List of Faculty Publications

Below is a list of Faculty publications imported from PubMed or manually added. By default, publications are sorted by year with titles displayed in ascending alphabetical order.
Shortcuts: Wühr, Martin | Wingreen, Ned | Wieschaus, Eric | Troyanskaya, Olga | Tilghman, Shirley | Storey, John | Singh, Mona | Shvartsman, Stanislav | Shaevitz, Joshua | Rabinowitz, Joshua | Murphy, Coleen | Levine, Michael {Levine, Michael S.} | Gregor, Thomas | Botstein, David | Bialek, William | Ayroles, Julien | Andolfatto, Peter | Akey, Joshua

Filters: Author is Troyanskaya, Olga G  [Clear All Filters]
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Dosage Compensation, Genetic
Y. Guan, Dunham, M. J., and Troyanskaya, O. G., Functional analysis of gene duplications in Saccharomyces cerevisiae., Genetics, vol. 175, no. 2, pp. 933-43, 2007.
Disease
C. S. Greene and Troyanskaya, O. G., Chapter 2: Data-driven view of disease biology., PLoS Comput Biol, vol. 8, no. 12, p. e1002816, 2012.
Databases, Protein
Z. Barutcuoglu, Schapire, R. E., and Troyanskaya, O. G., Hierarchical multi-label prediction of gene function., Bioinformatics, vol. 22, no. 7, pp. 830-6, 2006.
M. A. Hibbs, Hess, D. C., Myers, C. L., Huttenhower, C., Li, K., and Troyanskaya, O. G., Exploring the functional landscape of gene expression: directed search of large microarray compendia., Bioinformatics, vol. 23, no. 20, pp. 2692-9, 2007.
C. Huttenhower, Mehmood, S. O., and Troyanskaya, O. G., Graphle: Interactive exploration of large, dense graphs., BMC Bioinformatics, vol. 10, p. 417, 2009.
C. Huttenhower, Myers, C. L., Hibbs, M. A., and Troyanskaya, O. G., Computational analysis of the yeast proteome: understanding and exploiting functional specificity in genomic data., Methods Mol Biol, vol. 548, pp. 273-93, 2009.
C. Huttenhower, Hibbs, M. A., Myers, C. L., Caudy, A. A., Hess, D. C., and Troyanskaya, O. G., The impact of incomplete knowledge on evaluation: an experimental benchmark for protein function prediction., Bioinformatics, vol. 25, no. 18, pp. 2404-10, 2009.
R. S. G. Sealfon, Hibbs, M. A., Huttenhower, C., Myers, C. L., and Troyanskaya, O. G., GOLEM: an interactive graph-based gene-ontology navigation and analysis tool., BMC Bioinformatics, vol. 7, p. 443, 2006.
C. L. Myers and Troyanskaya, O. G., Context-sensitive data integration and prediction of biological networks., Bioinformatics, vol. 23, no. 17, pp. 2322-30, 2007.
Databases, Genetic
C. Huttenhower, Flamholz, A. I., Landis, J. N., Sahi, S., Myers, C. L., Olszewski, K. L., Hibbs, M. A., Siemers, N. O., Troyanskaya, O. G., and Coller, H. A., Nearest Neighbor Networks: clustering expression data based on gene neighborhoods., BMC Bioinformatics, vol. 8, p. 250, 2007.
C. Y. Park, Hess, D. C., Huttenhower, C., and Troyanskaya, O. G., Simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway components., PLoS Comput Biol, vol. 6, no. 11, p. e1001009, 2010.
Y. Guan, Myers, C. L., Lu, R., Lemischka, I. R., Bult, C. J., and Troyanskaya, O. G., A genomewide functional network for the laboratory mouse., PLoS Comput Biol, vol. 4, no. 9, p. e1000165, 2008.
W. Ju, Greene, C. S., Eichinger, F., Nair, V., Hodgin, J. B., Bitzer, M., Lee, Y. -suk, Zhu, Q., Kehata, M., Li, M., Jiang, S., Rastaldi, M. Pia, Cohen, C. D., Troyanskaya, O. G., and Kretzler, M., Defining cell-type specificity at the transcriptional level in human disease., Genome Res, vol. 23, no. 11, pp. 1862-73, 2013.
O. G. Troyanskaya, Integrated analysis of microarray results., Methods Mol Biol, vol. 382, pp. 429-37, 2007.
C. L. Myers, Chiriac, C., and Troyanskaya, O. G., Discovering biological networks from diverse functional genomic data., Methods Mol Biol, vol. 563, pp. 157-75, 2009.
O. G. Troyanskaya, Putting the 'bio' into bioinformatics., Genome Biol, vol. 6, no. 10, p. 351, 2005.
V. N. Kristensen, Vaske, C. J., Ursini-Siegel, J., Van Loo, P., Nordgard, S. H., Sachidanandam, R., Sørlie, T., Wärnberg, F., Haakensen, V. D., Helland, Å., Naume, B., Perou, C. M., Haussler, D., Troyanskaya, O. G., and Børresen-Dale, A. - L., Integrated molecular profiles of invasive breast tumors and ductal carcinoma in situ (DCIS) reveal differential vascular and interleukin signaling., Proc Natl Acad Sci U S A, vol. 109, no. 8, pp. 2802-7, 2012.
C. Huttenhower, Myers, C. L., Hibbs, M. A., and Troyanskaya, O. G., Computational analysis of the yeast proteome: understanding and exploiting functional specificity in genomic data., Methods Mol Biol, vol. 548, pp. 273-93, 2009.
O. G. Troyanskaya, Arbell, O., Koren, Y., Landau, G. M., and Bolshoy, A., Sequence complexity profiles of prokaryotic genomic sequences: a fast algorithm for calculating linguistic complexity., Bioinformatics, vol. 18, no. 5, pp. 679-88, 2002.
C. L. Myers, Barrett, D. R., Hibbs, M. A., Huttenhower, C., and Troyanskaya, O. G., Finding function: evaluation methods for functional genomic data., BMC Genomics, vol. 7, p. 187, 2006.
Y. Guan, Ackert-Bicknell, C. L., Kell, B., Troyanskaya, O. G., and Hibbs, M. A., Functional genomics complements quantitative genetics in identifying disease-gene associations., PLoS Comput Biol, vol. 6, no. 11, p. e1000991, 2010.
C. S. Greene and Troyanskaya, O. G., PILGRM: an interactive data-driven discovery platform for expert biologists., Nucleic Acids Res, vol. 39, no. Web Server issue, pp. W368-74, 2011.
C. S. Greene and Troyanskaya, O. G., Accurate evaluation and analysis of functional genomics data and methods., Ann N Y Acad Sci, vol. 1260, pp. 95-100, 2012.
O. G. Troyanskaya, Putting microarrays in a context: integrated analysis of diverse biological data., Brief Bioinform, vol. 6, no. 1, pp. 34-43, 2005.
C. Huttenhower, Schroeder, M., Chikina, M. D., and Troyanskaya, O. G., The Sleipnir library for computational functional genomics., Bioinformatics, vol. 24, no. 13, pp. 1559-61, 2008.
M. A. Hibbs, Dirksen, N. C., Li, K., and Troyanskaya, O. G., Visualization methods for statistical analysis of microarray clusters., BMC Bioinformatics, vol. 6, p. 115, 2005.
C. Huttenhower, Hibbs, M., Myers, C., and Troyanskaya, O. G., A scalable method for integration and functional analysis of multiple microarray datasets., Bioinformatics, vol. 22, no. 23, pp. 2890-7, 2006.
Data Mining
C. S. Greene and Troyanskaya, O. G., PILGRM: an interactive data-driven discovery platform for expert biologists., Nucleic Acids Res, vol. 39, no. Web Server issue, pp. W368-74, 2011.
Computer Simulation
O. G. Troyanskaya, Garber, M. E., Brown, P. O., Botstein, D., and Altman, R. B., Nonparametric methods for identifying differentially expressed genes in microarray data., Bioinformatics, vol. 18, no. 11, pp. 1454-61, 2002.
W. Ju, Greene, C. S., Eichinger, F., Nair, V., Hodgin, J. B., Bitzer, M., Lee, Y. -suk, Zhu, Q., Kehata, M., Li, M., Jiang, S., Rastaldi, M. Pia, Cohen, C. D., Troyanskaya, O. G., and Kretzler, M., Defining cell-type specificity at the transcriptional level in human disease., Genome Res, vol. 23, no. 11, pp. 1862-73, 2013.
E. M. Airoldi, Huttenhower, C., Gresham, D., Lu, C., Caudy, A. A., Dunham, M. J., Broach, J. R., Botstein, D., and Troyanskaya, O. G., Predicting cellular growth from gene expression signatures., PLoS Comput Biol, vol. 5, no. 1, p. e1000257, 2009.
M. D. Chikina, Huttenhower, C., Murphy, C. T., and Troyanskaya, O. G., Global prediction of tissue-specific gene expression and context-dependent gene networks in Caenorhabditis elegans., PLoS Comput Biol, vol. 5, no. 6, p. e1000417, 2009.
J. Zhou, Schor, I. E., Yao, V., Theesfeld, C. L., Marco-Ferreres, R., Tadych, A., Furlong, E. E. M., and Troyanskaya, O. G., Accurate genome-wide predictions of spatio-temporal gene expression during embryonic development., PLoS Genet, vol. 15, no. 9, p. e1008382, 2019.
J. Zhou, Theesfeld, C. L., Yao, K., Chen, K. M., Wong, A. K., and Troyanskaya, O. G., Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk., Nat Genet, vol. 50, no. 8, pp. 1171-1179, 2018.
M. A. Hibbs, Myers, C. L., Huttenhower, C., Hess, D. C., Li, K., Caudy, A. A., and Troyanskaya, O. G., Directing experimental biology: a case study in mitochondrial biogenesis., PLoS Comput Biol, vol. 5, no. 3, p. e1000322, 2009.
Y. Guan, Gorenshteyn, D., Burmeister, M., Wong, A. K., Schimenti, J. C., Handel, M. Ann, Bult, C. J., Hibbs, M. A., and Troyanskaya, O. G., Tissue-specific functional networks for prioritizing phenotype and disease genes., PLoS Comput Biol, vol. 8, no. 9, p. e1002694, 2012.
Computational Biology
C. L. Myers, Robson, D., Wible, A., Hibbs, M. A., Chiriac, C., Theesfeld, C. L., Dolinski, K., and Troyanskaya, O. G., Discovery of biological networks from diverse functional genomic data., Genome Biol, vol. 6, no. 13, p. R114, 2005.
J. Zhou and Troyanskaya, O. G., Global quantitative modeling of chromatin factor interactions., PLoS Comput Biol, vol. 10, no. 3, p. e1003525, 2014.
Y. Guan, Myers, C. L., Lu, R., Lemischka, I. R., Bult, C. J., and Troyanskaya, O. G., A genomewide functional network for the laboratory mouse., PLoS Comput Biol, vol. 4, no. 9, p. e1000165, 2008.
Z. Barutcuoglu, Schapire, R. E., and Troyanskaya, O. G., Hierarchical multi-label prediction of gene function., Bioinformatics, vol. 22, no. 7, pp. 830-6, 2006.
C. Y. Park, Wong, A. K., Greene, C. S., Rowland, J., Guan, Y., Bongo, L. A., Burdine, R. D., and Troyanskaya, O. G., Functional knowledge transfer for high-accuracy prediction of under-studied biological processes., PLoS Comput Biol, vol. 9, no. 3, p. e1002957, 2013.
W. Ju, Greene, C. S., Eichinger, F., Nair, V., Hodgin, J. B., Bitzer, M., Lee, Y. -suk, Zhu, Q., Kehata, M., Li, M., Jiang, S., Rastaldi, M. Pia, Cohen, C. D., Troyanskaya, O. G., and Kretzler, M., Defining cell-type specificity at the transcriptional level in human disease., Genome Res, vol. 23, no. 11, pp. 1862-73, 2013.
F. Markowetz and Troyanskaya, O. G., Computational identification of cellular networks and pathways., Mol Biosyst, vol. 3, no. 7, pp. 478-82, 2007.
J. Zhou, Park, C. Y., Theesfeld, C. L., Wong, A. K., Yuan, Y., Scheckel, C., Fak, J. J., Funk, J., Yao, K., Tajima, Y., Packer, A., Darnell, R. B., and Troyanskaya, O. G., Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk., Nat Genet, vol. 51, no. 6, pp. 973-980, 2019.
C. Huttenhower, Mehmood, S. O., and Troyanskaya, O. G., Graphle: Interactive exploration of large, dense graphs., BMC Bioinformatics, vol. 10, p. 417, 2009.
C. L. Myers, Barrett, D. R., Hibbs, M. A., Huttenhower, C., and Troyanskaya, O. G., Finding function: evaluation methods for functional genomic data., BMC Genomics, vol. 7, p. 187, 2006.
D. Gorenshteyn, Zaslavsky, E., Fribourg, M., Park, C. Y., Wong, A. K., Tadych, A., Hartmann, B. M., Albrecht, R. A., García-Sastre, A., Kleinstein, S. H., Troyanskaya, O. G., and Sealfon, S. C., Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases., Immunity, vol. 43, no. 3, pp. 605-14, 2015.
C. Huttenhower, Myers, C. L., Hibbs, M. A., and Troyanskaya, O. G., Computational analysis of the yeast proteome: understanding and exploiting functional specificity in genomic data., Methods Mol Biol, vol. 548, pp. 273-93, 2009.
J. Zhou, Schor, I. E., Yao, V., Theesfeld, C. L., Marco-Ferreres, R., Tadych, A., Furlong, E. E. M., and Troyanskaya, O. G., Accurate genome-wide predictions of spatio-temporal gene expression during embryonic development., PLoS Genet, vol. 15, no. 9, p. e1008382, 2019.
C. Huttenhower and Troyanskaya, O. G., Bayesian data integration: a functional perspective., Comput Syst Bioinformatics Conf, pp. 341-51, 2006.
M. D. Chikina and Troyanskaya, O. G., Accurate quantification of functional analogy among close homologs., PLoS Comput Biol, vol. 7, no. 2, p. e1001074, 2011.
O. G. Troyanskaya, Putting the 'bio' into bioinformatics., Genome Biol, vol. 6, no. 10, p. 351, 2005.
Y. -suk Lee, Krishnan, A., Zhu, Q., and Troyanskaya, O. G., Ontology-aware classification of tissue and cell-type signals in gene expression profiles across platforms and technologies., Bioinformatics, vol. 29, no. 23, pp. 3036-44, 2013.
M. A. Hibbs, Dirksen, N. C., Li, K., and Troyanskaya, O. G., Visualization methods for statistical analysis of microarray clusters., BMC Bioinformatics, vol. 6, p. 115, 2005.
C. Huttenhower, Hibbs, M. A., Myers, C. L., Caudy, A. A., Hess, D. C., and Troyanskaya, O. G., The impact of incomplete knowledge on evaluation: an experimental benchmark for protein function prediction., Bioinformatics, vol. 25, no. 18, pp. 2404-10, 2009.
M. Costanzo, Baryshnikova, A., Bellay, J., Kim, Y., Spear, E. D., Sevier, C. S., Ding, H., L Y Koh, J., Toufighi, K., Mostafavi, S., Prinz, J., St Onge, R. P., VanderSluis, B., Makhnevych, T., Vizeacoumar, F. J., Alizadeh, S., Bahr, S., Brost, R. L., Chen, Y., Cokol, M., Deshpande, R., Li, Z., Lin, Z. - Y., Liang, W., Marback, M., Paw, J., San Luis, B. - J., Shuteriqi, E., Tong, A. Hin Yan, van Dyk, N., Wallace, I. M., Whitney, J. A., Weirauch, M. T., Zhong, G., Zhu, H., Houry, W. A., Brudno, M., Ragibizadeh, S., Papp, B., Pál, C., Roth, F. P., Giaever, G., Nislow, C., Troyanskaya, O. G., Bussey, H., Bader, G. D., Gingras, A. - C., Morris, Q. D., Kim, P. M., Kaiser, C. A., Myers, C. L., Andrews, B. J., and Boone, C., The genetic landscape of a cell., Science, vol. 327, no. 5964, pp. 425-31, 2010.
C. L. Myers and Troyanskaya, O. G., Context-sensitive data integration and prediction of biological networks., Bioinformatics, vol. 23, no. 17, pp. 2322-30, 2007.
C. Huttenhower, Schroeder, M., Chikina, M. D., and Troyanskaya, O. G., The Sleipnir library for computational functional genomics., Bioinformatics, vol. 24, no. 13, pp. 1559-61, 2008.
Z. Barutcuoglu, Airoldi, E. M., Dumeaux, V., Schapire, R. E., and Troyanskaya, O. G., Aneuploidy prediction and tumor classification with heterogeneous hidden conditional random fields., Bioinformatics, vol. 25, no. 10, pp. 1307-13, 2009.
K. M. Chen, Cofer, E. M., Zhou, J., and Troyanskaya, O. G., Selene: a PyTorch-based deep learning library for sequence data., Nat Methods, vol. 16, no. 4, pp. 315-318, 2019.
C. Huttenhower, Haley, E. M., Hibbs, M. A., Dumeaux, V., Barrett, D. R., Coller, H. A., and Troyanskaya, O. G., Exploring the human genome with functional maps., Genome Res, vol. 19, no. 6, pp. 1093-106, 2009.
F. Markowetz, Mulder, K. W., Airoldi, E. M., Lemischka, I. R., and Troyanskaya, O. G., Mapping dynamic histone acetylation patterns to gene expression in nanog-depleted murine embryonic stem cells., PLoS Comput Biol, vol. 6, no. 12, p. e1001034, 2010.
C. Huttenhower, K Mutungu, T., Indik, N., Yang, W., Schroeder, M., Forman, J. J., Troyanskaya, O. G., and Coller, H. A., Detailing regulatory networks through large scale data integration., Bioinformatics, vol. 25, no. 24, pp. 3267-74, 2009.
A. Pop, Huttenhower, C., Iyer-Pascuzzi, A., Benfey, P. N., and Troyanskaya, O. G., Integrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana., BMC Syst Biol, vol. 4, p. 180, 2010.
C. L. Myers, Chen, X., and Troyanskaya, O. G., Visualization-based discovery and analysis of genomic aberrations in microarray data., BMC Bioinformatics, vol. 6, p. 146, 2005.
Cluster Analysis
C. Huttenhower, Flamholz, A. I., Landis, J. N., Sahi, S., Myers, C. L., Olszewski, K. L., Hibbs, M. A., Siemers, N. O., Troyanskaya, O. G., and Coller, H. A., Nearest Neighbor Networks: clustering expression data based on gene neighborhoods., BMC Bioinformatics, vol. 8, p. 250, 2007.
C. Y. Park, Hess, D. C., Huttenhower, C., and Troyanskaya, O. G., Simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway components., PLoS Comput Biol, vol. 6, no. 11, p. e1001009, 2010.
Y. Guan, Ackert-Bicknell, C. L., Kell, B., Troyanskaya, O. G., and Hibbs, M. A., Functional genomics complements quantitative genetics in identifying disease-gene associations., PLoS Comput Biol, vol. 6, no. 11, p. e1000991, 2010.
M. A. Hibbs, Dirksen, N. C., Li, K., and Troyanskaya, O. G., Visualization methods for statistical analysis of microarray clusters., BMC Bioinformatics, vol. 6, p. 115, 2005.
J. A. Brown, Sherlock, G., Myers, C. L., Burrows, N. M., Deng, C., H Wu, I., McCann, K. E., Troyanskaya, O. G., and J Brown, M., Global analysis of gene function in yeast by quantitative phenotypic profiling., Mol Syst Biol, vol. 2, p. 2006.0001, 2006.
F. Markowetz, Mulder, K. W., Airoldi, E. M., Lemischka, I. R., and Troyanskaya, O. G., Mapping dynamic histone acetylation patterns to gene expression in nanog-depleted murine embryonic stem cells., PLoS Comput Biol, vol. 6, no. 12, p. e1001034, 2010.
C. Huttenhower, K Mutungu, T., Indik, N., Yang, W., Schroeder, M., Forman, J. J., Troyanskaya, O. G., and Coller, H. A., Detailing regulatory networks through large scale data integration., Bioinformatics, vol. 25, no. 24, pp. 3267-74, 2009.
M. J. Brauer, Huttenhower, C., Airoldi, E. M., Rosenstein, R., Matese, J. C., Gresham, D., Boer, V. M., Troyanskaya, O. G., and Botstein, D., Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast., Mol Biol Cell, vol. 19, no. 1, pp. 352-67, 2008.
Y. Guan, Myers, C. L., Lu, R., Lemischka, I. R., Bult, C. J., and Troyanskaya, O. G., A genomewide functional network for the laboratory mouse., PLoS Comput Biol, vol. 4, no. 9, p. e1000165, 2008.
Chromatin Immunoprecipitation
M. D. Chikina and Troyanskaya, O. G., An effective statistical evaluation of ChIPseq dataset similarity., Bioinformatics, vol. 28, no. 5, pp. 607-13, 2012.
Cell Line
C. S. Greene and Troyanskaya, O. G., Chapter 2: Data-driven view of disease biology., PLoS Comput Biol, vol. 8, no. 12, p. e1002816, 2012.
Cell Differentiation
Y. Guan, Myers, C. L., Lu, R., Lemischka, I. R., Bult, C. J., and Troyanskaya, O. G., A genomewide functional network for the laboratory mouse., PLoS Comput Biol, vol. 4, no. 9, p. e1000165, 2008.
W. Ju, Greene, C. S., Eichinger, F., Nair, V., Hodgin, J. B., Bitzer, M., Lee, Y. -suk, Zhu, Q., Kehata, M., Li, M., Jiang, S., Rastaldi, M. Pia, Cohen, C. D., Troyanskaya, O. G., and Kretzler, M., Defining cell-type specificity at the transcriptional level in human disease., Genome Res, vol. 23, no. 11, pp. 1862-73, 2013.
R. Lu, Markowetz, F., Unwin, R. D., Leek, J. T., Airoldi, E. M., MacArthur, B. D., Lachmann, A., Rozov, R., Ma'ayan, A., Boyer, L. A., Troyanskaya, O. G., Whetton, A. D., and Lemischka, I. R., Systems-level dynamic analyses of fate change in murine embryonic stem cells., Nature, vol. 462, no. 7271, pp. 358-62, 2009.
C. J. Nirschl, Suárez-Fariñas, M., Izar, B., Prakadan, S., Dannenfelser, R., Tirosh, I., Liu, Y., Zhu, Q., K Devi, S. P., Carroll, S. L., Chau, D., Rezaee, M., Kim, T. - G., Huang, R., Fuentes-Duculan, J., Song-Zhao, G. X., Gulati, N., Lowes, M. A., King, S. L., Quintana, F. J., Lee, Y. -suk, Krueger, J. G., Sarin, K. Y., Yoon, C. H., Garraway, L., Regev, iv, A., Shalek, A. K., Troyanskaya, O. G., and Anandasabapathy, N., IFNγ-Dependent Tissue-Immune Homeostasis Is Co-opted in the Tumor Microenvironment., Cell, vol. 170, no. 1, pp. 127-141.e15, 2017.
Bayes Theorem
C. Huttenhower, K Mutungu, T., Indik, N., Yang, W., Schroeder, M., Forman, J. J., Troyanskaya, O. G., and Coller, H. A., Detailing regulatory networks through large scale data integration., Bioinformatics, vol. 25, no. 24, pp. 3267-74, 2009.
A. Pop, Huttenhower, C., Iyer-Pascuzzi, A., Benfey, P. N., and Troyanskaya, O. G., Integrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana., BMC Syst Biol, vol. 4, p. 180, 2010.
C. Huttenhower, Hibbs, M., Myers, C., and Troyanskaya, O. G., A scalable method for integration and functional analysis of multiple microarray datasets., Bioinformatics, vol. 22, no. 23, pp. 2890-7, 2006.
Y. Guan, Myers, C. L., Hess, D. C., Barutcuoglu, Z., Caudy, A. A., and Troyanskaya, O. G., Predicting gene function in a hierarchical context with an ensemble of classifiers., Genome Biol, vol. 9 Suppl 1, p. S3, 2008.
C. S. Greene and Troyanskaya, O. G., Integrative systems biology for data-driven knowledge discovery., Semin Nephrol, vol. 30, no. 5, pp. 443-54, 2010.
Y. Guan, Dunham, M. J., and Troyanskaya, O. G., Functional analysis of gene duplications in Saccharomyces cerevisiae., Genetics, vol. 175, no. 2, pp. 933-43, 2007.
C. L. Myers, Robson, D., Wible, A., Hibbs, M. A., Chiriac, C., Theesfeld, C. L., Dolinski, K., and Troyanskaya, O. G., Discovery of biological networks from diverse functional genomic data., Genome Biol, vol. 6, no. 13, p. R114, 2005.
Z. Barutcuoglu, Schapire, R. E., and Troyanskaya, O. G., Hierarchical multi-label prediction of gene function., Bioinformatics, vol. 22, no. 7, pp. 830-6, 2006.
C. Y. Park, Wong, A. K., Greene, C. S., Rowland, J., Guan, Y., Bongo, L. A., Burdine, R. D., and Troyanskaya, O. G., Functional knowledge transfer for high-accuracy prediction of under-studied biological processes., PLoS Comput Biol, vol. 9, no. 3, p. e1002957, 2013.
O. G. Troyanskaya, Dolinski, K., Owen, A. B., Altman, R. B., and Botstein, D., A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae)., Proc Natl Acad Sci U S A, vol. 100, no. 14, pp. 8348-53, 2003.
C. Y. Park, Hess, D. C., Huttenhower, C., and Troyanskaya, O. G., Simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway components., PLoS Comput Biol, vol. 6, no. 11, p. e1001009, 2010.
Y. Guan, Myers, C. L., Lu, R., Lemischka, I. R., Bult, C. J., and Troyanskaya, O. G., A genomewide functional network for the laboratory mouse., PLoS Comput Biol, vol. 4, no. 9, p. e1000165, 2008.
P. H. Bradley, Brauer, M. J., Rabinowitz, J. D., and Troyanskaya, O. G., Coordinated concentration changes of transcripts and metabolites in Saccharomyces cerevisiae., PLoS Comput Biol, vol. 5, no. 1, p. e1000270, 2009.
M. D. Chikina and Troyanskaya, O. G., Accurate quantification of functional analogy among close homologs., PLoS Comput Biol, vol. 7, no. 2, p. e1001074, 2011.
D. Gorenshteyn, Zaslavsky, E., Fribourg, M., Park, C. Y., Wong, A. K., Tadych, A., Hartmann, B. M., Albrecht, R. A., García-Sastre, A., Kleinstein, S. H., Troyanskaya, O. G., and Sealfon, S. C., Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases., Immunity, vol. 43, no. 3, pp. 605-14, 2015.
Y. -suk Lee, Krishnan, A., Zhu, Q., and Troyanskaya, O. G., Ontology-aware classification of tissue and cell-type signals in gene expression profiles across platforms and technologies., Bioinformatics, vol. 29, no. 23, pp. 3036-44, 2013.
C. Huttenhower and Troyanskaya, O. G., Bayesian data integration: a functional perspective., Comput Syst Bioinformatics Conf, pp. 341-51, 2006.
Y. Guan, Ackert-Bicknell, C. L., Kell, B., Troyanskaya, O. G., and Hibbs, M. A., Functional genomics complements quantitative genetics in identifying disease-gene associations., PLoS Comput Biol, vol. 6, no. 11, p. e1000991, 2010.
C. Huttenhower, Haley, E. M., Hibbs, M. A., Dumeaux, V., Barrett, D. R., Coller, H. A., and Troyanskaya, O. G., Exploring the human genome with functional maps., Genome Res, vol. 19, no. 6, pp. 1093-106, 2009.
C. S. Greene and Troyanskaya, O. G., Chapter 2: Data-driven view of disease biology., PLoS Comput Biol, vol. 8, no. 12, p. e1002816, 2012.

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