Faculty & Research

Associated Faculty

Olga G. Troyanskaya

Associated Faculty, Computer Science
and the Lewis-Sigler Institute for Integrative Genomics

Olga Troyanskaya

lab Troyanskaya Research Lab
Phone (609) 258-1749
locationCarl Icahn Lab, 228
Phone Lab (609) 258-1749
Faculty Assistant
Marybeth Fedele
Phone (609) 258-7058

Research Focus

Bioinformatics and genomics

The new era of high-throughput experimental methods in molecular biology has created exciting challenges for computer science to develop novel algorithms for complex, accurate, and consistent interpretation of diverse biological information. In the next decades, large-scale explorations of complex molecular, cellular, and organismic systems at complementary levels of resolution will allow us to integrate our understanding of macroscopic physiology and microscopic biology. To realize the full potential of these developments, we need to develop sophisticated bioinformatics frameworks to integrate and synthesize diverse biological data produced by these methods.

The goal of the research in my laboratory is to bring the capabilities of computer science and statistics to the study of gene function and regulation in the biological networks through integrated analysis of biological data from diverse data sources--both existing and yet to come (e.g. from diverse gene expression data sets and proteomic studies). We are designing systematic and accurate computational and statistical algorithms for biological signal detection in high-throughput data sets. More specifically, our lab is interested in developing methods for better gene expression data processing and algorithms for integrated analysis of biological data from multiple genomic data sets and different types of data sources (e.g. genomic sequences, gene expression, and proteomics data).

My laboratory combines computational methods with an experimental component in a unified effort to develop comprehensive descriptions of genetic systems of cellular controls, including those whose malfunctioning becomes the basis of genetic disorders, such as cancer, and others whose failure might produce developmental defects in model systems. The experimental component the lab focuses on is S. cerevisiae (baker's yeast).

Selected Publications

Zhou J, Troyanskaya OG. (2016) Probabilistic modelling of chromatin code landscape reveals functional diversity of enhancer-like chromatin states. Nat Commun. 7:10528. Pubmed

Gorenshteyn D, Zaslavsky E, Fribourg M, ... Troyanskaya OG, Sealfon SC. (2015) Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases.  Immunity. 43(3): 605-14. Pubmed

Zhou J, Troyanskaya OG. (2015) Predicting effects of noncoding variants with deep learning-based sequence model. Nat Methods. 12(10):931-4. Pubmed

Dolinski K, Troyanskaya OG. (2015) Implications of big data for cell biology. Mol Biol Cell.  26 (14): 2575-8. Pubmed

Goya J, Wong AK, Yao V, Krishnan A, Homilius M, Troyanskaya OG. (2015) FNTM: a server for predicting functional networks of tissues in mouse. Nucleic Acids Res. 43(W1):W182-7. Pubmed

Wong AK, Krishnan A, Yao V, Tadych A, Troyanskaya OG. (2015) IMP 2.0: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks. Nucleic Acids Res. 43(W1):W128-33. Pubmed 

Greene CS, Krishnan A, Wong AK,...Troyanskaya OG. (2015) Understanding multicellular function and disease with human tissue-specific networks. Nat Genet. Pubmed

Zhu Q, Wong AK, Krishnan A,...Troyanskaya OG. (2015) Targeted exploration and analysis of large cross-platform human transcriptomic compendia. Nat Methods. 12:211-4. Pubmed

Park CY, Krishnan A, Zhu Q, Wong AK, Lee Y, Troyanskaya OG. (2014) Tissue-aware data integration approach for the inference of pathway interactions in metazoan organisms. Bioinformatics. 31:1093-101. Pubmed

Zhou J, Troyanskaya OG. (2014) Global quantitative modeling of chromatin factor interactions. PLoS Comput Biol. 10: e1003525. Pubmed

Lee YS, Krishnan A, Zhu Q, Troyanskaya OG. (2013) Ontology-aware classification of tissue and cell-type signals in gene expression profiles across platforms and technologies. Bioinformatics. 29: 3036-44 Pubmed

Park CY, Wong AK, Greene CS, Rowland J, Guan Y, Bongo LA, Burdine RD, Troyanskaya OG. (2013) Functional knowledge transfer for high-accuracy prediction of under-studied biological processes. PLoS Comput Biol. 9: e1002957. Pubmed

Guan Y, Dunham MJ, Troyanskaya OG, Caudy AA. (2013) Comparative gene expression between two yeast species. BMC Genomics. 14: 33. Pubmed

Greene CS, Troyanskaya OG. (2012) Chapter 2: data-driven view of disease biology. PLoS Comput Biol. 8: e1002816. Pubmed

Greene CS, Troyanskaya OG. (2012) Accurate evaluation and analysis of functional genomics data and methods. Ann N Y Acad Sci. 1260: 95-100. Pubmed

Wong AK, Park CY, Greene CS, Bongo LA, Guan Y, Troyanskaya OG. (2012) IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks. Nucleic Acids Res. 40: W484-490. PubMed

Guan Y, Yao V, Tsui K, Gebbia M, Dunham MJ, Nislow C, Troyanskaya OG. (2011) Nucleosome-coupled expression differences in closely-related species. BMC Genomics. 12: 466. PubMed

Greene CS, Troyanskaya OG. (2011) PILGRM: an interactive data-driven discovery platform for expert biologists. Nucleic Acids Res. 39: W368-374. PubMed

Chikina MD, Troyanskaya OG. (2011) Accurate quantification of functional analogy among close homologs. PLoS Comput Biol. 7: e1001074. PubMed

Pop A, Huttenhower C, Iyer-Pascuzzi A, Benfey PN, Troyanskaya OG. (2010) Integrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana. BMC Syst Biol. 4: 180. PubMed

Park CY, Hess DC, Huttenhower C, Troyanskaya OG. (2010) Simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway components. PLoS Comput Biol. 6: e1001009. PubMed

Guan Y, Ackert-Bicknell CL, Kell B, Troyanskaya OG, Hibbs MA. (2010) Functional genomics complements quantitative genetics in identifying disease-gene associations. PLoS Comput Biol. 6: e1000991. PubMed

Greene CS, Troyanskaya OG. (2010) Integrative systems biology for data-driven knowledge discovery. Semin Nephrol. 30: 443-454. PubMed

Huttenhower C, Mehmood SO, Troyanskaya OG. (2009) Graphle: Interactive exploration of large, dense graphs. BMC Bioinformatics. 10: 417. PubMed

Lu R, Markowetz F, Unwin RD, ... Troyanskaya OG, Whetton AD, Lemischka IR. (2009) Systems-level dynamic analyses of fate change in murine embryonic stem cells. Nature. 462: 358-362. PubMed

Huttenhower C, Mutungu KT, Indik N, ... Troyanskaya OG, Coller HA. (2009) Detailing regulatory networks through large scale data integration. Bioinformatics. 25: 3267-3274. PubMed

Huttenhower C, Haley EM, Hibbs MA, Dumeaux V, Barrett DR, Coller HA, Troyanskaya OG. (2009) Exploring the human genome with functional maps. Genome Res. 19: 1093-1106. PubMed

Huttenhower C, Hibbs MA, Myers CL, Caudy AA, Hess DC, Troyanskaya OG. (2009) The impact of incomplete knowledge on evaluation: an experimental benchmark for protein function prediction. Bioinformatics 25: 2404-2410. PubMed

Chikina MD, Huttenhower C, Murphy CT, Troyanskaya OG. (2009) Global prediction of tissue-specific gene expression and context-dependent gene networks in Caenorhabditis elegans. PLoS Comput Biol. 5: e1000417. PubMed

Huttenhower C, Myers CL, Hibbs MA, Troyanskaya OG. (2009) Computational analysis of the yeast proteome: understanding and exploiting functional specificity in genomic data. Methods Mol Biol. 548: 273-293. PubMed

Barutcuoglu Z, Airoldi EM, Dumeaux V, Schapire RE, Troyanskaya OG. (2009) Aneuploidy prediction and tumor classification with heterogeneous hidden conditional random fields. Bioinformatics. 25: 1307-1313. PubMed

Hibbs MA, Myers CL, Huttenhower C, Hess DC, Li K, Caudy AA, Troyanskaya OG. (2009) Directing experimental biology: a case study in mitochondrial biogenesis. PLoS Comput Biol. 5: e1000322. PubMed

Hess DC, Myers CL, Huttenhower C ... Troyanskaya OG, Caudy AA. (2009) Computationally driven, quantitative experiments discover genes required for mitochondrial biogenesis. PLoS Genet. 5: e1000407. PubMed

Huttenhower C, Haley EM, Hibbs MA, Dumeaux V, Barrett DR, Coller HA, Troyanskaya OG. (2009) Exploring the human genome with functional maps. Genome Res. 19: 1093-1106. PubMed

Bradley PH, Brauer MJ, Rabinowitz JD, Troyanskaya OG. (2009) Coordinated concentration changes of transcripts and metabolites in Saccharomyces cerevisiae. PLoS Comput Biol. 5: e1000270. PubMed

Airoldi EM, Huttenhower C, Gresham D ... Troyanskaya OG. (2009) Predicting cellular growth from gene expression signatures. PLoS Comput Biol. 5: e1000257. PubMed

Guan Y, Myers CL, Lu R, Lemischka IR, Bult CJ, Troyanskaya OG. (2008) A genomewide functional network for the laboratory mouse. PLoS Comput Biol. 4: e1000165. PubMed

Guan Y, Myers CL, Hess DC, Barutcuoglu Z, Caudy AA, Troyanskaya OG. (2008) Predicting gene function in a hierarchical context with an ensemble of classifiers. Genome Biol. Suppl 1:S3. PubMed

Huttenhower C, Troyanskaya OG. (2008) Assessing the functional structure of genomic data. Bioinformatics. 24: i330-38. PubMed

Huttenhower C, Schroeder M, Chikina MD, Troyanskaya OG. (2008) The Sleipnir library for computational functional genomics. Bioinformatics. 24: 1559-61. PubMed

Brauer MJ, Huttenhower C, Airoldi EM,...Troyanskaya OG, Botstein D. (2008) Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast. Mol Biol Cell. 19: 352-67. PubMed.

Troyanskaya OG. (2007) Integrated analysis of microarray results. Methods Mol Biol. 382: 429-37. PubMed

Hibbs MA, Hess DC, Myers CL, Huttenhower C, Li K, Troyanskaya OG. (2007) Exploring the functional landscape of gene expression: directed search of large microarray compendia. Bioinformatics. 23: 2692-99. PubMed

Huttenhower C, Flamholz AI, Landis JN,...Troyanskaya OG, Coller HA. (2007) Nearest Neighbor Networks: clustering expression data based on gene neighborhoods. BMC Bioinformatics. 8: 250. PubMed

Myers CL, Troyanskaya OG. (2007) Context-sensitive data integration and prediction of biological networks. Bioinformatics. 23: 2322-30. PubMed

Markowetz F, Kostka D, Troyanskaya OG, Spang R. (2007) Nested effects models for high-dimensional phenotyping screens. Bioinformatics. 23: i305-12. PubMed

Markowetz F, Troyanskaya OG. (2007) Computational identification of cellular networks and pathways. Mol Biosyst. 3: 478-82. PubMed

Huttenhower C, Troyanskaya OG. (2007) Bayesian data integration: a functional perspective. Comput Syst Bioinformatics Conf 2006. 341-51. PubMed

Guan Y, Dunham MJ, Troyanskaya OG. (2006) Functional analysis of gene duplications in Saccharomyces cerevisiae. Genetics. 175: 933-43. PubMed

Huttenhower C, Hibbs M, Myers C, Troyanskaya OG. (2006) A scalable method for integration and functional analysis of multiple microarray data sets. Bioinformatics. 22: 2890-97. PubMed

Sealfon RS, Hibbs MA, Huttenhower C, Myers CL, Troyanskaya OG. (2006) GOLEM: an interactive graph-based gene-ontology navigation and analysis tool. BMC Bioinformatics. 7: 443. PubMed

Myers CL, Barrett DR, Hibbs MA, Huttenhower C, Troyanskaya OG. (2006) Finding function: evaluation methods for functional genomic data. BMC Genomics. 7: 187. PubMed

Barutcuoglu Z, Schapire RE, Troyanskaya OG (2006). Hierarchical multi-label prediction of gene function. Bioinformatics 22: 830-836. PubMed

Myers CL, Chen X, Troyanskaya OG. (2005) Visualization-based discovery and analysis of genomic aberrations in microarray data. BMC Bioinformatics. 6: 146. PubMed

Hibbs MA, Dirksen NC, Li K, Troyanskaya OG. (2005) Visualization methods for statistical analysis of microarray clusters. BMC Bioinformatics. 6: 115. PubMed

Troyanskaya OG. (2005) Putting microarrays in a context: integrated analysis of diverse biological data. Brief Bioinform. 6: 34-43. PubMed

Myers CL, Robson D, Wible A,...Troyanskaya OG. (2005) Discovery of biological networks from diverse functional genomic data. Genome Biol. 6: R114. PubMed

Troyanskaya OG. (2005) Putting the 'bio' into bioinformatics. Genome Biol. 6: 351. PubMed

Myers CL, Dunham MJ, Kung SY, Troyanskaya OG. (2003) Accurate detection of aneuploidies in array CGH and gene expression microarray data. Bioinformatics. 20: 3533-43. PubMed

Chen X, Leung SY, Yuen ST,...Troyanskaya OG,...Brown PO. (2003) Variation in gene expression patterns in human gastric cancers. Mol Biol Cell. 14: 3208-15. PubMed

Troyanskaya OG, Dolinski K, Owen AB, Altman RB, Botstein D. (2003) A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae). Proc Natl Acad Sci. 100: 8348-53. PubMed

Bohen SP, Troyanskaya OG, Alter O,...Levy R. (2003) Variation in gene expression patterns in follicular lymphoma and the response to rituximab. Proc Natl Acad Sci. 100: 1926-30. PubMed

Troyanskaya OG, Garber ME, Brown PO, Botstein D, Altman RB. (2002) Nonparametric methods for identifying differentially expressed genes in microarray data. Bioinformatics. 18: 1454-61. PubMed

Troyanskaya OG, Arbell O, Koren Y, Landau GM, Bolshoy A. (2002) Sequence complexity profiles of prokaryotic genomic sequences: a fast algorithm for calculating linguistic complexity. Bioinformatics. 18: 679-88. PubMed

Troyanskaya O, Cantor M, Sherlock G,...Altman RB. (2001) Missing value estimation methods for DNA microarrays. Bioinformatics. 17: 520-25. PubMed

Garber ME, Troyanskaya OG, Schluens K,...Petersen I. (2001) Diversity of gene expression in adenocarcinoma of the lung. Proc Natl Acad Sci. 98: 13784-89. PubMed


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