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

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2020
S. Zhao, Jang, C., Liu, J., Uehara, K., Gilbert, M., Izzo, L., Zeng, X., Trefely, S., Fernandez, S., Carrer, A., Miller, K. D., Schug, Z. T., Snyder, N. W., Gade, T. P., Titchenell, P. M., Rabinowitz, J. D., and Wellen, K. E., Dietary fructose feeds hepatic lipogenesis via microbiota-derived acetate., Nature, vol. 579, no. 7800, pp. 586-591, 2020.
S. Zhao, Jang, C., Liu, J., Uehara, K., Gilbert, M., Izzo, L., Zeng, X., Trefely, S., Fernandez, S., Carrer, A., Miller, K. D., Schug, Z. T., Snyder, N. W., Gade, T. P., Titchenell, P. M., Rabinowitz, J. D., and Wellen, K. E., Dietary fructose feeds hepatic lipogenesis via microbiota-derived acetate., Nature, vol. 579, no. 7800, pp. 586-591, 2020.
A. M. Li, Ducker, G. S., Li, Y., Seoane, J. A., Xiao, Y., Melemenides, S., Zhou, Y., Liu, L., Vanharanta, S., Graves, E. E., Rankin, E. B., Curtis, C., Massague, J., Rabinowitz, J. D., Thompson, C. B., and Ye, J., Metabolic profiling reveals a dependency of human metastatic breast cancer on mitochondrial serine and one-carbon unit metabolism., Mol. Cancer Res., vol. 18, no. 4, pp. 599-611, 2020.
R. Menon, Otto, E. A., Hoover, P., Eddy, S., Mariani, L., Godfrey, B., Berthier, C. C., Eichinger, F., Subramanian, L., Harder, J., Ju, W., Nair, V., Larkina, M., Naik, A. S., Luo, J., Jain, S., Sealfon, R., Troyanskaya, O., Hacohen, N., Hodgin, J. B., Kretzler, M., and Kpmp, K. Precision, Single cell transcriptomics identifies focal segmental glomerulosclerosis remission endothelial biomarker., JCI Insight, vol. 5, no. 6, 2020.
Q. Zhu, Tekpli, X., Troyanskaya, O. G., and Kristensen, V. N., Subtype-specific transcriptional regulators in breast tumors subjected to genetic and epigenetic alterations., Bioinformatics, vol. 36, no. 4, pp. 994-999, 2020.
Q. Zhu, Tekpli, X., Troyanskaya, O. G., and Kristensen, V. N., Subtype-specific transcriptional regulators in breast tumors subjected to genetic and epigenetic alterations., Bioinformatics, vol. 36, no. 4, pp. 994-999, 2020.
2019
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, 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, 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.
Y. -suk Lee, Krishnan, A., Oughtred, R., Rust, J., Chang, C. S., Ryu, J., Kristensen, V. N., Dolinski, K., Theesfeld, C. L., and Troyanskaya, O. G., A Computational Framework for Genome-wide Characterization of the Human Disease Landscape., Cell Syst, vol. 8, no. 2, pp. 152-162.e6, 2019.
Y. -suk Lee, Krishnan, A., Oughtred, R., Rust, J., Chang, C. S., Ryu, J., Kristensen, V. N., Dolinski, K., Theesfeld, C. L., and Troyanskaya, O. G., A Computational Framework for Genome-wide Characterization of the Human Disease Landscape., Cell Syst, vol. 8, no. 2, pp. 152-162.e6, 2019.
Y. Song, Park, J. O., Tanner, L., Nagano, Y., Rabinowitz, J. D., and Shvartsman, S. Y., Energy budget of Drosophila embryogenesis., Curr Biol, vol. 29, no. 12, pp. R566-R567, 2019.
S. Tucci and Akey, J. M., The long walk to African genomics., Genome Biol, vol. 20, no. 1, p. 130, 2019.
D. Sargin, Chottekalapanda, R. U., Perit, K. E., Yao, V., Chu, D., Sparks, D. W., Kalik, S., Power, S. K., Troyanskaya, O. G., Schmidt, E. F., Greengard, P., and Lambe, E. K., Mapping the physiological and molecular markers of stress and SSRI antidepressant treatment in S100a10 corticostriatal neurons., Mol Psychiatry, 2019.
P. H. Bradley, Gibney, P. A., Botstein, D., Troyanskaya, O. G., and Rabinowitz, J. D., Minor Isozymes Tailor Yeast Metabolism to Carbon Availability., mSystems, vol. 4, no. 1, 2019.
J. O. Park, Tanner, L. B., Wei, M. H., Khana, D. B., Jacobson, T. B., Zhang, Z., Rubin, S. A., Li, S. Hsin- Jung, Higgins, M. B., Stevenson, D. M., Amador-Noguez, D., and Rabinowitz, J. D., Near-equilibrium glycolysis supports metabolic homeostasis and energy yield., Nat Chem Biol, vol. 15, no. 10, pp. 1001-1008, 2019.
J. L. Harder, Menon, R., Otto, E. A., Zhou, J., Eddy, S., Wys, N. L., O'Connor, C., Luo, J., Nair, V., Cebrián, C., Spence, J. R., Bitzer, M., Troyanskaya, O. G., Hodgin, J. B., Wiggins, R. C., Freedman, B. S., and Kretzler, M., Organoid single cell profiling identifies a transcriptional signature of glomerular disease., JCI Insight, vol. 4, no. 1, 2019.
Q. Liu, Johnson, E. M., Lam, R. K., Wang, Q., Ye, H. Bo, Wilson, E. N., Minhas, P. S., Liu, L., Swarovski, M. S., Tran, S., Wang, J., Mehta, S. S., Yang, X., Rabinowitz, J. D., Yang, S. S., Shamloo, M., Mueller, C., James, M. L., and Andreasson, K. I., Peripheral TREM1 responses to brain and intestinal immunogens amplify stroke severity., Nat Immunol, vol. 20, no. 8, pp. 1023-1034, 2019.
R. R. Stine, Sakers, A. P., TeSlaa, T., Kissig, M., Stine, Z. E., Kwon, C. Wook, Cheng, L., Lim, H. - W., Kaestner, K. H., Rabinowitz, J. D., and Seale, P., PRDM16 Maintains Homeostasis of the Intestinal Epithelium by Controlling Region-Specific Metabolism., Cell Stem Cell, 2019.
W. Wang, Ishibashi, J., Trefely, S., Shao, M., Cowan, A. J., Sakers, A., Lim, H. - W., O'Connor, S., Doan, M. T., Cohen, P., Baur, J. A., M King, T., Veech, R. L., Won, K. - J., Rabinowitz, J. D., Snyder, N. W., Gupta, R. K., and Seale, P., A PRDM16-Driven Metabolic Signal from Adipocytes Regulates Precursor Cell Fate., Cell Metab, vol. 30, no. 1, pp. 174-189.e5, 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.
N. Ron-Harel, Ghergurovich, J. M., Notarangelo, G., LaFleur, M. W., Tsubosaka, Y., Sharpe, A. H., Rabinowitz, J. D., and Haigis, M. C., T Cell Activation Depends on Extracellular Alanine., Cell Rep, vol. 28, no. 12, pp. 3011-3021.e4, 2019.
P. Anikeeva, Boyden, E., Brangwynne, C., Troyanskaya, O., and al., et., Voices in methods development., Nat Methods, vol. 16, no. 10, pp. 945-951, 2019.
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.
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.
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.
2018
S. R. Browning, Browning, B. L., Zhou, Y., Tucci, S., and Akey, J. M., Analysis of Human Sequence Data Reveals Two Pulses of Archaic Denisovan Admixture., Cell, vol. 173, no. 1, pp. 53-61.e9, 2018.
N. N. Pavlova, Hui, S., Ghergurovich, J. M., Fan, J., Intlekofer, A. M., White, R. M., Rabinowitz, J. D., Thompson, C. B., and Zhang, J., As Extracellular Glutamine Levels Decline, Asparagine Becomes an Essential Amino Acid., Cell Metab, vol. 27, no. 2, pp. 428-438.e5, 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.
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.
Y. - F. Xu, Lu, W., Chen, J. C., Johnson, S. A., Gibney, P. A., Thomas, D. G., Brown, G., May, A. L., Campagna, S. R., Yakunin, A. F., Botstein, D., and Rabinowitz, J. D., Discovery and Functional Characterization of a Yeast Sugar Alcohol Phosphatase., ACS Chem Biol, vol. 13, no. 10, pp. 3011-3020, 2018.
V. Yao, Wong, A. K., and Troyanskaya, O. G., Enabling Precision Medicine through Integrative Network Models., J Mol Biol, vol. 430, no. 18 Pt A, pp. 2913-2923, 2018.
S. Tucci, Vohr, S. H., McCoy, R. C., Vernot, B., Robinson, M. R., Barbieri, C., Nelson, B. J., Fu, W., Purnomo, G. A., Sudoyo, H., Eichler, E. E., Barbujani, G., Visscher, P. M., Akey, J. M., and Green, R. E., Evolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia., Science, vol. 361, no. 6401, pp. 511-516, 2018.
L. Bahati Tanner, Goglia, A. G., Wei, M. H., Sehgal, T., Parsons, L. R., Park, J. O., White, E., Toettcher, J. E., and Rabinowitz, J. D., Four Key Steps Control Glycolytic Flux in Mammalian Cells., Cell Syst, vol. 7, no. 1, pp. 49-62.e8, 2018.
L. Bahati Tanner, Goglia, A. G., Wei, M. H., Sehgal, T., Parsons, L. R., Park, J. O., White, E., Toettcher, J. E., and Rabinowitz, J. D., Four Key Steps Control Glycolytic Flux in Mammalian Cells., Cell Syst, vol. 7, no. 1, pp. 49-62.e8, 2018.
A. K. Wong, Krishnan, A., and Troyanskaya, O. G., GIANT 2.0: genome-scale integrated analysis of gene networks in tissues., Nucleic Acids Research, vol. 46, no. W1, pp. W65-W70, 2018.
V. Yao, Kaletsky, R., Keyes, W., Mor, D. E., Wong, A. K., Sohrabi, S., Murphy, C. T., and Troyanskaya, O. G., An integrative tissue-network approach to identify and test human disease genes., Nat Biotechnol, 2018.
Y. -suk Lee, Wong, A. K., Tadych, A., Hartmann, B. M., Park, C. Y., DeJesus, V. A., Ramos, I., Zaslavsky, E., Sealfon, S. C., and Troyanskaya, O. G., Interpretation of an individual functional genomics experiment guided by massive public data., Nat Methods, vol. 15, no. 12, pp. 1049-1052, 2018.
Y. -suk Lee, Wong, A. K., Tadych, A., Hartmann, B. M., Park, C. Y., DeJesus, V. A., Ramos, I., Zaslavsky, E., Sealfon, S. C., and Troyanskaya, O. G., Interpretation of an individual functional genomics experiment guided by massive public data., Nat Methods, vol. 15, no. 12, pp. 1049-1052, 2018.
M. A. Lanaspa, Andres-Hernando, A., Orlicky, D. J., Cicerchi, C., Jang, C., Li, N., Milagres, T., Kuwabara, M., Wempe, M. F., Rabinowitz, J. D., Johnson, R. J., and Tolan, D. R., Ketohexokinase C blockade ameliorates fructose-induced metabolic dysfunction in fructose-sensitive mice., J Clin Invest, vol. 128, no. 6, pp. 2226-2238, 2018.
A. V. Rangan, McGrouther, C. C., Kelsoe, J., Schork, N., Stahl, E., Zhu, Q., Krishnan, A., Yao, V., Troyanskaya, O., Bilaloglu, S., Raghavan, P., Bergen, S., Jureus, A., and Landen, M., A loop-counting method for covariate-corrected low-rank biclustering of gene-expression and genome-wide association study data., PLoS Comput Biol, vol. 14, no. 5, p. e1006105, 2018.
S. Jabeen, Zucknick, M., Nome, M., Dannenfelser, R., Fleischer, T., Kumar, S., Lüders, T., Gythfeldt, Hvon der Li, Troyanskaya, O., Kyte, J. Amund, Børresen-Dale, A. - L., Naume, B., Tekpli, X., Engebraaten, O., and Kristensen, V., Serum cytokine levels in breast cancer patients during neoadjuvant treatment with bevacizumab., Oncoimmunology, vol. 7, no. 11, p. e1457598, 2018.
S. Jabeen, Zucknick, M., Nome, M., Dannenfelser, R., Fleischer, T., Kumar, S., Lüders, T., Gythfeldt, Hvon der Li, Troyanskaya, O., Kyte, J. Amund, Børresen-Dale, A. - L., Naume, B., Tekpli, X., Engebraaten, O., and Kristensen, V., Serum cytokine levels in breast cancer patients during neoadjuvant treatment with bevacizumab., Oncoimmunology, vol. 7, no. 11, p. e1457598, 2018.
R. Menon, Otto, E. A., Kokoruda, A., Zhou, J., Zhang, Z., Yoon, E., Chen, Y. - C., Troyanskaya, O., Spence, J. R., Kretzler, M., and Cebrián, C., Single-cell analysis of progenitor cell dynamics and lineage specification in the human fetal kidney., Development, vol. 145, no. 16, 2018.
C. Jang, Hui, S., Lu, W., Cowan, A. J., Morscher, R. J., Lee, G., Liu, W., Tesz, G. J., Birnbaum, M. J., and Rabinowitz, J. D., The Small Intestine Converts Dietary Fructose into Glucose and Organic Acids., Cell Metab, vol. 27, no. 2, pp. 351-361.e3, 2018.
R. Kaletsky, Yao, V., Williams, A., Runnels, A. M., Tadych, A., Zhou, S., Troyanskaya, O. G., and Murphy, C. T., Transcriptome analysis of adult Caenorhabditis elegans cells reveals tissue-specific gene and isoform expression., PLoS Genetics, vol. 14, no. 8, p. e1007559, 2018.
R. Kaletsky, Yao, V., Williams, A., Runnels, A. M., Tadych, A., Zhou, S., Troyanskaya, O. G., and Murphy, C. T., Transcriptome analysis of adult Caenorhabditis elegans cells reveals tissue-specific gene and isoform expression., PLoS Genetics, vol. 14, no. 8, p. e1007559, 2018.
2017
T. Clancy, Dannenfelser, R., Troyanskaya, O. G., Malmberg, K. Johan, Hovig, E., and Kristensen, V., Bioinformatics approaches to profile the tumor microenvironment for immunotherapeutic discovery., Curr Pharm Des, 2017.
R. Dannenfelser, Nome, M., Tahiri, A., Ursini-Siegel, J., Vollan, H. Kristian M., Haakensen, V. D., Helland, Å., Naume, B., Caldas, C., Børresen-Dale, A. - L., Kristensen, V. N., and Troyanskaya, O. G., Data-driven analysis of immune infiltrate in a large cohort of breast cancer and its association with disease progression, ER activity, and genomic complexity., Oncotarget, vol. 8, no. 34, pp. 57121-57133, 2017.
R. Dannenfelser, Nome, M., Tahiri, A., Ursini-Siegel, J., Vollan, H. Kristian M., Haakensen, V. D., Helland, Å., Naume, B., Caldas, C., Børresen-Dale, A. - L., Kristensen, V. N., and Troyanskaya, O. G., Data-driven analysis of immune infiltrate in a large cohort of breast cancer and its association with disease progression, ER activity, and genomic complexity., Oncotarget, vol. 8, no. 34, pp. 57121-57133, 2017.
S. Hui, Ghergurovich, J. M., Morscher, R. J., Jang, C., Teng, X., Lu, W., Esparza, L. A., Reya, T., Guo, J. Yanxiang, White, E., and Rabinowitz, J. D., Glucose feeds the TCA cycle via circulating lactate., Nature, vol. 551, no. 7678, pp. 115-118, 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.
L. Chen, Ducker, G. S., Lu, W., Teng, X., and Rabinowitz, J. D., An LC-MS chemical derivatization method for the measurement of five different one-carbon states of cellular tetrahydrofolate., Anal Bioanal Chem, 2017.
N. V. Rajeshkumar, Yabuuchi, S., Pai, S. G., De Oliveira, E., Kamphorst, J. J., Rabinowitz, J. D., Tejero, H., Al-Shahrour, F., Hidalgo, M., Maitra, A., and Dang, C. V., Treatment of Pancreatic Cancer Patient-Derived Xenograft Panel with Metabolic Inhibitors Reveals Efficacy of Phenformin., Clin Cancer Res, vol. 23, no. 18, pp. 5639-5647, 2017.
2016
J. Yanxiang Guo, Teng, X., Laddha, S. V., Ma, S., Van Nostrand, S. C., Yang, Y., Khor, S., Chan, C. S., Rabinowitz, J. D., and White, E., Autophagy provides metabolic substrates to maintain energy charge and nucleotide pools in Ras-driven lung cancer cells., Genes Dev, vol. 30, no. 15, pp. 1704-17, 2016.
P. M. Titchenell, Quinn, W. J., Lu, M., Chu, Q., Lu, W., Li, C., Chen, H., Monks, B. R., Chen, J., Rabinowitz, J. D., and Birnbaum, M. J., Direct Hepatocyte Insulin Signaling Is Required for Lipogenesis but Is Dispensable for the Suppression of Glucose Production., Cell Metab, 2016.
X. Nuttle, Giannuzzi, G., Duyzend, M. H., Schraiber, J. G., Narvaiza, I., Sudmant, P. H., Penn, O., Chiatante, G., Malig, M., Huddleston, J., Benner, C., Camponeschi, F., Ciofi-Baffoni, S., Stessman, H. A. F., Marchetto, M. C. N., Denman, L., Harshman, L., Baker, C., Raja, A., Penewit, K., Janke, N., W Tang, J., Ventura, M., Banci, L., Antonacci, F., Akey, J. M., Amemiya, C. T., Gage, F. H., Reymond, A., and Eichler, E. E., Emergence of a Homo sapiens-specific gene family and chromosome 16p11.2 CNV susceptibility., Nature, vol. 536, no. 7615, pp. 205-9, 2016.
A. Krishnan, Zhang, R., Yao, V., Theesfeld, C. L., Wong, A. K., Tadych, A., Volfovsky, N., Packer, A., Lash, A., and Troyanskaya, O. G., Genome-wide prediction and functional characterization of the genetic basis of autism spectrum disorder., Nat Neurosci, vol. 19, no. 11, pp. 1454-1462, 2016.
A. Krishnan, Zhang, R., Yao, V., Theesfeld, C. L., Wong, A. K., Tadych, A., Volfovsky, N., Packer, A., Lash, A., and Troyanskaya, O. G., Genome-wide prediction and functional characterization of the genetic basis of autism spectrum disorder., Nat Neurosci, vol. 19, no. 11, pp. 1454-1462, 2016.
A. Krishnan, Zhang, R., Yao, V., Theesfeld, C. L., Wong, A. K., Tadych, A., Volfovsky, N., Packer, A., Lash, A., and Troyanskaya, O. G., Genome-wide prediction and functional characterization of the genetic basis of autism spectrum disorder., Nat Neurosci, vol. 19, no. 11, pp. 1454-1462, 2016.
H. D. Møller, Bojsen, R. K., Tachibana, C., Parsons, L., Botstein, D., and Regenberg, B., Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells., J Vis Exp, no. 110, p. e54239 |, 2016.
A. M. Roberts, Wong, A. K., Fisk, I., and Troyanskaya, O. G., GIANT API: an application programming interface for functional genomics., Nucleic Acids Res, 2016.
M. Costanzo, VanderSluis, B., Koch, E. N., Baryshnikova, A., Pons, C., Tan, G., Wang, W., Usaj, M., Hanchard, J., Lee, S. D., Pelechano, V., Styles, E. B., Billmann, M., van Leeuwen, J., van Dyk, N., Lin, Z. - Y., Kuzmin, E., Nelson, J., Piotrowski, J. S., Srikumar, T., Bahr, S., Chen, Y., Deshpande, R., Kurat, C. F., Li, S. C., Li, Z., Usaj, M. Mattiazzi, Okada, H., Pascoe, N., San Luis, B. - J., Sharifpoor, S., Shuteriqi, E., Simpkins, S. W., Snider, J., Suresh, H. Garadi, Tan, Y., Zhu, H., Malod-Dognin, N., Janjic, V., Przulj, N., Troyanskaya, O. G., Stagljar, I., Xia, T., Ohya, Y., Gingras, A. - C., Raught, B., Boutros, M., Steinmetz, L. M., Moore, C. L., Rosebrock, A. P., Caudy, A. A., Myers, C. L., Andrews, B., and Boone, C., A global genetic interaction network maps a wiring diagram of cellular function., Science, vol. 353, no. 6306, 2016.
M. Costanzo, VanderSluis, B., Koch, E. N., Baryshnikova, A., Pons, C., Tan, G., Wang, W., Usaj, M., Hanchard, J., Lee, S. D., Pelechano, V., Styles, E. B., Billmann, M., van Leeuwen, J., van Dyk, N., Lin, Z. - Y., Kuzmin, E., Nelson, J., Piotrowski, J. S., Srikumar, T., Bahr, S., Chen, Y., Deshpande, R., Kurat, C. F., Li, S. C., Li, Z., Usaj, M. Mattiazzi, Okada, H., Pascoe, N., San Luis, B. - J., Sharifpoor, S., Shuteriqi, E., Simpkins, S. W., Snider, J., Suresh, H. Garadi, Tan, Y., Zhu, H., Malod-Dognin, N., Janjic, V., Przulj, N., Troyanskaya, O. G., Stagljar, I., Xia, T., Ohya, Y., Gingras, A. - C., Raught, B., Boutros, M., Steinmetz, L. M., Moore, C. L., Rosebrock, A. P., Caudy, A. A., Myers, C. L., Andrews, B., and Boone, C., A global genetic interaction network maps a wiring diagram of cellular function., Science, vol. 353, no. 6306, 2016.
M. Costanzo, VanderSluis, B., Koch, E. N., Baryshnikova, A., Pons, C., Tan, G., Wang, W., Usaj, M., Hanchard, J., Lee, S. D., Pelechano, V., Styles, E. B., Billmann, M., van Leeuwen, J., van Dyk, N., Lin, Z. - Y., Kuzmin, E., Nelson, J., Piotrowski, J. S., Srikumar, T., Bahr, S., Chen, Y., Deshpande, R., Kurat, C. F., Li, S. C., Li, Z., Usaj, M. Mattiazzi, Okada, H., Pascoe, N., San Luis, B. - J., Sharifpoor, S., Shuteriqi, E., Simpkins, S. W., Snider, J., Suresh, H. Garadi, Tan, Y., Zhu, H., Malod-Dognin, N., Janjic, V., Przulj, N., Troyanskaya, O. G., Stagljar, I., Xia, T., Ohya, Y., Gingras, A. - C., Raught, B., Boutros, M., Steinmetz, L. M., Moore, C. L., Rosebrock, A. P., Caudy, A. A., Myers, C. L., Andrews, B., and Boone, C., A global genetic interaction network maps a wiring diagram of cellular function., Science, vol. 353, no. 6306, 2016.
A. Bren, Park, J. O., Towbin, B. D., Dekel, E., Rabinowitz, J. D., and Alon, U., Glucose becomes one of the worst carbon sources for E.coli on poor nitrogen sources due to suboptimal levels of cAMP., Sci Rep, vol. 6, p. 24834, 2016.
X. Teng, Emmett, M. J., Lazar, M. A., Goldberg, E., and Rabinowitz, J. D., Lactate Dehydrogenase C Produces S-2-Hydroxyglutarate in Mouse Testis., ACS Chem Biol, 2016.
D. W. Frederick, Loro, E., Liu, L., Davila, A., Chellappa, K., Silverman, I. M., Quinn, W. J., Gosai, S. J., Tichy, E. D., Davis, J. G., Mourkioti, F., Gregory, B. D., Dellinger, R. W., Redpath, P., Migaud, M. E., Nakamaru-Ogiso, E., Rabinowitz, J. D., Khurana, T. S., and Baur, J. A., Loss of NAD Homeostasis Leads to Progressive and Reversible Degeneration of Skeletal Muscle., Cell Metab, vol. 24, no. 2, pp. 269-82, 2016.
E. Watson, Olin-Sandoval, V., Hoy, M. J., Li, C. - H., Louisse, T., Yao, V., Mori, A., Holdorf, A. D., Troyanskaya, O. G., Ralser, M., and Walhout, A. Jm, Metabolic network rewiring of propionate flux compensates vitamin B12 deficiency in C. elegans., Elife, vol. 5, 2016.
R. Papazyan, Sun, Z., Kim, Y. Hoon, Titchenell, P. M., Hill, D. A., Lu, W., Damle, M., Wan, M., Zhang, Y., Briggs, E. R., Rabinowitz, J. D., and Lazar, M. A., Physiological Suppression of Lipotoxic Liver Damage by Complementary Actions of HDAC3 and SCAP/SREBP., Cell Metab, vol. 24, no. 6, pp. 863-874, 2016.
J. Zhou and Troyanskaya, O. G., Probabilistic modelling of chromatin code landscape reveals functional diversity of enhancer-like chromatin states., Nat Commun, vol. 7, p. 10528, 2016.
Q. Wang, J Taliaferro, M., Klibaite, U., Hilgers, V., Shaevitz, J. W., and Rio, D. C., The PSI-U1 snRNP interaction regulates male mating behavior in Drosophila., Proc Natl Acad Sci U S A, vol. 113, no. 19, pp. 5269-74, 2016.
G. S. Ducker, Chen, L., Morscher, R. J., Ghergurovich, J. M., Esposito, M., Teng, X., Kang, Y., and Rabinowitz, J. D., Reversal of Cytosolic One-Carbon Flux Compensates for Loss of the Mitochondrial Folate Pathway., Cell Metab, 2016.
2015
S. Thutupalli, Sun, M., Bunyak, F., Palaniappan, K., and Shaevitz, J. W., Directional reversals enable Myxococcus xanthus cells to produce collective one-dimensional streams during fruiting-body formation., J R Soc Interface, vol. 12, no. 109, p. 20150049, 2015.
J. Goya, Wong, A. K., Yao, V., Krishnan, A., Homilius, M., and Troyanskaya, O. G., FNTM: a server for predicting functional networks of tissues in mouse., Nucleic Acids Res, 2015.
J. J. Kamphorst, Nofal, M., Commisso, C., Hackett, S. R., Lu, W., Grabocka, E., Heiden, M. G. Vander, Miller, G., Drebin, J. A., Bar-Sagi, D., Thompson, C. B., and Rabinowitz, J. D., Human pancreatic cancer tumors are nutrient poor and tumor cells actively scavenge extracellular protein., Cancer Res, vol. 75, no. 3, pp. 544-53, 2015.
A. K. Wong, Krishnan, A., Yao, V., Tadych, A., and Troyanskaya, O. G., IMP 2.0: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks., Nucleic Acids Res, 2015.
A. K. Wong, Krishnan, A., Yao, V., Tadych, A., and Troyanskaya, O. G., IMP 2.0: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks., Nucleic Acids Res, 2015.
K. Dolinski and Troyanskaya, O. G., Implications of Big Data for cell biology., Mol Biol Cell, vol. 26, no. 14, pp. 2575-8, 2015.
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.
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.
M. Tikhonov, Leach, R. W., and Wingreen, N. S., Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution., ISME J, vol. 9, no. 1, pp. 68-80, 2015.
M. D. Chikina, Gerald, C. P., Li, X., Ge, Y., Pincas, H., Nair, V. D., Wong, A. K., Krishnan, A., Troyanskaya, O. G., Raymond, D., Saunders-Pullman, R., Bressman, S. B., Yue, Z., and Sealfon, S. C., Low-variance RNAs identify Parkinson's disease molecular signature in blood., Mov Disord, vol. 30, no. 6, pp. 813-21, 2015.
G. Tkačik, Dubuis, J. O., Petkova, M. D., and Gregor, T., Positional information, positional error, and readout precision in morphogenesis: a mathematical framework., Genetics, vol. 199, no. 1, pp. 39-59, 2015.
J. Zhou and Troyanskaya, O. G., Predicting effects of noncoding variants with deep learning-based sequence model., Nat Methods, 2015.
P. Barron Abitua, T Gainous, B., Kaczmarczyk, A. N., Winchell, C. J., Hudson, C., Kamata, K., Nakagawa, M., Tsuda, M., Kusakabe, T. G., and Levine, M., The pre-vertebrate origins of neurogenic placodes., Nature, vol. 524, no. 7566, pp. 462-5, 2015.
J. M. Buescher, Antoniewicz, M. R., Boros, L. G., Burgess, S. C., Brunengraber, H., Clish, C. B., DeBerardinis, R. J., Feron, O., Frezza, C., Ghesquiere, B., Gottlieb, E., Hiller, K., Jones, R. G., Kamphorst, J. J., Kibbey, R. G., Kimmelman, A. C., Locasale, J. W., Lunt, S. Y., Maddocks, O. Dk, Malloy, C., Metallo, C. M., Meuillet, E. J., Munger, J., Nöh, K., Rabinowitz, J. D., Ralser, M., Sauer, U., Stephanopoulos, G., St-Pierre, J., Tennant, D. A., Wittmann, C., Heiden, M. G. Vander, Vazquez, A., Vousden, K., Young, J. D., Zamboni, N., and Fendt, S. - M., A roadmap for interpreting (13)C metabolite labeling patterns from cells., Curr Opin Biotechnol, vol. 34, pp. 189-201, 2015.
S. D. Kocher, Tsuruda, J. M., Gibson, J. D., Emore, C. M., Arechavaleta-Velasco, M. E., Queller, D. C., Strassmann, J. E., Grozinger, C. M., Gribskov, M. R., San Miguel, P., Westerman, R., and Hunt, G. J., A Search for Parent-of-Origin Effects on Honey Bee Gene Expression., G3 (Bethesda), vol. 5, no. 8, pp. 1657-62, 2015.
K. M. Kapheim, Pan, H., Li, C., Salzberg, S. L., Puiu, D., Magoc, T., Robertson, H. M., Hudson, M. E., Venkat, A., Fischman, B. J., Hernandez, A., Yandell, M., Ence, D., Holt, C., Yocum, G. D., Kemp, W. P., Bosch, J., Waterhouse, R. M., Zdobnov, E. M., Stolle, E., F Kraus, B., Helbing, S., Moritz, R. F. A., Glastad, K. M., Hunt, B. G., Goodisman, M. A. D., Hauser, F., Grimmelikhuijzen, C. J. P., Pinheiro, D. Guariz, Nunes, F. Morais Fra, Soares, M. Prioli Mir, Tanaka, É. Donato, Simões, Z. Luz Paulin, Hartfelder, K., Evans, J. D., Barribeau, S. M., Johnson, R. M., Massey, J. H., Southey, B. R., Hasselmann, M., Hamacher, D., Biewer, M., Kent, C. F., Zayed, A., Blatti, C., Sinha, S., J Johnston, S., Hanrahan, S. J., Kocher, S. D., Wang, J., Robinson, G. E., and Zhang, G., Social evolution. Genomic signatures of evolutionary transitions from solitary to group living., Science, vol. 348, no. 6239, pp. 1139-43, 2015.
Q. Zhu, Wong, A. K., Krishnan, A., Aure, M. R., Tadych, A., Zhang, R., Corney, D. C., Greene, C. S., Bongo, L. A., Kristensen, V. N., Charikar, M., Li, K., and Troyanskaya, O. G., Targeted exploration and analysis of large cross-platform human transcriptomic compendia., Nat Methods, vol. 12, no. 3, pp. 211-4, 3 p following 214, 2015.
Q. Zhu, Wong, A. K., Krishnan, A., Aure, M. R., Tadych, A., Zhang, R., Corney, D. C., Greene, C. S., Bongo, L. A., Kristensen, V. N., Charikar, M., Li, K., and Troyanskaya, O. G., Targeted exploration and analysis of large cross-platform human transcriptomic compendia., Nat Methods, vol. 12, no. 3, pp. 211-4, 3 p following 214, 2015.
C. S. Greene, Krishnan, A., Wong, A. K., Ricciotti, E., Zelaya, R. A., Himmelstein, D. S., Zhang, R., Hartmann, B. M., Zaslavsky, E., Sealfon, S. C., Chasman, D. I., FitzGerald, G. A., Dolinski, K., Grosser, T., and Troyanskaya, O. G., Understanding multicellular function and disease with human tissue-specific networks., Nat Genet, vol. 47, no. 6, pp. 569-76, 2015.
2014
J. Zhang, Fan, J., Venneti, S., Cross, J. R., Takagi, T., Bhinder, B., Djaballah, H., Kanai, M., Cheng, E. H., Judkins, A. R., Pawel, B., Baggs, J., Cherry, S., Rabinowitz, J. D., and Thompson, C. B., Asparagine plays a critical role in regulating cellular adaptation to glutamine depletion., Mol Cell, vol. 56, no. 2, pp. 205-18, 2014.
J. Zhang, Fan, J., Venneti, S., Cross, J. R., Takagi, T., Bhinder, B., Djaballah, H., Kanai, M., Cheng, E. H., Judkins, A. R., Pawel, B., Baggs, J., Cherry, S., Rabinowitz, J. D., and Thompson, C. B., Asparagine plays a critical role in regulating cellular adaptation to glutamine depletion., Mol Cell, vol. 56, no. 2, pp. 205-18, 2014.
G. Karsli-Uzunbas, Guo, J. Yanxiang, Price, S., Teng, X., Laddha, S. V., Khor, S., Kalaany, N. Y., Jacks, T., Chan, C. S., Rabinowitz, J. D., and White, E., Autophagy is required for glucose homeostasis and lung tumor maintenance., Cancer Discov, vol. 4, no. 8, pp. 914-27, 2014.
B. VanderSluis, Hess, D. C., Pesyna, C., Krumholz, E. W., Syed, T., Szappanos, B., Nislow, C., Papp, B., Troyanskaya, O. G., Myers, C. L., and Caudy, A. A., Broad metabolic sensitivity profiling of a prototrophic yeast deletion collection., Genome Biol, vol. 15, no. 4, p. R64, 2014.
R. G. Tepper, Murphy, C. T., and Bussemaker, H. J., DAF-16 and PQM-1: partners in longevity., Aging (Albany NY), vol. 6, no. 1, pp. 5-6, 2014.
J. Zhou and Troyanskaya, O. G., Global quantitative modeling of chromatin factor interactions., PLoS Comput Biol, vol. 10, no. 3, p. e1003525, 2014.
J. Fan, Teng, X., Liu, L., Mattaini, K. R., Looper, R. E., Heiden, M. G. Vander, and Rabinowitz, J. D., Human Phosphoglycerate Dehydrogenase Produces the Oncometabolite d-2-Hydroxyglutarate., ACS Chem Biol, 2014.
R. L. Rogers, Cridland, J. M., Shao, L., Hu, T. T., Andolfatto, P., and Thornton, K. R., Landscape of standing variation for tandem duplications in Drosophila yakuba and Drosophila simulans., Mol Biol Evol, vol. 31, no. 7, pp. 1750-66, 2014.
M. Levine, Cattoglio, C., and Tjian, R., Looping back to leap forward: transcription enters a new era., Cell, vol. 157, no. 1, pp. 13-25, 2014.
D. Quigley, Silwal-Pandit, L., Dannenfelser, R., Langerod, A., Vollan, H. Kristian M., Vaske, C., Ursini-Siegel, J., Troyanskaya, O., Chin, S. - F., Caldas, C., Balmain, A., Borresen-Dale, A. - L., and Kristensen, V., Lymphocyte invasion in IC10/Basal-like breast tumors is associated with wild-type TP53., Mol Cancer Res, 2014.
J. Fan, Ye, J., Kamphorst, J. J., Shlomi, T., Thompson, C. B., and Rabinowitz, J. D., Quantitative flux analysis reveals folate-dependent NADPH production., Nature, vol. 510, no. 7504, pp. 298-302, 2014.
R. L. Rogers, Shao, L., Sanjak, J. S., Andolfatto, P., and Thornton, K. R., Revised Annotations, Sex-Biased Expression, and Lineage-Specific Genes in the Drosophila melanogaster Group., G3 (Bethesda), vol. 4, no. 12, pp. 2345-51, 2014.
G. Tkačik, Marre, O., Amodei, D., Schneidman, E., Bialek, W., and Berry, M. J., Searching for collective behavior in a large network of sensory neurons., PLoS Comput Biol, vol. 10, no. 1, p. e1003408, 2014.
J. Ye, Fan, J., Venneti, S., Wan, Y. - W., Pawel, B. R., Zhang, J., Finley, L. W. S., Lu, C., Lindsten, T., Cross, J. R., Qing, G., Liu, Z., M Simon, C., Rabinowitz, J. D., and Thompson, C. B., Serine Catabolism Regulates Mitochondrial Redox Control during Hypoxia., Cancer Discov, vol. 4, no. 12, pp. 1406-17, 2014.
C. Y. Park, Krishnan, A., Zhu, Q., Wong, A. K., Lee, Y. -suk, and Troyanskaya, O. G., Tissue-aware data integration approach for the inference of pathway interactions in metazoan organisms., Bioinformatics, 2014.
S. M. Tilghman, Twists and turns: a scientific journey., Annu Rev Cell Dev Biol, vol. 30, pp. 1-21, 2014.
2013
T. Slotte, Hazzouri, K. M., J Ågren, A., Koenig, D., Maumus, F., Guo, Y. - L., Steige, K., Platts, A. E., Escobar, J. S., L Newman, K., Wang, W., Mandáková, T., Vello, E., Smith, L. M., Henz, S. R., Steffen, J., Takuno, S., Brandvain, iv, Y., Coop, G., Andolfatto, P., Hu, T. T., Blanchette, M., Clark, R. M., Quesneville, H., Nordborg, M., Gaut, B. S., Lysak, M. A., Jenkins, J., Grimwood, J., Chapman, J., Prochnik, S., Shu, S., Rokhsar, D., Schmutz, J., Weigel, D., and Wright, S. I., The Capsella rubella genome and the genomic consequences of rapid mating system evolution., Nat Genet, vol. 45, no. 7, pp. 831-5, 2013.
J. I. Kliegman, Fiedler, D., Ryan, C. J., Xu, Y. - F., Su, X. - Y., Thomas, D., Caccese, M. C., Cheng, A., Shales, M., Rabinowitz, J. D., Krogan, N. J., and Shokat, K. M., Chemical genetics of rapamycin-insensitive TORC2 in S. cerevisiae., Cell Rep, vol. 5, no. 6, pp. 1725-36, 2013.
Y. Guan, Dunham, M. J., Troyanskaya, O. G., and Caudy, A. A., Comparative gene expression between two yeast species., BMC Genomics, vol. 14, p. 33, 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.
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.
J. J. Kamphorst, Cross, J. R., Fan, J., de Stanchina, E., Mathew, R., White, E. P., Thompson, C. B., and Rabinowitz, J. D., Hypoxic and Ras-transformed cells support growth by scavenging unsaturated fatty acids from lysophospholipids., Proc Natl Acad Sci U S A, vol. 110, no. 22, pp. 8882-7, 2013.
M. Ragle Aure, Leivonen, S. - K., Fleischer, T., Zhu, Q., Overgaard, J., Alsner, J., Tramm, T., Louhimo, R., Alnæs, G. I. Grenaker, Perälä, M., Busato, F., Touleimat, N., Tost, J., Børresen-Dale, A. - L., Hautaniemi, S., Troyanskaya, O. G., Lingjærde, O. Christian, Sahlberg, K. Kleivi, and Kristensen, V. N., Individual and combined effects of DNA methylation and copy number alterations on miRNA expression in breast tumors., Genome Biol, vol. 14, no. 11, p. R126, 2013.
M. Ragle Aure, Leivonen, S. - K., Fleischer, T., Zhu, Q., Overgaard, J., Alsner, J., Tramm, T., Louhimo, R., Alnæs, G. I. Grenaker, Perälä, M., Busato, F., Touleimat, N., Tost, J., Børresen-Dale, A. - L., Hautaniemi, S., Troyanskaya, O. G., Lingjærde, O. Christian, Sahlberg, K. Kleivi, and Kristensen, V. N., Individual and combined effects of DNA methylation and copy number alterations on miRNA expression in breast tumors., Genome Biol, vol. 14, no. 11, p. R126, 2013.
M. Ragle Aure, Leivonen, S. - K., Fleischer, T., Zhu, Q., Overgaard, J., Alsner, J., Tramm, T., Louhimo, R., Alnæs, G. I. Grenaker, Perälä, M., Busato, F., Touleimat, N., Tost, J., Børresen-Dale, A. - L., Hautaniemi, S., Troyanskaya, O. G., Lingjærde, O. Christian, Sahlberg, K. Kleivi, and Kristensen, V. N., Individual and combined effects of DNA methylation and copy number alterations on miRNA expression in breast tumors., Genome Biol, vol. 14, no. 11, p. R126, 2013.
M. Ragle Aure, Leivonen, S. - K., Fleischer, T., Zhu, Q., Overgaard, J., Alsner, J., Tramm, T., Louhimo, R., Alnæs, G. I. Grenaker, Perälä, M., Busato, F., Touleimat, N., Tost, J., Børresen-Dale, A. - L., Hautaniemi, S., Troyanskaya, O. G., Lingjærde, O. Christian, Sahlberg, K. Kleivi, and Kristensen, V. N., Individual and combined effects of DNA methylation and copy number alterations on miRNA expression in breast tumors., Genome Biol, vol. 14, no. 11, p. R126, 2013.
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.
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.
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. Lagha, Bothma, J. P., Esposito, E., Ng, S., Stefanik, L., Tsui, C., Johnston, J., Chen, K., Gilmour, D. S., Zeitlinger, J., and Levine, M. S., Paused Pol II coordinates tissue morphogenesis in the Drosophila embryo., Cell, vol. 153, no. 5, pp. 976-87, 2013.
J. O. Dubuis, Tkačik, G., Wieschaus, E. F., Gregor, T., and Bialek, W., Positional information, in bits., Proc Natl Acad Sci U S A, vol. 110, no. 41, pp. 16301-8, 2013.
R. G. Tepper, Ashraf, J., Kaletsky, R., Kleemann, G., Murphy, C. T., and Bussemaker, H. J., PQM-1 complements DAF-16 as a key transcriptional regulator of DAF-2-mediated development and longevity., Cell, vol. 154, no. 3, pp. 676-90, 2013.
S. C. Little, Tikhonov, M., and Gregor, T., Precise developmental gene expression arises from globally stochastic transcriptional activity., Cell, vol. 154, no. 4, pp. 789-800, 2013.
H. G. Garcia, Tikhonov, M., Lin, A., and Gregor, T., Quantitative imaging of transcription in living Drosophila embryos links polymerase activity to patterning., Curr Biol, vol. 23, no. 21, pp. 2140-5, 2013.
T. T. Hu, Eisen, M. B., Thornton, K. R., and Andolfatto, P., A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence., Genome Res, vol. 23, no. 1, pp. 89-98, 2013.
G. J. Stephens, Mora, T., Tkačik, G., and Bialek, W., Statistical thermodynamics of natural images., Phys Rev Lett, vol. 110, no. 1, p. 018701, 2013.
2012
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.
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.
T. F. C. Mackay, Richards, S., Stone, E. A., Barbadilla, A., Ayroles, J. F., Zhu, D., Casillas, S., Han, Y., Magwire, M. M., Cridland, J. M., Richardson, M. F., Anholt, R. R. H., Barrón, M., Bess, C., Blankenburg, K. Petra, Carbone, M. Anna, Castellano, D., Chaboub, L., Duncan, L., Harris, Z., Javaid, M., Jayaseelan, J. Christina, Jhangiani, S. N., Jordan, K. W., Lara, F., Lawrence, F., Lee, S. L., Librado, P., Linheiro, R. S., Lyman, R. F., Mackey, A. J., Munidasa, M., Muzny, D. Marie, Nazareth, L., Newsham, I., Perales, L., Pu, L. - L., Qu, C., Ràmia, M., Reid, J. G., Rollmann, S. M., Rozas, J., Saada, N., Turlapati, L., Worley, K. C., Wu, Y. - Q., Yamamoto, A., Zhu, Y., Bergman, C. M., Thornton, K. R., Mittelman, D., and Gibbs, R. A., The Drosophila melanogaster Genetic Reference Panel., Nature, vol. 482, no. 7384, pp. 173-8, 2012.
T. F. C. Mackay, Richards, S., Stone, E. A., Barbadilla, A., Ayroles, J. F., Zhu, D., Casillas, S., Han, Y., Magwire, M. M., Cridland, J. M., Richardson, M. F., Anholt, R. R. H., Barrón, M., Bess, C., Blankenburg, K. Petra, Carbone, M. Anna, Castellano, D., Chaboub, L., Duncan, L., Harris, Z., Javaid, M., Jayaseelan, J. Christina, Jhangiani, S. N., Jordan, K. W., Lara, F., Lawrence, F., Lee, S. L., Librado, P., Linheiro, R. S., Lyman, R. F., Mackey, A. J., Munidasa, M., Muzny, D. Marie, Nazareth, L., Newsham, I., Perales, L., Pu, L. - L., Qu, C., Ràmia, M., Reid, J. G., Rollmann, S. M., Rozas, J., Saada, N., Turlapati, L., Worley, K. C., Wu, Y. - Q., Yamamoto, A., Zhu, Y., Bergman, C. M., Thornton, K. R., Mittelman, D., and Gibbs, R. A., The Drosophila melanogaster Genetic Reference Panel., Nature, vol. 482, no. 7384, pp. 173-8, 2012.
M. D. Chikina and Troyanskaya, O. G., An effective statistical evaluation of ChIPseq dataset similarity., Bioinformatics, vol. 28, no. 5, pp. 607-13, 2012.
D. Garrigan, Kingan, S. B., Geneva, A. J., Andolfatto, P., Clark, A. G., Thornton, K. R., and Presgraves, D. C., Genome sequencing reveals complex speciation in the Drosophila simulans clade., Genome Res, vol. 22, no. 8, pp. 1499-511, 2012.
L. J. Terry, Vastag, L., Rabinowitz, J. D., and Shenk, T., Human kinome profiling identifies a requirement for AMP-activated protein kinase during human cytomegalovirus infection., Proc Natl Acad Sci U S A, vol. 109, no. 8, pp. 3071-6, 2012.
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.
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.
V. D. Nair, Ge, Y., Balasubramaniyan, N., Kim, J., Okawa, Y., Chikina, M., Troyanskaya, O., and Sealfon, S. C., Involvement of histone demethylase LSD1 in short-time-scale gene expression changes during cell cycle progression in embryonic stem cells., Mol Cell Biol, vol. 32, no. 23, pp. 4861-76, 2012.
G. Tkačik, Walczak, A. M., and Bialek, W., Optimizing information flow in small genetic networks. III. A self-interacting gene., Phys Rev E Stat Nonlin Soft Matter Phys, vol. 85, no. 4 Pt 1, p. 041903, 2012.
J. A. Drocco, Wieschaus, E. F., and Tank, D. W., The synthesis-diffusion-degradation model explains Bicoid gradient formation in unfertilized eggs., Phys Biol, vol. 9, no. 5, p. 055004, 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.
M. A. Gelbart, He, B., Martin, A. C., Thiberge, S. Y., Wieschaus, E. F., and Kaschube, M., Volume conservation principle involved in cell lengthening and nucleus movement during tissue morphogenesis., Proc Natl Acad Sci U S A, vol. 109, no. 47, pp. 19298-303, 2012.
2011
Z. Khan, Amini, S., Bloom, J. S., Ruse, C., Caudy, A. A., Kruglyak, L., Singh, M., Perlman, D. H., and Tavazoie, S., Accurate proteome-wide protein quantification from high-resolution 15N mass spectra., Genome Biol, vol. 12, no. 12, p. R122, 2011.
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.
S. - W. Teng, Schaffer, J. N., Tu, K. C., Mehta, P., Lu, W., Ong, N. P., Bassler, B. L., and Wingreen, N. S., Active regulation of receptor ratios controls integration of quorum-sensing signals in Vibrio harveyi., Mol Syst Biol, vol. 7, p. 491, 2011.
S. - W. Teng, Schaffer, J. N., Tu, K. C., Mehta, P., Lu, W., Ong, N. P., Bassler, B. L., and Wingreen, N. S., Active regulation of receptor ratios controls integration of quorum-sensing signals in Vibrio harveyi., Mol Syst Biol, vol. 7, p. 491, 2011.
J. S. Kanodia, Kim, Y., Tomer, R., Khan, Z., Chung, K., Storey, J. D., Lu, H., Keller, P. J., and Shvartsman, S. Y., A computational statistics approach for estimating the spatial range of morphogen gradients., Development, vol. 138, no. 22, pp. 4867-74, 2011.
K. H. Desai, Tan, C. Seng, Leek, J. T., Maier, R. V., Tompkins, R. G., and Storey, J. D., Dissecting inflammatory complications in critically injured patients by within-patient gene expression changes: a longitudinal clinical genomics study., PLoS Med, vol. 8, no. 9, p. e1001093, 2011.
K. H. Desai, Tan, C. Seng, Leek, J. T., Maier, R. V., Tompkins, R. G., and Storey, J. D., Dissecting inflammatory complications in critically injured patients by within-patient gene expression changes: a longitudinal clinical genomics study., PLoS Med, vol. 8, no. 9, p. e1001093, 2011.
S. C. Little, Tkačik, G., Kneeland, T. B., Wieschaus, E. F., and Gregor, T., The formation of the Bicoid morphogen gradient requires protein movement from anteriorly localized mRNA., PLoS Biol, vol. 9, no. 3, p. e1000596, 2011.
Y. Kim, Andreu, M. José, Lim, B., Chung, K., Terayama, M., Jiménez, G., Berg, C. A., Lu, H., and Shvartsman, S. Y., Gene regulation by MAPK substrate competition., Dev Cell, vol. 20, no. 6, pp. 880-7, 2011.
J. A. Drocco, Grimm, O., Tank, D. W., and Wieschaus, E., Measurement and perturbation of morphogen lifetime: effects on gradient shape., Biophys J, vol. 101, no. 8, pp. 1807-15, 2011.
A. Stolfi, Wagner, E., J Taliaferro, M., Chou, S., and Levine, M., Neural tube patterning by Ephrin, FGF and Notch signaling relays., Development, vol. 138, no. 24, pp. 5429-39, 2011.
Y. Guan, Yao, V., Tsui, K., Gebbia, M., Dunham, M. J., Nislow, C., and Troyanskaya, O. G., Nucleosome-coupled expression differences in closely-related species., BMC Genomics, vol. 12, p. 466, 2011.
Y. Guan, Yao, V., Tsui, K., Gebbia, M., Dunham, M. J., Nislow, C., and Troyanskaya, O. G., Nucleosome-coupled expression differences in closely-related species., BMC Genomics, vol. 12, p. 466, 2011.
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.
V. S. Chopra, Hendrix, D. A., Core, L. J., Tsui, C., Lis, J. T., and Levine, M., The polycomb group mutant esc leads to augmented levels of paused Pol II in the Drosophila embryo., Mol Cell, vol. 42, no. 6, pp. 837-44, 2011.
Y. Wang, Tu, K. C., Ong, N. P., Bassler, B. L., and Wingreen, N. S., Protein-level fluctuation correlation at the microcolony level and its application to the Vibrio harveyi quorum-sensing circuit., Biophys J, vol. 100, no. 12, pp. 3045-53, 2011.
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. 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.
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.
P. L. Nara, Tobin, G. J., A Chaudhuri, R., Trujillo, J. D., Lin, G., Cho, M. W., Levin, S. A., Ndifon, W., and Wingreen, N. S., How can vaccines against influenza and other viral diseases be made more effective?, PLoS Biol, vol. 8, no. 12, p. e1000571, 2010.
P. L. Nara, Tobin, G. J., A Chaudhuri, R., Trujillo, J. D., Lin, G., Cho, M. W., Levin, S. A., Ndifon, W., and Wingreen, N. S., How can vaccines against influenza and other viral diseases be made more effective?, PLoS Biol, vol. 8, no. 12, p. e1000571, 2010.
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. S. Greene and Troyanskaya, O. G., Integrative systems biology for data-driven knowledge discovery., Semin Nephrol, vol. 30, no. 5, pp. 443-54, 2010.
S. M. Tilghman, It's all about the talent., Mol Biol Cell, vol. 21, no. 22, p. 3823, 2010.
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.
S. - W. Teng, Wang, Y., Tu, K. C., Long, T., Mehta, P., Wingreen, N. S., Bassler, B. L., and Ong, N. P., Measurement of the copy number of the master quorum-sensing regulator of a bacterial cell., Biophys J, vol. 98, no. 9, pp. 2024-31, 2010.
S. - W. Teng, Wang, Y., Tu, K. C., Long, T., Mehta, P., Wingreen, N. S., Bassler, B. L., and Ong, N. P., Measurement of the copy number of the master quorum-sensing regulator of a bacterial cell., Biophys J, vol. 98, no. 9, pp. 2024-31, 2010.
S. J. Silverman, Petti, A. A., Slavov, N., Parsons, L., Briehof, R., Thiberge, S. Y., Zenklusen, D., Gandhi, S. J., Larson, D. R., Singer, R. H., and Botstein, D., Metabolic cycling in single yeast cells from unsynchronized steady-state populations limited on glucose or phosphate., Proc Natl Acad Sci U S A, vol. 107, no. 15, pp. 6946-51, 2010.
K. C. Tu, Long, T., Svenningsen, S. L., Wingreen, N. S., and Bassler, B. L., Negative feedback loops involving small regulatory RNAs precisely control the Vibrio harveyi quorum-sensing response., Mol Cell, vol. 37, no. 4, pp. 567-79, 2010.
A. M. Walczak, Tkačik, G., and Bialek, W., Optimizing information flow in small genetic networks. II. Feed-forward interactions., Phys Rev E Stat Nonlin Soft Matter Phys, vol. 81, no. 4 Pt 1, p. 041905, 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.
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.
H. Goodarzi, Bennett, B. D., Amini, S., Reaves, M. L., Hottes, A. K., Rabinowitz, J. D., and Tavazoie, S., Regulatory and metabolic rewiring during laboratory evolution of ethanol tolerance in E. coli., Mol Syst Biol, vol. 6, p. 378, 2010.
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, Dunham, M., Caudy, A., and Troyanskaya, O., Systematic planning of genome-scale experiments in poorly studied species., PLoS Comput Biol, vol. 6, no. 3, p. e1000698, 2010.
M. Tipping, Kim, Y., Kyriakakis, P., Tong, M., Shvartsman, S. Y., and Veraksa, A., β-arrestin Kurtz inhibits MAPK and Toll signalling in Drosophila development., EMBO J, vol. 29, no. 19, pp. 3222-35, 2010.
M. Tipping, Kim, Y., Kyriakakis, P., Tong, M., Shvartsman, S. Y., and Veraksa, A., β-arrestin Kurtz inhibits MAPK and Toll signalling in Drosophila development., EMBO J, vol. 29, no. 19, pp. 3222-35, 2010.
2009
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.
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.
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.
X. Lu, Li, J. M., Elemento, O., Tavazoie, S., and Wieschaus, E. F., Coupling of zygotic transcription to mitotic control at the Drosophila mid-blastula transition., Development, vol. 136, no. 12, pp. 2101-10, 2009.
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.
G. Tkačik and Bialek, W., Diffusion, dimensionality, and noise in transcriptional regulation., Phys Rev E Stat Nonlin Soft Matter Phys, vol. 79, no. 5 Pt 1, p. 051901, 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.
M. Rebeiz, Ramos-Womack, M., Jeong, S., Andolfatto, P., Werner, T., True, J., Stern, D. L., and Carroll, S. B., Evolution of the tan locus contributed to pigment loss in Drosophila santomea: a response to Matute et al., Cell, vol. 139, no. 6, pp. 1189-96, 2009.
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.
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.
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, 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.
G. Tkačik, Walczak, A. M., and Bialek, W., Optimizing information flow in small genetic networks., Phys Rev E Stat Nonlin Soft Matter Phys, vol. 80, no. 3 Pt 1, p. 031920, 2009.
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.
J. A. Capra, Laskowski, R. A., Thornton, J. M., Singh, M., and Funkhouser, T. A., Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure., PLoS Comput Biol, vol. 5, no. 12, p. e1000585, 2009.
T. Long, Tu, K. C., Wang, Y., Mehta, P., Ong, N. P., Bassler, B. L., and Wingreen, N. S., Quantifying the integration of quorum-sensing signals with single-cell resolution., PLoS Biol, vol. 7, no. 3, p. e68, 2009.
L. Salwinski, Licata, L., Winter, A., Thorneycroft, D., Khadake, J., Ceol, A., Aryamontri, A. Chatr, Oughtred, R., Livstone, M., Boucher, L., Botstein, D., Dolinski, K., Berardini, T., Huala, E., Tyers, M., Eisenberg, D., Cesareni, G., and Hermjakob, H., Recurated protein interaction datasets., Nat Methods, vol. 6, no. 12, pp. 860-1, 2009.

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