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.
S. Gokhale, Lu, W., Zhu, S., Liu, Y., Hart, R. P., Rabinowitz, J. D., and Xie, P., Elevated Choline Kinase α-Mediated Choline Metabolism Supports the Prolonged Survival of TRAF3-Deficient B Lymphocytes., J Immunol, vol. 204, no. 2, pp. 459-471, 2020.
D. Hermans, Gautam, S., García-Cañaveras, J. C., Gromer, D., Mitra, S., Spolski, R., Li, P., Christensen, S., Nguyen, R., Lin, J. - X., Oh, J., Du, N., Veenbergen, S., Fioravanti, J., Ebina-Shibuya, R., Bleck, C., Neckers, L. M., Rabinowitz, J. D., Gattinoni, L., and Leonard, W. J., Lactate dehydrogenase inhibition synergizes with IL-21 to promote CD8 T cell stemness and antitumor immunity., Proc Natl Acad Sci U S A, vol. 117, no. 11, pp. 6047-6055, 2020.
D. Hermans, Gautam, S., García-Cañaveras, J. C., Gromer, D., Mitra, S., Spolski, R., Li, P., Christensen, S., Nguyen, R., Lin, J. - X., Oh, J., Du, N., Veenbergen, S., Fioravanti, J., Ebina-Shibuya, R., Bleck, C., Neckers, L. M., Rabinowitz, J. D., Gattinoni, L., and Leonard, W. J., Lactate dehydrogenase inhibition synergizes with IL-21 to promote CD8 T cell stemness and antitumor immunity., Proc Natl Acad Sci U S A, vol. 117, no. 11, pp. 6047-6055, 2020.
D. Hermans, Gautam, S., García-Cañaveras, J. C., Gromer, D., Mitra, S., Spolski, R., Li, P., Christensen, S., Nguyen, R., Lin, J. - X., Oh, J., Du, N., Veenbergen, S., Fioravanti, J., Ebina-Shibuya, R., Bleck, C., Neckers, L. M., Rabinowitz, J. D., Gattinoni, L., and Leonard, W. J., Lactate dehydrogenase inhibition synergizes with IL-21 to promote CD8 T cell stemness and antitumor immunity., Proc Natl Acad Sci U S A, vol. 117, no. 11, pp. 6047-6055, 2020.
D. Hermans, Gautam, S., García-Cañaveras, J. C., Gromer, D., Mitra, S., Spolski, R., Li, P., Christensen, S., Nguyen, R., Lin, J. - X., Oh, J., Du, N., Veenbergen, S., Fioravanti, J., Ebina-Shibuya, R., Bleck, C., Neckers, L. M., Rabinowitz, J. D., Gattinoni, L., and Leonard, W. J., Lactate dehydrogenase inhibition synergizes with IL-21 to promote CD8 T cell stemness and antitumor immunity., Proc Natl Acad Sci U S A, vol. 117, no. 11, pp. 6047-6055, 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.
L. Yang, Canaveras, J. Carlos Gar, Chen, Z., Wang, L., Liang, L., Jang, C., Mayr, J. A., Zhang, Z., Ghergurovich, J. M., Zhan, L., Joshi, S., Hu, Z., McReynolds, M. R., Su, X., White, E., Morscher, R. J., and Rabinowitz, J. D., Serine Catabolism Feeds NADH when Respiration Is Impaired., Cell Metab, vol. 31, no. 4, pp. 809-821.e6, 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.
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.
C. Jang, Hui, S., Zeng, X., Cowan, A. J., Wang, L., Chen, L., Morscher, R. J., Reyes, J., Frezza, C., Hwang, H. Y., Imai, A., Saito, Y., Okamoto, K., Vaspoli, C., Kasprenski, L., Zsido, G. A. 2nd, Gorman, J. H. 3rd, Gorman, R. C., and Rabinowitz, J. D., Metabolite exchange between mammalian organs quantified in pigs., Cell Metab., vol. 30, no. 3, pp. 594-606, 2019.
C. Jang, Hui, S., Zeng, X., Cowan, A. J., Wang, L., Chen, L., Morscher, R. J., Reyes, J., Frezza, C., Hwang, H. Y., Imai, A., Saito, Y., Okamoto, K., Vaspoli, C., Kasprenski, L., Zsido, G. A. 2nd, Gorman, J. H. 3rd, Gorman, R. C., and Rabinowitz, J. D., Metabolite exchange between mammalian organs quantified in pigs., Cell Metab., vol. 30, no. 3, pp. 594-606, 2019.
C. Jang, Hui, S., Zeng, X., Cowan, A. J., Wang, L., Chen, L., Morscher, R. J., Reyes, J., Frezza, C., Hwang, H. Young, Imai, A., Saito, Y., Okamoto, K., Vaspoli, C., Kasprenski, L., Zsido, G. A., Gorman, J. H., Gorman, R. C., and Rabinowitz, J. D., Metabolite Exchange between Mammalian Organs Quantified in Pigs., Cell Metab, vol. 30, no. 3, pp. 594-606.e3, 2019.
C. Jang, Hui, S., Zeng, X., Cowan, A. J., Wang, L., Chen, L., Morscher, R. J., Reyes, J., Frezza, C., Hwang, H. Young, Imai, A., Saito, Y., Okamoto, K., Vaspoli, C., Kasprenski, L., Zsido, G. A., Gorman, J. H., Gorman, R. C., and Rabinowitz, J. D., Metabolite Exchange between Mammalian Organs Quantified in Pigs., Cell Metab, vol. 30, no. 3, pp. 594-606.e3, 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.
A. S. Dekhne, Shah, K., Ducker, G. S., Katinas, J. M., Wong-Roushar, J., Nayeen, M. Junayed, Doshi, A., Ning, C., Bao, X., Frühauf, J., Liu, J., Wallace-Povirk, A., O'Connor, C., Dzinic, S. H., White, K., Kushner, J., Kim, S., Hüttemann, M., Polin, L., Rabinowitz, J. D., Li, J., Hou, Z., Dann, C. E., Gangjee, A., and Matherly, L. H., Novel pyrrolo[3,2-d]pyrimidine compounds target mitochondrial and cytosolic one-carbon metabolism with broad-spectrum antitumor efficacy., Mol Cancer Ther, 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.
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.
J. C. García-Cañaveras, Chen, L., and Rabinowitz, J. D., The Tumor Metabolic Microenvironment: Lessons from Lactate., Cancer Res, vol. 79, no. 13, pp. 3155-3162, 2019.
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.
L. Poillet-Perez, Xie, X., Zhan, L., Yang, Y., Sharp, D. W., Hu, Z. Sherrie, Su, X., Maganti, A., Jiang, C., Lu, W., Zheng, H., Bosenberg, M. W., Mehnert, J. M., Guo, J. Yanxiang, Lattime, E., Rabinowitz, J. D., and White, E., Autophagy maintains tumour growth through circulating arginine., Nature, vol. 563, no. 7732, pp. 569-573, 2018.
P. A. Gibney, Schieler, A., Chen, J. C., Bacha-Hummel, J. M., Botstein, M., Volpe, M., Silverman, S. J., Xu, Y., Bennett, B. D., Rabinowitz, J. D., and Botstein, D., Common and divergent features of galactose-1-phosphate and fructose-1-phosphate toxicity in yeast., Mol Biol Cell, vol. 29, no. 8, pp. 897-910, 2018.
N. Ron-Harel, Notarangelo, G., Ghergurovich, J. M., Paulo, J. A., Sage, P. T., Santos, D., F Satterstrom, K., Gygi, S. P., Rabinowitz, J. D., Sharpe, A. H., and Haigis, M. C., Defective respiration and one-carbon metabolism contribute to impaired naïve T cell activation in aged mice., Proc Natl Acad Sci U S A, vol. 115, no. 52, pp. 13347-13352, 2018.
N. Ron-Harel, Notarangelo, G., Ghergurovich, J. M., Paulo, J. A., Sage, P. T., Santos, D., F Satterstrom, K., Gygi, S. P., Rabinowitz, J. D., Sharpe, A. H., and Haigis, M. C., Defective respiration and one-carbon metabolism contribute to impaired naïve T cell activation in aged mice., Proc Natl Acad Sci U S A, vol. 115, no. 52, pp. 13347-13352, 2018.
D. Guan, Xiong, Y., Borck, P. C., Jang, C., Doulias, P. - T., Papazyan, R., Fang, B., Jiang, C., Zhang, Y., Briggs, E. R., Hu, W., Steger, D., Ischiropoulos, H., Rabinowitz, J. D., and Lazar, M. A., Diet-Induced Circadian Enhancer Remodeling Synchronizes Opposing Hepatic Lipid Metabolic Processes., Cell, vol. 174, no. 4, pp. 831-842.e12, 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.
S. Hsin- Jung Li, Li, Z., Park, J. O., King, C. G., Rabinowitz, J. D., Wingreen, N. S., and Gitai, Z., Escherichia coli translation strategies differ across carbon, nitrogen and phosphorus limitation conditions., Nat Microbiol, vol. 3, no. 8, pp. 939-947, 2018.
J. M. Akey, Evolution of DNAase I hypersensitive sites in MHC regulatory regions of primates., Genetics, vol. 209, no. 2, pp. 579-589, 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.
R. J. Morscher, Ducker, G. S., Li, S. Hsin- Jung, Mayer, J. A., Gitai, Z., Sperl, W., and Rabinowitz, J. D., Mitochondrial translation requires folate-dependent tRNA methylation., Nature, vol. 554, no. 7690, pp. 128-132, 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.
D. Munro, Ghersi, D., and Singh, M., Two critical positions in zinc finger domains are heavily mutated in three human cancer types., PLoS Comput Biol, vol. 14, no. 6, p. e1006290, 2018.
2017
R. C. Oslund, Su, X., Haugbro, M., Kee, J. - M., Esposito, M., David, Y., Wang, B., Ge, E., Perlman, D. H., Kang, Y., Muir, T. W., and Rabinowitz, J. D., Bisphosphoglycerate mutase controls serine pathway flux via 3-phosphoglycerate., Nat Chem Biol, vol. 13, no. 10, pp. 1081-1087, 2017.
G. S. Liu, Bratton, B. P., Gitai, Z., and Shaevitz, J. W., The effect of antibiotics on protein diffusion in the Escherichia coli cytoplasmic membrane., PLoS One, vol. 12, no. 10, p. e0185810, 2017.
Y. Zhang, Kurupati, R., Liu, L., Zhou, X. Yang, Zhang, G., Hudaihed, A., Filisio, F., Giles-Davis, W., Xu, X., Karakousis, G. C., Schuchter, L. M., Xu, W., Amaravadi, R., Xiao, M., Sadek, N., Krepler, C., Herlyn, M., Freeman, G. J., Rabinowitz, J. D., and Ertl, H. C. J., Enhancing CD8(+) T Cell Fatty Acid Catabolism within a Metabolically Challenging Tumor Microenvironment Increases the Efficacy of Melanoma Immunotherapy., Cancer Cell, vol. 32, no. 3, pp. 377-391.e9, 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.
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.
G. S. Ducker, Ghergurovich, J. M., Mainolfi, N., Suri, V., Jeong, S. K., Li, S. Hsin- Jung, Friedman, A., Manfredi, M. G., Gitai, Z., Kim, H., and Rabinowitz, J. D., Human SHMT inhibitors reveal defective glycine import as a targetable metabolic vulnerability of diffuse large B-cell lymphoma., Proc Natl Acad Sci U S A, vol. 114, no. 43, pp. 11404-11409, 2017.
G. S. Ducker, Ghergurovich, J. M., Mainolfi, N., Suri, V., Jeong, S. K., Li, S. Hsin- Jung, Friedman, A., Manfredi, M. G., Gitai, Z., Kim, H., and Rabinowitz, J. D., Human SHMT inhibitors reveal defective glycine import as a targetable metabolic vulnerability of diffuse large B-cell lymphoma., Proc Natl Acad Sci U S A, vol. 114, no. 43, pp. 11404-11409, 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.
Y. Gong, Cao, R., Ding, G., Hong, S., Zhou, W., Lu, W., Damle, M., Fang, B., Wang, C. C., Qian, J., Lie, N., Lanzillotta, C., Rabinowitz, J. D., and Sun, Z., Integrated omics approaches to characterize a nuclear receptor corepressor-associated histone deacetylase in mouse skeletal muscle., Mol Cell Endocrinol, 2017.
A. L. Wooldridge, Bischof, R. J., Liu, H., Heinemann, G. K., Hunter, D. S., Giles, L. C., Simmons, R. A., Lien, Y. - C., Lu, W., Rabinowitz, J. D., Kind, K. L., Owens, J. A., Clifton, V. L., and Gatford, K. L., Late gestation maternal dietary methyl donor and cofactor supplementation in sheep partially reverses protection against allergic sensitization by IUGR., Am J Physiol Regul Integr Comp Physiol, p. ajpregu.00549.2016, 2017.
A. L. Wooldridge, Bischof, R. J., Liu, H., Heinemann, G. K., Hunter, D. S., Giles, L. C., Simmons, R. A., Lien, Y. - C., Lu, W., Rabinowitz, J. D., Kind, K. L., Owens, J. A., Clifton, V. L., and Gatford, K. L., Late gestation maternal dietary methyl donor and cofactor supplementation in sheep partially reverses protection against allergic sensitization by IUGR., Am J Physiol Regul Integr Comp Physiol, p. ajpregu.00549.2016, 2017.
T. M. Bartlett, Bratton, B. P., Duvshani, A., Miguel, A., Sheng, Y., Martin, N. R., Nguyen, J. P., Persat, A., Desmarais, S. M., VanNieuwenhze, M. S., Huang, K. Casey, Zhu, J., Shaevitz, J. W., and Gitai, Z., A Periplasmic Polymer Curves Vibrio cholerae and Promotes Pathogenesis., Cell, vol. 168, no. 1-2, pp. 172-185.e15, 2017.
W. A. Rogers, Goyal, Y., Yamaya, K., Shvartsman, S. Y., and Levine, M. S., Uncoupling neurogenic gene networks in the Drosophila embryo., Genes Dev, vol. 31, no. 7, pp. 634-638, 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. Engel, Kwong, W. K., McFrederick, Q., Anderson, K. E., Barribeau, S. Michael, Chandler, J. Angus, R Cornman, S., Dainat, J., de Miranda, J. R., Doublet, V., Emery, O., Evans, J. D., Farinelli, L., Flenniken, M. L., Granberg, F., Grasis, J. A., Gauthier, L., Hayer, J., Koch, H., Kocher, S., Martinson, V. G., Moran, N., Munoz-Torres, M., Newton, I., Paxton, R. J., Powell, E., Sadd, B. M., Schmid-Hempel, P., Schmid-Hempel, R., Song, S. Jin, Schwarz, R. S., vanEngelsdorp, D., and Dainat, B., The Bee Microbiome: Impact on Bee Health and Model for Evolution and Ecology of Host-Microbe Interactions., MBio, vol. 7, no. 2, pp. e02164-15, 2016.
P. Engel, Kwong, W. K., McFrederick, Q., Anderson, K. E., Barribeau, S. Michael, Chandler, J. Angus, R Cornman, S., Dainat, J., de Miranda, J. R., Doublet, V., Emery, O., Evans, J. D., Farinelli, L., Flenniken, M. L., Granberg, F., Grasis, J. A., Gauthier, L., Hayer, J., Koch, H., Kocher, S., Martinson, V. G., Moran, N., Munoz-Torres, M., Newton, I., Paxton, R. J., Powell, E., Sadd, B. M., Schmid-Hempel, P., Schmid-Hempel, R., Song, S. Jin, Schwarz, R. S., vanEngelsdorp, D., and Dainat, B., The Bee Microbiome: Impact on Bee Health and Model for Evolution and Ecology of Host-Microbe Interactions., MBio, vol. 7, no. 2, pp. e02164-15, 2016.
P. Engel, Kwong, W. K., McFrederick, Q., Anderson, K. E., Barribeau, S. Michael, Chandler, J. Angus, R Cornman, S., Dainat, J., de Miranda, J. R., Doublet, V., Emery, O., Evans, J. D., Farinelli, L., Flenniken, M. L., Granberg, F., Grasis, J. A., Gauthier, L., Hayer, J., Koch, H., Kocher, S., Martinson, V. G., Moran, N., Munoz-Torres, M., Newton, I., Paxton, R. J., Powell, E., Sadd, B. M., Schmid-Hempel, P., Schmid-Hempel, R., Song, S. Jin, Schwarz, R. S., vanEngelsdorp, D., and Dainat, B., The Bee Microbiome: Impact on Bee Health and Model for Evolution and Ecology of Host-Microbe Interactions., MBio, vol. 7, no. 2, pp. e02164-15, 2016.
C. Jang, Oh, S. F., Wada, S., Rowe, G. C., Liu, L., Chan, M. Chun, Rhee, J., Hoshino, A., Kim, B., Ibrahim, A., Baca, L. G., Kim, E., Ghosh, C. C., Parikh, S. M., Jiang, A., Chu, Q., Forman, D. E., Lecker, S. H., Krishnaiah, S., Rabinowitz, J. D., Weljie, A. M., Baur, J. A., Kasper, D. L., and Arany, Z., A branched-chain amino acid metabolite drives vascular fatty acid transport and causes insulin resistance., Nat Med, vol. 22, no. 4, pp. 421-6, 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.
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.
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.
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.
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.
N. Ron-Harel, Santos, D., Ghergurovich, J. M., Sage, P. T., Reddy, A., Lovitch, S. B., Dephoure, N., F Satterstrom, K., Sheffer, M., Spinelli, J. B., Gygi, S., Rabinowitz, J. D., Sharpe, A. H., and Haigis, M. C., Mitochondrial Biogenesis and Proteome Remodeling Promote One-Carbon Metabolism for T Cell Activation., Cell Metab, vol. 24, no. 1, pp. 104-17, 2016.
N. Ron-Harel, Santos, D., Ghergurovich, J. M., Sage, P. T., Reddy, A., Lovitch, S. B., Dephoure, N., F Satterstrom, K., Sheffer, M., Spinelli, J. B., Gygi, S., Rabinowitz, J. D., Sharpe, A. H., and Haigis, M. C., Mitochondrial Biogenesis and Proteome Remodeling Promote One-Carbon Metabolism for T Cell Activation., Cell Metab, vol. 24, no. 1, pp. 104-17, 2016.
E. Esposito, Lim, B., Guessous, G., Falahati, H., and Levine, M., Mitosis-associated repression in development., Genes Dev, vol. 30, no. 13, pp. 1503-8, 2016.
N. Ouzounov, Nguyen, J. P., Bratton, B. P., Jacobowitz, D., Gitai, Z., and Shaevitz, J. W., MreB Orientation Correlates with Cell Diameter in Escherichia coli., Biophys J, vol. 111, no. 5, pp. 1035-43, 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.
S. R. Hackett, Zanotelli, V. R. T., Xu, W., Goya, J., Park, J. O., Perlman, D. H., Gibney, P. A., Botstein, D., Storey, J. D., and Rabinowitz, J. D., Systems-level analysis of mechanisms regulating yeast metabolic flux., Science, vol. 354, no. 6311, 2016.
S. R. Hackett, Zanotelli, V. R. T., Xu, W., Goya, J., Park, J. O., Perlman, D. H., Gibney, P. A., Botstein, D., Storey, J. D., and Rabinowitz, J. D., Systems-level analysis of mechanisms regulating yeast metabolic flux., Science, vol. 354, no. 6311, 2016.
D. A. Galbraith, Kocher, S. D., Glenn, T., Albert, I., Hunt, G. J., Strassmann, J. E., Queller, D. C., and Grozinger, C. M., Testing the kinship theory of intragenomic conflict in honey bees (Apis mellifera)., Proc Natl Acad Sci U S A, vol. 113, no. 4, pp. 1020-5, 2016.
D. A. Galbraith, Kocher, S. D., Glenn, T., Albert, I., Hunt, G. J., Strassmann, J. E., Queller, D. C., and Grozinger, C. M., Testing the kinship theory of intragenomic conflict in honey bees (Apis mellifera)., Proc Natl Acad Sci U S A, vol. 113, no. 4, pp. 1020-5, 2016.
D. A. Galbraith, Kocher, S. D., Glenn, T., Albert, I., Hunt, G. J., Strassmann, J. E., Queller, D. C., and Grozinger, C. M., Testing the kinship theory of intragenomic conflict in honey bees (Apis mellifera)., Proc Natl Acad Sci U S A, vol. 113, no. 4, pp. 1020-5, 2016.
2015
J. F. Ayroles, Buchanan, S. M., O'Leary, C., Skutt-Kakaria, K., Grenier, J. K., Clark, A. G., Hartl, D. L., and de Bivort, B. L., Behavioral idiosyncrasy reveals genetic control of phenotypic variability., Proc Natl Acad Sci U S A, vol. 112, no. 21, pp. 6706-11, 2015.
J. Wang, Kaletsky, R., Silva, M., Williams, A., Haas, L. A., Androwski, R. J., Landis, J. N., Patrick, C., Rashid, A., Santiago-Martinez, D., Gravato-Nobre, M., Hodgkin, J., Hall, D. H., Murphy, C. T., and Barr, M. M., Cell-Specific Transcriptional Profiling of Ciliated Sensory Neurons Reveals Regulators of Behavior and Extracellular Vesicle Biogenesis., Curr Biol, vol. 25, no. 24, pp. 3232-8, 2015.
P. A. Gibney, Schieler, A., Chen, J. C., Rabinowitz, J. D., and Botstein, D., Characterizing the in vivo role of trehalose in Saccharomyces cerevisiae using the AGT1 transporter., Proc Natl Acad Sci U S A, 2015.
B. T Gainous, Wagner, E., and Levine, M., Diverse ETS transcription factors mediate FGF signaling in the Ciona anterior neural plate., Dev Biol, 2015.
J. P. Bothma, Garcia, H. G., Ng, S., Perry, M. W., Gregor, T., and Levine, M., Enhancer additivity and non-additivity are determined by enhancer strength in the Drosophila embryo., Elife, vol. 4, 2015.
J. P. Bothma, Garcia, H. G., Ng, S., Perry, M. W., Gregor, T., and Levine, M., Enhancer additivity and non-additivity are determined by enhancer strength in the Drosophila embryo., Elife, vol. 4, 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.
Y. Pritykin, Ghersi, D., and Singh, M., Genome-Wide Detection and Analysis of Multifunctional Genes., PLoS Comput Biol, vol. 11, no. 10, p. e1004467, 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.
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. 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.
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.
A. J. Bott, Peng, I. - C., Fan, Y., Faubert, B., Zhao, L., Li, J., Neidler, S., Sun, Y., Jaber, N., Krokowski, D., Lu, W., Pan, J. - A., Powers, S., Rabinowitz, J., Hatzoglou, M., Murphy, D. J., Jones, R., Wu, S., Girnun, G., and Zong, W. - X., Oncogenic Myc Induces Expression of Glutamine Synthetase through Promoter Demethylation., Cell Metab, vol. 22, no. 6, pp. 1068-77, 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.
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.
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.
R. M. Morgenstein, Bratton, B. P., Nguyen, J. P., Ouzounov, N., Shaevitz, J. W., and Gitai, Z., RodZ links MreB to cell wall synthesis to mediate MreB rotation and robust morphogenesis., Proc Natl Acad Sci U S A, vol. 112, no. 40, pp. 12510-5, 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.
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.
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.
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.
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.
N. V. Rajeshkumar, Dutta, P., Yabuuchi, S., de Wilde, R. F., Martinez, G. V., Le, A., Kamphorst, J. J., Rabinowitz, J. D., Jain, S. K., Hidalgo, M., Dang, C. V., Gillies, R. J., and Maitra, A., Therapeutic Targeting of the Warburg Effect in Pancreatic Cancer Relies on an Absence of p53 Function., Cancer Res, vol. 75, no. 16, pp. 3355-64, 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.
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
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.
D. G. Robinson, Chen, W., Storey, J. D., and Gresham, D., Design and analysis of Bar-seq experiments., G3 (Bethesda), vol. 4, no. 1, pp. 11-8, 2014.
J. P. Bothma, Garcia, H. G., Esposito, E., Schlissel, G., Gregor, T., and Levine, M., Dynamic regulation of eve stripe 2 expression reveals transcriptional bursts in living Drosophila embryos., Proc Natl Acad Sci U S A, vol. 111, no. 29, pp. 10598-603, 2014.
J. P. Bothma, Garcia, H. G., Esposito, E., Schlissel, G., Gregor, T., and Levine, M., Dynamic regulation of eve stripe 2 expression reveals transcriptional bursts in living Drosophila embryos., Proc Natl Acad Sci U S A, vol. 111, no. 29, pp. 10598-603, 2014.
T. Gregor, Garcia, H. G., and Little, S. C., The embryo as a laboratory: quantifying transcription in Drosophila., Trends Genet, vol. 30, no. 8, pp. 364-75, 2014.
T. Gregor, Garcia, H. G., and Little, S. C., The embryo as a laboratory: quantifying transcription in Drosophila., Trends Genet, vol. 30, no. 8, pp. 364-75, 2014.
M. Castellana, Wilson, M. Z., Xu, Y., Joshi, P., Cristea, I. M., Rabinowitz, J. D., Gitai, Z., and Wingreen, N. S., Enzyme clustering accelerates processing of intermediates through metabolic channeling., Nat Biotechnol, vol. 32, no. 10, pp. 1011-8, 2014.
L. Abouchar, Petkova, M. D., Steinhardt, C. R., and Gregor, T., Fly wing vein patterns have spatial reproducibility of a single cell., J R Soc Interface, vol. 11, no. 97, p. 20140443, 2014.
J. Kim, Ghasemzadeh, N., Eapen, D. J., Chung, N. Christophe, Storey, J. D., Quyyumi, A. A., and Gibson, G., Gene expression profiles associated with acute myocardial infarction and risk of cardiovascular death., Genome Med, vol. 6, no. 5, p. 40, 2014.
J. Kim, Ghasemzadeh, N., Eapen, D. J., Chung, N. Christophe, Storey, J. D., Quyyumi, A. A., and Gibson, G., Gene expression profiles associated with acute myocardial infarction and risk of cardiovascular death., Genome Med, vol. 6, no. 5, p. 40, 2014.
D. Ghersi and Singh, M., Interaction-based discovery of functionally important genes in cancers., Nucleic Acids Res, vol. 42, no. 3, p. e18, 2014.
R. M. Barry, Bitbol, A. - F., Lorestani, A., Charles, E. J., Habrian, C. H., Hansen, J. M., Li, H. - J., Baldwin, E. P., Wingreen, N. S., Kollman, J. M., and Gitai, Z., Large-scale filament formation inhibits the activity of CTP synthetase., Elife, vol. 3, p. e03638, 2014.
M. D. Petkova, Little, S. C., Liu, F., and Gregor, T., Maternal origins of developmental reproducibility., Curr Biol, vol. 24, no. 11, pp. 1283-8, 2014.
D. Ghersi and Singh, M., molBLOCKS: decomposing small molecule sets and uncovering enriched fragments., Bioinformatics, vol. 30, no. 14, pp. 2081-3, 2014.
D. Krotov, Dubuis, J. O., Gregor, T., and Bialek, W., Morphogenesis at criticality., Proc Natl Acad Sci U S A, vol. 111, no. 10, pp. 3683-8, 2014.
T. S. Ursell, Nguyen, J., Monds, R. D., Colavin, A., Billings, G., Ouzounov, N., Gitai, Z., Shaevitz, J. W., and Huang, K. Casey, Rod-like bacterial shape is maintained by feedback between cell curvature and cytoskeletal localization., Proc Natl Acad Sci U S A, vol. 111, no. 11, pp. E1025-34, 2014.
W. Bialek, Cavagna, A., Giardina, I., Mora, T., Pohl, O., Silvestri, E., Viale, M., and Walczak, A. M., Social interactions dominate speed control in poising natural flocks near criticality., Proc Natl Acad Sci U S A, vol. 111, no. 20, pp. 7212-7, 2014.
S. R McIsaac, Gibney, P. A., Chandran, S. S., Benjamin, K. R., and Botstein, D., Synthetic biology tools for programming gene expression without nutritional perturbations in Saccharomyces cerevisiae., Nucleic Acids Res, vol. 42, no. 6, p. e48, 2014.
2013
J. O. Dubuis, Samanta, R., and Gregor, T., Accurate measurements of dynamics and reproducibility in small genetic networks., Mol Syst Biol, vol. 9, p. 639, 2013.
S. L. Grady, Purdy, J. G., Rabinowitz, J. D., and Shenk, T., Argininosuccinate synthetase 1 depletion produces a metabolic state conducive to herpes simplex virus 1 infection., Proc Natl Acad Sci U S A, vol. 110, no. 51, pp. E5006-15, 2013.
A. Munivenkatappa, Devi, B. Indira, Gregor, T. Issac, Bhat, D. I., Kumarsamy, A. Deepika, and Shukla, D. P., Bicycle accident-related head injuries in India., J Neurosci Rural Pract, vol. 4, no. 3, pp. 262-6, 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.
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.
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.
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.
D. Ghersi and Singh, M., Disentangling function from topology to infer the network properties of disease genes., BMC Syst Biol, vol. 7, p. 5, 2013.
F. Liu, Morrison, A. H., and Gregor, T., Dynamic interpretation of maternal inputs by the Drosophila segmentation gene network., Proc Natl Acad Sci U S A, vol. 110, no. 17, pp. 6724-9, 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.
P. V. Gordon, Muratov, C. B., and Shvartsman, S. Y., Local accumulation times for source, diffusion, and degradation models in two and three dimensions., J Chem Phys, vol. 138, no. 10, p. 104121, 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.
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.
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.
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.
P. A. Gibney, Hickman, M. J., Bradley, P. H., Matese, J. C., and Botstein, D., Phylogenetic portrait of the Saccharomyces cerevisiae functional genome., G3 (Bethesda), vol. 3, no. 8, pp. 1335-40, 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.
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.
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.
S. C. Little and Gregor, T., Sorting sloppy Sonic., Cell, vol. 153, no. 3, pp. 509-10, 2013.
A. Z. Welch, Gibney, P. A., Botstein, D., and Koshland, D. E., TOR and RAS pathways regulate desiccation tolerance in Saccharomyces cerevisiae., Mol Biol Cell, vol. 24, no. 2, pp. 115-28, 2013.
P. A. Gibney, Lu, C., Caudy, A. A., Hess, D. C., and Botstein, D., Yeast metabolic and signaling genes are required for heat-shock survival and have little overlap with the heat-induced genes., Proc Natl Acad Sci U S A, vol. 110, no. 46, pp. E4393-402, 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.
W. Huang, Richards, S., Carbone, M. Anna, Zhu, D., Anholt, R. R. H., Ayroles, J. F., Duncan, L., Jordan, K. W., Lawrence, F., Magwire, M. M., Warner, C. B., Blankenburg, K., Han, Y., Javaid, M., Jayaseelan, J., Jhangiani, S. N., Muzny, D., Ongeri, F., Perales, L., Wu, Y. - Q., Zhang, Y., Zou, X., Stone, E. A., Gibbs, R. A., and Mackay, T. F. C., Epistasis dominates the genetic architecture of Drosophila quantitative traits., Proc Natl Acad Sci U S A, vol. 109, no. 39, pp. 15553-9, 2012.
J. Cande, Andolfatto, P., Prud'homme, B., Stern, D. L., and Gompel, N., Evolution of multiple additive loci caused divergence between Drosophila yakuba and D. santomea in wing rowing during male courtship., PLoS One, vol. 7, no. 8, p. e43888, 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.
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.
S. L. Grady, Hwang, J., Vastag, L., Rabinowitz, J. D., and Shenk, T., Herpes simplex virus 1 infection activates poly(ADP-ribose) polymerase and triggers the degradation of poly(ADP-ribose) glycohydrolase., J Virol, vol. 86, no. 15, pp. 8259-68, 2012.
S. van Teeffelen, Shaevitz, J. W., and Gitai, Z., Image analysis in fluorescence microscopy: bacterial dynamics as a case study., Bioessays, vol. 34, no. 5, pp. 427-36, 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.
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.
J. C. Gerhart, Martin, G. R., and Wieschaus, E. F., Introducing WIREs Developmental Biology., Wiley Interdiscip Rev Dev Biol, vol. 1, no. 1, pp. 1-2, 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.
A. H. Morrison, Scheeler, M., Dubuis, J., and Gregor, T., Quantifying the Bicoid morphogen gradient in living fly embryos., Cold Spring Harb Protoc, vol. 2012, no. 4, pp. 398-406, 2012.
Y. - F. Xu, Zhao, X., Glass, D. S., Absalan, F., Perlman, D. H., Broach, J. R., and Rabinowitz, J. D., Regulation of yeast pyruvate kinase by ultrasensitive allostery independent of phosphorylation., Mol Cell, vol. 48, no. 1, pp. 52-62, 2012.
W. Bialek, Cavagna, A., Giardina, I., Mora, T., Silvestri, E., Viale, M., and Walczak, A. M., Statistical mechanics for natural flocks of birds., Proc Natl Acad Sci U S A, vol. 109, no. 13, pp. 4786-91, 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.
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.
O. Grimm, Zini, V. Sanchez, Kim, Y., Casanova, J., Shvartsman, S. Y., and Wieschaus, E., Torso RTK controls Capicua degradation by changing its subcellular localization., Development, vol. 139, no. 21, pp. 3962-8, 2012.
U. Ober, Ayroles, J. F., Stone, E. A., Richards, S., Zhu, D., Gibbs, R. A., Stricker, C., Gianola, D., Schlather, M., Mackay, T. F. C., and Simianer, H., Using whole-genome sequence data to predict quantitative trait phenotypes in Drosophila melanogaster., PLoS Genet, vol. 8, no. 5, p. e1002685, 2012.
U. Ober, Ayroles, J. F., Stone, E. A., Richards, S., Zhu, D., Gibbs, R. A., Stricker, C., Gianola, D., Schlather, M., Mackay, T. F. C., and Simianer, H., Using whole-genome sequence data to predict quantitative trait phenotypes in Drosophila melanogaster., PLoS Genet, vol. 8, no. 5, p. e1002685, 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
S. van Teeffelen, Wang, S., Furchtgott, L., Huang, K. Casey, Wingreen, N. S., Shaevitz, J. W., and Gitai, Z., The bacterial actin MreB rotates, and rotation depends on cell-wall assembly., Proc Natl Acad Sci U S A, vol. 108, no. 38, pp. 15822-7, 2011.
D. Papatsenko, Levine, M., and Goltsev, Y., Clusters of temporal discordances reveal distinct embryonic patterning mechanisms in Drosophila and anopheles., PLoS Biol, vol. 9, no. 1, p. e1000584, 2011.
L. Vastag, Koyuncu, E., Grady, S. L., Shenk, T. E., and Rabinowitz, J. D., Divergent effects of human cytomegalovirus and herpes simplex virus-1 on cellular metabolism., PLoS Pathog, vol. 7, no. 7, p. e1002124, 2011.
S. R McIsaac, Silverman, S. J., McClean, M. N., Gibney, P. A., Macinskas, J., Hickman, M. J., Petti, A. A., and Botstein, D., Fast-acting and nearly gratuitous induction of gene expression and protein depletion in Saccharomyces cerevisiae., Mol Biol Cell, vol. 22, no. 22, pp. 4447-59, 2011.
E. J. Banigan, Gelbart, M. A., Gitai, Z., Wingreen, N. S., and Liu, A. J., Filament depolymerization can explain chromosome pulling during bacterial mitosis., PLoS Comput Biol, vol. 7, no. 9, p. e1002145, 2011.
E. J. Banigan, Gelbart, M. A., Gitai, Z., Wingreen, N. S., and Liu, A. J., Filament depolymerization can explain chromosome pulling during bacterial mitosis., PLoS Comput Biol, vol. 7, no. 9, p. e1002145, 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.
P. V. Gordon, Sample, C., Berezhkovskii, A. M., Muratov, C. B., and Shvartsman, S. Y., Local kinetics of morphogen gradients., Proc Natl Acad Sci U S A, vol. 108, no. 15, pp. 6157-62, 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.
K. Chung, Kim, Y., Kanodia, J. S., Gong, E., Shvartsman, S. Y., and Lu, H., A microfluidic array for large-scale ordering and orientation of embryos., Nat Methods, vol. 8, no. 2, pp. 171-6, 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.
M. F. Clasquin, Melamud, E., Singer, A., Gooding, J. R., Xu, X., Dong, A., Cui, H., Campagna, S. R., Savchenko, A., Yakunin, A. F., Rabinowitz, J. D., and Caudy, A. A., Riboneogenesis in yeast., Cell, vol. 145, no. 6, pp. 969-80, 2011.
C. B. Muratov, Gordon, P. V., and Shvartsman, S. Y., Self-similar dynamics of morphogen gradients., Phys Rev E Stat Nonlin Soft Matter Phys, vol. 84, no. 4 Pt 1, p. 041916, 2011.
D. Gresham, Boer, V. M., Caudy, A., Ziv, N., Brandt, N. J., Storey, J. D., and Botstein, D., System-level analysis of genes and functions affecting survival during nutrient starvation in Saccharomyces cerevisiae., Genetics, vol. 187, no. 1, pp. 299-317, 2011.
2010
S. Goyal, Yuan, J., Chen, T., Rabinowitz, J. D., and Wingreen, N. S., Achieving optimal growth through product feedback inhibition in metabolism., PLoS Comput Biol, vol. 6, no. 6, p. e1000802, 2010.
D. Gresham, Usaite, R., Germann, S. Manuela, Lisby, M., Botstein, D., and Regenberg, B., Adaptation to diverse nitrogen-limited environments by deletion or extrachromosomal element formation of the GAP1 locus., Proc Natl Acad Sci U S A, vol. 107, no. 43, pp. 18551-6, 2010.
D. Gresham, Usaite, R., Germann, S. Manuela, Lisby, M., Botstein, D., and Regenberg, B., Adaptation to diverse nitrogen-limited environments by deletion or extrachromosomal element formation of the GAP1 locus., Proc Natl Acad Sci U S A, vol. 107, no. 43, pp. 18551-6, 2010.
P. Mehta and Gregor, T., Approaching the molecular origins of collective dynamics in oscillating cell populations., Curr Opin Genet Dev, vol. 20, no. 6, pp. 574-80, 2010.
O. Grimm and Wieschaus, E., The Bicoid gradient is shaped independently of nuclei., Development, vol. 137, no. 17, pp. 2857-62, 2010.
K. L. Olszewski, Mather, M. W., Morrisey, J. M., Garcia, B. A., Vaidya, A. B., Rabinowitz, J. D., and Llinás, M., Branched tricarboxylic acid metabolism in Plasmodium falciparum., Nature, vol. 466, no. 7307, pp. 774-8, 2010.
A. Stolfi, T Gainous, B., Young, J. J., Mori, A., Levine, M., and Christiaen, L., Early chordate origins of the vertebrate second heart field., Science, vol. 329, no. 5991, pp. 565-8, 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.
The Gene Ontology in 2010: extensions and refinements., Nucleic Acids Res, vol. 38, no. Database issue, pp. D331-5, 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.
B. M. Zee, Levin, R. S., Xu, B., LeRoy, G., Wingreen, N. S., and Garcia, B. A., In vivo residue-specific histone methylation dynamics., J Biol Chem, vol. 285, no. 5, pp. 3341-50, 2010.
S. D. Kocher, Ayroles, J. F., Stone, E. A., and Grozinger, C. M., Individual variation in pheromone response correlates with reproductive traits and brain gene expression in worker honey bees., PLoS One, vol. 5, no. 2, p. e9116, 2010.
A. C. Martin, Gelbart, M., Fernandez-Gonzalez, R., Kaschube, M., and Wieschaus, E. F., Integration of contractile forces during tissue invagination., J Cell Biol, vol. 188, no. 5, pp. 735-49, 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.
Y. Kim, Coppey, M., Grossman, R., Ajuria, L., Jiménez, G., Paroush, Z. 'ev, and Shvartsman, S. Y., MAPK substrate competition integrates patterning signals in the Drosophila embryo., Curr Biol, vol. 20, no. 5, pp. 446-51, 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.
O. Grimm, Coppey, M., and Wieschaus, E., Modelling the Bicoid gradient., Development, vol. 137, no. 14, pp. 2253-64, 2010.

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