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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Proteins
M. Louis Reaves and Rabinowitz, J. D., “Metabolomics in systems microbiology.”, Curr Opin Biotechnol, vol. 22, no. 1, pp. 17-25, 2011.
J. D. Rabinowitz and White, E., “Autophagy and metabolism.”, Science, vol. 330, no. 6009, pp. 1344-8, 2010.
Proteolysis
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.
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.
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.
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.
Proteome
R. Mathew, Khor, S., Hackett, S. R., Rabinowitz, J. D., Perlman, D. H., and White, E., “Functional role of autophagy-mediated proteome remodeling in cell survival signaling and innate immunity.”, Mol Cell, vol. 55, no. 6, pp. 916-30, 2014.
Proteomics
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.
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.
Proto-Oncogene Proteins p21(ras)
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.
Protozoan Proteins
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.
Psychomotor Disorders
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.
Purine-Nucleoside Phosphorylase
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.
Purines
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.
Pyridoxal Phosphate
R. C. Kelly, Bolitho, M. E., Higgins, D. A., Lu, W., Ng, W. - L., Jeffrey, P. D., Rabinowitz, J. D., Semmelhack, M. F., Hughson, F. M., and Bassler, B. L., “The Vibrio cholerae quorum-sensing autoinducer CAI-1: analysis of the biosynthetic enzyme CqsA.”, Nat Chem Biol, vol. 5, no. 12, pp. 891-5, 2009.
Pyrimidine Nucleotides
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.
Pyrimidines
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.
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.
Pyroglutamate Hydrolase
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.
Pyruvate Carboxylase
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.
Pyruvate Kinase
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.
J. D. Rabinowitz and Vastag, L., “Teaching the design principles of metabolism.”, Nat Chem Biol, vol. 8, no. 6, pp. 497-501, 2012.
Pyruvates
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.
Pyruvic Acid
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.
Qb-SNARE Proteins
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.
Qc-SNARE Proteins
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.
Quantitative Structure-Activity Relationship
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.
Quantitative Trait Loci
J. S. Breunig, Hackett, S. R., Rabinowitz, J. D., and Kruglyak, L., “Genetic basis of metabolome variation in yeast.”, PLoS Genet, vol. 10, no. 3, p. e1004142, 2014.
Quaternary Ammonium Compounds
V. M. Boer, Crutchfield, C. A., Bradley, P. H., Botstein, D., and Rabinowitz, J. D., “Growth-limiting intracellular metabolites in yeast growing under diverse nutrient limitations.”, Mol Biol Cell, vol. 21, no. 1, pp. 198-211, 2010.
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.
Quorum Sensing
R. C. Kelly, Bolitho, M. E., Higgins, D. A., Lu, W., Ng, W. - L., Jeffrey, P. D., Rabinowitz, J. D., Semmelhack, M. F., Hughson, F. M., and Bassler, B. L., “The Vibrio cholerae quorum-sensing autoinducer CAI-1: analysis of the biosynthetic enzyme CqsA.”, Nat Chem Biol, vol. 5, no. 12, pp. 891-5, 2009.
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.
Randomized Controlled Trials as Topic
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.
ras Proteins
R. Mathew, Khor, S., Hackett, S. R., Rabinowitz, J. D., Perlman, D. H., and White, E., “Functional role of autophagy-mediated proteome remodeling in cell survival signaling and innate immunity.”, Mol Cell, vol. 55, no. 6, pp. 916-30, 2014.
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.
Real-Time Polymerase Chain Reaction
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.
Recombinant Proteins
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.
Reference Standards
E. Kimball and Rabinowitz, J. D., “Identifying decomposition products in extracts of cellular metabolites.”, Anal Biochem, vol. 358, no. 2, pp. 273-80, 2006.
Reproducibility of Results
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.
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.
Respiration
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.
Ribose
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.
Ribosemonophosphates
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.
Ribosomes
M. Nofal and Rabinowitz, J. D., “Ribosomes on the night shift.”, Science, vol. 360, no. 6390, pp. 710-711, 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.
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.
Risk Factors
M. Nofal and Rabinowitz, J. D., “Ribosomes on the night shift.”, Science, vol. 360, no. 6390, pp. 710-711, 2018.
RNA Interference
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.
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.
RNA, Messenger
V. M. Boer, Crutchfield, C. A., Bradley, P. H., Botstein, D., and Rabinowitz, J. D., “Growth-limiting intracellular metabolites in yeast growing under diverse nutrient limitations.”, Mol Biol Cell, vol. 21, no. 1, pp. 198-211, 2010.
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.
RNA, Small Interfering
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.
RNA, Transfer
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.
Saccharomyces cerevisiae
V. M. Boer, Crutchfield, C. A., Bradley, P. H., Botstein, D., and Rabinowitz, J. D., “Growth-limiting intracellular metabolites in yeast growing under diverse nutrient limitations.”, Mol Biol Cell, vol. 21, no. 1, pp. 198-211, 2010.
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. A. DiMaggio, McAllister, S. R., Floudas, C. A., Feng, X. - J., Rabinowitz, J. D., and Rabitz, H. A., “Biclustering via optimal re-ordering of data matrices in systems biology: rigorous methods and comparative studies.”, BMC Bioinformatics, vol. 9, p. 458, 2008.
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.
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.
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.
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.
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.
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.
J. S. Breunig, Hackett, S. R., Rabinowitz, J. D., and Kruglyak, L., “Genetic basis of metabolome variation in yeast.”, PLoS Genet, vol. 10, no. 3, p. e1004142, 2014.
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.
W. Lu, Kwon, Y. Kyung, and Rabinowitz, J. D., “Isotope ratio-based profiling of microbial folates.”, J Am Soc Mass Spectrom, vol. 18, no. 5, pp. 898-909, 2007.
M. M. Klosinska, Crutchfield, C. A., Bradley, P. H., Rabinowitz, J. D., and Broach, J. R., “Yeast cells can access distinct quiescent states.”, Genes Dev, vol. 25, no. 4, pp. 336-49, 2011.
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.
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.
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.
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.
Saccharomyces cerevisiae Proteins
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.
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.
J. I. Kliegman, Fiedler, D., Ryan, C. J., Xu, Y. - F., Su, X. - Y., Thomas, D., Caccese, M. C., Cheng, A., Shales, M., Rabinowitz, J. D., Krogan, N. J., and Shokat, K. M., “Chemical genetics of rapamycin-insensitive TORC2 in S. cerevisiae.”, Cell Rep, vol. 5, no. 6, pp. 1725-36, 2013.
Y. - 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.
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.
Salmonella enterica
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.
Sarcosine
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.
Serine
J. Fan, Ye, J., Kamphorst, J. J., Shlomi, T., Thompson, C. B., and Rabinowitz, J. D., “Quantitative flux analysis reveals folate-dependent NADPH production.”, Nature, vol. 510, no. 7504, pp. 298-302, 2014.
R. 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.
Serum Albumin
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.
Sex Characteristics
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.
Sigma Factor
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.
Signal Transduction
R. C. Kelly, Bolitho, M. E., Higgins, D. A., Lu, W., Ng, W. - L., Jeffrey, P. D., Rabinowitz, J. D., Semmelhack, M. F., Hughson, F. M., and Bassler, B. L., “The Vibrio cholerae quorum-sensing autoinducer CAI-1: analysis of the biosynthetic enzyme CqsA.”, Nat Chem Biol, vol. 5, no. 12, pp. 891-5, 2009.
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.
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.
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.
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.
J. D. Rabinowitz and White, E., “Autophagy and metabolism.”, Science, vol. 330, no. 6009, pp. 1344-8, 2010.
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.
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.
Single-Cell Analysis
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.
Sirolimus
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.
SNARE Proteins
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.
Software
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.
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.
Solubility
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.
Solvents
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.
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.
Species Specificity
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.
Spectrometry, Mass, Electrospray Ionization
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.
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.
J. Yuan, Bennett, B. D., and Rabinowitz, J. D., “Kinetic flux profiling for quantitation of cellular metabolic fluxes.”, Nat Protoc, vol. 3, no. 8, pp. 1328-40, 2008.
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.
W. Lu, Kwon, Y. Kyung, and Rabinowitz, J. D., “Isotope ratio-based profiling of microbial folates.”, J Am Soc Mass Spectrom, vol. 18, no. 5, pp. 898-909, 2007.
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.
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.
Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
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.
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.
Starvation
M. Nofal and Rabinowitz, J. D., “Ribosomes on the night shift.”, Science, vol. 360, no. 6390, pp. 710-711, 2018.
M. M. Klosinska, Crutchfield, C. A., Bradley, P. H., Rabinowitz, J. D., and Broach, J. R., “Yeast cells can access distinct quiescent states.”, Genes Dev, vol. 25, no. 4, pp. 336-49, 2011.
J. D. Rabinowitz and White, E., “Autophagy and metabolism.”, Science, vol. 330, no. 6009, pp. 1344-8, 2010.
Statistics, Nonparametric
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.
Stearoyl-CoA Desaturase
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.
Sterol Regulatory Element Binding Protein 1
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.
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.
Stress, Physiological
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, 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.
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.
Structure-Activity Relationship
C. D. Doucette, Schwab, D. J., Wingreen, N. S., and Rabinowitz, J. D., “α-Ketoglutarate coordinates carbon and nitrogen utilization via enzyme I inhibition.”, Nat Chem Biol, vol. 7, no. 12, pp. 894-901, 2011.
Substrate Specificity
R. C. Kelly, Bolitho, M. E., Higgins, D. A., Lu, W., Ng, W. - L., Jeffrey, P. D., Rabinowitz, J. D., Semmelhack, M. F., Hughson, F. M., and Bassler, B. L., “The Vibrio cholerae quorum-sensing autoinducer CAI-1: analysis of the biosynthetic enzyme CqsA.”, Nat Chem Biol, vol. 5, no. 12, pp. 891-5, 2009.
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.
Succinic Acid
S. Hui and Rabinowitz, J. D., “An unexpected trigger for calorie burning in brown fat.”, Nature, vol. 560, no. 7716, pp. 38-39, 2018.
Sugar Phosphates
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.
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.
Synaptic Vesicles
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.
Systems Biology
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.
J. D. Rabinowitz, “Cellular metabolomics of Escherchia coli.”, Expert Rev Proteomics, vol. 4, no. 2, pp. 187-98, 2007.
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.
P. A. DiMaggio, McAllister, S. R., Floudas, C. A., Feng, X. - J., Rabinowitz, J. D., and Rabitz, H. A., “Biclustering via optimal re-ordering of data matrices in systems biology: rigorous methods and comparative studies.”, BMC Bioinformatics, vol. 9, p. 458, 2008.
J. Fan, Kamphorst, J. J., Mathew, R., Chung, M. K., White, E., Shlomi, T., and Rabinowitz, J. D., “Glutamine-driven oxidative phosphorylation is a major ATP source in transformed mammalian cells in both normoxia and hypoxia.”, Mol Syst Biol, vol. 9, p. 712, 2013.
M. Louis Reaves and Rabinowitz, J. D., “Metabolomics in systems microbiology.”, Curr Opin Biotechnol, vol. 22, no. 1, pp. 17-25, 2011.
Systems Integration
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.
T-Lymphocytes
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.
Tandem Mass Spectrometry
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.
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.
J. Yuan, Bennett, B. D., and Rabinowitz, J. D., “Kinetic flux profiling for quantitation of cellular metabolic fluxes.”, Nat Protoc, vol. 3, no. 8, pp. 1328-40, 2008.
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.
J. S. Breunig, Hackett, S. R., Rabinowitz, J. D., and Kruglyak, L., “Genetic basis of metabolome variation in yeast.”, PLoS Genet, vol. 10, no. 3, p. e1004142, 2014.
W. Lu, Kwon, Y. Kyung, and Rabinowitz, J. D., “Isotope ratio-based profiling of microbial folates.”, J Am Soc Mass Spectrom, vol. 18, no. 5, pp. 898-909, 2007.
Teaching
J. D. Rabinowitz and Vastag, L., “Teaching the design principles of metabolism.”, Nat Chem Biol, vol. 8, no. 6, pp. 497-501, 2012.
Tetrahydrofolate Dehydrogenase
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.
Tetrahydrofolates
J. Fan, Ye, J., Kamphorst, J. J., Shlomi, T., Thompson, C. B., and Rabinowitz, J. D., “Quantitative flux analysis reveals folate-dependent NADPH production.”, Nature, vol. 510, no. 7504, pp. 298-302, 2014.
R. 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. 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.
Thermodynamics
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.
Thermogenesis
S. Hui and Rabinowitz, J. D., “An unexpected trigger for calorie burning in brown fat.”, Nature, vol. 560, no. 7716, pp. 38-39, 2018.
Thiazolidinediones
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.
Thymine
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.
Thymine Nucleotides
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.
Time Factors
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.
J. Yuan, Fowler, W. U., Kimball, E., Lu, W., and Rabinowitz, J. D., “Kinetic flux profiling of nitrogen assimilation in Escherichia coli.”, Nat Chem Biol, vol. 2, no. 10, pp. 529-30, 2006.
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.
Tissue Distribution
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.
TOR Serine-Threonine Kinases
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.
G. S. Ducker and Rabinowitz, J. D., “ZMP: a master regulator of one-carbon metabolism.”, Mol Cell, vol. 57, no. 2, pp. 203-4, 2015.
J. D. Rabinowitz and White, E., “Autophagy and metabolism.”, Science, vol. 330, no. 6009, pp. 1344-8, 2010.
Trans-Activators
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.
Transaldolase
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.
Transcription, Genetic
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.
M. M. Klosinska, Crutchfield, C. A., Bradley, P. H., Rabinowitz, J. D., and Broach, J. R., “Yeast cells can access distinct quiescent states.”, Genes Dev, vol. 25, no. 4, pp. 336-49, 2011.
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.
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.
Transcriptome
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.
Transfection
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.
Transferases
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.
Transport Vesicles
R. Mathew, Khor, S., Hackett, S. R., Rabinowitz, J. D., Perlman, D. H., and White, E., “Functional role of autophagy-mediated proteome remodeling in cell survival signaling and innate immunity.”, Mol Cell, vol. 55, no. 6, pp. 916-30, 2014.
Treatment Outcome
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.
Tricarboxylic Acids
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.
Triglycerides
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.
Trimethoprim
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.
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.
Tryptophan
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.
Tumor Cells, Cultured
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.
Tumor Microenvironment
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.
Tumor Suppressor Proteins
G. S. Ducker and Rabinowitz, J. D., “ZMP: a master regulator of one-carbon metabolism.”, Mol Cell, vol. 57, no. 2, pp. 203-4, 2015.
Ubiquitin-Protein Ligases
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.
Uracil
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.
Uridine Monophosphate
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.
Uridine Triphosphate
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.
Vero Cells
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.
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.
Vibrio cholerae
R. C. Kelly, Bolitho, M. E., Higgins, D. A., Lu, W., Ng, W. - L., Jeffrey, P. D., Rabinowitz, J. D., Semmelhack, M. F., Hughson, F. M., and Bassler, B. L., “The Vibrio cholerae quorum-sensing autoinducer CAI-1: analysis of the biosynthetic enzyme CqsA.”, Nat Chem Biol, vol. 5, no. 12, pp. 891-5, 2009.
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.
Virion
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.
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.
Virus Replication
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.
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.
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.
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.
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.
Water
E. Kimball and Rabinowitz, J. D., “Identifying decomposition products in extracts of cellular metabolites.”, Anal Biochem, vol. 358, no. 2, pp. 273-80, 2006.
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.
Workflow
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.
X-Ray Diffraction
J. D. Rabinowitz, Lloyd, P. M., Munzar, P., Myers, D. J., Cross, S., Damani, R., Quintana, R., Spyker, D. A., Soni, P., and Cassella, J. V., “Ultra-fast absorption of amorphous pure drug aerosols via deep lung inhalation.”, J Pharm Sci, vol. 95, no. 11, pp. 2438-51, 2006.
Xenopus laevis
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.
Yeasts
M. M. Klosinska, Crutchfield, C. A., Bradley, P. H., Rabinowitz, J. D., and Broach, J. R., “Yeast cells can access distinct quiescent states.”, Genes Dev, vol. 25, no. 4, pp. 336-49, 2011.
P. A. DiMaggio, McAllister, S. R., Floudas, C. A., Feng, X. - J., Rabinowitz, J. D., and Rabitz, H. A., “Biclustering via optimal re-ordering of data matrices in systems biology: rigorous methods and comparative studies.”, BMC Bioinformatics, vol. 9, p. 458, 2008.
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.
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.

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