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.

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 Genetics. 2018 Aug. [Website]

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.

Nature Genetics. 2018 Jul 16. [Website] [Code] [Simons Foundation: Press]

Enabling Precision Medicine through Integrative Network Models.

Yao V*, Wong AK*, Troyanskaya OG.

Journal of Molecular Biology. 2018 Jul 9.

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

Wong AK, Krishnan A, Troyanskaya OG.

Nucleic Acids Research. 2018 May 25. [Website]

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 Computational Biology. 2018 May 14.


Bioinformatics approaches to profile the tumor microenvironment for immunotherapeutic discovery.

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

Current Pharmaceutical Design. 2017 Jul 10.

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, Moen Vollan HK, Haakensen VD, Helland Å, Naume B, Caldas C, Børresen-Dale AL, Kristensen VN, Troyanskaya OG.

Oncotarget. 2017 Jul 7.

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, ..., Quintana FJ, Lee YS, Krueger JG, Sarin KY, Yoon CH, Garraway L, Regev A, Shalek AK, Troyanskaya O, Anandasabapathy N.

Cell. 2017 Jun 29.


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.

Nature Neuroscience. 2016 Nov. [Website] [Simons Foundation: Press] [Princeton University: Press]

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, ..., 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.

GIANT API: an application programming interface for functional genomics.

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

Nucleic Acids Research. 2016 Jul 8. [Website] [Code]

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.


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. [Website]

Implications of Big Data for cell biology.

Dolinski K, Troyanskaya OG.

Molecular Biology of the Cell. 2015 Jul 15.

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 Research. 2015 Jul 1. [Website]

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.

Nature Genetics. 2015 Jun. [Website] [Nature Biotechnology: News and Views]

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.

Movement Disorders. 2015 May.

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.

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.

Nature Methods. 2015 Mar. [Website]

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.

Molecular Cancer Research. 2015 Mar.


Deep Supervised and Convolutional Generative Stochastic Network for Protein Secondary Structure Prediction

Zhou JTroyanskaya OG.

Proceedings of the International Conference of Machine Learning (ICML 2014), JMLR W&CP. 2014 Jun 21.

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 Biology. 2014 Apr 10.

Global quantitative modeling of chromatin factor interactions.

Zhou J, Troyanskaya OG.

PLoS Computational Biology. 2014 Mar.


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 Biology. 2013 Nov 20.

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 Research. 2013 Nov. [Website]

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, ..., Wolf A, Young C, Yuan J, Crutchfield C, McClean M, Murphy CT, Llinás M, Botstein D, Troyanskaya OG, Dunham MJ.

Genetics. 2013 Sep.

Comparative gene expression between two yeast species.

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

BMC Genomics. 2013 Jan 16.

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 Computational Biology. 2013.


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.

Molecular and Cellular Biology. 2012 Dec.

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 Research. 2012 Jul.

Accurate evaluation and analysis of functional genomics data and methods.

Greene CS, Troyanskaya OG.

Annals of the New York Academy of Sciences. 2012 Jul.

An effective statistical evaluation of ChIPseq dataset similarity.

Chikina MD, Troyanskaya OG.

Bioinformatics. 2012 Mar 1.

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.

Proceedings of the National Academy of Sciences of the United States of America. 2012 Feb 21.

Chapter 2: Data-driven view of disease biology.

Greene CS, Troyanskaya OG.

PLoS Computational Biology. 2012.

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 Computational Biology. 2012.


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.

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

Greene CS, Troyanskaya OG.

Nucleic Acids Research. 2011 Jul.

Accurate quantification of functional analogy among close homologs.

Chikina MD, Troyanskaya OG.

PLoS Computational Biology. 2011 Feb 3.


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 Systems Biology. 2010 Dec 31.

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 Computational Biology. 2010 Dec 16.

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.

Nature Methods. 2010 Dec.

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

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

PLoS Computational Biology. 2010 Nov 24.

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

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

PLoS Computational Biology. 2010 Nov 11.

Integrative systems biology for data-driven knowledge discovery.

Greene CS, Troyanskaya OG.

Seminars in Nephrology. 2010 Sep.

Systematic planning of genome-scale experiments in poorly studied species.

Guan Y, Dunham M, Caudy A, Troyanskaya O.

PLoS Computational Biology. 2010 Mar 5.

The genetic landscape of a cell.

Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear ED, Sevier CS, Ding H, Koh JL, Toufighi K, Mostafavi S, ..., Troyanskaya OG, Bussey H, Bader GD, Gingras AC, Morris QD, Kim PM, Kaiser CA, Myers CL, Andrews BJ, Boone C.

Science. 2010 Jan 22.


Detailing regulatory networks through large scale data integration.

Huttenhower C, Mutungu KT, Indik N, Yang W, Schroeder M, Forman JJ, Troyanskaya OG, Coller HA.

Bioinformatics. 2009 Dec 15.

Graphle: Interactive exploration of large, dense graphs.

Huttenhower C, Mehmood SO, Troyanskaya OG.

BMC Bioinformatics. 2009 Dec 14.

Systems-level dynamic analyses of fate change in murine embryonic stem cells.

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.

Nature. 2009 Nov 19.

The impact of incomplete knowledge on evaluation: an experimental benchmark for protein function prediction.

Huttenhower C, Hibbs MA, Myers CL, Caudy AA, Hess DC, Troyanskaya OG.

Bioinformatics. 2009 Sep 15.

Global prediction of tissue-specific gene expression and context-dependent gene networks in Caenorhabditis elegans.

Chikina MD, Huttenhower C, Murphy CT, Troyanskaya OG.

PLoS Computational Biology. 2009 Jun.

Exploring the human genome with functional maps.

Huttenhower C, Haley EM, Hibbs MA, Dumeaux V, Barrett DR, Coller HA, Troyanskaya OG.

Genome Research. 2009 Jun.

Aneuploidy prediction and tumor classification with heterogeneous hidden conditional random fields.

Barutcuoglu Z, Airoldi EM, Dumeaux V, Schapire RE, Troyanskaya OG.

Bioinformatics. 2009 May 15.

Directing experimental biology: a case study in mitochondrial biogenesis.

Hibbs MA, Myers CL, Huttenhower C, Hess DC, Li K, Caudy AA, Troyanskaya OG.

PLoS Computational Biology. 2009 Mar.

Computationally driven, quantitative experiments discover genes required for mitochondrial biogenesis.

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.

PLoS Genetics. 2009 Mar.

Selected proceedings of the First Summit on Translational Bioinformatics 2008.

Butte AJ, Sarkar IN, Ramoni M, Lussier Y, Troyanskaya O.

BMC Bioinformatics. 2009 Feb 5.

Coordinated concentration changes of transcripts and metabolites in Saccharomyces cerevisiae.

Bradley PH, Brauer MJ, Rabinowitz JD, Troyanskaya OG.

PLoS Computational Biology. 2009 Jan.

Predicting cellular growth from gene expression signatures.

Airoldi EM, Huttenhower C, Gresham D, Lu C, Caudy AA, Dunham MJ, Broach JR, Botstein D, Troyanskaya OG.

PLoS Computational Biology. 2009 Jan.

Discovering biological networks from diverse functional genomic data.

Myers CL, Chiriac C, Troyanskaya OG.

Methods in Molecular Biology. 2009.

Computational analysis of the yeast proteome: understanding and exploiting functional specificity in genomic data.

Huttenhower C, Myers CL, Hibbs MA, Troyanskaya OG.

Methods in Molecular Biology. 2009.


A genomewide functional network for the laboratory mouse.

Guan Y, Myers CL, Lu R, Lemischka IR, Bult CJ, Troyanskaya OG.

PLoS Computational Biology. 2008 Sep 26.

The Sleipnir library for computational functional genomics.

Huttenhower C, Schroeder M, Chikina MD, Troyanskaya OG.

Bioinformatics. 2008 Jul 1. [Website] [Code]

Assessing the functional structure of genomic data.

Huttenhower C, Troyanskaya OG.

Bioinformatics. 2008 Jul 1.

Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast.

Brauer MJ, Huttenhower C, Airoldi EM, Rosenstein R, Matese JC, Gresham D, Boer VM, Troyanskaya OG, Botstein D.

Molecular Biology of the Cell. 2008 Jan.

Predicting gene function in a hierarchical context with an ensemble of classifiers.

Guan Y, Myers CL, Hess DC, Barutcuoglu Z, Caudy AA, Troyanskaya OG.

Genome Biology. 2008.

A critical assessment of Mus musculus gene function prediction using integrated genomic evidence.

Peña-Castillo L, Tasan M, Myers CL, Lee H, Joshi T, Zhang C, Guan Y, Leone M, Pagnani A, Kim WK, ..., Morris Q, Klein-Seetharaman J, Bar-Joseph Z, Chen T, Sun F, Troyanskaya OG, Marcotte EM, Xu D, Hughes TR, Roth FP.

Genome Biology. 2008.


Exploring the functional landscape of gene expression: directed search of large microarray compendia.

Hibbs MA, Hess DC, Myers CL, Huttenhower C, Li K, Troyanskaya OG.

Bioinformatics. 2007 Oct 15. [Website]

"Getting started in...": a series not to miss.

Troyanskaya O.

PLoS Computational Biology. 2007 Oct.

Context-sensitive data integration and prediction of biological networks.

Myers CL, Troyanskaya OG.

Bioinformatics. 2007 Sep 1.

Nearest Neighbor Networks: clustering expression data based on gene neighborhoods.

Huttenhower C, Flamholz AI, Landis JN, Sahi S, Myers CL, Olszewski KL, Hibbs MA, Siemers NO, Troyanskaya OG, Coller HA.

BMC Bioinformatics. 2007 Jul 12.

Nested effects models for high-dimensional phenotyping screens.

Markowetz F, Kostka D, Troyanskaya OG, Spang R.

Bioinformatics. 2007 Jul 1.

Computational identification of cellular networks and pathways.

Markowetz F, Troyanskaya OG.

Molecular Biosystems. 2007 Jul.

Viewing the Larger Context of Genomic Data through Horizontal Integration

Hibbs MA, Wallace G, Dunham MJ, Li K, Troyanskaya OG.

IV '07 Proceedings of the 11th International Conference Information Visualization. 2007 Jul.

Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry.

Chi A, Huttenhower C, Geer LY, Coon JJ, Syka JE, Bai DL, Shabanowitz J, Burke DJ, Troyanskaya OG, Hunt DF.

Proceedings of the National Academy of Sciences of the United States of America. 2007 Feb 13.

Functional analysis of gene duplications in Saccharomyces cerevisiae.

Guan Y, Dunham MJ, Troyanskaya OG.

Genetics. 2007 Feb.

Modeling complex genetic interactions in a simple eukaryotic genome: actin displays a rich spectrum of complex haploinsufficiencies.

Haarer B, Viggiano S, Hibbs MA, Troyanskaya OG, Amberg DC.

Genes & Development. 2007 Jan 15.

Systems support for remote visualization of genomics applications over wide area networks

Bongo LA, Wallace G, Larsen T, Li K, Troyanskaya OG.

GCCB'06 Proceedings of the 2006 international conference on Distributed, high-performance and grid computing in computational biology. 2007 Jan.

Integrated analysis of microarray results.

Troyanskaya OG.

Methods in Molecular Biology. 2007.


A scalable method for integration and functional analysis of multiple microarray datasets.

Huttenhower C, Hibbs M, Myers C, Troyanskaya OG.

Bioinformatics. 2006 Dec 1.

GOLEM: an interactive graph-based gene-ontology navigation and analysis tool.

Sealfon RS, Hibbs MA, Huttenhower C, Myers CL, Troyanskaya OG.

BMC Bioinformatics. 2006 Oct 10.

Finding function: evaluation methods for functional genomic data.

Myers CL, Barrett DR, Hibbs MA, Huttenhower C, Troyanskaya OG.

BMC Genomics. 2006 Jul 25.

Hierarchical multi-label prediction of gene function.

Barutcuoglu Z, Schapire RE, Troyanskaya OG.

Bioinformatics. 2006 Apr 1.

Bayesian data integration: a functional perspective.

Huttenhower C, Troyanskaya OG.

Computational Systems Bioinformatics. Computational Systems Bioinformatics Conference. 2006.

Global analysis of gene function in yeast by quantitative phenotypic profiling.

Brown JA, Sherlock G, Myers CL, Burrows NM, Deng C, Wu HI, McCann KE, Troyanskaya OG, Brown JM.

Molecular Systems Biology. 2006.


Tools and applications for large-scale display walls.

Wallace G, Anshus OJ, Bi P, Chen H, Chen Y, Clark D, Cook P, Finkelstein A, Funkhouser T, Gupta A, Hibbs M, Li K, Liu Z, Samanta R, Sukthankar R, Troyanskaya O.

IEEE Computer Graphics and Applications. 2005 Aug.

A General Methodology for Integration of Microarray Data

Huttenhower C, Troyanskaya OG.

CSBW '05: Proceedings of the 2005 IEEE Computational Systems Bioinformatics Conference - Workshops. 2005 Aug.

Visualization-based discovery and analysis of genomic aberrations in microarray data.

Myers CL, Chen X, Troyanskaya OG.

BMC Bioinformatics. 2005 Jun 13.

Visualization methods for statistical analysis of microarray clusters.

Hibbs MA, Dirksen NC, Li K, Troyanskaya OG.

BMC Bioinformatics. 2005 May 12.

Dynamic Scalable Visualization for Collaborative Scientific Applications

Li K, Hibbs MA, Wallace G, Troyanskaya OG.

IPDPS '05 Proceedings of the 19th IEEE International Parallel and Distributed Processing Symposium (IPDPS'05) - Workshop 10 - Volume 11. 2005 Apr.

Discovery of biological networks from diverse functional genomic data.

Myers CL, Robson D, Wible A, Hibbs MA, Chiriac C, Theesfeld CL, Dolinski K, Troyanskaya OG.

Genome Biology. 2005.

Putting the 'bio' into bioinformatics.

Troyanskaya OG.

Genome Biology. 2005.


Accurate detection of aneuploidies in array CGH and gene expression microarray data.

Myers CL, Dunham MJ, Kung SY, Troyanskaya OG.

Bioinformatics. 2004 Dec 12.


Gene expression patterns in ovarian carcinomas.

Schaner ME, Ross DT, Ciaravino G, Sorlie T, Troyanskaya O, Diehn M, Wang YC, Duran GE, Sikic TL, Caldeira S, ..., Kristensen GB, Borresen-Dale AL, Hastie T, Tibshirani R, van de Rijn M, Teng NN, Longacre TA, Botstein D, Brown PO, Sikic BI.

Molecular Biology of the Cell. 2003 Nov.

Systemic and cell type-specific gene expression patterns in scleroderma skin.

Whitfield ML, Finlay DR, Murray JI, Troyanskaya OG, Chi JT, Pergamenschikov A, McCalmont TH, Brown PO, Botstein D, Connolly MK.

Proceedings of the National Academy of Sciences of the United States of America. 2003 Oct 14.

Endothelial cell diversity revealed by global expression profiling.

Chi JT, Chang HY, Haraldsen G, Jahnsen FL, Troyanskaya OG, Chang DS, Wang Z, Rockson SG, van de Rijn M, Botstein D, Brown PO.

Proceedings of the National Academy of Sciences of the United States of America. 2003 Sep 16.

Variation in gene expression patterns in human gastric cancers.

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.

Molecular Biology of the Cell. 2003 Aug.

A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae).

Troyanskaya OG, Dolinski K, Owen AB, Altman RB, Botstein D.

Proceedings of the National Academy of Sciences of the United States of America. 2003 Jul 8.

Variation in gene expression patterns in follicular lymphoma and the response to rituximab.

Bohen SP, Troyanskaya OG, Alter O, Warnke R, Botstein D, Brown PO, Levy R.

Proceedings of the National Academy of Sciences of the United States of America. 2003 Feb 18.


Phospholipase A2 group IIA expression in gastric adenocarcinoma is associated with prolonged survival and less frequent metastasis.

Leung SY, Chen X, Chu KM, Yuen ST, Mathy J, Ji J, Chan AS, Li R, Law S, Troyanskaya OG, Tu IP, Wong J, So S, Botstein D, Brown PO.

Proceedings of the National Academy of Sciences of the United States of America. 2002 Dec 10.

Nonparametric methods for identifying differentially expressed genes in microarray data.

Troyanskaya OG, Garber ME, Brown PO, Botstein D, Altman RB.

Bioinformatics. 2002 Nov.

Sequence complexity profiles of prokaryotic genomic sequences: a fast algorithm for calculating linguistic complexity.

Troyanskaya OG, Arbell O, Koren Y, Landau GM, Bolshoy A.

Bioinformatics. 2002 May.


Diversity of gene expression in adenocarcinoma of the lung.

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.

Proceedings of the National Academy of Sciences of the United States of America. 2001 Nov 20.

Missing value estimation methods for DNA microarrays.

Troyanskaya O, Cantor M, Sherlock G, Brown P, Hastie T, Tibshirani R, Botstein D, Altman RB.

Bioinformatics. 2001 Jun. [Code]