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Items: 1 to 50 of 118

1.

Voices in methods development.

Anikeeva P, Boyden E, Brangwynne C, Cissé II, Fiehn O, Fromme P, Gingras AC, Greene CS, Heard E, Hell SW, Hillman E, Jensen GJ, Karchin R, Kiessling LL, Kleinstiver BP, Knight R, Kukura P, Lancaster MA, Loman N, Looger L, Lundberg E, Luo Q, Miyawaki A, Myers EW Jr, Nolan GP, Picotti P, Reik W, Sauer M, Shalek AK, Shendure J, Slavov N, Tanay A, Troyanskaya O, van Valen D, Wang HW, Yi C, Yin P, Zernicka-Goetz M, Zhuang X.

Nat Methods. 2019 Oct;16(10):945-951. doi: 10.1038/s41592-019-0585-6. No abstract available.

PMID:
31562479
2.

Accurate genome-wide predictions of spatio-temporal gene expression during embryonic development.

Zhou J, Schor IE, Yao V, Theesfeld CL, Marco-Ferreres R, Tadych A, Furlong EEM, Troyanskaya OG.

PLoS Genet. 2019 Sep 25;15(9):e1008382. doi: 10.1371/journal.pgen.1008382. eCollection 2019 Sep.

3.

Subtype-Specific Transcriptional Regulators in Breast Tumors Subjected to Genetic and Epigenetic Alterations.

Zhu Q, Tekpli X, Troyanskaya OG, Kristensen VN.

Bioinformatics. 2019 Sep 16. pii: btz709. doi: 10.1093/bioinformatics/btz709. [Epub ahead of print]

PMID:
31529022
4.

Mapping the physiological and molecular markers of stress and SSRI antidepressant treatment in S100a10 corticostriatal neurons.

Sargin D, Chottekalapanda RU, Perit KE, Yao V, Chu D, Sparks DW, Kalik S, Power SK, Troyanskaya OG, Schmidt EF, Greengard P, Lambe EK.

Mol Psychiatry. 2019 Aug 20. doi: 10.1038/s41380-019-0473-6. [Epub ahead of print]

PMID:
31431686
5.

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.

6.

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
7.

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
8.

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.

9.

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.

10.

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
11.

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]

12.

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
13.

Serum cytokine levels in breast cancer patients during neoadjuvant treatment with bevacizumab.

Jabeen S, Zucknick M, Nome M, Dannenfelser R, Fleischer T, Kumar S, Lüders T, von der Lippe Gythfeldt H, Troyanskaya O, Kyte JA, Børresen-Dale AL, Naume B, Tekpli X, Engebraaten O, Kristensen V.

Oncoimmunology. 2018 Aug 6;7(11):e1457598. doi: 10.1080/2162402X.2018.1457598. eCollection 2018.

14.

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
15.

Single-cell analysis of progenitor cell dynamics and lineage specification in the human fetal kidney.

Menon R, Otto EA, Kokoruda A, Zhou J, Zhang Z, Yoon E, Chen YC, Troyanskaya O, Spence JR, Kretzler M, Cebrián C.

Development. 2018 Aug 30;145(16). pii: dev164038. doi: 10.1242/dev.164038.

16.

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.

17.

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.

18.

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
19.

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.

20.

A loop-counting method for covariate-corrected low-rank biclustering of gene-expression and genome-wide association study data.

Rangan AV, McGrouther CC, Kelsoe J, Schork N, Stahl E, Zhu Q, Krishnan A, Yao V, Troyanskaya O, Bilaloglu S, Raghavan P, Bergen S, Jureus A, Landen M; Bipolar Disorders Working Group of the Psychiatric Genomics Consortium.

PLoS Comput Biol. 2018 May 14;14(5):e1006105. doi: 10.1371/journal.pcbi.1006105. eCollection 2018 May.

21.

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.

22.

Bioinformatics Approaches to Profile the Tumor Microenvironment for Immunotherapeutic Discovery.

Clancy T, Dannenfelser R, Troyanskaya O, Malmberg KJ, Hovig E, Kristensen V.

Curr Pharm Des. 2017;23(32):4716-4725. doi: 10.2174/1381612823666170710154936. Review.

PMID:
28699527
23.

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.

Cell. 2017 Jun 29;170(1):127-141.e15. doi: 10.1016/j.cell.2017.06.016.

24.

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.

25.

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.

26.

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.

27.

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.

28.
29.

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.

30.

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.

31.

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.

32.

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.

33.

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.

34.

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.

35.

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.

36.

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.

37.

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.

38.

Lymphocyte Invasion in IC10/Basal-Like Breast Tumors Is Associated with Wild-Type TP53.

Quigley D, Silwal-Pandit L, Dannenfelser R, Langerød A, Vollan HK, Vaske C, Siegel JU, Troyanskaya O, Chin SF, Caldas C, Balmain A, Børresen-Dale AL, Kristensen V.

Mol Cancer Res. 2015 Mar;13(3):493-501. doi: 10.1158/1541-7786.MCR-14-0387. Epub 2014 Oct 28.

39.

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.

40.

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.

41.

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.

42.

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.

43.

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.

44.

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.

45.

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.

46.

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.

47.

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.

48.

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.

49.

Involvement of histone demethylase LSD1 in short-time-scale gene expression changes during cell cycle progression in embryonic stem cells.

Nair VD, Ge Y, Balasubramaniyan N, Kim J, Okawa Y, Chikina M, Troyanskaya O, Sealfon SC.

Mol Cell Biol. 2012 Dec;32(23):4861-76. doi: 10.1128/MCB.00816-12. Epub 2012 Oct 1.

50.

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.

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