59. Boer, V. M., Crutchfield, C. A., Bradley, P. H., Botstein, D., Rabinowitz, J. D. (2009). Growth-limiting intracellular metabolites in yeast growing under diverse nutrient limitations. Mol. Biol. Cell in press.

58. 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.
 

57. 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.
 

56. 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.
 

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

54. 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.

53. DiMaggio, P. A., McAllister, S. R., Floudas, C. A., Feng, X. J., Rabinowitz, J. D., Rabitz, H. A. (2009). A network flow model for biclustering via optimal re-ordering of data matrices. J. Glob. Optim.

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.  PMCID: PMC2293178

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.  PMCID: PMC1909916

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.  PMCID: PMC1697828

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.
PMCID: PMC1698944

30. Hess, D. C., Lu, W., Rabinowitz, J. D., Botstein, D. (2006). Ammonium toxicity and potassium limitation in yeast. PLoS Biology, 4: 2012-2023.  PMCID: PMC1609136

29. Kimball, E., Rabinowitz, J. D. (2006). Identifying decomposition products in extracts of cellular metabolites. Anal. Biochem., 358: 273-80.   PMCID: PMC1868396

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.