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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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.
Risk Factors
M. Nofal and Rabinowitz, J. D., Ribosomes on the night shift., Science, vol. 360, no. 6390, pp. 710-711, 2018.
Saccharomyces cerevisiae
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.
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.
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.
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.
P. A. Gibney, Schieler, A., Chen, J. C., Bacha-Hummel, J. M., Botstein, M., Volpe, M., Silverman, S. J., Xu, Y., Bennett, B. D., Rabinowitz, J. D., and Botstein, D., Common and divergent features of galactose-1-phosphate and fructose-1-phosphate toxicity in yeast., Mol Biol Cell, vol. 29, no. 8, pp. 897-910, 2018.
P. 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.
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.
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. 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.
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.
Signal Transduction
J. D. Rabinowitz and White, E., Autophagy and metabolism., Science, vol. 330, no. 6009, pp. 1344-8, 2010.
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.
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.
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.
Spectrometry, Mass, Electrospray Ionization
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.
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.
Teaching
J. D. Rabinowitz and Vastag, L., Teaching the design principles of metabolism., Nat Chem Biol, vol. 8, no. 6, pp. 497-501, 2012.
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.

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