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Items: 1 to 50 of 101

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.

Nat Genet. 2019 Jun;51(6):973-980. doi: 10.1038/s41588-019-0420-0. Epub 2019 May 27.

PMID:
31133750
2.

Author Correction: New genetic signals for lung function highlight pathways and chronic obstructive pulmonary disease associations across multiple ancestries.

Shrine N, Guyatt AL, Erzurumluoglu AM, Jackson VE, Hobbs BD, Melbourne CA, Batini C, Fawcett KA, Song K, Sakornsakolpat P, Li X, Boxall R, Reeve NF, Obeidat M, Zhao JH, Wielscher M; Understanding Society Scientific Group, Weiss S, Kentistou KA, Cook JP, Sun BB, Zhou J, Hui J, Karrasch S, Imboden M, Harris SE, Marten J, Enroth S, Kerr SM, Surakka I, Vitart V, Lehtimäki T, Allen RJ, Bakke PS, Beaty TH, Bleecker ER, Bossé Y, Brandsma CA, Chen Z, Crapo JD, Danesh J, DeMeo DL, Dudbridge F, Ewert R, Gieger C, Gulsvik A, Hansell AL, Hao K, Hoffman JD, Hokanson JE, Homuth G, Joshi PK, Joubert P, Langenberg C, Li X, Li L, Lin K, Lind L, Locantore N, Luan J, Mahajan A, Maranville JC, Murray A, Nickle DC, Packer R, Parker MM, Paynton ML, Porteous DJ, Prokopenko D, Qiao D, Rawal R, Runz H, Sayers I, Sin DD, Smith BH, Artigas MS, Sparrow D, Tal-Singer R, Timmers PRHJ, Van den Berge M, Whittaker JC, Woodruff PG, Yerges-Armstrong LM, Troyanskaya OG, Raitakari OT, Kähönen M, Polašek O, Gyllensten U, Rudan I, Deary IJ, Probst-Hensch NM, Schulz H, James AL, Wilson JF, Stubbe B, Zeggini E, Jarvelin MR, Wareham N, Silverman EK, Hayward C, Morris AP, Butterworth AS, Scott RA, Walters RG, Meyers DA, Cho MH, Strachan DP, Hall IP, Tobin MD, Wain LV.

Nat Genet. 2019 Jun;51(6):1067. doi: 10.1038/s41588-019-0438-3.

PMID:
31110354
3.

Selene: a PyTorch-based deep learning library for sequence data.

Chen KM, Cofer EM, Zhou J, Troyanskaya OG.

Nat Methods. 2019 Apr;16(4):315-318. doi: 10.1038/s41592-019-0360-8. Epub 2019 Mar 28.

PMID:
30923381
4.

Minor Isozymes Tailor Yeast Metabolism to Carbon Availability.

Bradley PH, Gibney PA, Botstein D, Troyanskaya OG, Rabinowitz JD.

mSystems. 2019 Feb 26;4(1). pii: e00170-18. doi: 10.1128/mSystems.00170-18. eCollection 2019 Jan-Feb.

5.

New genetic signals for lung function highlight pathways and chronic obstructive pulmonary disease associations across multiple ancestries.

Shrine N, Guyatt AL, Erzurumluoglu AM, Jackson VE, Hobbs BD, Melbourne CA, Batini C, Fawcett KA, Song K, Sakornsakolpat P, Li X, Boxall R, Reeve NF, Obeidat M, Zhao JH, Wielscher M, Weiss S, Kentistou KA, Cook JP, Sun BB, Zhou J, Hui J, Karrasch S, Imboden M, Harris SE, Marten J, Enroth S, Kerr SM, Surakka I, Vitart V, Lehtimäki T, Allen RJ, Bakke PS, Beaty TH, Bleecker ER, Bossé Y, Brandsma CA, Chen Z, Crapo JD, Danesh J, DeMeo DL, Dudbridge F, Ewert R, Gieger C, Gulsvik A, Hansell AL, Hao K, Hoffman JD, Hokanson JE, Homuth G, Joshi PK, Joubert P, Langenberg C, Li X, Li L, Lin K, Lind L, Locantore N, Luan J, Mahajan A, Maranville JC, Murray A, Nickle DC, Packer R, Parker MM, Paynton ML, Porteous DJ, Prokopenko D, Qiao D, Rawal R, Runz H, Sayers I, Sin DD, Smith BH, Soler Artigas M, Sparrow D, Tal-Singer R, Timmers PRHJ, Van den Berge M, Whittaker JC, Woodruff PG, Yerges-Armstrong LM, Troyanskaya OG, Raitakari OT, Kähönen M, Polašek O, Gyllensten U, Rudan I, Deary IJ, Probst-Hensch NM, Schulz H, James AL, Wilson JF, Stubbe B, Zeggini E, Jarvelin MR, Wareham N, Silverman EK, Hayward C, Morris AP, Butterworth AS, Scott RA, Walters RG, Meyers DA, Cho MH, Strachan DP, Hall IP, Tobin MD, Wain LV; Understanding Society Scientific Group.

Nat Genet. 2019 Mar;51(3):481-493. doi: 10.1038/s41588-018-0321-7. Epub 2019 Feb 25. Erratum in: Nat Genet. 2019 Jun;51(6):1067.

PMID:
30804560
6.

A Computational Framework for Genome-wide Characterization of the Human Disease Landscape.

Lee YS, Krishnan A, Oughtred R, Rust J, Chang CS, Ryu J, Kristensen VN, Dolinski K, Theesfeld CL, Troyanskaya OG.

Cell Syst. 2019 Feb 27;8(2):152-162.e6. doi: 10.1016/j.cels.2018.12.010. Epub 2019 Jan 23.

PMID:
30685436
7.

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).

JCI Insight. 2019 Jan 10;4(1). pii: 122697. doi: 10.1172/jci.insight.122697. [Epub ahead of print]

8.

Interpretation of an individual functional genomics experiment guided by massive public data.

Lee YS, Wong AK, Tadych A, Hartmann BM, Park CY, DeJesus VA, Ramos I, Zaslavsky E, Sealfon SC, Troyanskaya OG.

Nat Methods. 2018 Dec;15(12):1049-1052. doi: 10.1038/s41592-018-0218-5. Epub 2018 Nov 26.

PMID:
30478325
9.

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.

Nat Biotechnol. 2018 Oct 22. doi: 10.1038/nbt.4246. [Epub ahead of print]

PMID:
30346941
10.

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.

PLoS Genet. 2018 Aug 10;14(8):e1007559. doi: 10.1371/journal.pgen.1007559. eCollection 2018 Aug.

11.

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.

Nat Genet. 2018 Aug;50(8):1171-1179. doi: 10.1038/s41588-018-0160-6. Epub 2018 Jul 16.

12.

Enabling Precision Medicine through Integrative Network Models.

Yao V, Wong AK, Troyanskaya OG.

J Mol Biol. 2018 Sep 14;430(18 Pt A):2913-2923. doi: 10.1016/j.jmb.2018.07.004. Epub 2018 Jul 9. Review.

PMID:
30003887
13.

GIANT 2.0: genome-scale integrated analysis of gene networks in tissues.

Wong AK, Krishnan A, Troyanskaya OG.

Nucleic Acids Res. 2018 Jul 2;46(W1):W65-W70. doi: 10.1093/nar/gky408.

14.

Data-driven analysis of immune infiltrate in a large cohort of breast cancer and its association with disease progression, ER activity, and genomic complexity.

Dannenfelser R, Nome M, Tahiri A, Ursini-Siegel J, Vollan HKM, Haakensen VD, Helland Å, Naume B, Caldas C, Børresen-Dale AL, Kristensen VN, Troyanskaya OG.

Oncotarget. 2017 Jul 7;8(34):57121-57133. doi: 10.18632/oncotarget.19078. eCollection 2017 Aug 22.

15.

Genome-wide prediction and functional characterization of the genetic basis of autism spectrum disorder.

Krishnan A, Zhang R, Yao V, Theesfeld CL, Wong AK, Tadych A, Volfovsky N, Packer A, Lash A, Troyanskaya OG.

Nat Neurosci. 2016 Nov;19(11):1454-1462. doi: 10.1038/nn.4353. Epub 2016 Aug 1.

16.

A global genetic interaction network maps a wiring diagram of cellular function.

Costanzo M, VanderSluis B, Koch EN, Baryshnikova A, Pons C, Tan G, Wang W, Usaj M, Hanchard J, Lee SD, Pelechano V, Styles EB, Billmann M, van Leeuwen J, van Dyk N, Lin ZY, Kuzmin E, Nelson J, Piotrowski JS, Srikumar T, Bahr S, Chen Y, Deshpande R, Kurat CF, Li SC, Li Z, Usaj MM, Okada H, Pascoe N, San Luis BJ, Sharifpoor S, Shuteriqi E, Simpkins SW, Snider J, Suresh HG, Tan Y, Zhu H, Malod-Dognin N, Janjic V, Przulj N, Troyanskaya OG, Stagljar I, Xia T, Ohya Y, Gingras AC, Raught B, Boutros M, Steinmetz LM, Moore CL, Rosebrock AP, Caudy AA, Myers CL, Andrews B, Boone C.

Science. 2016 Sep 23;353(6306). pii: aaf1420.

17.

Metabolic network rewiring of propionate flux compensates vitamin B12 deficiency in C. elegans.

Watson E, Olin-Sandoval V, Hoy MJ, Li CH, Louisse T, Yao V, Mori A, Holdorf AD, Troyanskaya OG, Ralser M, Walhout AJ.

Elife. 2016 Jul 6;5. pii: e17670. doi: 10.7554/eLife.17670.

18.

GIANT API: an application programming interface for functional genomics.

Roberts AM, Wong AK, Fisk I, Troyanskaya OG.

Nucleic Acids Res. 2016 Jul 8;44(W1):W587-92. doi: 10.1093/nar/gkw289. Epub 2016 Apr 20.

19.
20.

Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases.

Gorenshteyn D, Zaslavsky E, Fribourg M, Park CY, Wong AK, Tadych A, Hartmann BM, Albrecht RA, García-Sastre A, Kleinstein SH, Troyanskaya OG, Sealfon SC.

Immunity. 2015 Sep 15;43(3):605-14. doi: 10.1016/j.immuni.2015.08.014. Epub 2015 Sep 8.

21.

Predicting effects of noncoding variants with deep learning-based sequence model.

Zhou J, Troyanskaya OG.

Nat Methods. 2015 Oct;12(10):931-4. doi: 10.1038/nmeth.3547. Epub 2015 Aug 24.

22.

Implications of Big Data for cell biology.

Dolinski K, Troyanskaya OG.

Mol Biol Cell. 2015 Jul 15;26(14):2575-8. doi: 10.1091/mbc.E13-12-0756.

23.

IMP 2.0: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks.

Wong AK, Krishnan A, Yao V, Tadych A, Troyanskaya OG.

Nucleic Acids Res. 2015 Jul 1;43(W1):W128-33. doi: 10.1093/nar/gkv486. Epub 2015 May 12.

24.

FNTM: a server for predicting functional networks of tissues in mouse.

Goya J, Wong AK, Yao V, Krishnan A, Homilius M, Troyanskaya OG.

Nucleic Acids Res. 2015 Jul 1;43(W1):W182-7. doi: 10.1093/nar/gkv443. Epub 2015 May 4.

25.

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.

Nat Genet. 2015 Jun;47(6):569-76. doi: 10.1038/ng.3259. Epub 2015 Apr 27.

26.

Low-variance RNAs identify Parkinson's disease molecular signature in blood.

Chikina MD, Gerald CP, Li X, Ge Y, Pincas H, Nair VD, Wong AK, Krishnan A, Troyanskaya OG, Raymond D, Saunders-Pullman R, Bressman SB, Yue Z, Sealfon SC.

Mov Disord. 2015 May;30(6):813-21. doi: 10.1002/mds.26205. Epub 2015 Mar 18.

27.

Targeted exploration and analysis of large cross-platform human transcriptomic compendia.

Zhu Q, Wong AK, Krishnan A, Aure MR, Tadych A, Zhang R, Corney DC, Greene CS, Bongo LA, Kristensen VN, Charikar M, Li K, Troyanskaya OG.

Nat Methods. 2015 Mar;12(3):211-4, 3 p following 214. doi: 10.1038/nmeth.3249. Epub 2015 Jan 12.

28.

Tissue-aware data integration approach for the inference of pathway interactions in metazoan organisms.

Park CY, Krishnan A, Zhu Q, Wong AK, Lee YS, Troyanskaya OG.

Bioinformatics. 2015 Apr 1;31(7):1093-101. doi: 10.1093/bioinformatics/btu786. Epub 2014 Nov 26.

29.

Broad metabolic sensitivity profiling of a prototrophic yeast deletion collection.

VanderSluis B, Hess DC, Pesyna C, Krumholz EW, Syed T, Szappanos B, Nislow C, Papp B, Troyanskaya OG, Myers CL, Caudy AA.

Genome Biol. 2014 Apr 10;15(4):R64. doi: 10.1186/gb-2014-15-4-r64.

30.

Global quantitative modeling of chromatin factor interactions.

Zhou J, Troyanskaya OG.

PLoS Comput Biol. 2014 Mar 27;10(3):e1003525. doi: 10.1371/journal.pcbi.1003525. eCollection 2014 Mar.

31.

Individual and combined effects of DNA methylation and copy number alterations on miRNA expression in breast tumors.

Aure MR, Leivonen SK, Fleischer T, Zhu Q, Overgaard J, Alsner J, Tramm T, Louhimo R, Alnæs GI, Perälä M, Busato F, Touleimat N, Tost J, Børresen-Dale AL, Hautaniemi S, Troyanskaya OG, Lingjærde OC, Sahlberg KK, Kristensen VN.

Genome Biol. 2013 Nov 20;14(11):R126. doi: 10.1186/gb-2013-14-11-r126.

32.

Ontology-aware classification of tissue and cell-type signals in gene expression profiles across platforms and technologies.

Lee YS, Krishnan A, Zhu Q, Troyanskaya OG.

Bioinformatics. 2013 Dec 1;29(23):3036-44. doi: 10.1093/bioinformatics/btt529. Epub 2013 Sep 12.

33.

Defining cell-type specificity at the transcriptional level in human disease.

Ju W, Greene CS, Eichinger F, Nair V, Hodgin JB, Bitzer M, Lee YS, Zhu Q, Kehata M, Li M, Jiang S, Rastaldi MP, Cohen CD, Troyanskaya OG, Kretzler M.

Genome Res. 2013 Nov;23(11):1862-73. doi: 10.1101/gr.155697.113. Epub 2013 Aug 15.

34.

A new system for comparative functional genomics of Saccharomyces yeasts.

Caudy AA, Guan Y, Jia Y, Hansen C, DeSevo C, Hayes AP, Agee J, Alvarez-Dominguez JR, Arellano H, Barrett D, Bauerle C, Bisaria N, Bradley PH, Breunig JS, Bush E, Cappel D, Capra E, Chen W, Clore J, Combs PA, Doucette C, Demuren O, Fellowes P, Freeman S, Frenkel E, Gadala-Maria D, Gawande R, Glass D, Grossberg S, Gupta A, Hammonds-Odie L, Hoisos A, Hsi J, Hsu YH, Inukai S, Karczewski KJ, Ke X, Kojima M, Leachman S, Lieber D, Liebowitz A, Liu J, Liu Y, Martin T, Mena J, Mendoza R, Myhrvold C, Millian C, Pfau S, Raj S, Rich M, Rokicki J, Rounds W, Salazar M, Salesi M, Sharma R, Silverman S, Singer C, Sinha S, Staller M, Stern P, Tang H, Weeks S, Weidmann M, Wolf A, Young C, Yuan J, Crutchfield C, McClean M, Murphy CT, Llinás M, Botstein D, Troyanskaya OG, Dunham MJ.

Genetics. 2013 Sep;195(1):275-87. doi: 10.1534/genetics.113.152918. Epub 2013 Jul 12.

35.

Functional knowledge transfer for high-accuracy prediction of under-studied biological processes.

Park CY, Wong AK, Greene CS, Rowland J, Guan Y, Bongo LA, Burdine RD, Troyanskaya OG.

PLoS Comput Biol. 2013;9(3):e1002957. doi: 10.1371/journal.pcbi.1002957. Epub 2013 Mar 14.

36.

Comparative gene expression between two yeast species.

Guan Y, Dunham MJ, Troyanskaya OG, Caudy AA.

BMC Genomics. 2013 Jan 16;14:33. doi: 10.1186/1471-2164-14-33.

37.

Chapter 2: Data-driven view of disease biology.

Greene CS, Troyanskaya OG.

PLoS Comput Biol. 2012;8(12):e1002816. doi: 10.1371/journal.pcbi.1002816. Epub 2012 Dec 27.

38.

Tissue-specific functional networks for prioritizing phenotype and disease genes.

Guan Y, Gorenshteyn D, Burmeister M, Wong AK, Schimenti JC, Handel MA, Bult CJ, Hibbs MA, Troyanskaya OG.

PLoS Comput Biol. 2012;8(9):e1002694. doi: 10.1371/journal.pcbi.1002694. Epub 2012 Sep 27.

39.

IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks.

Wong AK, Park CY, Greene CS, Bongo LA, Guan Y, Troyanskaya OG.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W484-90. doi: 10.1093/nar/gks458. Epub 2012 Jun 7.

40.

Accurate evaluation and analysis of functional genomics data and methods.

Greene CS, Troyanskaya OG.

Ann N Y Acad Sci. 2012 Jul;1260:95-100. doi: 10.1111/j.1749-6632.2011.06383.x. Epub 2012 Jan 23.

41.

An effective statistical evaluation of ChIPseq dataset similarity.

Chikina MD, Troyanskaya OG.

Bioinformatics. 2012 Mar 1;28(5):607-13. doi: 10.1093/bioinformatics/bts009. Epub 2012 Jan 19.

42.

Nucleosome-coupled expression differences in closely-related species.

Guan Y, Yao V, Tsui K, Gebbia M, Dunham MJ, Nislow C, Troyanskaya OG.

BMC Genomics. 2011 Sep 26;12:466. doi: 10.1186/1471-2164-12-466.

43.

Integrated molecular profiles of invasive breast tumors and ductal carcinoma in situ (DCIS) reveal differential vascular and interleukin signaling.

Kristensen VN, Vaske CJ, Ursini-Siegel J, Van Loo P, Nordgard SH, Sachidanandam R, Sørlie T, Wärnberg F, Haakensen VD, Helland Å, Naume B, Perou CM, Haussler D, Troyanskaya OG, Børresen-Dale AL.

Proc Natl Acad Sci U S A. 2012 Feb 21;109(8):2802-7. doi: 10.1073/pnas.1108781108. Epub 2011 Sep 9.

44.

PILGRM: an interactive data-driven discovery platform for expert biologists.

Greene CS, Troyanskaya OG.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W368-74. doi: 10.1093/nar/gkr440. Epub 2011 Jun 7.

45.

Accurate quantification of functional analogy among close homologs.

Chikina MD, Troyanskaya OG.

PLoS Comput Biol. 2011 Feb 3;7(2):e1001074. doi: 10.1371/journal.pcbi.1001074.

46.

Integrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana.

Pop A, Huttenhower C, Iyer-Pascuzzi A, Benfey PN, Troyanskaya OG.

BMC Syst Biol. 2010 Dec 31;4:180. doi: 10.1186/1752-0509-4-180.

47.

Mapping dynamic histone acetylation patterns to gene expression in nanog-depleted murine embryonic stem cells.

Markowetz F, Mulder KW, Airoldi EM, Lemischka IR, Troyanskaya OG.

PLoS Comput Biol. 2010 Dec 16;6(12):e1001034. doi: 10.1371/journal.pcbi.1001034.

48.

Simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway components.

Park CY, Hess DC, Huttenhower C, Troyanskaya OG.

PLoS Comput Biol. 2010 Nov 24;6(11):e1001009. doi: 10.1371/journal.pcbi.1001009.

49.

Functional genomics complements quantitative genetics in identifying disease-gene associations.

Guan Y, Ackert-Bicknell CL, Kell B, Troyanskaya OG, Hibbs MA.

PLoS Comput Biol. 2010 Nov 11;6(11):e1000991. doi: 10.1371/journal.pcbi.1000991.

50.

Quantitative analysis of fitness and genetic interactions in yeast on a genome scale.

Baryshnikova A, Costanzo M, Kim Y, Ding H, Koh J, Toufighi K, Youn JY, Ou J, San Luis BJ, Bandyopadhyay S, Hibbs M, Hess D, Gingras AC, Bader GD, Troyanskaya OG, Brown GW, Andrews B, Boone C, Myers CL.

Nat Methods. 2010 Dec;7(12):1017-24. doi: 10.1038/nmeth.1534. Epub 2010 Nov 14.

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