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Olga Troyanskaya, PhD

Publications since 2011

Gorenshteyn, D. Zaslavsky, E. Fribourg, M. Park, C. Y. Wong, A. K. Tadych, A. Hartmann, B. M. Albrecht, R. A. Garcia-Sastre, A. Kleinstein, S. H. Troyanskaya, O. G. Sealfon, S. C. Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases. Immunity, 43:605-614, . (PMID: 26362267)

Zhou, J. Troyanskaya, O. G. Predicting effects of noncoding variants with deep learning-based sequence model. Nat Methods, In process, . (PMID: 26301843)

Dolinski, K. Troyanskaya, O. G. Implications of Big Data for cell biology. Mol Biol Cell, 26:2575-2578, . (PMID: 26174066)

Wong, A. K. Krishnan, A. Yao, V. Tadych, A. Troyanskaya, O. G. IMP 2.0: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks. Nucleic Acids Res, In process, . (PMID: 25969450)

Goya, J. Wong, A. K. Yao, V. Krishnan, A. Homilius, M. Troyanskaya, O. G. FNTM: a server for predicting functional networks of tissues in mouse. Nucleic Acids Res, In process, . (PMID: 25940632)

Greene, C. S. Krishnan, A. Wong, A. K. Ricciotti, E. Zelaya, R. A. Himmelstein, D. S. Zhang, R. Hartmann, B. M. Zaslavsky, E. Sealfon, S. C. Chasman, D. I. FitzGerald, G. A. Dolinski, K. Grosser, T. Troyanskaya, O. G. Understanding multicellular function and disease with human tissue-specific networks. Nat Genet, In process, . (PMID: 25915600)

Zhu, Q. Wong, A. K. Krishnan, A. Aure, M. R. Tadych, A. Zhang, R. Corney, D. C. Greene, C. S. Bongo, L. A. Kristensen, V. N. Charikar, M. Li, K. Troyanskaya, O. G. Targeted exploration and analysis of large cross-platform human transcriptomic compendia. Nat Methods, In process, . (PMID: 25581801)

Park, C. Y. Krishnan, A. Zhu, Q. Wong, A. K. Lee, Y. S. Troyanskaya, O. G. Tissue-aware data integration approach for the inference of pathway interactions in metazoan organisms. Bioinformatics, In process, . (PMID: 25431329)

Quigley, D. Silwal-Pandit, L. Dannenfelser, R. Langerod, A. Vollan, H. K. Vaske, C. Ursini-Siegel, J. Troyanskaya, O. Chin, S. F. Caldas, C. Balmain, A. Borresen-Dale, A. L. Kristensen, V. Lymphocyte invasion in IC10/Basal-like breast tumors is associated with wild-type TP53. Mol Cancer Res, In process, . (PMID: 25351767)

Zhou, J. Troyanskaya, O. G. Global quantitative modeling of chromatin factor interactions. PLoS Comput Biol, 10:e1003525, . (PMID: 24675896, PMCID: PMC3967939)

Vandersluis, B. Hess, D. C. Pesyna, C. Krumholz, E. W. Syed, T. Szappanos, B. Nislow, C. Papp, B. Troyanskaya, O. G. Myers, C. L. Caudy, A. A. Broad metabolic sensitivity profiling of a prototrophic yeast deletion collection. Genome Biol, 15:R64, . (PMID: 24721214, PMCID: PMC4053978)

Lee, Y. S. Krishnan, A. Zhu, Q. Troyanskaya, O. G. Ontology-aware classification of tissue and cell-type signals in gene expression profiles across platforms and technologies. Bioinformatics, 29:3036-3044, . (PMID: 24037214, PMCID: PMC3834796)

Aure, M. R. Leivonen, S. K. Fleischer, T. Zhu, Q. Overgaard, J. Alsner, J. Tramm, T. Louhimo, R. Alnaes, G. I. Perala, M. Busato, F. Touleimat, N. Tost, J. Borresen-Dale, A. L. Hautaniemi, S. Troyanskaya, O. G. Lingjaerde, O. C. Sahlberg, K. K. Kristensen, V. N. Individual and combined effects of DNA methylation and copy number alterations on miRNA expression in breast tumors. Genome Biol, In process, . (PMID: 24257477, PMCID: PMC4053776)

Ju, W. Greene, C. S. Eichinger, F. Nair, V. Hodgin, J. B. Bitzer, M. Lee, Y. S. Zhu, Q. Kehata, M. Li, M. Jiang, S. Rastaldi, M. P. Cohen, C. D. Troyanskaya, O. G. Kretzler, M. Defining cell-type specificity at the transcriptional level in human disease. Genome Res, 23:1862-1873, . (PMID: 23950145, PMCID: PMC3814886)

Caudy, A. A. Guan, Y. Jia, Y. Hansen, C. Desevo, C. Hayes, A. P. Agee, J. Alvarez-Dominguez, J. R. Arellano, H. Barrett, D. Bauerle, C. Bisaria, N. Bradley, P. H. Breunig, J. S. Bush, E. Cappel, D. Capra, E. Chen, W. Clore, J. Combs, P. A. 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, Y. H. Inukai, S. Karczewski, K. J. 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, C. T. Llinas, M. Botstein, D. Troyanskaya, O. G. Dunham, M. J. A new system for comparative functional genomics of Saccharomyces yeasts. Genetics, 195:275-287, . (PMID: 23852385, PMCID: PMC3761308)

Park, C. Y. Wong, A. K. Greene, C. S. Rowland, J. Guan, Y. Bongo, L. A. Burdine, R. D. Troyanskaya, O. G. Functional knowledge transfer for high-accuracy prediction of under-studied biological processes. PLoS Comput Biol, 9:e1002957, . (PMID: 23516347, PMCID: PMC3597527)

Guan, Y. Dunham, M. J. Troyanskaya, O. G. Caudy, A. A. Comparative gene expression between two yeast species. BMC Genomics, 14:33, . (PMID: 23324262, PMCID: PMC3556494)

Wong, A. K. Park, C. Y. Greene, C. S. Bongo, L. A. Guan, Y. Troyanskaya, O. G. IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks. Nucleic Acids Res, 40:W484-W490, . (PMID: 22684505, PMCID: PMC3394282)

Chikina, M. D. Troyanskaya, O. G. An effective statistical evaluation of ChIPseq dataset similarity. Bioinformatics, 28:607-613, . (PMID: 22262674, PMCID: PMC3339511)

Greene, C. S. Troyanskaya, O. G. Chapter 2: Data-driven view of disease biology. PLoS Comput Biol, 8:e1002816, . (PMID: 23300408, PMCID: PMC3531282)

Guan, Y. Gorenshteyn, D. Burmeister, M. Wong, A. K. Schimenti, J. C. Handel, M. A. Bult, C. J. Hibbs, M. A. Troyanskaya, O. G. Tissue-specific functional networks for prioritizing phenotype and disease genes. PLoS Comput Biol, 8:e1002694, . (PMID: 23028291, PMCID: PMC3459891)