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Table representation of search results timeline featuring number of search results per year.

Year Number of Results
2005 2
2006 6
2007 8
2008 8
2009 10
2010 6
2011 3
2012 6
2013 5
2014 3
2015 8
2016 3
2017 2
2018 5
2019 8
2020 7
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83 results
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Page 1
Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk.
Zhou J, Park CY, Theesfeld CL, Wong AK, Yuan Y, Scheckel C, Fak JJ, Funk J, Yao K, Tajima Y, Packer A, Darnell RB, Troyanskaya OG. Zhou J, et al. Nat Genet. 2019 Jun;51(6):973-980. doi: 10.1038/s41588-019-0420-0. Epub 2019 May 27. Nat Genet. 2019. PMID: 31133750 Free PMC article.
Predicting effects of noncoding variants with deep learning-based sequence model.
Zhou J, Troyanskaya OG. Zhou J, et al. Nat Methods. 2015 Oct;12(10):931-4. doi: 10.1038/nmeth.3547. Epub 2015 Aug 24. Nat Methods. 2015. PMID: 26301843 Free PMC article.
IFNγ-Dependent Tissue-Immune Homeostasis Is Co-opted in the Tumor Microenvironment.
Nirschl CJ, Suárez-Fariñas M, Izar B, Prakadan S, Dannenfelser R, Tirosh I, Liu Y, Zhu Q, Devi KSP, Carroll SL, Chau D, Rezaee M, Kim TG, Huang R, Fuentes-Duculan J, Song-Zhao GX, Gulati N, Lowes MA, King SL, Quintana FJ, Lee YS, Krueger JG, Sarin KY, Yoon CH, Garraway L, Regev A, Shalek AK, Troyanskaya O, Anandasabapathy N. Nirschl CJ, et al. Cell. 2017 Jun 29;170(1):127-141.e15. doi: 10.1016/j.cell.2017.06.016. Cell. 2017. PMID: 28666115 Free PMC article.
Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk.
Zhou J, Theesfeld CL, Yao K, Chen KM, Wong AK, Troyanskaya OG. Zhou J, et al. Nat Genet. 2018 Aug;50(8):1171-1179. doi: 10.1038/s41588-018-0160-6. Epub 2018 Jul 16. Nat Genet. 2018. PMID: 30013180 Free PMC article.
Selene: a PyTorch-based deep learning library for sequence data.
Chen KM, Cofer EM, Zhou J, Troyanskaya OG. Chen KM, et al. Nat Methods. 2019 Apr;16(4):315-318. doi: 10.1038/s41592-019-0360-8. Epub 2019 Mar 28. Nat Methods. 2019. PMID: 30923381 Free PMC article.
Understanding multicellular function and disease with human tissue-specific networks.
Greene CS, Krishnan A, Wong AK, Ricciotti E, Zelaya RA, Himmelstein DS, Zhang R, Hartmann BM, Zaslavsky E, Sealfon SC, Chasman DI, FitzGerald GA, Dolinski K, Grosser T, Troyanskaya OG. Greene CS, et al. Nat Genet. 2015 Jun;47(6):569-76. doi: 10.1038/ng.3259. Epub 2015 Apr 27. Nat Genet. 2015. PMID: 25915600 Free PMC article.
Organoid single cell profiling identifies a transcriptional signature of glomerular disease.
Harder JL, Menon R, Otto EA, Zhou J, Eddy S, Wys NL, O'Connor C, Luo J, Nair V, Cebrian C, Spence JR, Bitzer M, Troyanskaya OG, Hodgin JB, Wiggins RC, Freedman BS, Kretzler M; European Renal cDNA Bank (ERCB); Nephrotic Syndrome Study Network (NEPTUNE). Harder JL, et al. JCI Insight. 2019 Jan 10;4(1):e122697. doi: 10.1172/jci.insight.122697. JCI Insight. 2019. PMID: 30626756 Free PMC article.
RNA Identification of PRIME Cells Predicting Rheumatoid Arthritis Flares.
Orange DE, Yao V, Sawicka K, Fak J, Frank MO, Parveen S, Blachere NE, Hale C, Zhang F, Raychaudhuri S, Troyanskaya OG, Darnell RB. Orange DE, et al. N Engl J Med. 2020 Jul 16;383(3):218-228. doi: 10.1056/NEJMoa2004114. N Engl J Med. 2020. PMID: 32668112
An integrative tissue-network approach to identify and test human disease genes.
Yao V, Kaletsky R, Keyes W, Mor DE, Wong AK, Sohrabi S, Murphy CT, Troyanskaya OG. Yao V, et al. Nat Biotechnol. 2018 Oct 22:10.1038/nbt.4246. doi: 10.1038/nbt.4246. Online ahead of print. Nat Biotechnol. 2018. PMID: 30346941 Free PMC article.
Transcriptome analysis of adult Caenorhabditis elegans cells reveals tissue-specific gene and isoform expression.
Kaletsky R, Yao V, Williams A, Runnels AM, Tadych A, Zhou S, Troyanskaya OG, Murphy CT. Kaletsky R, et al. PLoS Genet. 2018 Aug 10;14(8):e1007559. doi: 10.1371/journal.pgen.1007559. eCollection 2018 Aug. PLoS Genet. 2018. PMID: 30096138 Free PMC article.
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