Huddleston J, Yang H, Han X, Fu A, Li Q, Li N, Gong S, Lintner K, Ding Q, Wang Z, Hu J, Wang D, Wang F, Wang L, Lyon G, Guan Y, Shen Y, Evgrafov O, Knowles J, Thibaud-Nissen F, Schneider V, Yu C, Zhou L, Eichler E, So K, Wang K. (2016) Long-read sequencing and de novo assembly of a Chinese genome. Nature communications. PMID: 27356984.
  85. Sims J, Grinshpun B, Feng Y, Ung T, Neira J, Samanamud J, Canoll P, Shen Y [+], Sims P [+], Bruce J [+]. (2016) Diversity and divergence of the glioma-infiltrating T-cell receptor repertoire. PNAS. PMID: 27261081. PDF
  86. Beck D, Cho M, Millan F, Yates C, Hannibal M, O'Connor B, Shinawi M, Connolly A, Waggoner D, Halbach S, Angle B, Sanders V, Shen Y, Retterer K, Begtrup A, Bai R, Chung W. (2016) A recurrent de novo CTBP1 mutation is associated with developmental delay, hypotonia, ataxia, and tooth enamel defects. Neurogenetics. PMID: 27094857.
  87. Nicoletti P, Werk A, Sawle A, Shen Y, Urban T, Coulthard S, Bjornsson E, Cascorbi I, Floratos A, Stammschulte T, Gundert-Remy U, Nelson M, Aithal G, Daly A. (2016) HLA-DRB1*16: 01-DQB1*05: 02 is a novel genetic risk factor for flupirtine-induced liver injury. Pharmacogenetics and genomics. PMID: 26959717.
  88. DeWolf S, Shen Y, Sykes M. (2016) A New Window into the Human Alloresponse. Transplantation. PMID: 26760572.

    89. 2015

  89. Homsy J *, Zaidi S *, Shen Y *, Ware J, Samocha K, Karczewski K, DePalma S, McKean D, Wakimoto H, Gorham J, Jin S, Deanfield J, Giardini A, Porter G, Kim R, Bilguvar K, López-Giráldez F, Tikhonova I, Mane S, Romano-Adesman A, Qi H, Vardarajan B, Ma L, Daly M, Roberts A, Russell M, Mital S, Newburger J, Gaynor J, Breitbart R, Iossifov I, Ronemus M, Sanders S, Kaltman J, Seidman J, Brueckner M, Gelb B, Goldmuntz E, Lifton R, Seidman C, Chung W. (2015) De novo mutations in congenital heart disease with neurodevelopmental and other congenital anomalies. Science. PMID: 26785492. PDF
  90. Guo Y, Ding X, Shen Y, Lyon G, Wang K. (2015) SeqMule: automated pipeline for analysis of human exome/genome sequencing data. Scientific reports. PMID: 26381817.
  91. Jiang K, Sun X, Chen Y, Shen Y [+], Jarvis J [+]. (2015) RNA sequencing from human neutrophils reveals distinct transcriptional differences associated with chronic inflammatory states. BMC medical genomics. PMID: 26310571.
  92. Shang L, Cho M, Retterer K, Folk L, Humberson J, Rohena L, Sidhu A, Saliganan S, Iglesias A, Vitazka P, Juusola J, O'Donnell-Luria A, Shen Y, Chung W. (2015) Mutations in ARID2 are associated with intellectual disabilities. Neurogenetics. PMID: 26238514.
  93. Liu X, Jia Y, Stoopler M, Shen Y, Cheng H, Chen J, Mansukhani M, Koul S, Halmos B, Borczuk A. (2015) Next-Generation Sequencing of Pulmonary Sarcomatoid Carcinoma Reveals High Frequency of Actionable MET Gene Mutations. Journal of clinical oncology. PMID: 26215952.
  94. Nelson M, Tipney H, Painter J, Shen J, Nicoletti P, Shen Y, Floratos A, Sham P, Li M, Wang J, Cardon L, Whittaker J, Sanseau P. (2015) The support of human genetic evidence for approved drug indications. Nature genetics. PMID: 26121088.
  95. Nicoletti P, Bansal M, Lefebvre C, Guarnieri P, Shen Y, Pe'er I, Califano A, Floratos A. (2015) ABC transporters and the proteasome complex are implicated in susceptibility to Stevens-Johnson syndrome and toxic epidermal necrolysis across multiple drugs. PloS one. PMID: 26110827.
  96. Ostrowski E, Shen Y, Tian X, Sucgang R, Jiang H, Qu J, Katoh-Kurasawa M, Brock D, Dinh C, Lara-Garduno F, Lee S, Kovar C, Dinh H, Korchina V, Jackson L, Patil S, Han Y, Chaboub L, Shaulsky G, Muzny D, Worley K, Gibbs R, Richards S, Kuspa A, Strassmann J, Queller D. (2015) Genomic signatures of cooperation and conflict in the social amoeba. Current biology. PMID: 26051890.
  97. Yu L *, Sawle A *, Wynn J, Aspelund G, Stolar C, Arkovitz M, Potoka D, Azarow K, Mychaliska G, Shen Y [+], Chung W [+]. (2015) Increased burden of de novo predicted deleterious variants in complex congenital diaphragmatic hernia. Human molecular genetics. PMID: 26034137. PDF
  98. Morris H *, DeWolf S *, Robins H, Sprangers B, LoCascio S, Shonts B, 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. PDF

    99. 2014

  99. Johannesson B, Sagi I, Gore A, Paull D, Yamada M, Golan-Lev T, Li Z, LeDuc C, Shen Y, Stern S, Xu N, Ma H, Kang E, Mitalipov S, Sauer M, Zhang K, Benvenisty N, Egli D. (2014) Comparable frequencies of coding mutations and loss of imprinting in human pluripotent cells derived by nuclear transfer and defined factors. Cell stem cell. PMID: 25517467.
  100. Thome J, Yudanin N, Ohmura Y, Kubota M, Grinshpun B, Sathaliyawala T, Kato T, Lerner H, Shen Y, Farber D. (2014) Spatial map of human T cell compartmentalization and maintenance over decades of life. Cell. PMID: 25417158. PDF
  101. Vardarajan B, Zhang Y, Lee J, Cheng R, Bohm C, Ghani M, Reitz C, Reyes-Dumeyer D, Shen Y, Rogaeva E, Mayeux R. (2014) Coding mutations in SORL1 and Alzheimer disease. Annals of neurology. PMID: 25382023.
  102. Glessner J, Bick A, Ito K, Homsy J, Rodriguez-Murillo L, Fromer M, Mazaika E, Vardarajan B, Italia M, Leipzig J, DePalma S, Golhar R, Sanders S, Yamrom B, Ronemus M, Iossifov I, Willsey A, State M, Kaltman J, White P, Shen Y, Warburton D, Brueckner M, Seidman C, Goldmuntz E, Gelb B, Lifton R, Seidman J, Hakonarson H, Chung W. (2014) Increased frequency of de novo copy number variants in congenital heart disease by integrative analysis of single nucleotide polymorphism array and exome sequence data. Circulation research. PMID: 25205790.
  103. Overby C, Hripcsak G, Shen Y. (2014) Estimating heritability of drug-induced liver injury from common variants and implications for future study designs. Scientific reports. PMID: 25042059.
  104. Backenroth D, Homsy J, Murillo L, Glessner J, Lin E, Brueckner M, Lifton R, Goldmuntz E, Chung W, Shen Y. (2014) CANOES: detecting rare copy number variants from whole exome sequencing data. Nucleic acids research. PMID: 24771342. PDF
  105. Yu L, Bennett J, Wynn J, Carvill G, Cheung Y, Shen Y, Mychaliska G, Azarow K, Crombleholme T, Chung D, Potoka D, Warner B, Bucher B, Lim F, Pietsch J, Stolar C, Aspelund G, Arkovitz M, Mefford H, Chung W. (2014) Whole exome sequencing identifies de novo mutations in GATA6 associated with congenital diaphragmatic hernia. Journal of medical genetics. PMID: 24385578.

    106. 2013

  106. Leduc C, Crouch E, Wilson A, Lefkowitch J, Wamelink M, Jakobs C, Salomons G, Sun X, Shen Y, Chung W. (2013) Novel association of early onset hepatocellular carcinoma with transaldolase deficiency. JIMD reports. PMID: 24097415.
  107. Boland M, Hripcsak G, Shen Y, Chung W, Weng C. (2013) Defining a comprehensive verotype using electronic health records for personalized medicine. Journal of the American Medical Informatics Association. PMID: 24001516.
  108. Overby C, Pathak J, Gottesman O, Haerian K, Perotte A, Murphy S, Bruce K, Johnson S, Talwalkar J, Shen Y, Ellis S, Kullo I, Chute C, Friedman C, Bottinger E, Hripcsak G, Weng C. (2013) A collaborative approach to developing an electronic health record phenotyping algorithm for drug-induced liver injury. Journal of the American Medical Informatics Association. PMID: 23837993.
  109. Gill R, Cheung Y, Shen Y, Lanzano P, Mirza N, Ten S, Maclaren N, Motaghedi R, Han J, Yanovski J, Leibel R, Chung W. (2013) Whole-exome sequencing identifies novel LEPR mutations in individuals with severe early onset obesity. Obesity. PMID: 23616257.
  110. DeStefano G, Fantauzzo K, Petukhova L, Kurban M, Tadin-Strapps M, Levy B, Warburton D, Cirulli E, Han Y, Sun X, Shen Y, Shirazi M, Jobanputra V, Cepeda-Valdes R, Christiano A. (2013) Position effect on FGF13 associated with X-linked congenital generalized hypertrichosis. PNAS. PMID: 23603273.

    111. 2012

  111. Yu L, Wynn J, Cheung Y, Shen Y, Mychaliska G, Crombleholme T, Azarow K, Lim F, Chung D, Potoka D, Warner B, Bucher B, Stolar C, Aspelund G, Arkovitz M, Chung W. (2012) Variants in GATA4 are a rare cause of familial and sporadic congenital diaphragmatic hernia. Human genetics. PMID: 23138528.
  112. Urban T, Shen Y, Stolz A, Chalasani N, Fontana R, Rochon J, Ge D, Shianna K, Daly A, Lucena M, Nelson M, Molokhia M, Aithal G, Floratos A, Pe'er I, Serrano J, Bonkovsky H, Davern T, Lee W, Navarro V, Talwalkar J, Goldstein D, Watkins P, Daly A, Aithal G, Dillon J, Pirmohamed M, Day C, Donaldson P, Bernal W, Park B, Khoo S, Gilmore I, Henderson J, Davies C, Hawkins K, Hanson A, Evely J, Hussaini H, Mills P, Griffiths W, Collier J, Brind A, Fisher N, Shearman J, Elias E, Grant A, Austin A, Gordon F, Cramp M, Saksena S, McMurtry H, Thompson N, Williams R, Morgan M, Phillips E, Patel M, Mitchison H, Kingham J, Das D, Collier J, Hellier S, Groome M, Miller M, McKeigue P, Stricker B, Yue Q, Wadelius M, Eliasson E, Hallberg P, Melhus H, Carvajal A, Ibáñez L, Bondon-Guitton E, Lapeyre-Mestre M, Montastruc J, Conforti A, Velo G, Eichelbaum M, Salado I, Sainz M, Vendrell L, Succurro F, Smerghetto M, Buyukcelik R, Arp P, Andrade R, Lucena M, Stephens C, Ulzurrun E, Borraz Y, Ruiz-Cabello F, Lopez-Nevot M, Romero-Gomez M, Fernández M, Peláez G, Casado M, Navarro J, Guarner C, Soriano G, Roman E, Muñoz-Yague T, Solís-Herruzo J, Castiella A, Zapata E, Moreno M, Calleja J. (2012) Limited contribution of common genetic variants to risk for liver injury due to a variety of drugs. Pharmacogenetics and genomics. PMID: 22968431.
  113. Nicoletti P, Cartsos V, Palaska P, Shen Y, Floratos A, Zavras A. (2012) Genomewide pharmacogenetics of bisphosphonate-induced osteonecrosis of the jaw: the role of RBMS3. The oncologist. PMID: 22267851.

    114. 2011

  114. Shen Y, Gu Y, Pe'er I. (2011) A hidden Markov model for copy number variant prediction from whole genome resequencing data. BMC bioinformatics. PMID: 21989326.
  115. Shen Y, Song R, Pe'er I. (2011) Coverage tradeoffs and power estimation in the design of whole-genome sequencing experiments for detecting association. Bioinformatics. PMID: 21636589.
  116. Lucena M *, Molokhia M *, Shen Y *, Urban T, Aithal G, Andrade R, Day C, Ruiz-Cabello F, Donaldson P, Stephens C, Pirmohamed M, Romero-Gomez M, Navarro J, Fontana R, Miller M, Groome M, Bondon-Guitton E, Conforti A, Stricker B, Carvajal A, Ibanez L, Yue Q, Eichelbaum M, Floratos A, Pe'er I, Daly M, Goldstein D, Dillon J, Nelson M, Watkins P, Daly A. (2011) Susceptibility to amoxicillin-clavulanate-induced liver injury is influenced by multiple HLA class I and II alleles. Gastroenterology. PMID: 21570397.
  117. Shen Y, Nicoletti P, Floratos A, Pirmohamed M, Molokhia M, Geppetti P, Benemei S, Giomi B, Schena D, Vultaggio A, Stern R, Daly M, John S, Nelson M, Pe'er I. (2011) Genome-wide association study of serious blistering skin rash caused by drugs. The pharmacogenomics journal. PMID: 21221126.

    118. 2009

  118. Shen Y [+], Wan Z, Coarfa C, Drabek R, Chen L, Ostrowski E, Liu Y, Weinstock G, Wheeler D, Gibbs R, Yu F [+]. (2009) A SNP discovery method to assess variant allele probability from next-generation resequencing data. Genome research. PMID: 20019143.
  119. Daly A, Donaldson P, Bhatnagar P, Shen Y, Pe'er I, Floratos A, Daly M, Goldstein D, John S, Nelson M, Graham J, Park B, Dillon J, Bernal W, Cordell H, Pirmohamed M, Aithal G, Day C. (2009) HLA-B*5701 genotype is a major determinant of drug-induced liver injury due to flucloxacillin. Nature genetics. PMID: 19483685.
  120. Liu Y, Qin X, Song X, Jiang H, Shen Y, Durbin K, Lien S, Kent M, Sodeland M, Ren Y, Zhang L, Sodergren E, Havlak P, Worley K, Weinstock G, Gibbs R. (2009) Bos taurus genome assembly. BMC genomics. PMID: 19393050.

    121. 2008

  121. Shen Y, 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. PMID: 19107202.
  122. Wang X, Gao H, Shen Y, Weinstock G, Zhou J, Palzkill T. (2008) A high-throughput percentage-of-binding strategy to measure binding energies in DNA-protein interactions: application to genome-scale site discovery. Nucleic acids research. PMID: 18653527.
  123. Wheeler D *, Srinivasan M *, Egholm M *, Shen Y *, Chen L, McGuire A, He W, Chen Y, Makhijani V, Roth G, Gomes X, Tartaro K, Niazi F, Turcotte C, Irzyk G, Lupski J, Chinault C, Song X, Liu Y, Yuan Y, Nazareth L, Qin X, Muzny D, Margulies M, Weinstock G, Gibbs R, Rothberg J. (2008) The complete genome of an individual by massively parallel DNA sequencing. Nature. PMID: 18421352.

    124. 2007

  124. Gibbs R, Rogers J, Katze M, Bumgarner R, Weinstock G, Mardis E, Remington K, Strausberg R, Venter J, Wilson R, Batzer M, Bustamante C, Eichler E, Hahn M, Hardison R, Makova K, Miller W, Milosavljevic A, Palermo R, Siepel A, Sikela J, Attaway T, Bell S, Bernard K, Buhay C, Chandrabose M, Dao M, Davis C, Delehaunty K, Ding Y, Dinh H, Dugan-Rocha S, Fulton L, Gabisi R, Garner T, Godfrey J, Hawes A, Hernandez J, Hines S, Holder M, Hume J, Jhangiani S, Joshi V, Khan Z, Kirkness E, Cree A, Fowler R, Lee S, Lewis L, Li Z, Liu Y, Moore S, Muzny D, Nazareth L, Ngo D, Okwuonu G, Pai G, Parker D, Paul H, Pfannkoch C, Pohl C, Rogers Y, Ruiz S, Sabo A, Santibanez J, Schneider B, Smith S, Sodergren E, Svatek A, Utterback T, Vattathil S, Warren W, White C, Chinwalla A, Feng Y, Halpern A, Hillier L, Huang X, Minx P, Nelson J, Pepin K, Qin X, Sutton G, Venter E, Walenz B, Wallis J, Worley K, Yang S, Jones S, Marra M, Rocchi M, Schein J, Baertsch R, Clarke L, Csürös M, Glasscock J, Harris R, Havlak P, Jackson A, Jiang H, Liu Y, Messina D, Shen Y, Song H, Wylie T, Zhang L, Birney E, Han K, Konkel M, Lee J, Smit A, Ullmer B, Wang H, Xing J, Burhans R, Cheng Z, Karro J, Ma J, Raney B, She X, Cox M, Demuth J, Dumas L, Han S, Hopkins J, Karimpour-Fard A, Kim Y, Pollack J, Vinar T, Addo-Quaye C, Degenhardt J, Denby A, Hubisz M, Indap A, Kosiol C, Lahn B, Lawson H, Marklein A, Nielsen R, Vallender E, Clark A, Ferguson B, Hernandez R, Hirani K, Kehrer-Sawatzki H, Kolb J, Patil S, Pu L, Ren Y, Smith D, Wheeler D, Schenck I, Ball E, Chen R, Cooper D, Giardine B, Hsu F, Kent W, Lesk A, Nelson D, O'brien W, Prüfer K, Stenson P, Wallace J, Ke H, Liu X, Wang P, Xiang A, Yang F, Barber G, Haussler D, Karolchik D, Kern A, Kuhn R, Smith K, Zwieg A. (2007) Evolutionary and biomedical insights from the rhesus macaque genome. Science. PMID: 17431167.

    125. 2006

  125. Sodergren E, Shen Y, Song X, Zhang L, Gibbs R, Weinstock G. (2006) Shedding genomic light on Aristotle's lantern. Developmental biology. PMID: 17097628.

    126. 2002

  126. Kong Y, Shen Y, Warth T, Ma J. (2002) Conformational pathways in the gating of Escherichia coli mechanosensitive channel. PNAS. PMID: 11972047.
  127. Shen Y, Kong Y, Ma J. (2002) Intrinsic flexibility and gating mechanism of the potassium channel KcsA. PNAS. PMID: 11842204.

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