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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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. 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.
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.
N. V. Rajeshkumar, Dutta, P., Yabuuchi, S., de Wilde, R. F., Martinez, G. V., Le, A., Kamphorst, J. J., Rabinowitz, J. D., Jain, S. K., Hidalgo, M., Dang, C. V., Gillies, R. J., and Maitra, A., Therapeutic Targeting of the Warburg Effect in Pancreatic Cancer Relies on an Absence of p53 Function., Cancer Res, vol. 75, no. 16, pp. 3355-64, 2015.
J. D. Rabinowitz and Vastag, L., Teaching the design principles of metabolism., Nat Chem Biol, vol. 8, no. 6, pp. 497-501, 2012.
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.
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. Munger, Bennett, B. D., Parikh, A., Feng, X. - J., McArdle, J., Rabitz, H. A., Shenk, T., and Rabinowitz, J. D., Systems-level metabolic flux profiling identifies fatty acid synthesis as a target for antiviral therapy., Nat Biotechnol, vol. 26, no. 10, pp. 1179-86, 2008.
D. Amador-Noguez, Feng, X. - J., Fan, J., Roquet, N., Rabitz, H., and Rabinowitz, J. D., Systems-level metabolic flux profiling elucidates a complete, bifurcated tricarboxylic acid cycle in Clostridium acetobutylicum., J Bacteriol, vol. 192, no. 17, pp. 4452-61, 2010.
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.
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.
S. T. H. Liu, Sharon-Friling, R., Ivanova, P., Milne, S. B., Myers, D. S., Rabinowitz, J. D., H Brown, A., and Shenk, T., Synaptic vesicle-like lipidome of human cytomegalovirus virions reveals a role for SNARE machinery in virion egress., Proc Natl Acad Sci U S A, vol. 108, no. 31, pp. 12869-74, 2011.
A. A. Petti, Crutchfield, C. A., Rabinowitz, J. D., and Botstein, D., Survival of starving yeast is correlated with oxidative stress response and nonrespiratory mitochondrial function., Proc Natl Acad Sci U S A, vol. 108, no. 45, pp. E1089-98, 2011.
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.
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.
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.
J. Ye, Fan, J., Venneti, S., Wan, Y. - W., Pawel, B. R., Zhang, J., Finley, L. W. S., Lu, C., Lindsten, T., Cross, J. R., Qing, G., Liu, Z., M Simon, C., Rabinowitz, J. D., and Thompson, C. B., Serine Catabolism Regulates Mitochondrial Redox Control during Hypoxia., Cancer Discov, vol. 4, no. 12, pp. 1406-17, 2014.
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.
S. U. Bajad, Lu, W., Kimball, E. H., Yuan, J., Peterson, C., and Rabinowitz, J. D., Separation and quantitation of water soluble cellular metabolites by hydrophilic interaction chromatography-tandem mass spectrometry., J Chromatogr A, vol. 1125, no. 1, pp. 76-88, 2006.
E. Koyuncu, Purdy, J. G., Rabinowitz, J. D., and Shenk, T., Saturated very long chain fatty acids are required for the production of infectious human cytomegalovirus progeny., PLoS Pathog, vol. 9, no. 5, p. e1003333, 2013.
C. N. Peterson, Levchenko, I., Rabinowitz, J. D., Baker, T. A., and Silhavy, T. J., RpoS proteolysis is controlled directly by ATP levels in Escherichia coli., Genes Dev, vol. 26, no. 6, pp. 548-53, 2012.
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.
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.
M. Nofal and Rabinowitz, J. D., Ribosomes on the night shift., Science, vol. 360, no. 6390, pp. 710-711, 2018.
M. F. Clasquin, Melamud, E., Singer, A., Gooding, J. R., Xu, X., Dong, A., Cui, H., Campagna, S. R., Savchenko, A., Yakunin, A. F., Rabinowitz, J. D., and Caudy, A. A., Riboneogenesis in yeast., Cell, vol. 145, no. 6, pp. 969-80, 2011.
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.
L. Vastag, Jorgensen, P., Peshkin, L., Wei, R., Rabinowitz, J. D., and Kirschner, M. W., Remodeling of the metabolome during early frog development., PLoS One, vol. 6, no. 2, p. e16881, 2011.
H. Goodarzi, Bennett, B. D., Amini, S., Reaves, M. L., Hottes, A. K., Rabinowitz, J. D., and Tavazoie, S., Regulatory and metabolic rewiring during laboratory evolution of ethanol tolerance in E. coli., Mol Syst Biol, vol. 6, p. 378, 2010.
Y. - F. Xu, Zhao, X., Glass, D. S., Absalan, F., Perlman, D. H., Broach, J. R., and Rabinowitz, J. D., Regulation of yeast pyruvate kinase by ultrasensitive allostery independent of phosphorylation., Mol Cell, vol. 48, no. 1, pp. 52-62, 2012.
C. M. Waters, Lu, W., Rabinowitz, J. D., and Bassler, B. L., Quorum sensing controls biofilm formation in Vibrio cholerae through modulation of cyclic di-GMP levels and repression of vpsT., J Bacteriol, vol. 190, no. 7, pp. 2527-36, 2008.
J. M. S. Lemons, Feng, X. - J., Bennett, B. D., Legesse-Miller, A., Johnson, E. L., Raitman, I., Pollina, E. A., Rabitz, H. A., Rabinowitz, J. D., and Coller, H. A., Quiescent fibroblasts exhibit high metabolic activity., PLoS Biol, vol. 8, no. 10, p. e1000514, 2010.
J. Fan, Ye, J., Kamphorst, J. J., Shlomi, T., Thompson, C. B., and Rabinowitz, J. D., Quantitative flux analysis reveals folate-dependent NADPH production., Nature, vol. 510, no. 7504, pp. 298-302, 2014.
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.
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.
J. J. Kamphorst, Chung, M. K., Fan, J., and Rabinowitz, J. D., Quantitative analysis of acetyl-CoA production in hypoxic cancer cells reveals substantial contribution from acetate., Cancer Metab, vol. 2, p. 23, 2014.
M. Louis Reaves, Young, B. D., Hosios, A. M., Xu, Y. - F., and Rabinowitz, J. D., Pyrimidine homeostasis is accomplished by directed overflow metabolism., Nature, vol. 500, no. 7461, pp. 237-41, 2013.
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.
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. 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.
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.
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. 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.
J. D. Rabinowitz and Coller, H. A., Partners in the Warburg effect., Elife, vol. 5, 2016.
Y. - F. Xu, Létisse, F., Absalan, F., Lu, W., Kuznetsova, E., Brown, G., Caudy, A. A., Yakunin, A. F., Broach, J. R., and Rabinowitz, J. D., Nucleotide degradation and ribose salvage in yeast., Mol Syst Biol, vol. 9, p. 665, 2013.
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.
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.
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.
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.
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.
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.
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.
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.
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.
W. - X. Zong, Rabinowitz, J. D., and White, E., Mitochondria and Cancer., Mol Cell, vol. 61, no. 5, pp. 667-76, 2016.
P. H. Bradley, Gibney, P. A., Botstein, D., Troyanskaya, O. G., and Rabinowitz, J. D., Minor Isozymes Tailor Yeast Metabolism to Carbon Availability., mSystems, vol. 4, no. 1, 2019.
J. Yuan, Doucette, C. D., Fowler, W. U., Feng, X. - J., Piazza, M., Rabitz, H. A., Wingreen, N. S., and Rabinowitz, J. D., Metabolomics-driven quantitative analysis of ammonia assimilation in E. coli., Mol Syst Biol, vol. 5, p. 302, 2009.
M. Louis Reaves and Rabinowitz, J. D., Metabolomics in systems microbiology., Curr Opin Biotechnol, vol. 22, no. 1, pp. 17-25, 2011.
C. Jang, Chen, L., and Rabinowitz, J. D., Metabolomics and Isotope Tracing., Cell, vol. 173, no. 4, pp. 822-837, 2018.
W. Lu, Clasquin, M. F., Melamud, E., Amador-Noguez, D., Caudy, A. A., and Rabinowitz, J. D., Metabolomic analysis via reversed-phase ion-pairing liquid chromatography coupled to a stand alone orbitrap mass spectrometer., Anal Chem, vol. 82, no. 8, pp. 3212-21, 2010.
E. Melamud, Vastag, L., and Rabinowitz, J. D., Metabolomic analysis and visualization engine for LC-MS data., Anal Chem, vol. 82, no. 23, pp. 9818-26, 2010.
D. Amador-Noguez, Brasg, I. A., Feng, X. - J., Roquet, N., and Rabinowitz, J. D., Metabolome remodeling during the acidogenic-solventogenic transition in Clostridium acetobutylicum., Appl Environ Microbiol, vol. 77, no. 22, pp. 7984-97, 2011.
X. Su, Lu, W., and Rabinowitz, J. D., Metabolite Spectral Accuracy on Orbitraps., Anal Chem, vol. 89, no. 11, pp. 5940-5948, 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.
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.
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.
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.
C. A. Crutchfield, Lu, W., Melamud, E., and Rabinowitz, J. D., Mass spectrometry-based metabolomics of yeast., Methods Enzymol, vol. 470, pp. 393-426, 2010.
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.
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. 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.
J. J. Kamphorst, Fan, J., Lu, W., White, E., and Rabinowitz, J. D., Liquid chromatography-high resolution mass spectrometry analysis of fatty acid metabolism., Anal Chem, vol. 83, no. 23, pp. 9114-22, 2011.
M. F. Clasquin, Melamud, E., and Rabinowitz, J. D., LC-MS data processing with MAVEN: a metabolomic analysis and visualization engine., Curr Protoc Bioinformatics, vol. Chapter 14, p. Unit14.11, 2012.
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.
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.
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.
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.
J. J. Kamphorst, Cross, J. R., Fan, J., de Stanchina, E., Mathew, R., White, E. P., Thompson, C. B., and Rabinowitz, J. D., Hypoxic and Ras-transformed cells support growth by scavenging unsaturated fatty acids from lysophospholipids., Proc Natl Acad Sci U S A, vol. 110, no. 22, pp. 8882-7, 2013.
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.
J. Fan, Teng, X., Liu, L., Mattaini, K. R., Looper, R. E., Heiden, M. G. Vander, and Rabinowitz, J. D., Human Phosphoglycerate Dehydrogenase Produces the Oncometabolite d-2-Hydroxyglutarate., ACS Chem Biol, 2014.
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.
L. J. Terry, Vastag, L., Rabinowitz, J. D., and Shenk, T., Human kinome profiling identifies a requirement for AMP-activated protein kinase during human cytomegalovirus infection., Proc Natl Acad Sci U S A, vol. 109, no. 8, pp. 3071-6, 2012.
K. L. Olszewski, Morrisey, J. M., Wilinski, D., Burns, J. M., Vaidya, A. B., Rabinowitz, J. D., and Llinás, M., Host-parasite interactions revealed by Plasmodium falciparum metabolomics., Cell Host Microbe, vol. 5, no. 2, pp. 191-9, 2009.
W. Lu, Kimball, E., and Rabinowitz, J. D., A high-performance liquid chromatography-tandem mass spectrometry method for quantitation of nitrogen-containing intracellular metabolites., J Am Soc Mass Spectrom, vol. 17, no. 1, pp. 37-50, 2006.
L. Aristilde, Lewis, I. A., Park, J. O., and Rabinowitz, J. D., Hierarchy in Pentose Sugar Metabolism in Clostridium Acetobutylicum., Appl Environ Microbiol, 2014.
S. L. Grady, Hwang, J., Vastag, L., Rabinowitz, J. D., and Shenk, T., Herpes simplex virus 1 infection activates poly(ADP-ribose) polymerase and triggers the degradation of poly(ADP-ribose) glycohydrolase., J Virol, vol. 86, no. 15, pp. 8259-68, 2012.
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.
J. Hwang, Purdy, J. G., Wu, K., Rabinowitz, J. D., and Shenk, T., Estrogen-related receptor α is required for efficient human cytomegalovirus replication., Proc Natl Acad Sci U S A, vol. 111, no. 52, pp. E5706-15, 2014.
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.
M. Castellana, Wilson, M. Z., Xu, Y., Joshi, P., Cristea, I. M., Rabinowitz, J. D., Gitai, Z., and Wingreen, N. S., Enzyme clustering accelerates processing of intermediates through metabolic channeling., Nat Biotechnol, vol. 32, no. 10, pp. 1011-8, 2014.
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. Song, Park, J. O., Tanner, L., Nagano, Y., Rabinowitz, J. D., and Shvartsman, S. Y., Energy budget of Drosophila embryogenesis., Curr Biol, vol. 29, no. 12, pp. R566-R567, 2019.
S. 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.
J. Munger, Bajad, S. U., Coller, H. A., Shenk, T., and Rabinowitz, J. D., Dynamics of the cellular metabolome during human cytomegalovirus infection., PLoS Pathog, vol. 2, no. 12, p. e132, 2006.
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. Kyung Kwon, Lu, W., Melamud, E., Khanam, N., Bognar, A., and Rabinowitz, J. D., A domino effect in antifolate drug action in Escherichia coli., Nat Chem Biol, vol. 4, no. 10, pp. 602-8, 2008.
M. Piazza, Feng, X. - J., Rabinowitz, J. D., and Rabitz, H., Diverse metabolic model parameters generate similar methionine cycle dynamics., J Theor Biol, vol. 251, no. 4, pp. 628-39, 2008.
L. Vastag, Koyuncu, E., Grady, S. L., Shenk, T. E., and Rabinowitz, J. D., Divergent effects of human cytomegalovirus and herpes simplex virus-1 on cellular metabolism., PLoS Pathog, vol. 7, no. 7, p. e1002124, 2011.
S. 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.
J. D. Rabinowitz, Hsiao, J. J., Gryncel, K. R., Kantrowitz, E. R., Feng, X. - J., Li, G., and Rabitz, H., Dissecting enzyme regulation by multiple allosteric effectors: nucleotide regulation of aspartate transcarbamoylase., Biochemistry, vol. 47, no. 21, pp. 5881-8, 2008.
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.
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.
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.
J. Yuan and Rabinowitz, J. D., Differentiating metabolites formed from de novo synthesis versus macromolecule decomposition., J Am Chem Soc, vol. 129, no. 30, pp. 9294-5, 2007.
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. 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. R. McAllister, Feng, X. - J., DiMaggio, P. A., Floudas, C. A., Rabinowitz, J. D., and Rabitz, H., Descriptor-free molecular discovery in large libraries by adaptive substituent reordering., Bioorg Med Chem Lett, vol. 18, no. 22, pp. 5967-70, 2008.
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.
P. H. Bradley, Brauer, M. J., Rabinowitz, J. D., and Troyanskaya, O. G., Coordinated concentration changes of transcripts and metabolites in Saccharomyces cerevisiae., PLoS Comput Biol, vol. 5, no. 1, p. e1000270, 2009.
M. J. Brauer, Yuan, J., Bennett, B. D., Lu, W., Kimball, E., Botstein, D., and Rabinowitz, J. D., Conservation of the metabolomic response to starvation across two divergent microbes., Proc Natl Acad Sci U S A, vol. 103, no. 51, pp. 19302-7, 2006.
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.
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. I. Kliegman, Fiedler, D., Ryan, C. J., Xu, Y. - F., Su, X. - Y., Thomas, D., Caccese, M. C., Cheng, A., Shales, M., Rabinowitz, J. D., Krogan, N. J., and Shokat, K. M., Chemical genetics of rapamycin-insensitive TORC2 in S. cerevisiae., Cell Rep, vol. 5, no. 6, pp. 1725-36, 2013.
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. 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.
M. Louis Reaves and Rabinowitz, J. D., Characteristic phenotypes associated with ptsN-null mutants in Escherichia coli K-12 are absent in strains with functional ilvG., J Bacteriol, vol. 193, no. 18, pp. 4576-81, 2011.
J. D. Rabinowitz, Cellular metabolomics of Escherchia coli., Expert Rev Proteomics, vol. 4, no. 2, pp. 187-98, 2007.
Q. Bao, Lu, W., Rabinowitz, J. D., and Shi, Y., Calcium blocks formation of apoptosome by preventing nucleotide exchange in Apaf-1., Mol Cell, vol. 25, no. 2, pp. 181-92, 2007.
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. 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.
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.
G. Karsli-Uzunbas, Guo, J. Yanxiang, Price, S., Teng, X., Laddha, S. V., Khor, S., Kalaany, N. Y., Jacks, T., Chan, C. S., Rabinowitz, J. D., and White, E., Autophagy is required for glucose homeostasis and lung tumor maintenance., Cancer Discov, vol. 4, no. 8, pp. 914-27, 2014.
J. D. Rabinowitz and White, E., Autophagy and metabolism., Science, vol. 330, no. 6009, pp. 1344-8, 2010.
J. Zhang, Fan, J., Venneti, S., Cross, J. R., Takagi, T., Bhinder, B., Djaballah, H., Kanai, M., Cheng, E. H., Judkins, A. R., Pawel, B., Baggs, J., Cherry, S., Rabinowitz, J. D., and Thompson, C. B., Asparagine plays a critical role in regulating cellular adaptation to glutamine depletion., Mol Cell, vol. 56, no. 2, pp. 205-18, 2014.
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.
S. L. Grady, Purdy, J. G., Rabinowitz, J. D., and Shenk, T., Argininosuccinate synthetase 1 depletion produces a metabolic state conducive to herpes simplex virus 1 infection., Proc Natl Acad Sci U S A, vol. 110, no. 51, pp. E5006-15, 2013.
Y. Kyung Kwon, Higgins, M. B., and Rabinowitz, J. D., Antifolate-induced depletion of intracellular glycine and purines inhibits thymineless death in E. coli., ACS Chem Biol, vol. 5, no. 8, pp. 787-95, 2010.
W. Lu, Bennett, B. D., and Rabinowitz, J. D., Analytical strategies for LC-MS-based targeted metabolomics., J Chromatogr B Analyt Technol Biomed Life Sci, vol. 871, no. 2, pp. 236-42, 2008.
D. C. Hess, Lu, W., Rabinowitz, J. D., and Botstein, D., Ammonium toxicity and potassium limitation in yeast., PLoS Biol, vol. 4, no. 11, p. e351, 2006.
J. D. Rabinowitz and Kimball, E., Acidic acetonitrile for cellular metabolome extraction from Escherichia coli., Anal Chem, vol. 79, no. 16, pp. 6167-73, 2007.
S. Goyal, Yuan, J., Chen, T., Rabinowitz, J. D., and Wingreen, N. S., Achieving optimal growth through product feedback inhibition in metabolism., PLoS Comput Biol, vol. 6, no. 6, p. e1000802, 2010.
B. D. Bennett, Yuan, J., Kimball, E. H., and Rabinowitz, J. D., Absolute quantitation of intracellular metabolite concentrations by an isotope ratio-based approach., Nat Protoc, vol. 3, no. 8, pp. 1299-311, 2008.
B. D. Bennett, Kimball, E. H., Gao, M., Osterhout, R., Van Dien, S. J., and Rabinowitz, J. D., Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli., Nat Chem Biol, vol. 5, no. 8, pp. 593-9, 2009.
M. Louis Reaves, Sinha, S., Rabinowitz, J. D., Kruglyak, L., and Redfield, R. J., Absence of detectable arsenate in DNA from arsenate-grown GFAJ-1 cells., Science, vol. 337, no. 6093, pp. 470-3, 2012.