Olga G. Troyanskaya

This email address is being protected from spambots. You need JavaScript enabled to view it.	Troyanskaya Research Lab
(609) 258-1749	Carl Icahn Lab, 228
	Lab (609) 258-1749
Faculty Assistant	Barbara Brinker
This email address is being protected from spambots. You need JavaScript enabled to view it.	(609) 258-7014

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

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, Leek JT, Airoldi EM, MacArthur BD, Lachmann A, Rozov R, Ma'ayan A, Boyer LA, 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, Yang W, Schroeder M, Forman JJ, 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, Hibbs MA, Hayes AP, Paw J, Clore JJ, Mendoza RM, Luis BS, Nislow C, Giaever G, Costanzo M, 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, Lu C, Caudy AA, Dunham MJ, Broach JR, Botstein 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: i330-338. PubMed

Huttenhower C, Schroeder M, Chikina MD, Troyanskaya OG. (2008) The Sleipnir library for computational functional genomics. Bioinformatics 24: 1559-1561. PubMed

Brauer MJ, Huttenhower C, Airoldi EM, Rosenstein R, Matese JC, Gresham D, Boer VM, Troyanskaya OG, Botstein D. (2008) Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast. Mol Biol Cell 19: 352-367 PubMed.

Troyanskaya OG. (2007) Integrated analysis of microarray results. Methods Mol Biol 382: 429-437. 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: 2692-2699. PubMed

Huttenhower C, Flamholz AI, Landis JN, Sahi S, Myers CL, Olszewski KL, Hibbs MA, Siemers NO, Troyanskaya OG, Coller HA. (2007) Nearest Neighbor Networks: clustering expression data based on gene neighborhoods. BMC Bioinformatics.8: 250. PubMed

Myers CL and Troyanskaya OG (2007). Context-sensitive data integration and prediction of biological networks. Bioinformatics 23: 2322-2330. PubMed

Markowetz F, Kostka D, Troyanskaya OG, Spang R (2007). Nested effects models for high-dimensional phenotyping screens. Bioinformatics 23: i305-i312. PubMed

Markowetz F and Troyanskaya OG (2007). Computational identification of cellular networks and pathways. Mol Biosyst 3: 478-482. PubMed

Huttenhower C and Troyanskaya OG (2007). Bayesian data integration: a functional perspective. Comput Syst Bioinformatics Conf 2006. 341-351. PubMed

Guan Y, Dunham MJ, Troyanskaya OG (2006). Functional analysis of gene duplications in Saccharomyces cerevisiae. Genetics 175: 933-943. 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: 2890-2897. 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, Hibbs MA, Chiriac C, Theesfeld CL, Dolinski K, 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: 3533-3543. PubMed

Chen X, Leung SY, Yuen ST, Chu KM, Ji J, Li R, Chan AS, Law S, Troyanskaya OG, Wong J, So S, Botstein D, Brown PO (2003). Variation in gene expression patterns in human gastric cancers. Mol Biol Cell 14: 3208-3215. PubMed

Troyanskaya OG, Dolinski K, Owen AB, Altman RB and Botstein D (2003). A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae). Proc Natl Acad Sci USA 100: 8348-8353. PubMed

Bohen SP, Troyanskaya OG, Alter O, Warnke R, Botstein D, Brown PO, Levy R (2003). Variation in gene expression patterns in follicular lymphoma and the response to rituximab. Proc Natl Acad Sci USA 100: 1926-1930. PubMed

Troyanskaya OG, Garber ME, Brown PO, Botstein D and Altman RB (2002). Nonparametric methods for identifying differentially expressed genes in microarray data. Bioinformatics 18: 1454-1461. PubMed

Troyanskaya OG, Arbell O, Koren Y, Landau GM and Bolshoy A (2002). Sequence complexity profiles of prokaryotic genomic sequences: a fast algorithm for calculating linguistic complexity. Bioinformatics 18: 679-688. PubMed

Troyanskaya O, Cantor M, Sherlock G, Brown P, Hastie T, Tibshirani R, Botstein D, Altman RB (2001). Missing value estimation methods for DNA microarrays. Bioinformatics 17: 520-525. PubMed

Garber ME, Troyanskaya OG, Schluens K, Petersen S, Thaesler Z, Pacyna-Gengelbach M, van de Rijn M, Rosen GD, Perou CM, Whyte RI, Altman RB, Brown PO, Botstein D, Petersen I (2001). Diversity of gene expression in adenocarcinoma of the lung. Proc Natl Acad Sci USA 98: 13784-13789. PubMed