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Publications

129. Kamphorst, J. J., Chung, M. K., Fan, J., Rabinowitz, J. D. (2014) Quantitative analysis of acetyl-CoA production in hypoxic cancer cells reveals substantial contribution from acetate. Cancer & Metabolism, 2: 23.

128. Fan, J., Teng, X., Liu, L., Mattaini, K. R., Looper, R. E., Vander Heiden, M. G., Rabinowitz, J. D. (2014) Human phosphoglycerate dehydrogenase produces the oncometabolite d-2-hydroxyglutarate. ACS Chem Biol., 2014 Nov. 18. Epub ahead of print.

127. Castellana, M., Wilson, M. Z., Xu, Y., Joshi, P., Cristea, I. M., Rabinowitz, J. D., Gitai, Z., Wingreen, W. S. (2014) Enzyme clustering accelerates processing of intermediates through metabolic channeling. Nat. Biotechnol., 32(10): 1011-8. 

126. Stincone, A., Prigione, A., Cramer, T., Wamelink, M. M., Campbell, K., Cheung, E., Olin-Sandoval, V., Gruening, N. M., Krueger, A., Tauqeer Alam, M., Keller, M. A., Breitenbach, M., Brindle, K. M., Rabinowitz, J. D., Raiser, M. (2014) The return of metabolism: biochemistry and physiology of the pentose phosphate pathway. Biol. Rev. Camb. Philos. Soc., 2014 Sep 22. Epub ahead of print.

125. Zhang, J., 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., Thompson, C. B. (2014) Asparagine plays a critical role in regulating cellular adaptation to glutamine depletion. Mol. Cell, 56(2): 205-18.

124. Ye, J., Fan, J., Venneti, S., Wan, Y. W., Pawel, B. R., Zhang, J., Finley, L. W., Lu, C., Linsten, T., Cross, J., Qing, G., Liu, Z., Simon, M. C., Rabinowitz, J. D., Thompson, C. (2014) Serine catabolism regulates mitochondrial redox control during hypoxia. Cancer Discov., pii: CD-14-0250. Epub ahead of print. 

123. Mathew, R., Khor, S., Hackett, S. R., Rabinowitz, J. D., Perlman, D. H., White, E. (2014) Functional role of autophagy-mediated proteome remodeling in cell survival signaling and innate immunity. Mol. Cell, 55(6): 916-30.

122. Karsli-Uzunbas, G., Guo, J. Y., Price, S. M., Teng, X., Laddha, S. V., Khor, S., Kalaany, N. Y., Jacks, T., Chan, C. S., Rabinowitz, J. D., White, E. (2014) Autophagy is required for glucose homeostasis and lung tumor maintenance. Cancer Discov., 4(8): 914-27. 

121. Fan, J., Ye, J., Kamphorst, J. J., Shlomi, T., Thompson, C. B., Rabinowitz, J. D. (2014) Quantitative flux analysis reveals folate-dependent NADPH production. Nature, 510(7504): 298-302.

120. Breunig, J. S., Hackett, S. R., Rabinowitz, J. D., Krugkyak, L. (2014) Genetic basis of metabolome variation in yeast. PLoS Genet., 10(3): e1004142.

119. Shlomi, T., Fan, J., Tang, B., Kruger, W. D., Rabinowitz, J. D. (2014) Quantitation of cellular metabolic fluxes in methionine. Anal. Chem., 86(3): 1583-91.

118. Kliegman, J. I., 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., Shokat, K. M. (2013) Chemical genetics of rapamycin-insensitive TORC2 in s. cerevisiae. Cell Rep., 5(6): 1725-36.

117. Fan, J., Kamphorst, J. J., Mathew, R., Chung, M. K., White, E., Shlomi, T., Rabinowitz, J. D. (2013) Glutamine-driven oxidative phosphorylation is a major ATP source in transformed mammalian cells in both normoxia and hypoxia. Mol. Syst. Biol., 9: 712.

116. Grady, S. L., Purdy, J. G., Rabinowitz, J. D., Shenk, T. (2013) Argininosuccinate synthetase 1 depletion produces a metabolic state conducive to herpes simplex virus 1 infection. Proc. Natl. Acad. Sci. USA, 110(51): E5006-15.

115. Tchigvintsev, A., Tchigvintsev, D., Flick, R., Popovic, A., Dong, A., Xu, X., Brown, G., Lu, W., Wu, H., Dombrowski, L., Joo, J. C., Beloglazova, N., Min, J., Savchenko, A., Caudy, A. A., Rabinowitz, J. D., Murin, A. G., Yakunin, A. F. (2013) Biochemical and structural studies of conserved maf proteins revealed nucleotide pyrophosphatases with a preference for modified nucleotides.Chem. Biol., 20(11): 1386-98.

114. Tepper, N., Noor, E., Amador-Noguez, D., Haraldsdóttir, H. S., Milo, R., Rabinowitz, J.,Liebermeister, W., Shlomi, T. (2013) Steady-state metabolite concentrations reflect a balance between maximizing enzyme efficiency and minimizing totalk metabolite load. PLoS One, 8(9): e75370.

113. Fan, J., Kamphorst, J. J., Rabinowitz, J. D., Shlomi, T. (2013) Fatty acid labeling from glutamine in hypoxia can be explained by isotope exchange without net reductive IDH flux. J. Biol. Chem., 288(43): 31363-9.

112. Rabinowitz, J. D. and Silhavy, T. J. (2013) Systems biology: metabolite turns master regulator. Nature, 500(7462): 283-4.

111. Reaves, M.L., Young, B. D., Hosios, A. M., Xu, Y. F., Rabinowitz, J. D. (2013) Pyrimidine homeostasis is accomplished by directed overflow metabolism. Nature, 500(7461): 237-41.

110. Guo, L. Y., Karsli-Uzunbas, G., Mathew, R., Aisner, S. C., Kamphorst, J.J., Strohecker, A. M., Chen, G., Price, S., Lu, W., Teng, X., Snyder, E., Santanam, U., Dipaola, R. S., Jacks, T., Rabinowitz, J. D., White, E. (2013) Autophagy suppresses progression of K-ras-induced lung tumors to oncocytomas and maintains lipid homeostasis. Genes Dev., 27(13): 1447-61.

109. Koyuncu, E., Purdy, J. G., Rabinowitz, J. D., Shenk, T. (2013) Saturated very long fatty acids are required for the production of infectious human cytomegalovirus progeny. PLoS Pathog., 9(5): e1003333.

108. Kamphorst, J. J., Cross, J. R., Fan, J., de Stanchina, E., Mathew, R., White, E. P., Thompson, C. B., Rabinowitz, J. D. (2013) Hypoxic and Ras-transformed cells support growth by scavenging unsaturated fatty acids from lysophospholipids. Proc. Natl. Acad. Sci. USA, 110(22): 8882-7.

107. Xu, Y. F., Létisse, F., Absalan, F., Lu, W., Kuznetsova, E., Brown, G., Caudy, A. A., Yakunin, A. F., Broach, J. R., Rabinowitz, J. D. (2013) Nucleotide degradation and ribose salvage in yeast. Mol. Syst. Biol., 9: 665.

106. Commiso, C., Davidson, S. M., Soydaner-Azeloglu, R. g., Parker, S. J., Kamphorst, J. J., Hackett, S., Grabocka, E., Nofal, M., Drebin, J. A., Thompson, C. B., Rabinowitz, J. D., Metallo, C. M. (2013) Macropinocytosis of protein is an amino acid supply route in Ras-transformed cells. Nature, 497(7451): 633-7.

105. Shlomi T. and Rabinowitz, J. D. (2013) Metabolism: Cancer mistunes methylation. Nat. Chem. Biol., 9(5): 293-4. 

104. Xu, Y. F., Zhao, X., Glass, D. S., Absalan, F., Perlman, D. h., Broach, J. R., Rabinowitz, J. D. (2012) Regulation of yeast pyruvate kinase by ultrasensitive allostery independent of phosphorylation. Mol. Cell, 48:52-62.

103. Bray, K., Mathew, R., Lau, A., Kamphorst, J. J., Fan, J., Chen, J., Chen, H. Y., Ghavami, A., Stein, M., Dipaola, R. S., Zhang, D., Rabinowitz, J. D., White, E. (2012) Autophagy suppresses RIP kinase-dependent necrosis enabling survival to mTOR inhibition. PLoS One, 7(7): e41831.

102. Reaves, M. L., Sinha, S., Rabinowitz, J. D., Kruglyak, L., Redfield, R. J. (2012) Absence of detectable arsenate in DNA from arsenate-grown GFAJ-1 cells. Science, 337(6093): 470-3.

101. Grady, S. L., Hwang, J., Vastag, L., Rabinowitz, J. D., Shenk, T. (2012) Herpes simplex virus type 1 infection activates poly (ADP-ribose) polymerase and triggers the degradation of poly (ADP-ribose) glycohydrolase. J. Virol., 86(15): 8259-68. 

100. Rabinowitz, J. D. and Vastag, L. (2012) Teaching the design principles of metabolism. Nat. Chem.Biol., 8(6):497-501.

99. Xu, Y., Amador-Noguez, D., Reaves, M. L., Feng, X. J., Rabinowitz, J. D. (2012) Ultrasensitive regulation of anapleurosis via allosteric activation of PEP carboxylaseNat. Chem. Biol., 8(6): 562-68.   

98.  Ye, J., Mancuso, A., Tong, X., Ward, P. S., Fan, J., Rabinowitz, J. D., Thompson, C. B. (2012). Pyruvate kinase M2 promotes de novo serine synthesis to sustain mTORC1 activity and cell proliferation. Proc. Natl. Acad. Sci. USA, 109(18): 6904-09.

97. Peterson, C. N., Levchenko, I., Rabinowitz, J. D., Baker, T. A., Silhavy, T. J. (2012). RpoS proteolysis is controlled directly by ATP levels in Escherichia coli. Genes Dev., 26(6): 548-53.

96. Clasquin, M. F, Melamud, E., Rabinowitz, J. D. (2012). LC-MS Data Processing with MAVEN: A Metabolomic Analysis and Visualization EngineCurr. Protoc. Bioinformatics, 14.11.1-14.11.23, March.

95. Terry, L. J., Vastag, L., Rabinowitz, J. D., Shenk, T. (2012). Human kinome profiling identifies a requirement for AMP-activated protein kinase during human cytomegalovirus infection. Proc. Natl. Acad. Sci. USA, 109(8):3071-6.

94. Rabinowitz, J. D., Purdy, J. G., Vastag, L., Shenk, T., Koyuncu, E. (2011).Metabolomics in drug target discovery. Cold Spring Harb. Symp. Quant. Biol., 76: 235-46.

93. Kamphorst, J. J., Fan, J., Lu, W., White, E., Rabinowitz, J. D. (2011). Liquid chromatography-high resolution mass spectrometry analysis of fatty acid metabolism. Anal. Chem., 83(23): 9114-22.  

92. Doucette, C. D., Schwab, D. J., Wingreen, N. S., Rabinowitz, J. D. (2011). α-Ketoglutarate coordinates carbon and nitrogen utilization via enzyme I inhibition. Nat. Chem. Biol., 7(12): 894-901. 

91. Amador-Noguez, D. Brasg, I. A., Feng, X. J., Roquet, N., Rabinowitz, J. D. (2011). Metabolome remodeling during the acidogenic-solventogenic transition in Clostridium acetobutylicum. Appl. Environ. Microbiol., 77(22): 7984-97. 

90. Strelko, J. L., Lu, W., Dufort, F. J., Seyfried, T. N., Chiles, T. C., Rabinowitz, J. D., Roberts, M. F. (2011). Itaconic acid is a mammalian metabolite induced during macrophage activation. J. Am. Chem. Soc., 133(41): 16386-9.

89. Vastag, L., Koyuncu, E., Grady, S. L., Shenk, T. E., Rabinowitz, J. D. (2011). Divergent effects of human cytomegalovirus and herpes simplex virus-1 on cellular metabolism. PLoS Pathog., 7(7): e1002124.

88.  Liu, S. T. H., Sharon-Frilling, R., Ivanova, P., Milne, S. B., Myers, D. S., Rabinowitz, J. D., Brown, H. A., Shenk, T. (2011). Synaptic vesicle-like lipidome of human cytomegalovirus virions reveals a role for SNARE machinery in virion egress. PNAS, 108(31): 12869-74. 

87. Petti, A. A., Crutchfield, C. A., Rabinowitz, J. D., Botstein, D. (2011). Survival of starving yeast is correlated with oxidative stress response and nonrespiratory mitochondrial function. Proc. Natl. Acad. Sci. USA, 108(45): E1089-98. 

86. Clasquin, M. F., Melamud, E., Singer, A., Gooding, J. R., Xu, X., Dong, A., Cui, H., Campagna, S. R., Savchenko, A., Yakunin, A. F., Rabinowitz, J. D., Caudy, A. A. (2011). Riboneogenesis in yeast. Cell, 145: 969-980.

85. Reaves, M. L. and Rabinowitz, J. D. (2011). Characteristic phenotypes associated with ptsN-null mutants in Escherichia coli K-12 are absent in strains with functional ilvG. J. Bacteriol., 193(18): 4676-81.  

84. Guo, J. X., Chen, H.Y., Mathew, R., Fan, J., Strohecker, A, M., Karsli-Uzunbas, G., Kamphorst, J. J., Chen, G., Lemmons, J. M. S., Karantza, V., Coller, H. A., DiPaola, R. S., Gelinase, C., Rabinowitz, J. D., White, E. (2011). Activated Ras requires autophagy to maintain oxidative metabolism and tumorigenesis. Genes & Dev., 25: 460-470.

83. Klosinska, M. M., Crutchfield, C., Bradley, P. J., Rabinowitz, J. D., Broach, J. R. (2011). Yeast cells can access distinct  quiescent states. Genes Dev., 25(4): 336-49.

82. Vastag, L., Jorgensen, P., Peshkin, L., Rabinowitz, J. D., Kirschner, M. W. (2011). Remodeling of the metabolome during early frog development. PLoS ONE, 6(2): e16881.

81. Hart, Y., Madar, D., Yuan, J., Bren, A., Mayo, A. E., Rabinowitz, J. D., Alon, U. (2011) Robust control of nitrogen assimilation by a bifunctional enzyme in E. coli. Mol. Cell, 41(1): 117-127.

80. Merritt, J. H., Ha, D.G., Cowles, K. N., Lu, W., Morales, D. K., Rabinowitz, J., Gitai, Z., O’Toole, G. A. (2010). Specific control of Pseudomonas aeruginosa surface-associated behaviors by two c-di-GMP diguanylate cyclases. mBio, 1(4): pii. e00183-10.

79. Wellen, K. E., Lu, Lu, C., Mancuso, A., Lemons, J. M., Ryczko, M., Dennis, J. W., Rabinowitz, J. D., Coller, H. A., Thompson, C. B. (2010). The hexosamine biosynthetic pathwaycouples growth factor -induced glutamine uptake to glucose metabolism. Genes Dev., 24: 2784-2799.  

78. Rabinowitz, J. D. and White, E. (2010). Autophagy and metabolism. Science, 330(6009): 1344-8.

77. Melamud, E., Vastag, L., Rabinowitz, J. D. (2010) Metabolomic analysis and visualization engine for LC-MS data. Anal. Chem., 82: 9818-9826.

76. Seltzer, M. J., Bennett, B. D., Joshi, A. D., Gao, P., Thomas, A. G., Ferraris, D. V., Tsukamoto, T., Rojas, C. J., Slusher, B. S., Rabinowitz, J. D., Dang, C. V., Riggins, G. L. (2010). Inhibition of glutaminase preferentially slows growth of glioma cells with mutant IDH1. Cancer Res., 70(22): 8981-7. 

75. Reaves, M. L. and Rabinowitz, J. D. (2010) Metabolomics in systems microbiology. Curr. Opin. Biotechnol., 22(1): 17-25. 

74. Lemons, J. M. S., Feng, X. J., Bennett, B. D., Legesse-Miller, A., Johnson, E. L., Raitman, I., Pollina, E. A., Rabitz, H. A., Rabinowitz, J. D., Coller, H. A. (2010). Quiescent fibroblasts exhibit high metabolic activity. PLoS Biol., 8 (10): e1000514.

73. Vander Heiden, M. G., Locasale, J. W., Swanson, K.D., Sharfi, H., Heffron, G.J., Amador-Noguez, D., Christofk, H. R., Wagner, G., Rabinowitz, J.D., Asara, J.M., Cantley, L.C. (2010) Evidence for an Alternative Glycolytic Pathway in Rapidly Proliferating Cells. Science, 329(5998): 1492-1499.

72. Amador-Noguez, D., Feng, X. F., Fan, J.,Roquet, N., Rabitz, H., Rabinowitz, J. D. (2010) Systems-level Metabolic Flux Profiling Elucidates a Complete, Bifurcated Tricarboxylic Acid Cycle in Clostridium acetobutylicum. J. Bacteriol., 192(17): 4452-4461.

71. Kwon., Y. K., Higgins, M. B., Rabinowitz, J. D. (2010) Antifolate-induced Depletion of Intracellular Glycine and Purines Inhibits Thymineless Death in E. coli. ACS Chem. Biol., 5: 787-795.

70. Goyal, S., Yuan, J., Chen, T., Rabinowitz, J. D., Wingreen, N. S. (2010) Achieving Optimal Growth through Product Feedback Inhibition in Metabolism. PLoS Comput. Biol., 6:e1000802.

69. Goodarzi, H., Bennett, B. D., Amini, S., Reaves, M. L., Hottes, A. K., Rabinowitz, J. D., Tavazoie, S. (2010) Regulatory and Metabolic Rewiring during Laboratory Evolution of Ethanol Tolerance in E. coli. Mol. Syst. Biol., 6: 378.

68. Crutchfield, C., Lu, W., Melamud, E., Rabinowitz, J. D. (2010)  Mass Spectrometry-Based Metabolomics of Yeast. Methods Enzymol. 470: 393-426. 

67. Kuchma, S. L., Ballok, A. E., Merritt, J. H., Hammond, J. H., Lu, W., Rabinowitz, J. D., O'Toole, G. A. (2010). Cyclic-di-GMP-Mediated Repression of Swarming Motility by Pseudomonas aeruginosa: The pilY1 Gene and its Impact on Surface-Associated Behaviors. J. Bacteriol., 192: 2950-64.

66. Lu, W., Clasquin, M. F., Melamud, E., Amador-Noguez, D., Caudy, A. A., Rabinowitz, J. D. (2010) Metabolomic analysis via reversed-phase ion-pairing liquid chromatography coupled to a stand alone orbitrap mass spectrometer. Anal. Chem., 82: 3212-3221.

65. Monds, R. D., Newell,, P. D., Wagner, J. C., Schwartzman, J. A., Lu, W., Rabinowitz, J. D., O'Toole, G. A. (2010). Di-adenosine tetraphosphate (Ap4A) metabolism impacts biofilm formation by Pseudomonas fluorescens via modulation of c-di-GMP-dependent pathways. J. Bacteriol., 192: 3011-23.

64. Ward, P. S., Patel, J., Wise, D. R., Abdel-Wahab, O., Bennett, B. D., Coller, H. A., Cross, J. R., Fantin, V. R., Hedvat, C. V., Perl, A. E., Rabinowitz, J. D., Carroll, M., Su, S. M., Sharp, K. A., Levine, T. L., Thompson, C. B. (2010). The common feature of leukemia-associated IDH1 and IDH2 mutations is a neomorphic enzyme activity converting alpha-ketoglutarate to 2-hydroxyglutarate. Cancer Cell, 17: 215-6. 

63. Lu., X., Bennett, B., Mu, E., Rabinowitz, J., Kang, Y. (2010). Metabolomic changes accompanying transformation and acquisition of metastatic potential in a syngeneic mouse mammary tumor model. J. Biol. Chem., 285: 9319-21.

62. DiMaggio, P. A., McAllister, S. R., Floudas, C. A., Feng, X. J., Rabinowitz, J. D., Rabitz, H. A. (2010). A network flow model for biclustering via optimal re-ordering of data matrices. J. Glob. Optim., 47: 343-354. 

61. DiMaggio, P. A., McAllister, S. R., Floudas, C. A., Feng, X. J., Li, G., Rabinowitz, J. D., Rabitz, H. A. (2010). Enhancing molecular discovery using descriptor-free rearrangement clustering techniques for sparse data sets. AIChE Journal, 56: 405-418.

60. Boer, V. M., Crutchfield, C. A., Bradley, P. H., Botstein, D., Rabinowitz, J. D. (2010). Growth-limiting intracellular metabolites in yeast growing under diverse nutrient limitations. Mol. Biol. Cell, 21: 198-211.

59. Dang, L., White, D.W., Gross, S., Bennett, B.D., Bittinger, M.A., Driggers, E.M., Fantin, V.R., Jang, H.G., Jin, S., Keenan, M.C., Marks, M., Prins, R.M., Ward, P.S., Yen, K.E., Liau, L.M., Rabinowitz, J.D., Cantley, L.C., Thompson, C.B., Vander Heiden, M.G., Su, S.M. (2009). Cancer-associated IDH1 mutations produce 2-hydroxyglutarate. Nature, 462: 739-44.

58.  Kelly, R. C., Bolitho, M. E., Higgins, D. A., Lu, W., Ng, W. L., Jeffrey, P. D., Rabinowitz, J. D., Semmelhack, M. F., Hughson, F. M., Bassler, B. L. (2009) The Vibrio cholerae quorum-sensing autoinducer CAI-1: analysis of the biosynthetic enzyme CqsA. Nat. Chem. Biol., 5: 891-5. 

57. Yuan, J., Doucette, C., Fowler, W. U., Feng, X. J., Piazza, M., Rabitz, H. A., Wingreen, N. S., Rabinowitz, J. D. (2009). Metabolomics-driven quantitative analysis of ammonia assimilation in E. coli. Mol. Syst. Biol., 5:302.

56. Bennett, B. D., Kimball, E. H., Gao, M., Osterhout, R., Van Dien, S. J., Rabinowitz, J. D. (2009). Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli. Nat. Chem. Biol., 5: 593-9.

55. Olszewski, K. L., Morrisey, J. M., Wilinski, D., Burns, J. M., Vaidya, A. B., Rabinowitz, J. D., Llinás, M. (2009). Host parasite interactions revealed by Plasmodium falciparum metabolomics. Cell Host Microbe, 5:191-9.

54. Shinar, G., Rabinowitz, J. D., Alon, U. (2009). Robustness in glyoxylate bypass regulation. PLoS Comp. Biol., 5: e1000297.

53. Bradley, P. H., Brauer, M. J., Rabinowitz, J. D., Troyanskaya, O. (2009). Coordinated concentration changes of transcript and metabolites in Saccharomyces cerevisiae. PLoS Comp. Biol., 5: e1000270.

52. DiMaggio, P. A., McAllister, S. R., Floudas, C. A., Feng, X. J., Rabinowitz, J. D., Rabitz, H. A. (2008). Biclustering via optimal re-ordering of data matrices in systems biology: Novel rigorous methods and comparative studies. BMC Bioinformatics, 9: 458.

51. McAllister, S. R., Feng, X. J., Dimaggio, P. A. Jr., Floudas, C. A., Rabinowitz, J. D., Rabitz, H. (2008). Descriptor-free molecular discovery in large libraries by adaptive substituent reordering. Bioorg. Med. Chem. Lett., 18: 5967-5970.

50. Munger, J., Bennett, B. D., Parikh, A., Feng, X. J., McArdle, J., Rabitz, H. A., Shenk, T., Rabinowitz, J. D. (2008). Systems-level metabolic flux profiling identifies fatty acid synthesis as a target for anti-viral therapy. Nat. Biotechnol., 26: 1179-1186.

49. Kwon, Y. K., Lu, W., Melamud, E., Khanam, N., Bognar, A., Rabinowitz, J. D. (2008). A domino effect in antifolate drug action in Escherichia coli. Nat. Chem. Biol., 4: 602-608.

48. Yuan, J., Bennett, B. D., Rabinowitz, J. D. (2008).Kinetic flux profiling for quantitation of cellular metabolic fluxes. Nat. Protocols, 3: 1328-1340.

47. Bennett, B. D., Yuan, J., Kimball, E. H., Rabinowitz, J. D. (2008). Absolute quantitation of intracellular metabolite concentrations by an isotope ratio-based approach. Nat. Protocols, 3: 1299-1311.

46. Lu, W., Bennett, B. D., Rabinowitz, J. D. (2008). Analytical strategies for LC-MS-based targeted metabolomics. J. Chrom. B., 871: 236-242.

45. Waters, C. M., Lu, W., Rabinowitz, J. D., Bassler, B. L. (2008). Quorum sensing controls biofilm formation in Vibrio cholerae through modulation of cyclic di-GMP levels and repression of vpsT. J. Bacteriol., 190: 2527-2536. 

44. Rabinowitz, J. D., Hsiao, J. J., Gryncel, K. R., Kantrowitz, E. R., Feng, X. J., Li, G., Rabitz, H. (2008). Dissecting enzyme regulation by multiple allosteric effectors: Nucleotide regulation of aspartate transcarbamoylase. Biochemistry, 47: 5881-5888.

43. Piazza, M., Feng, X. J., Rabinowitz, J. D., Rabitz, H. (2008). Diverse metabolic model parameters generate similar methionine cycle dynamics. J. Theor. Biol., 251: 628-639.

42. Cui, H., Hayashi, A., Sun, H. S., Belmares, M. P., Cobey, C., Phan, T., Schweizer, J., Salter, M. W., Wang, Y. T., Tasker, R. A., Garman, D., Rabinowitz, J., Lu, P. S., Tymianski, M. (2007). PDZ protein interactions underlying NMDA receptor-mediated excitotoxicity and neuroprotection by PSD-95 inhibitors. J. Neurosci., 27: 9901-9915.

41. Xavier, K. B., Miller, S. T., Lu, W., Kim, J. H., Rabinowitz, J., Pelczer, I., Semmelhack, M. F., Bassler, B. L. (2007). Phosphorylation and processing of the quorum-sensing molecule AI-2 in enteric bacteria. ACS Chem. Biol., 2: 128-136.

40. Yuan, J., Rabinowitz, J. D. (2007). Differentiating metabolites formed from de novo synthesis versus macromolecule decomposition. J. Am. Chem. Soc., 129: 9294-9295.  PMCID: PMC2547081

39. Rabinowitz, J. D., Kimball, E. (2007). Acidic acetonitrile for cellular metabolome extraction from Escherichia coli. Anal. Chem., 79: 6167-6173.

38. Lu, W., Kwon, Y. K., Rabinowitz, J.D. (2007).  Isotope ratio-based profiling of microbial folates. J. Am. Soc. Mass Spectr., 18: 898-909. 

37. Campagna, S. R., Rabinowitz, J. D. (2007). Metabolome quantitation mass spectrometry. G.I.T. Laboratory Journal, 7-8: 26-27.

36. Rabinowitz, J. D. (2007). Cellular metabolomics of Escherichia coli. Exp. Rev. Proteomics, 4: 187-198.

35. Avram, M. J., Henthorn, T. K., Spyker, D. A., Krejcie, T. C., Lloyd, P. M., Cassella, J. V., Rabinowitz, J. D. (2007). Recirculatory pharmacokinetic model of the uptake, distribution, and bioavailability of prochlorperazine administered as a thermally generated aerosol in a single breath to dogs. Drug. Metab. Dispos., 35: 262-267.

34. Bao, Q., Lu, W., Rabinowitz, J. D., Shi, Y. (2007). Calcium blocks formation of apoptosome by preventing nucleotide exchange in Apaf-1. Mol. Cell, 25: 181-192.

33. Myers, D. J., Timmons, R. D., Lu, A. T., Hale, R. L., Solas, D. W., Soni, P., Rabinowitz, J. D. (2007). Effect of film thickness on thermal aerosol generation. Pharm. Res., 24:336-342.

32. Brauer, M. J., Yuan, J., Bennett, B. D., Lu, W., Kimball, E., Botstein, D., Rabinowitz, J. D. (2006). Conservation of the metabolomic response to starvation across two divergent microbes. Proc. Natl. Acad. Sci. USA, 103: 19302-19307.  

31. Munger, J., Bajad, S. U., Coller, H. A., Shenk, T., Rabinowitz, J. D. (2006). Dynamics of the cellular metabolome during human cytomegalovirus infection. PLoS Pathogens, 2: 1165.

30. Hess, D. C., Lu, W., Rabinowitz, J. D., Botstein, D. (2006). Ammonium toxicity and potassium limitation in yeast.  PLos Biology, 4: 2012-2023. 

29. Kimball, E., Rabinowitz, J. D. (2006). Identifying decomposition products in extracts of cellular metabolites. Anal. Biochem., 358: 273-80.   

28. Yuan, J., Fowler, W. U., Kimball, E., Lu, W., Rabinowitz, J. D. (2006). Kinetic flux profiling of nitrogen assimilation in Escherichia coli. Nat. Chem. Biol., 2: 529-530.

27. Bajad, S. U., Lu, W., Kimball, E. H., Yuan, J., Peterson, C., Rabinowitz, J. D. (2006). Separation and quantitation of water soluble cellular metabolites by hydrophilic interaction chromatography – tandem mass spectrometry. J. Chrom. A., 1125: 76-88.

26. Rabinowitz, J. D., Lloyd, P. M., Munzar, P., Myers, D. J., Cross, S., Damani, R., Quintana, R., Spyker, D. A., Soni, P., Cassella, J. V. (2006). Ultra-fast absorption of amorphous pure drug aerosols via deep lung inhalation. J. Pharm. Sci., 95: 2438-2451. 

25. Lu, W., Kimball, E., Rabinowitz, J. D. (2006). A high-performance liquid chromatography-tandem mass spectrometry method for quantitation of nitrogen-containing intracellular metabolites. J. Am. Soc. Mass Spectr., 17: 37-50.

24. Rabinowitz, J. D., Wensley, M., Lloyd, P., Myers, D., Shen, W., Lu, A., Hodges, C., Hale, R., Mufson, D., Zaffaroni, A. (2004). Fast onset medications through thermally generated aerosols. J. Pharmacol. Exp. Ther., 309: 769-775.

23. Turner-Cobb J. M., Koopman, C., Rabinowitz, J. D., Terr, A. I., Sephton, S. E., Spiegel, D. (2004). The interaction of social network size and stressful life events predict delayed-type hypersensitivity among women with metastatic breast cancer. Int. J. Psychophysiol., 54: 241-249.

22. Hall, F. C., Rabinowitz, J. D., Busch, R., Visconti, K. C., Belmares, M., Patil, N. S., Cope, A. P., Patel, S., McConnell, H. M., Mellins, E. D., Sonderstrup, G. (2002). Relationship between kinetic stability and immunogenicity of HLA-DR4/peptide complexes. Eur. J. Immunol., 32: 662-670.
 

21. Patil, N. S., Pashine, A., Belmares, M. P., Liu, W., Kaneshiro, B., Rabinowitz, J., McConnell, H., Mellins, E. D. (2001). Rheumatoid arthritis (RA)-associated HLA-DR alleles form less stable complexes with class II-associated invariant chain peptide than non-RA-associated HLA-DR alleles. J. Immunol., 167: 7157-7168.

20. Belmares, M. P., Rabinowitz, J. D., Lui, W., Mellins, E. D., McConnell, H. M. (2000). pH stability of HLA-DR4 complexes with antigenic peptides. Biochemistry, 39: 14558-14566.

19. Kasson, P. M., Rabinowitz, J. D., Schmitt, L., Davis, M. M., McConnell, H. M. (2000). Kinetics of peptide binding to the class II MHC protein I-Ek. Biochemistry, 39: 1048-1058.

18. Rabinowitz, J. D., Vrljic, M., Kasson, P. M., Liang, M. N., Busch, R., Boniface, J. J., Davis, M. M., McConnell, H. M. (1998). Formation of a highly peptide-receptive state of class II MHC. Immunity, 9: 699-709.

17. Boniface, J. J., Rabinowitz, J. D., Wulfing, C., Hampl, J., Reich, Z., Altman, J. D., Kantor, R. M., Beeson, C., McConnell, H. M., Davis, M. M. (1998). Initiation of signal transduction through the T cell receptor requires the multivalent engagement of peptide/MHC ligands. Immunity, 9: 459-466.

16. Lee, C., Liang, M. N., Tate, K. M., Rabinowitz, J. D., Beeson, C., Jones, P. P., McConnell, H. M. (1998). Evidence that the autoimmune antigen myelin basic protein (MBP) Ac1-9 binds towards one end of the major histocompatibility complex (MHC) cleft. J. Exp. Med., 187: 1505-1516.

15. Rabinowitz, J. D., Vacchino, J. F., Beeson, C., McConnell, H. M. (1998). Potentiometric measurement of intracellular redox activity. J. Am. Chem. Soc., 120: 2464-2473.

14. Petros, W. P., Rabinowitz, J., Gibbs, J. P., Hall, I. H., Stuart, A. R., Peters, W. P. (1998).Effect of plasma TNF-α on filgrastim-stimulated hematopoiesis in mice and humans.   Pharmacotherapy, 18: 816-823.

13. Rabinowitz, J. D., Liang, M. N., Tate K., Lee C., Beeson C., McConnell H. M. (1997). Specific T cell recognition of kinetic isomers in the binding of peptide to class II major histocompatibility complex. Proc. Natl. Acad. Sci. USA, 94: 8702-8707.

12. Rabinowitz, J. D., Rigler P., Carswell-Crumpton, C., Beeson, C., McConnell, H. M. (1997). Screening for novel drug effects with a microphysiometer: a potent effect of clofilium unrelated to potassium channel blockade. Life Sci., 61: PL87-PL94.

11. Elkordy, M., Crump, M., Vredenburgh, J. J., Petros, W. P., Hussein, A., Rubin, P., Ross, M., Gilbert, C., Modlin, C., Meisenberg, B., Coniglio, D., Rabinowitz, J., Laughlin, M., Kurtzberg, J., Peters, W. P. (1997). A phase I trial of recombinant human interleukin-1 beta (OCT-43) following high-dose chemotherapy and autologous bone marrow transplantation. Bone Marrow Transpl., 19: 315-322.

10. Petros, W. P., Rabinowitz, J., Stuart, A., Peters W. P. (1997). Clinical pharmacology of filgrastim following high-dose chemotherapy and autologous bone marrow transplantation. Clin. Cancer Res., 3: 705-711.

9. Wulfing, C., Rabinowitz, J. D., Beeson C., Sjaastad M. D., McConnell H. M., Davis M. M. (1997). Kinetics and extent of T cell activation as measured with the calcium signal. J. Exp. Med., 185: 1815-1825.

8. Rabinowitz, J. D., Beeson, C., Wulfing C., Tate K., Allen P. M., Davis M. M., McConnell, H. M. (1996). Altered T cell receptor ligands trigger a subset of early T cell signals. Immunity, 5: 125-135.

7. Rabinowitz, J. D., Beeson C., Lyons D. S., Davis M. M., McConnell, H. M. (1996). Kinetic discrimination in T-cell activation. Proc. Natl. Acad. Sci. USA, 93: 1401-1405.

6. Beeson, C., Rabinowitz, J., Tate, K., Gutgemann, I., Chien, Y. H., Jones, P. P., Davis, M. M., McConnell, H. M. (1996). Early biochemical signals arise from low affinity TCR-ligand reactions at the cell-cell interface. J. Exp. Med., 184: 777-782.

5. Petros, W. P., Rosner, G. L., Rabinowitz, J., Gilbert, C. J., Coniglio, D., Vredenburgh J. J., Ross, M., Peters, W. P. (1996). The pharmacologic effects of recombinant, human colony-stimulating factors and their modulation by theophylline. Pharmacotherapy, 16: 742-748.

4. Petros W. P., Rabinowitz, J., Stuart A. R., Gupton C., Alderman, E. M., Peters, W. P. (1994). Elevated endogenous serum macrophage colony-stimulating factor in the early stage of fungemia following bone marrow transplantation. Exp. Hematol., 22: 582-586.

3. Rabinowitz, J., Petros, W. P., Peters, W. P. (1994). Cytokine kinetics: Clinical pharmacology studies complementing recombinant growth factor trials. Cancer Bulletin, 46: 40-47.

2. Rabinowitz, J., Petros, W. P., Stuart, A. R., Peters, W. P. (1993). Characterization of endogenous cytokine concentrations after high-dose chemotherapy with autologous bone marrow support. Blood, 81: 2452-2459.

1. Petros W. P., Rabinowitz, J., Stuart, A. R., Gilbert, C. J., Kanakura, Y., Griffin, J. D., Peters, W. P. (1992). Disposition of recombinant human granulocyte-macrophage colony-stimulating factor in patients receiving high-dose chemotherapy and autologous bone marrow support. Blood, 80: 1135-1140.