Olga G. Troyanskaya - Publications

Affiliations: 
Computer Science Princeton University, Princeton, NJ 
 2003 Stanford University, Palo Alto, CA 
Area:
Bioinformatics; analysis of large-scale biological data sets (genomics, gene expression, proteomics, biological networks); algorithms for integration of data from multiple data sources; visualization of biological data; machine learning methods in bioinfo

116 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Sargin D, Chottekalapanda RU, Perit KE, Yao V, Chu D, Sparks DW, Kalik S, Power SK, Troyanskaya OG, Schmidt EF, Greengard P, Lambe EK. Mapping the physiological and molecular markers of stress and SSRI antidepressant treatment in S100a10 corticostriatal neurons. Molecular Psychiatry. PMID 31431686 DOI: 10.1038/s41380-019-0473-6  0.32
2019 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. Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk. Nature Genetics. PMID 31133750 DOI: 10.1038/s41588-019-0420-0  0.48
2019 Bradley PH, Gibney PA, Botstein D, Troyanskaya OG, Rabinowitz JD. Minor Isozymes Tailor Yeast Metabolism to Carbon Availability. Msystems. 4. PMID 30834327 DOI: 10.1128/mSystems.00170-18  0.88
2019 Lee YS, Krishnan A, Oughtred R, Rust J, Chang CS, Ryu J, Kristensen VN, Dolinski K, Theesfeld CL, Troyanskaya OG. A Computational Framework for Genome-wide Characterization of the Human Disease Landscape. Cell Systems. PMID 30685436 DOI: 10.1016/j.cels.2018.12.010  0.68
2018 Lee YS, Wong AK, Tadych A, Hartmann BM, Park CY, DeJesus VA, Ramos I, Zaslavsky E, Sealfon SC, Troyanskaya OG. Interpretation of an individual functional genomics experiment guided by massive public data. Nature Methods. PMID 30478325 DOI: 10.1038/s41592-018-0218-5  0.48
2018 Yao V, Kaletsky R, Keyes W, Mor DE, Wong AK, Sohrabi S, Murphy CT, Troyanskaya OG. An integrative tissue-network approach to identify and test human disease genes. Nature Biotechnology. PMID 30346941 DOI: 10.1038/nbt.4246  0.6
2018 Kaletsky R, Yao V, Williams A, Runnels AM, Tadych A, Zhou S, Troyanskaya OG, Murphy CT. Transcriptome analysis of adult Caenorhabditis elegans cells reveals tissue-specific gene and isoform expression. Plos Genetics. 14: e1007559. PMID 30096138 DOI: 10.1371/journal.pgen.1007559  0.6
2018 Zhou J, Theesfeld CL, Yao K, Chen KM, Wong AK, Troyanskaya OG. Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk. Nature Genetics. PMID 30013180 DOI: 10.1038/s41588-018-0160-6  0.48
2018 Yao V, Wong AK, Troyanskaya OG. Enabling Precision Medicine through Integrative Network Models. Journal of Molecular Biology. PMID 30003887 DOI: 10.1016/j.jmb.2018.07.004  0.48
2018 Wong AK, Krishnan A, Troyanskaya OG. GIANT 2.0: genome-scale integrated analysis of gene networks in tissues. Nucleic Acids Research. PMID 29800226 DOI: 10.1093/nar/gky408  0.48
2016 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, ... ... Troyanskaya OG, et al. A global genetic interaction network maps a wiring diagram of cellular function. Science (New York, N.Y.). 353. PMID 27708008 DOI: 10.1126/science.aaf1420  1
2016 Krishnan A, Zhang R, Yao V, Theesfeld CL, Wong AK, Tadych A, Volfovsky N, Packer A, Lash A, Troyanskaya OG. Genome-wide prediction and functional characterization of the genetic basis of autism spectrum disorder. Nature Neuroscience. PMID 27479844 DOI: 10.1038/nn.4353  0.48
2016 Walhout AJ, Watson E, Olin-Sandoval V, Hoy MJ, Li CH, Louisse T, Yao V, Mori A, Holdorf AD, Troyanskaya OG, Ralser M. Metabolic network rewiring of propionate flux compensates vitamin B12 deficiency in C. elegans. Elife. 5. PMID 27383050 DOI: 10.7554/eLife.17670  1
2016 Roberts AM, Wong AK, Fisk I, Troyanskaya OG. GIANT API: an application programming interface for functional genomics. Nucleic Acids Research. PMID 27098035 DOI: 10.1093/nar/gkw289  0.48
2016 Zhou J, Troyanskaya OG. Probabilistic modelling of chromatin code landscape reveals functional diversity of enhancer-like chromatin states. Nature Communications. 7: 10528. PMID 26841971 DOI: 10.1038/ncomms10528  1
2015 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. Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases. Immunity. 43: 605-14. PMID 26362267 DOI: 10.1016/j.immuni.2015.08.014  1
2015 Dolinski K, Troyanskaya OG. Implications of Big Data for cell biology. Molecular Biology of the Cell. 26: 2575-8. PMID 26174066 DOI: 10.1091/mbc.E13-12-0756  0.68
2015 Wong AK, Krishnan A, Yao V, Tadych A, Troyanskaya OG. IMP 2.0: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks. Nucleic Acids Research. 43: W128-33. PMID 25969450 DOI: 10.1093/nar/gkv486  0.48
2015 Goya J, Wong AK, Yao V, Krishnan A, Homilius M, Troyanskaya OG. FNTM: a server for predicting functional networks of tissues in mouse. Nucleic Acids Research. 43: W182-7. PMID 25940632 DOI: 10.1093/nar/gkv443  0.48
2015 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. Understanding multicellular function and disease with human tissue-specific networks. Nature Genetics. 47: 569-76. PMID 25915600 DOI: 10.1038/ng.3259  0.68
2015 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. Low-variance RNAs identify Parkinson's disease molecular signature in blood. Movement Disorders : Official Journal of the Movement Disorder Society. 30: 813-21. PMID 25786808 DOI: 10.1002/mds.26205  1
2015 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. Targeted exploration and analysis of large cross-platform human transcriptomic compendia. Nature Methods. 12: 211-4, 3 p following. PMID 25581801 DOI: 10.1038/nmeth.3249  1
2015 Park CY, Krishnan A, Zhu Q, Wong AK, Lee YS, Troyanskaya OG. Tissue-aware data integration approach for the inference of pathway interactions in metazoan organisms. Bioinformatics (Oxford, England). 31: 1093-101. PMID 25431329 DOI: 10.1093/bioinformatics/btu786  1
2015 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. Lymphocyte Invasion in IC10/Basal-Like Breast Tumors Is Associated with Wild-Type TP53. Molecular Cancer Research : McR. 13: 493-501. PMID 25351767 DOI: 10.1158/1541-7786.MCR-14-0387  1
2015 Dolinski K, Troyanskaya OG. Implications of Big Data for cell biology Molecular Biology of the Cell. 26: 2575-2578. DOI: 10.1091/mbc.E13-12-0756  1
2015 Zhou J, Troyanskaya OG. Predicting effects of noncoding variants with deep learning–based sequence model Nature Methods. DOI: 10.1038/nmeth.3547  1
2014 VanderSluis B, Hess DC, Pesyna C, Krumholz EW, Syed T, Szappanos B, Nislow C, Papp B, Troyanskaya OG, Myers CL, Caudy AA. Broad metabolic sensitivity profiling of a prototrophic yeast deletion collection. Genome Biology. 15: R64. PMID 24721214 DOI: 10.1186/gb-2014-15-4-r64  1
2014 Zhou J, Troyanskaya OG. Global quantitative modeling of chromatin factor interactions. Plos Computational Biology. 10: e1003525. PMID 24675896 DOI: 10.1371/journal.pcbi.1003525  1
2014 Dress A, Linial M, Troyanskaya O, Vingron M. ISCB/SPRINGER series in computational biology Bioinformatics. 30: 146-147. DOI: 10.1093/bioinformatics/btt670  1
2014 Zhou J, Troyanskaya OG. Deep supervised and convolutional generative stochastic network for protein secondary structure prediction 31st International Conference On Machine Learning, Icml 2014. 2: 1121-1129.  1
2013 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, et al. Individual and combined effects of DNA methylation and copy number alterations on miRNA expression in breast tumors. Genome Biology. 14: R126. PMID 24257477 DOI: 10.1186/gb-2013-14-11-r126  1
2013 Lee YS, Krishnan A, Zhu Q, Troyanskaya OG. Ontology-aware classification of tissue and cell-type signals in gene expression profiles across platforms and technologies. Bioinformatics (Oxford, England). 29: 3036-44. PMID 24037214 DOI: 10.1093/bioinformatics/btt529  1
2013 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. Defining cell-type specificity at the transcriptional level in human disease. Genome Research. 23: 1862-73. PMID 23950145 DOI: 10.1101/gr.155697.113  1
2013 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, ... ... Troyanskaya OG, et al. A new system for comparative functional genomics of Saccharomyces yeasts. Genetics. 195: 275-87. PMID 23852385 DOI: 10.1534/genetics.113.152918  1
2013 Park CY, Wong AK, Greene CS, Rowland J, Guan Y, Bongo LA, Burdine RD, Troyanskaya OG. Functional knowledge transfer for high-accuracy prediction of under-studied biological processes. Plos Computational Biology. 9: e1002957. PMID 23516347 DOI: 10.1371/journal.pcbi.1002957  1
2013 Guan Y, Dunham MJ, Troyanskaya OG, Caudy AA. Comparative gene expression between two yeast species. Bmc Genomics. 14: 33. PMID 23324262 DOI: 10.1186/1471-2164-14-33  1
2012 Greene CS, Troyanskaya OG. Chapter 2: Data-driven view of disease biology. Plos Computational Biology. 8: e1002816. PMID 23300408 DOI: 10.1371/journal.pcbi.1002816  1
2012 Guan Y, Gorenshteyn D, Burmeister M, Wong AK, Schimenti JC, Handel MA, Bult CJ, Hibbs MA, Troyanskaya OG. Tissue-specific functional networks for prioritizing phenotype and disease genes. Plos Computational Biology. 8: e1002694. PMID 23028291 DOI: 10.1371/journal.pcbi.1002694  1
2012 Nair VD, Ge Y, Balasubramaniyan N, Kim J, Okawa Y, Chikina M, Troyanskaya O, Sealfon SC. Involvement of histone demethylase LSD1 in short-time-scale gene expression changes during cell cycle progression in embryonic stem cells. Molecular and Cellular Biology. 32: 4861-76. PMID 23028048 DOI: 10.1128/MCB.00816-12  1
2012 Wong AK, Park CY, Greene CS, Bongo LA, Guan Y, Troyanskaya OG. IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks. Nucleic Acids Research. 40: W484-90. PMID 22684505 DOI: 10.1093/nar/gks458  1
2012 Greene CS, Troyanskaya OG. Accurate evaluation and analysis of functional genomics data and methods. Annals of the New York Academy of Sciences. 1260: 95-100. PMID 22268703 DOI: 10.1111/j.1749-6632.2011.06383.x  1
2012 Chikina MD, Troyanskaya OG. An effective statistical evaluation of ChIPseq dataset similarity. Bioinformatics (Oxford, England). 28: 607-13. PMID 22262674 DOI: 10.1093/bioinformatics/bts009  1
2012 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. Integrated molecular profiles of invasive breast tumors and ductal carcinoma in situ (DCIS) reveal differential vascular and interleukin signaling. Proceedings of the National Academy of Sciences of the United States of America. 109: 2802-7. PMID 21908711 DOI: 10.1073/pnas.1108781108  1
2011 Guan Y, Yao V, Tsui K, Gebbia M, Dunham MJ, Nislow C, Troyanskaya OG. Nucleosome-coupled expression differences in closely-related species. Bmc Genomics. 12: 466. PMID 21942931 DOI: 10.1186/1471-2164-12-466  1
2011 Greene CS, Troyanskaya OG. PILGRM: an interactive data-driven discovery platform for expert biologists. Nucleic Acids Research. 39: W368-74. PMID 21653547 DOI: 10.1093/nar/gkr440  1
2011 Chikina MD, Troyanskaya OG. Accurate quantification of functional analogy among close homologs. Plos Computational Biology. 7: e1001074. PMID 21304936 DOI: 10.1371/journal.pcbi.1001074  1
2011 Mungall CJ, Anderson D, Bandrowski A, Canada B, Chatyr-Aryamontri A, Cheng K, Conn PM, Dolinski K, Ellisman M, Eppig J, Grethe JS, Kemnitz J, Iadonato S, Larson SD, Magness C, ... ... Troyanskaya O, et al. An ontology-based approach to linking model organisms and resources to human diseases Ceur Workshop Proceedings. 833: 263-265.  1
2010 Pop A, Huttenhower C, Iyer-Pascuzzi A, Benfey PN, Troyanskaya OG. Integrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana. Bmc Systems Biology. 4: 180. PMID 21194434 DOI: 10.1186/1752-0509-4-180  0.8
2010 Markowetz F, Mulder KW, Airoldi EM, Lemischka IR, Troyanskaya OG. Mapping dynamic histone acetylation patterns to gene expression in nanog-depleted murine embryonic stem cells. Plos Computational Biology. 6: e1001034. PMID 21187909 DOI: 10.1371/journal.pcbi.1001034  1
2010 Park CY, Hess DC, Huttenhower C, Troyanskaya OG. Simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway components. Plos Computational Biology. 6: e1001009. PMID 21124865 DOI: 10.1371/journal.pcbi.1001009  1
2010 Guan Y, Ackert-Bicknell CL, Kell B, Troyanskaya OG, Hibbs MA. Functional genomics complements quantitative genetics in identifying disease-gene associations. Plos Computational Biology. 6: e1000991. PMID 21085640 DOI: 10.1371/journal.pcbi.1000991  1
2010 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, et al. Quantitative analysis of fitness and genetic interactions in yeast on a genome scale. Nature Methods. 7: 1017-24. PMID 21076421 DOI: 10.1038/nmeth.1534  1
2010 Greene CS, Troyanskaya OG. Integrative systems biology for data-driven knowledge discovery. Seminars in Nephrology. 30: 443-54. PMID 21044756 DOI: 10.1016/j.semnephrol.2010.07.002  1
2010 Guan Y, Dunham M, Caudy A, Troyanskaya O. Systematic planning of genome-scale experiments in poorly studied species Plos Computational Biology. 6. PMID 20221257 DOI: 10.1371/journal.pcbi.1000698  1
2010 Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear ED, Sevier CS, Ding H, Koh JL, Toufighi K, Mostafavi S, Prinz J, St Onge RP, VanderSluis B, Makhnevych T, Vizeacoumar FJ, ... ... Troyanskaya OG, et al. The genetic landscape of a cell. Science (New York, N.Y.). 327: 425-31. PMID 20093466 DOI: 10.1126/science.1180823  1
2009 Huttenhower C, Mehmood SO, Troyanskaya OG. Graphle: Interactive exploration of large, dense graphs. Bmc Bioinformatics. 10: 417. PMID 20003429 DOI: 10.1186/1471-2105-10-417  1
2009 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. Systems-level dynamic analyses of fate change in murine embryonic stem cells. Nature. 462: 358-62. PMID 19924215 DOI: 10.1038/nature08575  1
2009 Huttenhower C, Mutungu KT, Indik N, Yang W, Schroeder M, Forman JJ, Troyanskaya OG, Coller HA. Detailing regulatory networks through large scale data integration. Bioinformatics (Oxford, England). 25: 3267-74. PMID 19825796 DOI: 10.1093/bioinformatics/btp588  1
2009 Myers CL, Chiriac C, Troyanskaya OG. Discovering biological networks from diverse functional genomic data. Methods in Molecular Biology (Clifton, N.J.). 563: 157-75. PMID 19597785 DOI: 10.1007/978-1-60761-175-2_9  1
2009 Huttenhower C, Hibbs MA, Myers CL, Caudy AA, Hess DC, Troyanskaya OG. The impact of incomplete knowledge on evaluation: an experimental benchmark for protein function prediction. Bioinformatics (Oxford, England). 25: 2404-10. PMID 19561015 DOI: 10.1093/bioinformatics/btp397  1
2009 Chikina MD, Huttenhower C, Murphy CT, Troyanskaya OG. Global prediction of tissue-specific gene expression and context-dependent gene networks in Caenorhabditis elegans. Plos Computational Biology. 5: e1000417. PMID 19543383 DOI: 10.1371/journal.pcbi.1000417  1
2009 Huttenhower C, Myers CL, Hibbs MA, Troyanskaya OG. Computational analysis of the yeast proteome: understanding and exploiting functional specificity in genomic data. Methods in Molecular Biology (Clifton, N.J.). 548: 273-93. PMID 19521830 DOI: 10.1007/978-1-59745-540-4_15  1
2009 Hibbs MA, Myers CL, Huttenhower C, Hess DC, Li K, Caudy AA, Troyanskaya OG. Directing experimental biology: a case study in mitochondrial biogenesis. Plos Computational Biology. 5: e1000322. PMID 19300515 DOI: 10.1371/journal.pcbi.1000322  1
2009 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. Computationally driven, quantitative experiments discover genes required for mitochondrial biogenesis. Plos Genetics. 5: e1000407. PMID 19300474 DOI: 10.1371/journal.pgen.1000407  1
2009 Huttenhower C, Haley EM, Hibbs MA, Dumeaux V, Barrett DR, Coller HA, Troyanskaya OG. Exploring the human genome with functional maps. Genome Research. 19: 1093-106. PMID 19246570 DOI: 10.1101/gr.082214.108  1
2009 Butte AJ, Sarkar IN, Ramoni M, Lussier Y, Troyanskaya O. Selected proceedings of the First Summit on Translational Bioinformatics 2008 Bmc Bioinformatics. 10: I1. PMID 19208183 DOI: 10.1186/1471-2105-10-S7-I1  1
2009 Bradley PH, Brauer MJ, Rabinowitz JD, Troyanskaya OG. Coordinated concentration changes of transcripts and metabolites in Saccharomyces cerevisiae. Plos Computational Biology. 5: e1000270. PMID 19180179 DOI: 10.1371/journal.pcbi.1000270  1
2009 Airoldi EM, Huttenhower C, Gresham D, Lu C, Caudy AA, Dunham MJ, Broach JR, Botstein D, Troyanskaya OG. Predicting cellular growth from gene expression signatures. Plos Computational Biology. 5: e1000257. PMID 19119411 DOI: 10.1371/journal.pcbi.1000257  1
2009 Barutcuoglu Z, Airoldi EM, Dumeaux V, Schapire RE, Troyanskaya OG. Aneuploidy prediction and tumor classification with heterogeneous hidden conditional random fields. Bioinformatics (Oxford, England). 25: 1307-13. PMID 19052061 DOI: 10.1093/bioinformatics/btn585  1
2009 Rocke DM, Ideker T, Troyanskaya O, Quackenbush J, Dopazo J. Papers on normalization, variable selection, classification or clustering of microarray data Bioinformatics. 25: 701-702. DOI: 10.1093/bioinformatics/btp038  1
2008 Guan Y, Myers CL, Lu R, Lemischka IR, Bult CJ, Troyanskaya OG. A genomewide functional network for the laboratory mouse. Plos Computational Biology. 4: e1000165. PMID 18818725 DOI: 10.1371/journal.pcbi.1000165  1
2008 Guan Y, Myers CL, Hess DC, Barutcuoglu Z, Caudy AA, Troyanskaya OG. Predicting gene function in a hierarchical context with an ensemble of classifiers. Genome Biology. 9: S3. PMID 18613947 DOI: 10.1186/gb-2008-9-s1-s3  1
2008 Peña-Castillo L, Tasan M, Myers CL, Lee H, Joshi T, Zhang C, Guan Y, Leone M, Pagnani A, Kim WK, Krumpelman C, Tian W, Obozinski G, Qi Y, Mostafavi S, ... ... Troyanskaya OG, et al. A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biology. 9: S2. PMID 18613946 DOI: 10.1186/gb-2008-9-s1-s2  1
2008 Huttenhower C, Troyanskaya OG. Assessing the functional structure of genomic data. Bioinformatics (Oxford, England). 24: i330-8. PMID 18586732 DOI: 10.1093/bioinformatics/btn160  1
2008 Huttenhower C, Schroeder M, Chikina MD, Troyanskaya OG. The Sleipnir library for computational functional genomics. Bioinformatics (Oxford, England). 24: 1559-61. PMID 18499696 DOI: 10.1093/bioinformatics/btn237  1
2008 Brauer MJ, Huttenhower C, Airoldi EM, Rosenstein R, Matese JC, Gresham D, Boer VM, Troyanskaya OG, Botstein D. Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast. Molecular Biology of the Cell. 19: 352-67. PMID 17959824 DOI: 10.1091/mbc.E07-08-0779  1
2007 Troyanskaya OG. Integrated analysis of microarray results. Methods in Molecular Biology (Clifton, N.J.). 382: 429-37. PMID 18220247 DOI: 10.1007/978-1-59745-304-2_27  1
2007 Troyanskaya O. "Getting started in...": A series not to miss Plos Computational Biology. 3: 1841. PMID 17967055 DOI: 10.1371/journal.pcbi.0030224  1
2007 Hibbs MA, Hess DC, Myers CL, Huttenhower C, Li K, Troyanskaya OG. Exploring the functional landscape of gene expression: directed search of large microarray compendia. Bioinformatics (Oxford, England). 23: 2692-9. PMID 17724061 DOI: 10.1093/bioinformatics/btm403  1
2007 Markowetz F, Kostka D, Troyanskaya OG, Spang R. Nested effects models for high-dimensional phenotyping screens. Bioinformatics (Oxford, England). 23: i305-12. PMID 17646311 DOI: 10.1093/bioinformatics/btm178  1
2007 Huttenhower C, Flamholz AI, Landis JN, Sahi S, Myers CL, Olszewski KL, Hibbs MA, Siemers NO, Troyanskaya OG, Coller HA. Nearest Neighbor Networks: clustering expression data based on gene neighborhoods. Bmc Bioinformatics. 8: 250. PMID 17626636 DOI: 10.1186/1471-2105-8-250  1
2007 Myers CL, Troyanskaya OG. Context-sensitive data integration and prediction of biological networks. Bioinformatics (Oxford, England). 23: 2322-30. PMID 17599939 DOI: 10.1093/bioinformatics/btm332  1
2007 Markowetz F, Troyanskaya OG. Computational identification of cellular networks and pathways. Molecular Biosystems. 3: 478-82. PMID 17579773 DOI: 10.1039/b617014p  1
2007 Chi A, Huttenhower C, Geer LY, Coon JJ, Syka JE, Bai DL, Shabanowitz J, Burke DJ, Troyanskaya OG, Hunt DF. Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry. Proceedings of the National Academy of Sciences of the United States of America. 104: 2193-8. PMID 17287358 DOI: 10.1073/pnas.0607084104  1
2007 Haarer B, Viggiano S, Hibbs MA, Troyanskaya OG, Amberg DC. Modeling complex genetic interactions in a simple eukaryotic genome: actin displays a rich spectrum of complex haploinsufficiencies. Genes & Development. 21: 148-59. PMID 17167106 DOI: 10.1101/gad.1477507  1
2007 Guan Y, Dunham MJ, Troyanskaya OG. Functional analysis of gene duplications in Saccharomyces cerevisiae. Genetics. 175: 933-43. PMID 17151249 DOI: 10.1534/genetics.106.064329  1
2007 Hibbs M, Wallace G, Dunham M, Li K, Troyanskaya O. Viewing the larger context of genomic data through horizontal integration Proceedings of the International Conference On Information Visualisation. 326-332. DOI: 10.1109/IV.2007.120  1
2007 Wallace G, Hibbs M, Dunham M, Sealfon R, Troyanskaya O, Li K. Scalable, dynamic analysis and visualization for genomic datasets Proceedings - 21st International Parallel and Distributed Processing Symposium, Ipdps 2007; Abstracts and Cd-Rom. DOI: 10.1109/IPDPS.2007.370529  1
2007 Bongo LA, Wallace G, Larsen T, Li K, Troyanskaya O. Systems support for remote visualization of genomics applications over wide area networks Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4360: 157-174.  1
2006 Huttenhower C, Troyanskaya OG. Bayesian data integration: a functional perspective. Computational Systems Bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference. 341-51. PMID 17369653  1
2006 Sealfon RS, Hibbs MA, Huttenhower C, Myers CL, Troyanskaya OG. GOLEM: an interactive graph-based gene-ontology navigation and analysis tool. Bmc Bioinformatics. 7: 443. PMID 17032457 DOI: 10.1186/1471-2105-7-443  1
2006 Huttenhower C, Hibbs M, Myers C, Troyanskaya OG. A scalable method for integration and functional analysis of multiple microarray datasets. Bioinformatics (Oxford, England). 22: 2890-7. PMID 17005538 DOI: 10.1093/bioinformatics/btl492  1
2006 Myers CL, Barrett DR, Hibbs MA, Huttenhower C, Troyanskaya OG. Finding function: evaluation methods for functional genomic data. Bmc Genomics. 7: 187. PMID 16869964 DOI: 10.1186/1471-2164-7-187  1
2006 Brown JA, Sherlock G, Myers CL, Burrows NM, Deng C, Wu HI, McCann KE, Troyanskaya OG, Brown JM. Global analysis of gene function in yeast by quantitative phenotypic profiling. Molecular Systems Biology. 2: 2006.0001. PMID 16738548 DOI: 10.1038/msb4100043  1
2006 Barutcuoglu Z, Schapire RE, Troyanskaya OG. Hierarchical multi-label prediction of gene function. Bioinformatics (Oxford, England). 22: 830-6. PMID 16410319 DOI: 10.1093/bioinformatics/btk048  1
2005 Myers CL, Robson D, Wible A, Hibbs MA, Chiriac C, Theesfeld CL, Dolinski K, Troyanskaya OG. Discovery of biological networks from diverse functional genomic data. Genome Biology. 6: R114. PMID 16420673 DOI: 10.1186/gb-2005-6-13-r114  1
2005 Troyanskaya OG. Putting the 'bio' into bioinformatics. Genome Biology. 6: 351. PMID 16207369 DOI: 10.1186/gb-2005-6-10-351  1
2005 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, et al. Tools and applications for large-scale display walls. Ieee Computer Graphics and Applications. 25: 24-33. PMID 16060571 DOI: 10.1109/MCG.2005.89  1
2005 Myers CL, Chen X, Troyanskaya OG. Visualization-based discovery and analysis of genomic aberrations in microarray data. Bmc Bioinformatics. 6: 146. PMID 15953389 DOI: 10.1186/1471-2105-6-146  1
2005 Hibbs MA, Dirksen NC, Li K, Troyanskaya OG. Visualization methods for statistical analysis of microarray clusters. Bmc Bioinformatics. 6: 115. PMID 15890080 DOI: 10.1186/1471-2105-6-115  1
2005 Troyanskaya OG. Putting microarrays in a context: integrated analysis of diverse biological data. Briefings in Bioinformatics. 6: 34-43. PMID 15826355 DOI: 10.1093/bib/6.1.34  1
2005 Li K, Hibbs M, Wallace G, Troyanskaya O. Dynamic scalable visualization for collaborative scientific applications Proceedings - 19th Ieee International Parallel and Distributed Processing Symposium, Ipdps 2005. 2005. DOI: 10.1109/IPDPS.2005.183  1
2005 Huttenhower C, Troyanskaya O. A general methodology for integration of microarray data 2005 Ieee Computational Systems Bioinformatics Conference, Workshops and Poster Abstracts. 109. DOI: 10.1109/CSBW.2005.8  1
2005 Troyanskaya OG. Unsupervised Machine Learning to Support Functional Characterization of Genes: Emphasis on Cluster Description and Class Discovery Data Analysis and Visualization in Genomics and Proteomics. 175-192. DOI: 10.1002/0470094419.ch11  1
2004 Myers CL, Dunham MJ, Kung SY, Troyanskaya OG. Accurate detection of aneuploidies in array CGH and gene expression microarray data. Bioinformatics (Oxford, England). 20: 3533-43. PMID 15284100 DOI: 10.1093/bioinformatics/bth440  1
2004 Liang MP, Troyanskaya OG, Laederach A, Brutlag DL, Altman RB. Computational functional genomics Ieee Signal Processing Magazine. 21: 62-69. DOI: 10.1109/MSP.2004.1359143  1
2003 Whitfield ML, Finlay DR, Murray JI, Troyanskaya OG, Chi JT, Pergamenschikov A, McCalmont TH, Brown PO, Botstein D, Connolly MK. Systemic and cell type-specific gene expression patterns in scleroderma skin. Proceedings of the National Academy of Sciences of the United States of America. 100: 12319-24. PMID 14530402 DOI: 10.1073/pnas.1635114100  1
2003 Chi JT, Chang HY, Haraldsen G, Jahnsen FL, Troyanskaya OG, Chang DS, Wang Z, Rockson SG, van de Rijn M, Botstein D, Brown PO. Endothelial cell diversity revealed by global expression profiling. Proceedings of the National Academy of Sciences of the United States of America. 100: 10623-8. PMID 12963823 DOI: 10.1073/pnas.1434429100  1
2003 Schaner ME, Ross DT, Ciaravino G, Sorlie T, Troyanskaya O, Diehn M, Wang YC, Duran GE, Sikic TL, Caldeira S, Skomedal H, Tu IP, Hernandez-Boussard T, Johnson SW, O'Dwyer PJ, et al. Gene expression patterns in ovarian carcinomas. Molecular Biology of the Cell. 14: 4376-86. PMID 12960427 DOI: 10.1091/mbc.E03-05-0279  1
2003 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. Variation in gene expression patterns in human gastric cancers. Molecular Biology of the Cell. 14: 3208-15. PMID 12925757 DOI: 10.1091/mbc.E02-12-0833  1
2003 Troyanskaya OG, Dolinski K, Owen AB, Altman RB, Botstein D. A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae). Proceedings of the National Academy of Sciences of the United States of America. 100: 8348-53. PMID 12826619 DOI: 10.1073/pnas.0832373100  1
2003 Bohen SP, Troyanskaya OG, Alter O, Warnke R, Botstein D, Brown PO, Levy R. Variation in gene expression patterns in follicular lymphoma and the response to rituximab. Proceedings of the National Academy of Sciences of the United States of America. 100: 1926-30. PMID 12571354 DOI: 10.1073/pnas.0437875100  1
2002 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. Phospholipase A2 group IIA expression in gastric adenocarcinoma is associated with prolonged survival and less frequent metastasis. Proceedings of the National Academy of Sciences of the United States of America. 99: 16203-8. PMID 12456890 DOI: 10.1073/pnas.212646299  1
2002 Troyanskaya OG, Garber ME, Brown PO, Botstein D, Altman RB. Nonparametric methods for identifying differentially expressed genes in microarray data. Bioinformatics (Oxford, England). 18: 1454-61. PMID 12424116  1
2002 Troyanskaya OG, Arbell O, Koren Y, Landau GM, Bolshoy A. Sequence complexity profiles of prokaryotic genomic sequences: a fast algorithm for calculating linguistic complexity. Bioinformatics (Oxford, England). 18: 679-88. PMID 12050064  1
2001 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. Diversity of gene expression in adenocarcinoma of the lung. Proceedings of the National Academy of Sciences of the United States of America. 98: 13784-9. PMID 11707590 DOI: 10.1073/pnas.241500798  1
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