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: First Letter Of Keyword is M and Author is Troyanskaya, Olga G  [Clear All Filters]
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 
A
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.
B
C. Huttenhower and Troyanskaya, O. G., “Bayesian data integration: a functional perspective.”, Comput Syst Bioinformatics Conf, pp. 341-51, 2006.
C
F. Markowetz and Troyanskaya, O. G., “Computational identification of cellular networks and pathways.”, Mol Biosyst, vol. 3, no. 7, pp. 478-82, 2007.
D. C. Hess, Myers, C. L., Huttenhower, C., Hibbs, M. A., Hayes, A. P., Paw, J., Clore, J. J., Mendoza, R. M., San Luis, B., Nislow, C., Giaever, G., Costanzo, M., Troyanskaya, O. G., and Caudy, A. A., “Computationally driven, quantitative experiments discover genes required for mitochondrial biogenesis.”, PLoS Genet, vol. 5, no. 3, p. e1000407, 2009.
D. C. Hess, Myers, C. L., Huttenhower, C., Hibbs, M. A., Hayes, A. P., Paw, J., Clore, J. J., Mendoza, R. M., San Luis, B., Nislow, C., Giaever, G., Costanzo, M., Troyanskaya, O. G., and Caudy, A. A., “Computationally driven, quantitative experiments discover genes required for mitochondrial biogenesis.”, PLoS Genet, vol. 5, no. 3, p. e1000407, 2009.
D. C. Hess, Myers, C. L., Huttenhower, C., Hibbs, M. A., Hayes, A. P., Paw, J., Clore, J. J., Mendoza, R. M., San Luis, B., Nislow, C., Giaever, G., Costanzo, M., Troyanskaya, O. G., and Caudy, A. A., “Computationally driven, quantitative experiments discover genes required for mitochondrial biogenesis.”, PLoS Genet, vol. 5, no. 3, p. e1000407, 2009.
D. C. Hess, Myers, C. L., Huttenhower, C., Hibbs, M. A., Hayes, A. P., Paw, J., Clore, J. J., Mendoza, R. M., San Luis, B., Nislow, C., Giaever, G., Costanzo, M., Troyanskaya, O. G., and Caudy, A. A., “Computationally driven, quantitative experiments discover genes required for mitochondrial biogenesis.”, PLoS Genet, vol. 5, no. 3, p. e1000407, 2009.
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. 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.
L. Peña-Castillo, Tasan, M., Myers, C. L., Lee, H., Joshi, T., Zhang, C., Guan, Y., Leone, M., Pagnani, A., Kim, W. Kyu, Krumpelman, C., Tian, W., Obozinski, G., Qi, Y., Mostafavi, S., Lin, G. Ning, Berriz, G. F., Gibbons, F. D., Lanckriet, G., Qiu, J., Grant, C., Barutcuoglu, Z., Hill, D. P., Warde-Farley, D., Grouios, C., Ray, D., Blake, J. A., Deng, M., Jordan, M. I., Noble, W. S., Morris, Q., Klein-Seetharaman, J., Bar-Joseph, iv, Z., Chen, T., Sun, F., Troyanskaya, O. G., Marcotte, E. M., Xu, D., Hughes, T. R., and Roth, F. P., “A critical assessment of Mus musculus gene function prediction using integrated genomic evidence.”, Genome Biol, vol. 9 Suppl 1, p. S2, 2008.
D
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.
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.
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.
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.
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.
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.
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.
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.
E
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
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.
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. 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.
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.
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.
G
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.
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.
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.
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.
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.
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.
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.
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.
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 and Troyanskaya, O. G., “Global quantitative modeling of chromatin factor interactions.”, PLoS Comput Biol, vol. 10, no. 3, p. e1003525, 2014.
C. Huttenhower, Mehmood, S. O., and Troyanskaya, O. G., “Graphle: Interactive exploration of large, dense graphs.”, BMC Bioinformatics, vol. 10, p. 417, 2009.
H
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.
I
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.
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.
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.
A. K. Wong, Park, C. Y., Greene, C. S., Bongo, L. A., Guan, Y., and Troyanskaya, O. G., “IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks.”, Nucleic Acids Res, vol. 40, no. Web Server issue, pp. W484-90, 2012.
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.
O. G. Troyanskaya, “Integrated analysis of microarray results.”, Methods Mol Biol, vol. 382, pp. 429-37, 2007.
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.
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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.
B. Haarer, Viggiano, S., Hibbs, M. A., Troyanskaya, O. G., and Amberg, D. C., “Modeling complex genetic interactions in a simple eukaryotic genome: actin displays a rich spectrum of complex haploinsufficiencies.”, Genes Dev, vol. 21, no. 2, pp. 148-59, 2007.
B. Haarer, Viggiano, S., Hibbs, M. A., Troyanskaya, O. G., and Amberg, D. C., “Modeling complex genetic interactions in a simple eukaryotic genome: actin displays a rich spectrum of complex haploinsufficiencies.”, Genes Dev, vol. 21, no. 2, pp. 148-59, 2007.
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F. Markowetz, Kostka, D., Troyanskaya, O. G., and Spang, R., “Nested effects models for high-dimensional phenotyping screens.”, Bioinformatics, vol. 23, no. 13, pp. i305-12, 2007.
A. A. Caudy, Guan, Y., Jia, Y., Hansen, C., DeSevo, C., Hayes, A. P., Agee, J., Alvarez-Dominguez, J. R., Arellano, H., Barrett, D., Bauerle, C., Bisaria, N., Bradley, P. H., J Breunig, S., Bush, E., Cappel, D., Capra, E., Chen, W., Clore, J., Combs, P. A., Doucette, C., Demuren, O., Fellowes, P., Freeman, S., Frenkel, E., Gadala-Maria, D., Gawande, R., Glass, D., Grossberg, S., Gupta, A., Hammonds-Odie, L., Hoisos, A., Hsi, J., Hsu, Y. - H. Huang, Inukai, S., Karczewski, K. J., Ke, X., Kojima, M., Leachman, S., Lieber, D., Liebowitz, A., Liu, J., Liu, Y., Martin, T., Mena, J., Mendoza, R., Myhrvold, C., Millian, C., Pfau, S., Raj, S., Rich, M., Rokicki, J., Rounds, W., Salazar, M., Salesi, M., Sharma, R., Silverman, S., Singer, C., Sinha, S., Staller, M., Stern, P., Tang, H., Weeks, S., Weidmann, M., Wolf, A., Young, C., Yuan, J., Crutchfield, C., McClean, M., Murphy, C. T., Llinás, M., Botstein, D., Troyanskaya, O. G., and Dunham, M. J., “A new system for comparative functional genomics of Saccharomyces yeasts.”, Genetics, vol. 195, no. 1, pp. 275-87, 2013.
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.
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.
O
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.
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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.
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.
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.
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.
O. G. Troyanskaya, “Putting microarrays in a context: integrated analysis of diverse biological data.”, Brief Bioinform, vol. 6, no. 1, pp. 34-43, 2005.
O. G. Troyanskaya, “Putting the 'bio' into bioinformatics.”, Genome Biol, vol. 6, no. 10, p. 351, 2005.
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A. Baryshnikova, Costanzo, M., Kim, Y., Ding, H., Koh, J., Toufighi, K., Youn, J. - Y., Ou, J., San Luis, B. - J., Bandyopadhyay, S., Hibbs, M., Hess, D., Gingras, A. - C., Bader, G. D., Troyanskaya, O. G., Brown, G. W., Andrews, B., Boone, C., and Myers, C. L., “Quantitative analysis of fitness and genetic interactions in yeast on a genome scale.”, Nat Methods, vol. 7, no. 12, pp. 1017-24, 2010.
A. Baryshnikova, Costanzo, M., Kim, Y., Ding, H., Koh, J., Toufighi, K., Youn, J. - Y., Ou, J., San Luis, B. - J., Bandyopadhyay, S., Hibbs, M., Hess, D., Gingras, A. - C., Bader, G. D., Troyanskaya, O. G., Brown, G. W., Andrews, B., Boone, C., and Myers, C. L., “Quantitative analysis of fitness and genetic interactions in yeast on a genome scale.”, Nat Methods, vol. 7, no. 12, pp. 1017-24, 2010.
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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.
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.
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.
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.
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. 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.
M. L. Whitfield, Finlay, D. R., Murray, J. Isaac, Troyanskaya, O. G., Chi, J. - T., Pergamenschikov, A., McCalmont, T. H., Brown, P. O., Botstein, D., and M Connolly, K., “Systemic and cell type-specific gene expression patterns in scleroderma skin.”, Proc Natl Acad Sci U S A, vol. 100, no. 21, pp. 12319-24, 2003.
M. L. Whitfield, Finlay, D. R., Murray, J. Isaac, Troyanskaya, O. G., Chi, J. - T., Pergamenschikov, A., McCalmont, T. H., Brown, P. O., Botstein, D., and M Connolly, K., “Systemic and cell type-specific gene expression patterns in scleroderma skin.”, Proc Natl Acad Sci U S A, vol. 100, no. 21, pp. 12319-24, 2003.
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.
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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.
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.
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S. P. Bohen, Troyanskaya, O. G., Alter, O., Warnke, R., Botstein, D., Brown, P. O., and Levy, R., “Variation in gene expression patterns in follicular lymphoma and the response to rituximab.”, Proc Natl Acad Sci U S A, vol. 100, no. 4, pp. 1926-30, 2003.
S. P. Bohen, Troyanskaya, O. G., Alter, O., Warnke, R., Botstein, D., Brown, P. O., and Levy, R., “Variation in gene expression patterns in follicular lymphoma and the response to rituximab.”, Proc Natl Acad Sci U S A, vol. 100, no. 4, pp. 1926-30, 2003.
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.
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