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.
P. F. Przytycki and Singh, M., Differential Allele-Specific Expression Uncovers Breast Cancer Genes Dysregulated by Cis Noncoding Mutations., Cell Syst, vol. 10, no. 2, pp. 193-203.e4, 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.
J. L. Wetzel and Singh, M., Sharing DNA-binding information across structurally similar proteins enables accurate specificity determination., Nucleic Acids Res, vol. 48, no. 2, p. e9, 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.
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
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.
M. Stadlmeier, Runtsch, L. Simon, Streshnev, F., Wühr, M., and Carell, T., A Click-chemistry based enrichable cross-linker for structural and protein interaction analysis by mass spectrometry., Chembiochem, 2019.
M. Stadlmeier, Runtsch, L. Simon, Streshnev, F., Wühr, M., and Carell, T., A Click-chemistry based enrichable cross-linker for structural and protein interaction analysis by mass spectrometry., Chembiochem, 2019.
H. V. Dinh, Suthers, P. F., Chan, S. Hung Joshu, Shen, Y., Xiao, T., Deewan, A., Jagtap, S. S., Zhao, H., Rao, C. V., Rabinowitz, J. D., and Maranas, C. D., A comprehensive genome-scale model for IFO0880 accounting for functional genomics and phenotypic data., Metab Eng Commun, vol. 9, p. e00101, 2019.
H. V. Dinh, Suthers, P. F., Chan, S. Hung Joshu, Shen, Y., Xiao, T., Deewan, A., Jagtap, S. S., Zhao, H., Rao, C. V., Rabinowitz, J. D., and Maranas, C. D., A comprehensive genome-scale model for IFO0880 accounting for functional genomics and phenotypic data., Metab Eng Commun, vol. 9, p. e00101, 2019.
W. Bailis, Shyer, J. A., Zhao, J., Canaveras, J. Carlos Gar, Khazal, F. J. Al, Qu, R., Steach, H. R., Bielecki, P., Khan, O., Jackson, R., Kluger, Y., Maher, L. J., Rabinowitz, J., Craft, J., and Flavell, R. A., Distinct modes of mitochondrial metabolism uncouple T cell differentiation and function., Nature, vol. 571, no. 7765, pp. 403-407, 2019.
W. Bailis, Shyer, J. A., Zhao, J., Canaveras, J. Carlos Gar, Khazal, F. J. Al, Qu, R., Steach, H. R., Bielecki, P., Khan, O., Jackson, R., Kluger, Y., Maher, L. J., Rabinowitz, J., Craft, J., and Flavell, R. A., Distinct modes of mitochondrial metabolism uncouple T cell differentiation and function., Nature, vol. 571, no. 7765, pp. 403-407, 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.
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.
P. S. Minhas, Liu, L., Moon, P. K., Joshi, A. U., Dove, C., Mhatre, S., Contrepois, K., Wang, Q., Lee, B. A., Coronado, M., Bernstein, D., Snyder, M. P., Migaud, M., Majeti, R., Mochly-Rosen, D., Rabinowitz, J. D., and Andreasson, K. I., Macrophage de novo NAD synthesis specifies immune function in aging and inflammation., Nat Immunol, vol. 20, no. 1, pp. 50-63, 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.
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.
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. 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.
M. A. Estrella, Du, J., Chen, L., Rath, S., Prangley, E., Chitrakar, A., Aoki, T., Schedl, P., Rabinowitz, J., and Korennykh, A., The metabolites NADP and NADPH are the targets of the circadian protein Nocturnin (Curled)., Nat Commun, vol. 10, no. 1, p. 2367, 2019.
K. K. Benson, Hu, W., Weller, A. H., Bennett, A. H., Chen, E. R., Khetarpal, S. A., Yoshino, S., Bone, W. P., Wang, L., Rabinowitz, J. D., Voight, B. F., and Soccio, R. E., Natural human genetic variation determines basal and inducible expression of , an obesity-associated gene., Proc Natl Acad Sci U S A, vol. 116, no. 46, pp. 23232-23242, 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.
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.
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.
L. Wang, Xing, X., Chen, L., Yang, L., Su, X., Rabitz, H., Lu, W., and Rabinowitz, J. D., Peak Annotation and Verification Engine for Untargeted LC-MS Metabolomics., Anal Chem, vol. 91, no. 3, pp. 1838-1846, 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.
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.
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.
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.
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.
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.
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.
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.
A. E. Rodriguez, Ducker, G. S., Billingham, L. K., Martinez, C. A., Mainolfi, N., Suri, V., Friedman, A., Manfredi, M. G., Weinberg, S. E., Rabinowitz, J. D., and Chandel, N. S., Serine Metabolism Supports Macrophage IL-1β Production., Cell Metab, vol. 29, no. 4, pp. 1003-1011.e4, 2019.
S. Nadimpalli Kobren and Singh, M., Systematic domain-based aggregation of protein structures highlights DNA-, RNA- and other ligand-binding positions., Nucleic Acids Res, vol. 47, no. 2, pp. 582-593, 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.
A. F. Schober, Mathis, A. D., Ingle, C., Park, J. O., Chen, L., Rabinowitz, J. D., Junier, I., Rivoire, O., and Reynolds, K. A., A Two-Enzyme Adaptive Unit within Bacterial Folate Metabolism., Cell Rep, vol. 27, no. 11, pp. 3359-3370.e7, 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
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.
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.
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.
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.
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.
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.
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.
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.
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.
L. Liu, Su, X., Quinn, W. J., Hui, S., Krukenberg, K., Frederick, D. W., Redpath, P., Zhan, L., Chellappa, K., White, E., Migaud, M., Mitchison, T. J., Baur, J. A., and Rabinowitz, J. D., Quantitative Analysis of NAD Synthesis-Breakdown Fluxes., Cell Metab, vol. 27, no. 5, pp. 1067-1080.e5, 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.
R. A. Miller, Shi, Y., Lu, W., Pirman, D. A., Jatkar, A., Blatnik, M., Wu, H., Cárdenas, C., Wan, M., J Foskett, K., Park, J. O., Zhang, Y., Holland, W. L., Rabinowitz, J. D., and Birnbaum, M. J., Targeting hepatic glutaminase activity to ameliorate hyperglycemia., Nat Med, vol. 24, no. 4, pp. 518-524, 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
J. P. Nguyen, Linder, A. N., Plummer, G. S., Shaevitz, J. W., and Leifer, A. M., Automatically tracking neurons in a moving and deforming brain., PLoS Comput Biol, vol. 13, no. 5, p. e1005517, 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.
Z. Zhang, Chen, L., Liu, L., Su, X., and Rabinowitz, J. D., Chemical Basis for Deuterium Labeling of Fat and NADPH., J Am Chem Soc, vol. 139, no. 41, pp. 14368-14371, 2017.
P. F. Przytycki and Singh, M., Differential analysis between somatic mutation and germline variation profiles reveals cancer-related genes., Genome Med, vol. 9, no. 1, p. 79, 2017.
S. M. Davidson, Jonas, O., Keibler, M. A., Hou, H. Wei, Luengo, A., Mayers, J. R., Wyckoff, J., Del Rosario, A. M., Whitman, M., Chin, C. R., Condon, K. J., Lammers, A., Kellersberger, K. A., Stall, B. K., Stephanopoulos, G., Bar-Sagi, D., Han, J., Rabinowitz, J. D., Cima, M. J., Langer, R., and Heiden, M. G. Vander, Direct evidence for cancer-cell-autonomous extracellular protein catabolism in pancreatic tumors., Nat Med, vol. 23, no. 2, pp. 235-241, 2017.
S. M. Davidson, Jonas, O., Keibler, M. A., Hou, H. Wei, Luengo, A., Mayers, J. R., Wyckoff, J., Del Rosario, A. M., Whitman, M., Chin, C. R., Condon, K. J., Lammers, A., Kellersberger, K. A., Stall, B. K., Stephanopoulos, G., Bar-Sagi, D., Han, J., Rabinowitz, J. D., Cima, M. J., Langer, R., and Heiden, M. G. Vander, Direct evidence for cancer-cell-autonomous extracellular protein catabolism in pancreatic tumors., Nat Med, vol. 23, no. 2, pp. 235-241, 2017.
S. Hong, Zhou, W., Fang, B., Lu, W., Loro, E., Damle, M., Ding, G., Jager, J., Zhang, S., Zhang, Y., Feng, D., Chu, Q., Dill, B. D., Molina, H., Khurana, T. S., Rabinowitz, J. D., Lazar, M. A., and Sun, Z., Dissociation of muscle insulin sensitivity from exercise endurance in mice by HDAC3 depletion., Nat Med, vol. 23, no. 2, pp. 223-234, 2017.
A. Ochoa and Singh, M., Domain prediction with probabilistic directional context., Bioinformatics, vol. 33, no. 16, pp. 2471-2478, 2017.
Y. Song, Marmion, R. A., Park, J. O., Biswas, D., Rabinowitz, J. D., and Shvartsman, S. Y., Dynamic Control of dNTP Synthesis in Early Embryos., Dev Cell, vol. 42, no. 3, pp. 301-308.e3, 2017.
Y. Song, Marmion, R. A., Park, J. O., Biswas, D., Rabinowitz, J. D., and Shvartsman, S. Y., Dynamic Control of dNTP Synthesis in Early Embryos., Dev Cell, vol. 42, no. 3, pp. 301-308.e3, 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.
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.
H. In Kim, Raffler, J., Lu, W., Lee, J. - J., Abbey, D., Saleheen, D., Rabinowitz, J. D., Bennett, M. J., Hand, N. J., Brown, C., and Rader, D. J., Fine Mapping and Functional Analysis Reveal a Role of SLC22A1 in Acylcarnitine Transport., Am J Hum Genet, vol. 101, no. 4, pp. 489-502, 2017.
B. Sabass, Koch, M. D., Liu, G., Stone, H. A., and Shaevitz, J. W., Force generation by groups of migrating bacteria., Proc Natl Acad Sci U S A, vol. 114, no. 28, pp. 7266-7271, 2017.
B. Sabass, Koch, M. D., Liu, G., Stone, H. A., and Shaevitz, J. W., Force generation by groups of migrating bacteria., Proc Natl Acad Sci U S A, vol. 114, no. 28, pp. 7266-7271, 2017.
B. Sabass, Koch, M. D., Liu, G., Stone, H. A., and Shaevitz, J. W., Force generation by groups of migrating bacteria., Proc Natl Acad Sci U S A, vol. 114, no. 28, pp. 7266-7271, 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.
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.
Y. Pritykin, Brito, T., Schüpbach, T., Singh, M., and Pane, A., Integrative analysis unveils new functions for the Drosophila Cutoff protein in noncoding RNA biogenesis and gene regulation., RNA, vol. 23, no. 7, pp. 1097-1109, 2017.
Y. Pritykin, Brito, T., Schüpbach, T., Singh, M., and Pane, A., Integrative analysis unveils new functions for the Drosophila Cutoff protein in noncoding RNA biogenesis and gene regulation., RNA, vol. 23, no. 7, pp. 1097-1109, 2017.
M. D. Koch and Shaevitz, J. W., Introduction to Optical Tweezers., Methods Mol Biol, vol. 1486, pp. 3-24, 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.
C. Shi, Runnels, A. M., and Murphy, C. T., Mating and male pheromone kill Caenorhabditis males through distinct mechanisms., Elife, vol. 6, 2017.
W. Lu, Su, X., Klein, M. S., Lewis, I. A., Fiehn, O., and Rabinowitz, J. D., Metabolite Measurement: Pitfalls to Avoid and Practices to Follow., Annu Rev Biochem, vol. 86, pp. 277-304, 2017.
X. Su, Lu, W., and Rabinowitz, J. D., Metabolite Spectral Accuracy on Orbitraps., Anal Chem, vol. 89, no. 11, pp. 5940-5948, 2017.
B. H. Hristov and Singh, M., Network-Based Coverage of Mutational Profiles Reveals Cancer Genes., Cell Syst, vol. 5, no. 3, pp. 221-229.e4, 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.
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.
H. G. Son, Seo, M., Ham, S., Hwang, W., Lee, D., An, S. Woo A., Artan, M., Seo, K., Kaletsky, R., Arey, R. N., Ryu, Y., Ha, C. Man, Kim, Y. Ki, Murphy, C. T., Roh, T. - Y., Nam, H. Gil, and Lee, S. - J. V., RNA surveillance via nonsense-mediated mRNA decay is crucial for longevity in daf-2/insulin/IGF-1 mutant C. elegans., Nat Commun, vol. 8, p. 14749, 2017.
H. G. Son, Seo, M., Ham, S., Hwang, W., Lee, D., An, S. Woo A., Artan, M., Seo, K., Kaletsky, R., Arey, R. N., Ryu, Y., Ha, C. Man, Kim, Y. Ki, Murphy, C. T., Roh, T. - Y., Nam, H. Gil, and Lee, S. - J. V., RNA surveillance via nonsense-mediated mRNA decay is crucial for longevity in daf-2/insulin/IGF-1 mutant C. elegans., Nat Commun, vol. 8, p. 14749, 2017.
H. G. Son, Seo, M., Ham, S., Hwang, W., Lee, D., An, S. Woo A., Artan, M., Seo, K., Kaletsky, R., Arey, R. N., Ryu, Y., Ha, C. Man, Kim, Y. Ki, Murphy, C. T., Roh, T. - Y., Nam, H. Gil, and Lee, S. - J. V., RNA surveillance via nonsense-mediated mRNA decay is crucial for longevity in daf-2/insulin/IGF-1 mutant C. elegans., Nat Commun, vol. 8, p. 14749, 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.
U. Klibaite, Berman, G. J., Cande, J., Stern, D. L., and Shaevitz, J. W., An unsupervised method for quantifying the behavior of paired animals., Phys Biol, vol. 14, no. 1, p. 015006, 2017.
U. Klibaite, Berman, G. J., Cande, J., Stern, D. L., and Shaevitz, J. W., An unsupervised method for quantifying the behavior of paired animals., Phys Biol, vol. 14, no. 1, p. 015006, 2017.
2016
P. Koivunen, Fell, S. M., Lu, W., Rabinowitz, J. D., Kung, A. L., and Schlisio, S., The 2-oxoglutarate analog 3-oxoglutarate decreases normoxic hypoxia-inducible factor-1α in cancer cells, induces cell death, and reduces tumor xenograft growth., Hypoxia (Auckl), vol. 4, pp. 15-27, 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.
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.
J. P. Nguyen, Bratton, B. P., and Shaevitz, J. W., Biophysical Measurements of Bacterial Cell Shape., Methods Mol Biol, vol. 1440, pp. 227-45, 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.
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.
C. Shi and Murphy, C. T., Feeding the germline., Genes Dev, vol. 30, no. 3, pp. 249-50, 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.
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.
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.
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.
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.
L. Liu, Shah, S., Fan, J., Park, J. O., Wellen, K. E., and Rabinowitz, J. D., Malic enzyme tracers reveal hypoxia-induced switch in adipocyte NADPH pathway usage., Nat Chem Biol, vol. 12, no. 5, pp. 345-52, 2016.
X. Su, Wellen, K. E., and Rabinowitz, J. D., Metabolic control of methylation and acetylation., Curr Opin Chem Biol, vol. 30, pp. 52-60, 2016.
J. O. Park, Rubin, S. A., Xu, Y. - F., Amador-Noguez, D., Fan, J., Shlomi, T., and Rabinowitz, J. D., Metabolite concentrations, fluxes and free energies imply efficient enzyme usage., Nat Chem Biol, 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.
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.
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.
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.
L. - B. Li, Lei, H., Arey, R. N., Li, P., Liu, J., Murphy, C. T., Xu, X. Z. Shawn, and Shen, K., The Neuronal Kinesin UNC-104/KIF1A Is a Key Regulator of Synaptic Aging and Insulin Signaling-Regulated Memory., Curr Biol, vol. 26, no. 5, pp. 605-15, 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.
G. J. Berman, Bialek, W., and Shaevitz, J. W., Predictability and hierarchy in Drosophila behavior., Proc Natl Acad Sci U S A, vol. 113, no. 42, pp. 11943-11948, 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.
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.
J. P. Nguyen, Shipley, F. B., Linder, A. N., Plummer, G. S., Liu, M., Setru, S. U., Shaevitz, J. W., and Leifer, A. M., Whole-brain calcium imaging with cellular resolution in freely behaving Caenorhabditis elegans., Proc Natl Acad Sci U S A, vol. 113, no. 8, pp. E1074-81, 2016.
J. P. Nguyen, Shipley, F. B., Linder, A. N., Plummer, G. S., Liu, M., Setru, S. U., Shaevitz, J. W., and Leifer, A. M., Whole-brain calcium imaging with cellular resolution in freely behaving Caenorhabditis elegans., Proc Natl Acad Sci U S A, vol. 113, no. 8, pp. E1074-81, 2016.
J. P. Nguyen, Shipley, F. B., Linder, A. N., Plummer, G. S., Liu, M., Setru, S. U., Shaevitz, J. W., and Leifer, A. M., Whole-brain calcium imaging with cellular resolution in freely behaving Caenorhabditis elegans., Proc Natl Acad Sci U S A, vol. 113, no. 8, pp. E1074-81, 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.
A. Ochoa, Storey, J. D., Llinás, M., and Singh, M., Beyond the E-Value: Stratified Statistics for Protein Domain Prediction., PLoS Comput Biol, vol. 11, no. 11, p. e1004509, 2015.
A. Ochoa, Storey, J. D., Llinás, M., and Singh, M., Beyond the E-Value: Stratified Statistics for Protein Domain Prediction., PLoS Comput Biol, vol. 11, no. 11, p. e1004509, 2015.
J. - H. Hahm, Kim, S., DiLoreto, R., Shi, C., Lee, S. - J. V., Murphy, C. T., and Nam, H. Gil, C. elegans maximum velocity correlates with healthspan and is maintained in worms with an insulin receptor mutation., Nat Commun, vol. 6, p. 8919, 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.
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.
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.
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. G. Purdy, Shenk, T., and Rabinowitz, J. D., Fatty acid elongase 7 catalyzes lipidome remodeling essential for human cytomegalovirus replication., Cell Rep, vol. 10, no. 8, pp. 1375-85, 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.
V. Lakhina, Arey, R. N., Kaletsky, R., Kauffman, A., Stein, G., Keyes, W., Xu, D., and Murphy, C. T., Genome-wide functional analysis of CREB/long-term memory-dependent transcription reveals distinct basal and memory gene expression programs., Neuron, vol. 85, no. 2, pp. 330-45, 2015.
V. Lakhina, Arey, R. N., Kaletsky, R., Kauffman, A., Stein, G., Keyes, W., Xu, D., and Murphy, C. T., Genome-wide functional analysis of CREB/long-term memory-dependent transcription reveals distinct basal and memory gene expression programs., Neuron, vol. 85, no. 2, pp. 330-45, 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.
S. Li, Stone, H. A., and Murphy, C. T., A microfluidic device and automatic counting system for the study of C. elegans reproductive aging., Lab Chip, vol. 15, no. 2, pp. 524-31, 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.
S. Nadimpalli, Persikov, A. V., and Singh, M., Pervasive variation of transcription factor orthologs contributes to regulatory network evolution., PLoS Genet, vol. 11, no. 3, p. e1005011, 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.
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.
B. P. Bratton and Shaevitz, J. W., Simple Experimental Methods for Determining the Apparent Focal Shift in a Microscope System., PLoS One, vol. 10, no. 8, p. e0134616, 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.
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.
A. V. Persikov, Wetzel, J. L., Rowland, E. F., Oakes, B. L., Xu, D. J., Singh, M., and Noyes, M. B., A systematic survey of the Cys2His2 zinc finger DNA-binding landscape., Nucleic Acids Res, vol. 43, no. 3, pp. 1965-84, 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
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.
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.
G. M. Stein and Murphy, C. T., C. elegans positive olfactory associative memory is a molecularly conserved behavioral paradigm., Neurobiol Learn Mem, vol. 115, pp. 86-94, 2014.
P. Jiang and Singh, M., CCAT: Combinatorial Code Analysis Tool for transcriptional regulation., Nucleic Acids Res, vol. 42, no. 5, pp. 2833-47, 2014.
X. X. Du, Osterfield, M., and Shvartsman, S. Y., Computational analysis of three-dimensional epithelial morphogenesis using vertex models., Phys Biol, vol. 11, no. 6, p. 066007, 2014.
A. V. Persikov and Singh, M., De novo prediction of DNA-binding specificities for Cys2His2 zinc finger proteins., Nucleic Acids Res, vol. 42, no. 1, pp. 97-108, 2014.
A. V. Persikov, Rowland, E. F., Oakes, B. L., Singh, M., and Noyes, M. B., Deep sequencing of large library selections allows computational discovery of diverse sets of zinc fingers that bind common targets., Nucleic Acids Res, vol. 42, no. 3, pp. 1497-508, 2014.