| Year |
Citation |
Score |
| 2024 |
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, ... ... Shen Y, et al. Genome Sequencing is Critical for Forecasting Outcomes following Congenital Cardiac Surgery. Medrxiv : the Preprint Server For Health Sciences. PMID 38746151 DOI: 10.1101/2024.05.03.24306784 |
0.307 |
|
| 2024 |
Zhong G, Zhao Y, Zhuang D, Chung WK, Shen Y. PreMode predicts mode-of-action of missense variants by deep graph representation learning of protein sequence and structural context. Biorxiv : the Preprint Server For Biology. PMID 38746140 DOI: 10.1101/2024.02.20.581321 |
0.723 |
|
| 2024 |
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, et al. Functional dissection of human cardiac enhancers and noncoding de novo variants in congenital heart disease. Nature Genetics. PMID 38378865 DOI: 10.1038/s41588-024-01669-y |
0.321 |
|
| 2023 |
Zhao Y, Zhong G, Hagen J, Pan H, Chung WK, Shen Y. A probabilistic graphical model for estimating selection coefficient of missense variants from human population sequence data. Medrxiv : the Preprint Server For Health Sciences. PMID 38168397 DOI: 10.1101/2023.12.11.23299809 |
0.735 |
|
| 2023 |
Petit F, Longoni M, Wells J, Maser RS, Bogenschutz EL, Dysart MJ, Contreras HTM, Frénois F, Pober BR, Clark RD, Giampietro PF, Ropers HH, Hu H, Loscertales M, Wagner R, ... ... Shen Y, et al. PLS3 missense variants affecting the actin-binding domains cause X-linked congenital diaphragmatic hernia and body-wall defects. American Journal of Human Genetics. PMID 37751738 DOI: 10.1016/j.ajhg.2023.09.002 |
0.32 |
|
| 2023 |
Zhong G, Choi YA, Shen Y. VBASS enables integration of single cell gene expression data in Bayesian association analysis of rare variants. Communications Biology. 6: 774. PMID 37491581 DOI: 10.1038/s42003-023-05155-9 |
0.741 |
|
| 2023 |
Griffin EL, Nees SN, Morton SU, Wynn J, Patel N, Jobanputra V, Robinson S, Kochav SM, Tao A, Andrews C, Cross N, Geva J, Lanzilotta K, Ritter A, Taillie E, ... ... Shen Y, et al. Evidence-Based Assessment of Congenital Heart Disease Genes to Enable Returning Results in a Genomic Study. Circulation. Genomic and Precision Medicine. e003791. PMID 36803080 DOI: 10.1161/CIRCGEN.122.003791 |
0.383 |
|
| 2022 |
Zhang H, Xu MS, Fan X, Chung WK, Shen Y. Predicting functional effect of missense variants using graph attention neural networks. Nature Machine Intelligence. 4: 1017-1028. PMID 37484202 DOI: 10.1038/s42256-022-00561-w |
0.34 |
|
| 2022 |
Fan X, Pan H, Tian A, Chung WK, Shen Y. SHINE: protein language model-based pathogenicity prediction for short inframe insertion and deletion variants. Briefings in Bioinformatics. PMID 36575831 DOI: 10.1093/bib/bbac584 |
0.313 |
|
| 2022 |
Tan R, Shen Y. Accurate in silico confirmation of rare copy number variant calls from exome sequencing data using transfer learning. Nucleic Acids Research. PMID 36124672 DOI: 10.1093/nar/gkac788 |
0.374 |
|
| 2022 |
Zhou X, Feliciano P, Shu C, Wang T, Astrovskaya I, Hall JB, Obiajulu JU, Wright JR, Murali SC, Xu SX, Brueggeman L, Thomas TR, Marchenko O, Fleisch C, Barns SD, ... ... Shen Y, et al. Integrating de novo and inherited variants in 42,607 autism cases identifies mutations in new moderate-risk genes. Nature Genetics. PMID 35982159 DOI: 10.1038/s41588-022-01148-2 |
0.365 |
|
| 2022 |
Zhong G, Shen Y. Statistical models of the genetic etiology of congenital heart disease. Current Opinion in Genetics & Development. 76: 101967. PMID 35939966 DOI: 10.1016/j.gde.2022.101967 |
0.735 |
|
| 2022 |
Zhong G, Ahimaz P, Edwards NA, Hagen JJ, Faure C, Lu Q, Kingma P, Middlesworth W, Khlevner J, El Fiky M, Schindel D, Fialkowski E, Kashyap A, Forlenza S, Kenny AP, ... ... Shen Y, et al. Erratum: Identification and validation of candidate risk genes in endocytic vesicular trafficking associated with esophageal atresia and tracheoesophageal fistulas. Hgg Advances. 3: 100126. PMID 35800210 DOI: 10.1016/j.xhgg.2022.100126 |
0.709 |
|
| 2022 |
Lipman AR, Fan X, Shen Y, Chung WK. Clinical and genetic characterization of CACNA1A-related disease. Clinical Genetics. PMID 35722745 DOI: 10.1111/cge.14180 |
0.32 |
|
| 2022 |
Zhong G, Ahimaz P, Edwards NA, Hagen JJ, Faure C, Lu Q, Kingma P, Middlesworth W, Khlevner J, El Fiky M, Schindel D, Fialkowski E, Kashyap A, Forlenza S, Kenny AP, ... ... Shen Y, et al. Identification and validation of candidate risk genes in endocytic vesicular trafficking associated with esophageal atresia and tracheoesophageal fistulas. Hgg Advances. 3: 100107. PMID 35519826 DOI: 10.1016/j.xhgg.2022.100107 |
0.755 |
|
| 2022 |
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, et al. The genetic architecture of pediatric cardiomyopathy. American Journal of Human Genetics. PMID 35026164 DOI: 10.1016/j.ajhg.2021.12.006 |
0.373 |
|
| 2021 |
Qiao L, Xu L, Yu L, Wynn J, Hernan R, Zhou X, Farkouh-Karoleski C, Krishnan US, Khlevner J, De A, Zygmunt A, Crombleholme T, Lim FY, Needelman H, Cusick RA, ... ... Shen Y, et al. Rare and de novo variants in 827 congenital diaphragmatic hernia probands implicate LONP1 as candidate risk gene. American Journal of Human Genetics. PMID 34547244 DOI: 10.1016/j.ajhg.2021.08.011 |
0.407 |
|
| 2021 |
Khan A, Shang N, Petukhova L, Zhang J, Shen Y, Hebbring SJ, Moncrieffe H, Kottyan LC, Namjou-Khales B, Knevel R, Raychaudhuri S, Karlson EW, Harley JB, Stanaway IB, Crosslin D, et al. Medical Records-Based Genetic Studies of the Complement System. Journal of the American Society of Nephrology : Jasn. PMID 33941608 DOI: 10.1681/ASN.2020091371 |
0.339 |
|
| 2021 |
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. Functional interrogation of DNA damage response variants with base editing screens. Cell. 184: 1081-1097.e19. PMID 33606978 DOI: 10.1016/j.cell.2021.01.041 |
0.315 |
|
| 2021 |
Qi H, Zhang H, Zhao Y, Chen C, Long JJ, Chung WK, Guan Y, Shen Y. MVP predicts the pathogenicity of missense variants by deep learning. Nature Communications. 12: 510. PMID 33479230 DOI: 10.1038/s41467-020-20847-0 |
0.383 |
|
| 2020 |
Swietlik EM, Greene D, Zhu N, Megy K, Cogliano M, Rajaram S, Pandya D, Tilly T, Lutz KA, Welch CCL, Pauciulo MW, Southgate L, Martin JM, Treacy CM, Penkett CJ, ... ... Shen Y, et al. Bayesian Inference Associates Rare Variants with Specific Phenotypes in Pulmonary Arterial Hypertension. Circulation. Genomic and Precision Medicine. PMID 33320693 DOI: 10.1161/CIRCGEN.120.003155 |
0.353 |
|
| 2020 |
Bogenschutz EL, Fox ZD, Farrell A, Wynn J, Moore B, Yu L, Aspelund G, Marth G, Yandell M, Shen Y, Chung WK, Kardon G. Deep whole-genome sequencing of multiple proband tissues and parental blood reveals the complex genetic etiology of congenital diaphragmatic hernias. Hgg Advances. 1. PMID 33263113 DOI: 10.1016/j.xhgg.2020.100008 |
0.429 |
|
| 2020 |
Wang J, Ahimaz PR, Hashemifar S, Khlevner J, Picoraro JA, Middlesworth W, Elfiky MM, Que J, Shen Y, Chung WK. Novel candidate genes in esophageal atresia/tracheoesophageal fistula identified by exome sequencing. European Journal of Human Genetics : Ejhg. PMID 32641753 DOI: 10.1038/S41431-020-0680-2 |
0.428 |
|
| 2020 |
Richter F, Morton SU, Kim SW, Kitaygorodsky A, Wasson LK, Chen KM, Zhou J, Qi H, Patel N, DePalma SR, Parfenov M, Homsy J, Gorham JM, Manheimer KB, Velinder M, ... ... Shen Y, et al. Genomic analyses implicate noncoding de novo variants in congenital heart disease. Nature Genetics. PMID 32601476 DOI: 10.1038/S41588-020-0652-Z |
0.31 |
|
| 2019 |
Watkins WS, Hernandez EJ, Wesolowski S, Bisgrove BW, Sunderland RT, Lin E, Lemmon G, Demarest BL, Miller TA, Bernstein D, Brueckner M, Chung WK, Gelb BD, Goldmuntz E, Newburger JW, ... ... Shen Y, et al. De novo and recessive forms of congenital heart disease have distinct genetic and phenotypic landscapes. Nature Communications. 10: 4722. PMID 31624253 DOI: 10.1038/S41467-019-12582-Y |
0.367 |
|
| 2019 |
Feliciano P, Zhou X, Astrovskaya I, Turner TN, Wang T, Brueggeman L, Barnard R, Hsieh A, Snyder LG, Muzny DM, Sabo A, Gibbs RA, Eichler EE, O'Roak BJ, ... ... Shen Y, et al. Exome sequencing of 457 autism families recruited online provides evidence for autism risk genes. Npj Genomic Medicine. 4: 19. PMID 31452935 DOI: 10.1038/S41525-019-0093-8 |
0.389 |
|
| 2018 |
Qi H, Yu L, Zhou X, Wynn J, Zhao H, Guo Y, Zhu N, Kitaygorodsky A, Hernan R, Aspelund G, Lim FY, Crombleholme T, Cusick R, Azarow K, Danko ME, ... ... Shen Y, et al. De novo variants in congenital diaphragmatic hernia identify MYRF as a new syndrome and reveal genetic overlaps with other developmental disorders. Plos Genetics. 14: e1007822. PMID 30532227 DOI: 10.1371/Journal.Pgen.1007822 |
0.412 |
|
| 2018 |
Han X, Chen S, Flynn E, Wu S, Wintner D, Shen Y. Distinct epigenomic patterns are associated with haploinsufficiency and predict risk genes of developmental disorders. Nature Communications. 9: 2138. PMID 29849042 DOI: 10.1038/S41467-018-04552-7 |
0.385 |
|
| 2017 |
Jin SC, Homsy J, Zaidi S, Lu Q, Morton S, DePalma SR, Zeng X, Qi H, Chang W, Sierant MC, Hung WC, Haider S, Zhang J, Knight J, Bjornson RD, ... ... Shen Y, et al. Contribution of rare inherited and de novo variants in 2,871 congenital heart disease probands. Nature Genetics. PMID 28991257 DOI: 10.1038/Ng.3970 |
0.317 |
|
| 2017 |
Longoni M, High FA, Qi H, Joy MP, Hila R, Coletti CM, Wynn J, Loscertales M, Shan L, Bult CJ, Wilson JM, Shen Y, Chung WK, Donahoe PK. Genome-wide enrichment of damaging de novo variants in patients with isolated and complex congenital diaphragmatic hernia. Human Genetics. PMID 28303347 DOI: 10.1007/S00439-017-1774-Y |
0.356 |
|
| 2016 |
Shi L, Guo Y, Dong C, Huddleston J, Yang H, Han X, Fu A, Li Q, Li N, Gong S, Lintner KE, Ding Q, Wang Z, Hu J, Wang D, ... ... Shen Y, et al. Long-read sequencing and de novo assembly of a Chinese genome. Nature Communications. 7: 12065. PMID 27356984 DOI: 10.1038/Ncomms12065 |
0.311 |
|
| 2015 |
Guo Y, Ding X, Shen Y, Lyon GJ, Wang K. SeqMule: automated pipeline for analysis of human exome/genome sequencing data. Scientific Reports. 5: 14283. PMID 26381817 DOI: 10.1038/Srep14283 |
0.309 |
|
| 2015 |
Nicoletti P, Bansal M, Lefebvre C, Guarnieri P, Shen Y, Pe'er I, Califano A, Floratos A. ABC Transporters and the Proteasome Complex Are Implicated in Susceptibility to Stevens-Johnson Syndrome and Toxic Epidermal Necrolysis across Multiple Drugs. Plos One. 10: e0131038. PMID 26110827 DOI: 10.1371/Journal.Pone.0131038 |
0.391 |
|
| 2015 |
Yu L, Sawle AD, Wynn J, Aspelund G, Stolar CJ, Arkovitz MS, Potoka D, Azarow KS, Mychaliska GB, Shen Y, Chung WK. Increased burden of de novo predicted deleterious variants in complex congenital diaphragmatic hernia. Human Molecular Genetics. 24: 4764-73. PMID 26034137 DOI: 10.1093/Hmg/Ddv196 |
0.363 |
|
| 2014 |
Overby CL, Hripcsak G, Shen Y. Estimating heritability of drug-induced liver injury from common variants and implications for future study designs. Scientific Reports. 4: 5762. PMID 25042059 DOI: 10.1038/srep05762 |
0.323 |
|
| 2013 |
Behr ER, Ritchie MD, Tanaka T, Kääb S, Crawford DC, Nicoletti P, Floratos A, Sinner MF, Kannankeril PJ, Wilde AA, Bezzina CR, Schulze-Bahr E, Zumhagen S, Guicheney P, Bishopric NH, ... ... Shen Y, et al. Genome wide analysis of drug-induced torsades de pointes: lack of common variants with large effect sizes. Plos One. 8: e78511. PMID 24223155 DOI: 10.1371/Journal.Pone.0078511 |
0.308 |
|
| 2011 |
Shen Y, Gu Y, Pe'er I. A hidden Markov model for copy number variant prediction from whole genome resequencing data. Bmc Bioinformatics. S4. PMID 21989326 DOI: 10.1186/1471-2105-12-S6-S4 |
0.37 |
|
| 2010 |
Shen Y, Wan Z, Coarfa C, Drabek R, Chen L, Ostrowski EA, Liu Y, Weinstock GM, Wheeler DA, Gibbs RA, Yu F. A SNP discovery method to assess variant allele probability from next-generation resequencing data. Genome Research. 20: 273-80. PMID 20019143 DOI: 10.1101/Gr.096388.109 |
0.537 |
|
| 2009 |
Liu Y, Qin X, Song XZH, Jiang H, Shen Y, Durbin KJ, Lien S, Kent MP, Sodeland M, Ren Y, Zhang L, Sodergren E, Havlak P, Worley KC, Weinstock GM, et al. Bos taurus genome assembly Bmc Genomics. 10. PMID 19393050 DOI: 10.1186/1471-2164-10-180 |
0.582 |
|
| 2009 |
Elsik CG, Tellam RL, Worley KC, Gibbs RA, Muzny DM, Weinstock GM, Adelson DL, Eichler EE, Elnitski L, Guigó R, Hamernik DL, Kappes SM, Lewin HA, Lynn DJ, ... ... Shen Y, et al. The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science (New York, N.Y.). 324: 522-8. PMID 19390049 DOI: 10.1126/Science.1169588 |
0.65 |
|
| 2008 |
Shen Y, Sarin S, Liu Y, Hobert O, Pe'er I. Comparing platforms for C. elegans mutant identification using high-throughput whole-genome sequencing. Plos One. 3: e4012. PMID 19107202 DOI: 10.1371/Journal.Pone.0004012 |
0.342 |
|
| 2008 |
Wang X, Gao H, Shen Y, Weinstock GM, Zhou J, Palzkill T. A high-throughput percentage-of-binding strategy to measure binding energies in DNA-protein interactions: application to genome-scale site discovery. Nucleic Acids Research. 36: 4863-71. PMID 18653527 DOI: 10.1093/Nar/Gkn477 |
0.382 |
|
| 2008 |
Wheeler DA, Srinivasan M, Egholm M, Shen Y, Chen L, McGuire A, He W, Chen YJ, Makhijani V, Roth GT, Gomes X, Tartaro K, Niazi F, Turcotte CL, Irzyk GP, et al. The complete genome of an individual by massively parallel DNA sequencing. Nature. 452: 872-6. PMID 18421352 DOI: 10.1038/Nature06884 |
0.643 |
|
| 2007 |
Gibbs RA, Rogers J, Katze MG, Bumgarner R, Weinstock GM, Mardis ER, Remington KA, Strausberg RL, Venter JC, Wilson RK, Batzer MA, Bustamante CD, Eichler EE, Hahn MW, ... ... Shen Y, et al. Evolutionary and biomedical insights from the rhesus macaque genome. Science (New York, N.Y.). 316: 222-34. PMID 17431167 DOI: 10.1126/Science.1139247 |
0.643 |
|
| 2006 |
Sodergren E, Shen Y, Song X, Zhang L, Gibbs RA, Weinstock GM. Shedding genomic light on Aristotle's lantern Developmental Biology. 300: 2-8. PMID 17097628 DOI: 10.1016/J.Ydbio.2006.10.005 |
0.56 |
|
| 2006 |
Sodergren E, Weinstock GM, Davidson EH, Cameron RA, Gibbs RA, Angerer RC, Angerer LM, Arnone MI, Burgess DR, Burke RD, Coffman JA, Dean M, Elphick MR, Ettensohn CA, ... ... Shen Y, et al. The genome of the sea urchin Strongylocentrotus purpuratus. Science (New York, N.Y.). 314: 941-52. PMID 17095691 DOI: 10.1126/Science.1133609 |
0.537 |
|
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