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

2022
K. Olszewski, Barsotti, A., Feng, X. - J., Momcilovic, M., Liu, K. G., Kim, J. - I., Morris, K., Lamarque, C., Gaffney, J., Yu, X., Patel, J. P., Rabinowitz, J. D., Shackelford, D. B., and Poyurovsky, M. V., “Inhibition of glucose transport synergizes with chemical or genetic disruption of mitochondrial metabolism and suppresses TCA cycle-deficient tumors.”, Cell Chem Biol, vol. 29, no. 3, pp. 423-435.e10, 2022.
L. Yang, TeSlaa, T., Ng, S., Nofal, M., Wang, L., Lan, T., Zeng, X., Cowan, A., McBride, M., Lu, W., Davidson, S., Liang, G., Oh, T. Gyu, Downes, M., Evans, R., Von Hoff, D., Guo, J. Yanxiang, Han, H., and Rabinowitz, J. D., “Ketogenic diet and chemotherapy combine to disrupt pancreatic cancer metabolism and growth.”, Med (N Y), vol. 3, no. 2, pp. 119-136, 2022.
L. Wang, Xing, X., Zeng, X., S Jackson, R. E., TeSlaa, T., Al-Dalahmah, O., Samarah, L. Z., Goodwin, K., Yang, L., McReynolds, M. R., Li, X., Wolff, J. J., Rabinowitz, J. D., and Davidson, S. M., “Spatially resolved isotope tracing reveals tissue metabolic activity.”, Nat Methods, vol. 19, no. 2, pp. 223-230, 2022.
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.
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.
L. Chen, Wolf, A. B., Fu, W., Li, L., and Akey, J. M., “Identifying and Interpreting Apparent Neanderthal Ancestry in African Individuals.”, Cell, vol. 180, no. 4, pp. 677-687.e16, 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.
Q. Zhu, Tekpli, X., Troyanskaya, O. G., and Kristensen, V. N., “Subtype-specific transcriptional regulators in breast tumors subjected to genetic and epigenetic alterations.”, Bioinformatics, vol. 36, no. 4, pp. 994-999, 2020.
2019
J. Zhou, Schor, I. E., Yao, V., Theesfeld, C. L., Marco-Ferreres, R., Tadych, A., Furlong, E. E. M., and Troyanskaya, O. G., “Accurate genome-wide predictions of spatio-temporal gene expression during embryonic development.”, PLoS Genet, vol. 15, no. 9, p. e1008382, 2019.
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.
C. Cao, Lemaire, L. A., Wang, W., Yoon, P. H., Choi, Y. A., Parsons, L. R., Matese, J. C., Wang, W., Levine, M., and Chen, K., “Comprehensive single-cell transcriptome lineages of a proto-vertebrate.”, Nature, vol. 571, no. 7765, pp. 349-354, 2019.
Y. -suk Lee, Krishnan, A., Oughtred, R., Rust, J., Chang, C. S., Ryu, J., Kristensen, V. N., Dolinski, K., Theesfeld, C. L., and Troyanskaya, O. G., “A Computational Framework for Genome-wide Characterization of the Human Disease Landscape.”, Cell Syst, vol. 8, no. 2, pp. 152-162.e6, 2019.
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.
T. Heist, Fukaya, T., and Levine, M., “Large distances separate coregulated genes in living embryos.”, Proc Natl Acad Sci U S A, vol. 116, no. 30, pp. 15062-15067, 2019.
S. Tucci and Akey, J. M., “The long walk to African genomics.”, Genome Biol, vol. 20, no. 1, p. 130, 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.
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.
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.
L. Chen, Zhang, Z., Hoshino, A., Zheng, H. D., Morley, M., Arany, Z., and Rabinowitz, J. D., “NADPH production by the oxidative pentose-phosphate pathway supports folate metabolism.”, Nat Metab, vol. 1, pp. 404-415, 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.
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.
M. D. Neinast, Jang, C., Hui, S., Murashige, D. S., Chu, Q., Morscher, R. J., Li, X., Zhan, L., White, E., Anthony, T. G., Rabinowitz, J. D., and Arany, Z., “Quantitative Analysis of the Whole-Body Metabolic Fate of Branched-Chain Amino Acids.”, Cell Metab, vol. 29, no. 2, pp. 417-429.e4, 2019.
K. M. Chen, Cofer, E. M., Zhou, J., and Troyanskaya, O. G., “Selene: a PyTorch-based deep learning library for sequence data.”, Nat Methods, vol. 16, no. 4, pp. 315-318, 2019.
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.
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.
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.
P. Anikeeva, Boyden, E., Brangwynne, C., Troyanskaya, O., and al., et., “Voices in methods development.”, Nat Methods, vol. 16, no. 10, pp. 945-951, 2019.
J. Zhou, Park, C. Y., Theesfeld, C. L., Wong, A. K., Yuan, Y., Scheckel, C., Fak, J. J., Funk, J., Yao, K., Tajima, Y., Packer, A., Darnell, R. B., and Troyanskaya, O. G., “Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk.”, Nat Genet, vol. 51, no. 6, pp. 973-980, 2019.
2018
L. H. Rodan, Qi, W., Ducker, G. S., Demirbas, D., Laine, R., Yang, E., Walker, M. A., Eichler, F., Rabinowitz, J. D., Anselm, I., and Berry, G. T., “5,10-methenyltetrahydrofolate synthetase deficiency causes a neurometabolic disorder associated with microcephaly, epilepsy, and cerebral hypomyelination.”, Mol Genet Metab, vol. 125, no. 1-2, pp. 118-126, 2018.
S. R. Browning, Browning, B. L., Zhou, Y., Tucci, S., and Akey, J. M., “Analysis of Human Sequence Data Reveals Two Pulses of Archaic Denisovan Admixture.”, Cell, vol. 173, no. 1, pp. 53-61.e9, 2018.
N. N. Pavlova, Hui, S., Ghergurovich, J. M., Fan, J., Intlekofer, A. M., White, R. M., Rabinowitz, J. D., Thompson, C. B., and Zhang, J., “As Extracellular Glutamine Levels Decline, Asparagine Becomes an Essential Amino Acid.”, Cell Metab, vol. 27, no. 2, pp. 428-438.e5, 2018.
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.
J. Zhou, Theesfeld, C. L., Yao, K., Chen, K. M., Wong, A. K., and Troyanskaya, O. G., “Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk.”, Nat Genet, vol. 50, no. 8, pp. 1171-1179, 2018.
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.
V. Yao, Wong, A. K., and Troyanskaya, O. G., “Enabling Precision Medicine through Integrative Network Models.”, J Mol Biol, vol. 430, no. 18 Pt A, pp. 2913-2923, 2018.
S. 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.
A. K. Wong, Krishnan, A., and Troyanskaya, O. G., “GIANT 2.0: genome-scale integrated analysis of gene networks in tissues.”, Nucleic Acids Research, vol. 46, no. W1, pp. W65-W70, 2018.
V. Yao, Kaletsky, R., Keyes, W., Mor, D. E., Wong, A. K., Sohrabi, S., Murphy, C. T., and Troyanskaya, O. G., “An integrative tissue-network approach to identify and test human disease genes.”, Nat Biotechnol, 2018.
Y. -suk Lee, Wong, A. K., Tadych, A., Hartmann, B. M., Park, C. Y., DeJesus, V. A., Ramos, I., Zaslavsky, E., Sealfon, S. C., and Troyanskaya, O. G., “Interpretation of an individual functional genomics experiment guided by massive public data.”, Nat Methods, vol. 15, no. 12, pp. 1049-1052, 2018.
M. A. Lanaspa, Andres-Hernando, A., Orlicky, D. J., Cicerchi, C., Jang, C., Li, N., Milagres, T., Kuwabara, M., Wempe, M. F., Rabinowitz, J. D., Johnson, R. J., and Tolan, D. R., “Ketohexokinase C blockade ameliorates fructose-induced metabolic dysfunction in fructose-sensitive mice.”, J Clin Invest, vol. 128, no. 6, pp. 2226-2238, 2018.
A. V. Rangan, McGrouther, C. C., Kelsoe, J., Schork, N., Stahl, E., Zhu, Q., Krishnan, A., Yao, V., Troyanskaya, O., Bilaloglu, S., Raghavan, P., Bergen, S., Jureus, A., and Landen, M., “A loop-counting method for covariate-corrected low-rank biclustering of gene-expression and genome-wide association study data.”, PLoS Comput Biol, vol. 14, no. 5, p. e1006105, 2018.
M. O. Press, McCoy, R. C., Hall, A. N., Akey, J. M., and Queitsch, C., “Massive variation of short tandem repeats with functional consequences across strains of Arabidopsis thaliana.”, Genome Res, vol. 28, no. 8, pp. 1169-1178, 2018.
C. Jang, Chen, L., and Rabinowitz, J. D., “Metabolomics and Isotope Tracing.”, Cell, vol. 173, no. 4, pp. 822-837, 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.
A. Davila, Liu, L., Chellappa, K., Redpath, P., Nakamaru-Ogiso, E., Paolella, L. M., Zhang, Z., Migaud, M. E., Rabinowitz, J. D., and Baur, J. A., “Nicotinamide adenine dinucleotide is transported into mammalian mitochondria.”, Elife, vol. 7, 2018.
A. B. Wolf and Akey, J. M., “Outstanding questions in the study of archaic hominin admixture.”, PLoS Genet, vol. 14, no. 5, p. e1007349, 2018.
S. E. McKee, Zhang, S., Chen, L., Rabinowitz, J. D., and Reyes, T. M., “Perinatal high fat diet and early life methyl donor supplementation alter one carbon metabolism and DNA methylation in the brain.”, J Neurochem, vol. 145, no. 5, pp. 362-373, 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.
M. Nofal and Rabinowitz, J. D., “Ribosomes on the night shift.”, Science, vol. 360, no. 6390, pp. 710-711, 2018.
S. Jabeen, Zucknick, M., Nome, M., Dannenfelser, R., Fleischer, T., Kumar, S., Lüders, T., Gythfeldt, Hvon der Li, Troyanskaya, O., Kyte, J. Amund, Børresen-Dale, A. - L., Naume, B., Tekpli, X., Engebraaten, O., and Kristensen, V., “Serum cytokine levels in breast cancer patients during neoadjuvant treatment with bevacizumab.”, Oncoimmunology, vol. 7, no. 11, p. e1457598, 2018.
R. Menon, Otto, E. A., Kokoruda, A., Zhou, J., Zhang, Z., Yoon, E., Chen, Y. - C., Troyanskaya, O., Spence, J. R., Kretzler, M., and Cebrián, C., “Single-cell analysis of progenitor cell dynamics and lineage specification in the human fetal kidney.”, Development, vol. 145, no. 16, 2018.
C. Jang, Hui, S., Lu, W., Cowan, A. J., Morscher, R. J., Lee, G., Liu, W., Tesz, G. J., Birnbaum, M. J., and Rabinowitz, J. D., “The Small Intestine Converts Dietary Fructose into Glucose and Organic Acids.”, Cell Metab, vol. 27, no. 2, pp. 351-361.e3, 2018.
R. 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.
R. Kaletsky, Yao, V., Williams, A., Runnels, A. M., Tadych, A., Zhou, S., Troyanskaya, O. G., and Murphy, C. T., “Transcriptome analysis of adult Caenorhabditis elegans cells reveals tissue-specific gene and isoform expression.”, PLoS Genetics, vol. 14, no. 8, p. e1007559, 2018.
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.
S. Hui and Rabinowitz, J. D., “An unexpected trigger for calorie burning in brown fat.”, Nature, vol. 560, no. 7716, pp. 38-39, 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.
T. Clancy, Dannenfelser, R., Troyanskaya, O. G., Malmberg, K. Johan, Hovig, E., and Kristensen, V., “Bioinformatics approaches to profile the tumor microenvironment for immunotherapeutic discovery.”, Curr Pharm Des, 2017.
R. 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.
R. N. Arey and Murphy, C. T., “Conserved regulators of cognitive aging: From worms to humans.”, Behav Brain Res, vol. 322, no. Pt B, pp. 299-310, 2017.
R. Dannenfelser, Nome, M., Tahiri, A., Ursini-Siegel, J., Vollan, H. Kristian M., Haakensen, V. D., Helland, Å., Naume, B., Caldas, C., Børresen-Dale, A. - L., Kristensen, V. N., and Troyanskaya, O. G., “Data-driven analysis of immune infiltrate in a large cohort of breast cancer and its association with disease progression, ER activity, and genomic complexity.”, Oncotarget, vol. 8, no. 34, pp. 57121-57133, 2017.
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. 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.
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.
W. Lu, Wang, L., Chen, L., Hui, S., and Rabinowitz, J. D., “Extraction and Quantitation of Nicotinamide Adenine Dinucleotide Redox Cofactors.”, Antioxid Redox Signal, 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.
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.
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.
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.
L. Chen, Ducker, G. S., Lu, W., Teng, X., and Rabinowitz, J. D., “An LC-MS chemical derivatization method for the measurement of five different one-carbon states of cellular tetrahydrofolate.”, Anal Bioanal Chem, 2017.
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.
M. Nofal, Zhang, K., Han, S., and Rabinowitz, J. D., “mTOR Inhibition Restores Amino Acid Balance in Cells Dependent on Catabolism of Extracellular Protein.”, Mol Cell, vol. 67, no. 6, pp. 936-946.e5, 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.
L. X. Liu, Rowe, G. C., Yang, S., Li, J., Damilano, F., Chan, M. Chun, Lu, W., Jang, C., Wada, S., Morley, M., Hesse, M., Fleischmann, B. K., Rabinowitz, J., Das, S., Rosenzweig, A., and Arany, Z., “PDK4 Inhibits Cardiac Pyruvate Oxidation in Late Pregnancy.”, Circ Res, 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. Fukaya, Lim, B., and Levine, M., “Rapid Rates of Pol II Elongation in the Drosophila Embryo.”, Curr Biol, vol. 27, no. 9, pp. 1387-1391, 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.
J. Choi, Rajagopal, A., Xu, Y. - F., Rabinowitz, J. D., and O'Shea, E. K., “A systematic genetic screen for genes involved in sensing inorganic phosphate availability in Saccharomyces cerevisiae.”, PLoS One, vol. 12, no. 5, p. e0176085, 2017.
B. Lim, Levine, M., and Yamazaki, Y., “Transcriptional Pre-patterning of Drosophila Gastrulation.”, Curr Biol, vol. 27, no. 2, pp. 286-290, 2017.
T. Fukaya and Levine, M., “Transvection.”, Curr Biol, vol. 27, no. 19, pp. R1047-R1049, 2017.
N. V. Rajeshkumar, Yabuuchi, S., Pai, S. G., De Oliveira, E., Kamphorst, J. J., Rabinowitz, J. D., Tejero, H., Al-Shahrour, F., Hidalgo, M., Maitra, A., and Dang, C. V., “Treatment of Pancreatic Cancer Patient-Derived Xenograft Panel with Metabolic Inhibitors Reveals Efficacy of Phenformin.”, Clin Cancer Res, vol. 23, no. 18, pp. 5639-5647, 2017.
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.
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.
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.
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.
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.
R. Kaletsky, Lakhina, V., Arey, R., Williams, A., Landis, J., Ashraf, J., and Murphy, C. T., “The C. elegans adult neuronal IIS/FOXO transcriptome reveals adult phenotype regulators.”, Nature, vol. 529, no. 7584, pp. 92-6, 2016.
P. M. Titchenell, Quinn, W. J., Lu, M., Chu, Q., Lu, W., Li, C., Chen, H., Monks, B. R., Chen, J., Rabinowitz, J. D., and Birnbaum, M. J., “Direct Hepatocyte Insulin Signaling Is Required for Lipogenesis but Is Dispensable for the Suppression of Glucose Production.”, Cell Metab, 2016.
X. Nuttle, Giannuzzi, G., Duyzend, M. H., Schraiber, J. G., Narvaiza, I., Sudmant, P. H., Penn, O., Chiatante, G., Malig, M., Huddleston, J., Benner, C., Camponeschi, F., Ciofi-Baffoni, S., Stessman, H. A. F., Marchetto, M. C. N., Denman, L., Harshman, L., Baker, C., Raja, A., Penewit, K., Janke, N., W Tang, J., Ventura, M., Banci, L., Antonacci, F., Akey, J. M., Amemiya, C. T., Gage, F. H., Reymond, A., and Eichler, E. E., “Emergence of a Homo sapiens-specific gene family and chromosome 16p11.2 CNV susceptibility.”, Nature, vol. 536, no. 7615, pp. 205-9, 2016.
T. Fukaya, Lim, B., and Levine, M., “Enhancer Control of Transcriptional Bursting.”, Cell, vol. 166, no. 2, pp. 358-68, 2016.
C. Shi and Murphy, C. T., “Feeding the germline.”, Genes Dev, vol. 30, no. 3, pp. 249-50, 2016.
A. Krishnan, Zhang, R., Yao, V., Theesfeld, C. L., Wong, A. K., Tadych, A., Volfovsky, N., Packer, A., Lash, A., and Troyanskaya, O. G., “Genome-wide prediction and functional characterization of the genetic basis of autism spectrum disorder.”, Nat Neurosci, vol. 19, no. 11, pp. 1454-1462, 2016.
H. D. Møller, Bojsen, R. K., Tachibana, C., Parsons, L., Botstein, D., and Regenberg, B., “Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells.”, J Vis Exp, no. 110, p. e54239 |, 2016.
A. M. Roberts, Wong, A. K., Fisk, I., and Troyanskaya, O. G., “GIANT API: an application programming interface for functional genomics.”, Nucleic Acids Res, 2016.
M. Costanzo, VanderSluis, B., Koch, E. N., Baryshnikova, A., Pons, C., Tan, G., Wang, W., Usaj, M., Hanchard, J., Lee, S. D., Pelechano, V., Styles, E. B., Billmann, M., van Leeuwen, J., van Dyk, N., Lin, Z. - Y., Kuzmin, E., Nelson, J., Piotrowski, J. S., Srikumar, T., Bahr, S., Chen, Y., Deshpande, R., Kurat, C. F., Li, S. C., Li, Z., Usaj, M. Mattiazzi, Okada, H., Pascoe, N., San Luis, B. - J., Sharifpoor, S., Shuteriqi, E., Simpkins, S. W., Snider, J., Suresh, H. Garadi, Tan, Y., Zhu, H., Malod-Dognin, N., Janjic, V., Przulj, N., Troyanskaya, O. G., Stagljar, I., Xia, T., Ohya, Y., Gingras, A. - C., Raught, B., Boutros, M., Steinmetz, L. M., Moore, C. L., Rosebrock, A. P., Caudy, A. A., Myers, C. L., Andrews, B., and Boone, C., “A global genetic interaction network maps a wiring diagram of cellular function.”, Science, vol. 353, no. 6306, 2016.
A. Bren, Park, J. O., Towbin, B. D., Dekel, E., Rabinowitz, J. D., and Alon, U., “Glucose becomes one of the worst carbon sources for E.coli on poor nitrogen sources due to suboptimal levels of cAMP.”, Sci Rep, vol. 6, p. 24834, 2016.
X. Teng, Emmett, M. J., Lazar, M. A., Goldberg, E., and Rabinowitz, J. D., “Lactate Dehydrogenase C Produces S-2-Hydroxyglutarate in Mouse Testis.”, ACS Chem Biol, 2016.
D. W. Frederick, Loro, E., Liu, L., Davila, A., Chellappa, K., Silverman, I. M., Quinn, W. J., Gosai, S. J., Tichy, E. D., Davis, J. G., Mourkioti, F., Gregory, B. D., Dellinger, R. W., Redpath, P., Migaud, M. E., Nakamaru-Ogiso, E., Rabinowitz, J. D., Khurana, T. S., and Baur, J. A., “Loss of NAD Homeostasis Leads to Progressive and Reversible Degeneration of Skeletal Muscle.”, Cell Metab, vol. 24, no. 2, pp. 269-82, 2016.
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.
E. Watson, Olin-Sandoval, V., Hoy, M. J., Li, C. - H., Louisse, T., Yao, V., Mori, A., Holdorf, A. D., Troyanskaya, O. G., Ralser, M., and Walhout, A. Jm, “Metabolic network rewiring of propionate flux compensates vitamin B12 deficiency in C. elegans.”, Elife, vol. 5, 2016.
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.
W. - X. Zong, Rabinowitz, J. D., and White, E., “Mitochondria and Cancer.”, Mol Cell, vol. 61, no. 5, pp. 667-76, 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.
J. G. Moloughney, Kim, P. K., Vega-Cotto, N. M., Wu, C. - C., Zhang, S., Adlam, M., Lynch, T., Chou, P. - C., Rabinowitz, J. D., Werlen, G., and Jacinto, E., “mTORC2 Responds to Glutamine Catabolite Levels to Modulate the Hexosamine Biosynthesis Enzyme GFAT1.”, Mol Cell, vol. 63, no. 5, pp. 811-26, 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.
I. A. Navarrete and Levine, M., “Nodal and FGF coordinate ascidian neural tube morphogenesis.”, Development, vol. 143, no. 24, pp. 4665-4675, 2016.
G. S. Ducker and Rabinowitz, J. D., “One-Carbon Metabolism in Health and Disease.”, Cell Metab, 2016.
J. D. Rabinowitz and Coller, H. A., “Partners in the Warburg effect.”, Elife, vol. 5, 2016.
R. Papazyan, Sun, Z., Kim, Y. Hoon, Titchenell, P. M., Hill, D. A., Lu, W., Damle, M., Wan, M., Zhang, Y., Briggs, E. R., Rabinowitz, J. D., and Lazar, M. A., “Physiological Suppression of Lipotoxic Liver Damage by Complementary Actions of HDAC3 and SCAP/SREBP.”, Cell Metab, vol. 24, no. 6, pp. 863-874, 2016.
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.
J. Zhou and Troyanskaya, O. G., “Probabilistic modelling of chromatin code landscape reveals functional diversity of enhancer-like chromatin states.”, Nat Commun, vol. 7, p. 10528, 2016.
Q. Wang, J Taliaferro, M., Klibaite, U., Hilgers, V., Shaevitz, J. W., and Rio, D. C., “The PSI-U1 snRNP interaction regulates male mating behavior in Drosophila.”, Proc Natl Acad Sci U S A, vol. 113, no. 19, pp. 5269-74, 2016.
G. S. Ducker, Chen, L., Morscher, R. J., Ghergurovich, J. M., Esposito, M., Teng, X., Kang, Y., and Rabinowitz, J. D., “Reversal of Cytosolic One-Carbon Flux Compensates for Loss of the Mitochondrial Folate Pathway.”, Cell Metab, 2016.
E. El-Sherif and Levine, M., “Shadow Enhancers Mediate Dynamic Shifts of Gap Gene Expression in the Drosophila Embryo.”, Curr Biol, vol. 26, no. 9, pp. 1164-9, 2016.
E. K. Farley, Olson, K. M., Zhang, W., Rokhsar, D. S., and Levine, M. S., “Syntax compensates for poor binding sites to encode tissue specificity of developmental enhancers.”, Proc Natl Acad Sci U S A, vol. 113, no. 23, pp. 6508-13, 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.
T. Ferraro, Esposito, E., Mancini, L., Ng, S., Lucas, T., Coppey, M., Dostatni, N., Walczak, A. M., Levine, M., and Lagha, M., “Transcriptional Memory in the Drosophila Embryo.”, Curr Biol, vol. 26, no. 2, pp. 212-8, 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
Y. - F. Xu, Lu, W., and Rabinowitz, J. D., “Avoiding misannotation of in-source fragmentation products as cellular metabolites in liquid chromatography-mass spectrometry-based metabolomics.”, Anal Chem, vol. 87, no. 4, pp. 2273-81, 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.
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.
R. DiLoreto and Murphy, C. T., “The cell biology of aging.”, Mol Biol Cell, vol. 26, no. 25, pp. 4524-31, 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.
C. Y. Ewald, Landis, J. N., Abate, J. Porter, Murphy, C. T., and T Blackwell, K., “Dauer-independent insulin/IGF-1-signalling implicates collagen remodelling in longevity.”, Nature, vol. 519, no. 7541, pp. 97-101, 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.
B. T Gainous, Wagner, E., and Levine, M., “Diverse ETS transcription factors mediate FGF signaling in the Ciona anterior neural plate.”, Dev Biol, 2015.
K. Oktaba, Zhang, W., Lotz, T. Sabrina, Jun, D. Jayhyun, Lemke, S. Beatrice, Ng, S. Pak, Esposito, E., Levine, M., and Hilgers, V., “ELAV Links Paused Pol II to Alternative Polyadenylation in the Drosophila Nervous System.”, Mol Cell, vol. 57, no. 2, pp. 341-8, 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. 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.
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.
V. Lakhina and Murphy, C. T., “For longevity, perception is everything.”, Cell, vol. 160, no. 5, pp. 807-9, 2015.
V. Lakhina and Murphy, C. T., “For longevity, perception is everything.”, Cell, vol. 160, no. 5, pp. 807-9, 2015.
L. Zwarts, Broeck, L. Vanden, Cappuyns, E., Ayroles, J. F., Magwire, M. M., Vulsteke, V., Clements, J., Mackay, T. F. C., and Callaerts, P., “The genetic basis of natural variation in mushroom body size in Drosophila melanogaster.”, Nat Commun, vol. 6, p. 10115, 2015.
V. Lakhina and Murphy, C. T., “Genome Sequencing Fishes out Longevity Genes.”, Cell, vol. 163, no. 6, pp. 1312-3, 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.
J. J. Kamphorst, Nofal, M., Commisso, C., Hackett, S. R., Lu, W., Grabocka, E., Heiden, M. G. Vander, Miller, G., Drebin, J. A., Bar-Sagi, D., Thompson, C. B., and Rabinowitz, J. D., “Human pancreatic cancer tumors are nutrient poor and tumor cells actively scavenge extracellular protein.”, Cancer Res, vol. 75, no. 3, pp. 544-53, 2015.
A. K. Wong, Krishnan, A., Yao, V., Tadych, A., and Troyanskaya, O. G., “IMP 2.0: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks.”, Nucleic Acids Res, 2015.
K. Dolinski and Troyanskaya, O. G., “Implications of Big Data for cell biology.”, Mol Biol Cell, vol. 26, no. 14, pp. 2575-8, 2015.
D. Gorenshteyn, Zaslavsky, E., Fribourg, M., Park, C. Y., Wong, A. K., Tadych, A., Hartmann, B. M., Albrecht, R. A., García-Sastre, A., Kleinstein, S. H., Troyanskaya, O. G., and Sealfon, S. C., “Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases.”, Immunity, vol. 43, no. 3, pp. 605-14, 2015.
M. Tikhonov, Leach, R. W., and Wingreen, N. S., “Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution.”, ISME J, vol. 9, no. 1, pp. 68-80, 2015.
M. D. Chikina, Gerald, C. P., Li, X., Ge, Y., Pincas, H., Nair, V. D., Wong, A. K., Krishnan, A., Troyanskaya, O. G., Raymond, D., Saunders-Pullman, R., Bressman, S. B., Yue, Z., and Sealfon, S. C., “Low-variance RNAs identify Parkinson's disease molecular signature in blood.”, Mov Disord, vol. 30, no. 6, pp. 813-21, 2015.
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.
G. Tkačik, Dubuis, J. O., Petkova, M. D., and Gregor, T., “Positional information, positional error, and readout precision in morphogenesis: a mathematical framework.”, Genetics, vol. 199, no. 1, pp. 39-59, 2015.
J. Zhou and Troyanskaya, O. G., “Predicting effects of noncoding variants with deep learning-based sequence model.”, Nat Methods, 2015.
P. Barron Abitua, T Gainous, B., Kaczmarczyk, A. N., Winchell, C. J., Hudson, C., Kamata, K., Nakagawa, M., Tsuda, M., Kusakabe, T. G., and Levine, M., “The pre-vertebrate origins of neurogenic placodes.”, Nature, vol. 524, no. 7566, pp. 462-5, 2015.
W. W. K. Mok, Park, J. O., Rabinowitz, J. D., and Brynildsen, M. P., “RNA Futile Cycling in Model Persisters Derived from MazF Accumulation.”, MBio, vol. 6, no. 6, pp. e01588-15, 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.
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.
E. K. Farley, Olson, K. M., Zhang, W., Brandt, A. J., Rokhsar, D. S., and Levine, M. S., “Suboptimization of developmental enhancers.”, Science, vol. 350, no. 6258, pp. 325-8, 2015.

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