Joshua D Rabinowitz

Summary

Affiliation: Princeton University
Country: USA

Publications

  1. ncbi request reprint Acidic acetonitrile for cellular metabolome extraction from Escherichia coli
    Joshua D Rabinowitz
    Department of Chemistry and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
    Anal Chem 79:6167-73. 2007
  2. ncbi request reprint Cellular metabolomics of Escherchia coli
    Joshua D Rabinowitz
    Princeton University, Department of Chemistry and Lewis Sigler Institute for Integrative Genomics, Princeton, NJ 08544, USA
    Expert Rev Proteomics 4:187-98. 2007
  3. ncbi request reprint Ultra-fast absorption of amorphous pure drug aerosols via deep lung inhalation
    Joshua D Rabinowitz
    Department of Chemistry and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
    J Pharm Sci 95:2438-51. 2006
  4. pmc Dissecting enzyme regulation by multiple allosteric effectors: nucleotide regulation of aspartate transcarbamoylase
    Joshua D Rabinowitz
    Department of Chemistry, Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
    Biochemistry 47:5881-8. 2008
  5. pmc Yeast cells can access distinct quiescent states
    Maja M Klosinska
    Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
    Genes Dev 25:336-49. 2011
  6. doi request reprint Nucleotide degradation and ribose salvage in yeast
    Yi Fan Xu
    Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
    Mol Syst Biol 9:665. 2013
  7. pmc Metabolomics-driven quantitative analysis of ammonia assimilation in E. coli
    Jie Yuan
    Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton University, Princeton, NJ 08544, USA
    Mol Syst Biol 5:302. 2009
  8. pmc Quiescent fibroblasts exhibit high metabolic activity
    Johanna M S Lemons
    Department of Chemistry, Princeton University, Princeton, New Jersey, USA
    PLoS Biol 8:e1000514. 2010
  9. pmc α-Ketoglutarate coordinates carbon and nitrogen utilization via enzyme I inhibition
    Christopher D Doucette
    Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
    Nat Chem Biol 7:894-901. 2011
  10. pmc Biclustering via optimal re-ordering of data matrices in systems biology: rigorous methods and comparative studies
    Peter A DiMaggio
    Department of Chemical Engineering, Princeton University, Princeton, NJ, USA
    BMC Bioinformatics 9:458. 2008

Research Grants

  1. Migraine Headache Treatment by Drug Aerosol Inhalation
    Joshua Rabinowitz; Fiscal Year: 2004
  2. Metabolomics of the Virus-host Cell Interaction
    Joshua Rabinowitz; Fiscal Year: 2007
  3. Metabolomics of the Virus-host Cell Interaction
    Joshua D Rabinowitz; Fiscal Year: 2010

Collaborators

Detail Information

Publications74

  1. ncbi request reprint Acidic acetonitrile for cellular metabolome extraction from Escherichia coli
    Joshua D Rabinowitz
    Department of Chemistry and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
    Anal Chem 79:6167-73. 2007
    ..We recommend acidic solvent mixtures containing acetonitrile for extraction of the E. coli metabolome...
  2. ncbi request reprint Cellular metabolomics of Escherchia coli
    Joshua D Rabinowitz
    Princeton University, Department of Chemistry and Lewis Sigler Institute for Integrative Genomics, Princeton, NJ 08544, USA
    Expert Rev Proteomics 4:187-98. 2007
    ..Future challenges, both in terms of data collection and application of the data to obtain a comprehensive understanding of metabolic dynamics, are discussed...
  3. ncbi request reprint Ultra-fast absorption of amorphous pure drug aerosols via deep lung inhalation
    Joshua D Rabinowitz
    Department of Chemistry and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
    J Pharm Sci 95:2438-51. 2006
    ..Absorption of the thermal aerosol is nearly complete, with >80% absolute bioavailability found in both dogs and human normal volunteers...
  4. pmc Dissecting enzyme regulation by multiple allosteric effectors: nucleotide regulation of aspartate transcarbamoylase
    Joshua D Rabinowitz
    Department of Chemistry, Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
    Biochemistry 47:5881-8. 2008
    ..These findings support a predominant role of CTP and ATP in ATCase regulation. The general approach provides a new paradigm for dissecting multifactorial regulation of biological molecules and processes...
  5. pmc Yeast cells can access distinct quiescent states
    Maja M Klosinska
    Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
    Genes Dev 25:336-49. 2011
    ..Moreover, these survival strategies are not unique to quiescence, but are engaged by the cell in proportion to nutrient scarcity...
  6. doi request reprint Nucleotide degradation and ribose salvage in yeast
    Yi Fan Xu
    Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
    Mol Syst Biol 9:665. 2013
    ..Thus, ribose salvage provides means of surviving nutrient starvation and oxidative stress...
  7. pmc Metabolomics-driven quantitative analysis of ammonia assimilation in E. coli
    Jie Yuan
    Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton University, Princeton, NJ 08544, USA
    Mol Syst Biol 5:302. 2009
    ..Combined with covalent modification reactions controlling glutamine synthetase activity, such active-site competition was sufficient to explain and predict the complex dynamic response patterns of central nitrogen metabolites...
  8. pmc Quiescent fibroblasts exhibit high metabolic activity
    Johanna M S Lemons
    Department of Chemistry, Princeton University, Princeton, New Jersey, USA
    PLoS Biol 8:e1000514. 2010
    ..Quiescent fibroblasts, relieved of the biosynthetic requirements associated with generating progeny, direct their metabolic activity to preservation of self integrity and alternative functions beneficial to the organism as a whole...
  9. pmc α-Ketoglutarate coordinates carbon and nitrogen utilization via enzyme I inhibition
    Christopher D Doucette
    Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
    Nat Chem Biol 7:894-901. 2011
    ..Quantitative modeling shows that this previously unidentified regulatory connection is, in principle, sufficient to coordinate carbon and nitrogen utilization...
  10. pmc Biclustering via optimal re-ordering of data matrices in systems biology: rigorous methods and comparative studies
    Peter A DiMaggio
    Department of Chemical Engineering, Princeton University, Princeton, NJ, USA
    BMC Bioinformatics 9:458. 2008
    ....
  11. pmc Growth-limiting intracellular metabolites in yeast growing under diverse nutrient limitations
    Viktor M Boer
    Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
    Mol Biol Cell 21:198-211. 2010
    ..The complete data can be accessed at the interactive website http://growthrate.princeton.edu/metabolome...
  12. pmc Hypoxic and Ras-transformed cells support growth by scavenging unsaturated fatty acids from lysophospholipids
    Jurre J Kamphorst
    Lewis Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
    Proc Natl Acad Sci U S A 110:8882-7. 2013
    ..This renders Ras-driven cells, both in culture and in allografts, resistant to SCD1 inhibition. Thus, a mechanism by which oncogenic Ras confers metabolic robustness is through lipid scavenging...
  13. pmc Conservation of the metabolomic response to starvation across two divergent microbes
    Matthew J Brauer
    Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
    Proc Natl Acad Sci U S A 103:19302-7. 2006
    ..Metabolic similarity across organisms extends from the covalent reaction network of metabolism to include many elements of metabolome response to nutrient deprivation as well...
  14. pmc Metabolome remodeling during the acidogenic-solventogenic transition in Clostridium acetobutylicum
    Daniel Amador-Noguez
    Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
    Appl Environ Microbiol 77:7984-97. 2011
    ..Thus, the solventogenic transition involves global remodeling of metabolism to redirect resources (carbon and reducing power) from biomass production into solvent production...
  15. pmc Systems-level metabolic flux profiling elucidates a complete, bifurcated tricarboxylic acid cycle in Clostridium acetobutylicum
    Daniel Amador-Noguez
    Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
    J Bacteriol 192:4452-61. 2010
    ....
  16. pmc Ultrasensitive regulation of anapleurosis via allosteric activation of PEP carboxylase
    Yi Fan Xu
    Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
    Nat Chem Biol 8:562-8. 2012
    ..Thus, bacterial central carbon metabolism is intrinsically programmed with ultrasensitive allosteric regulation to enable rapid adaptation to changing environmental conditions...
  17. pmc Kinetic flux profiling for quantitation of cellular metabolic fluxes
    Jie Yuan
    241 Carl Icahn Laboratory, Department of Chemistry and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
    Nat Protoc 3:1328-40. 2008
    ..This protocol is exemplified using E. coli and nitrogen labeling, for which quantitative flux data for approximately 15 metabolites can be obtained over 3 d of work. Applications to adherent mammalian cells are also discussed...
  18. doi request reprint Pyrimidine homeostasis is accomplished by directed overflow metabolism
    Marshall Louis Reaves
    Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
    Nature 500:237-41. 2013
    ..Thus, pyrimidine homeostasis involves dual regulatory strategies, with classical feedback inhibition enhancing metabolic efficiency and directed overflow metabolism ensuring end-product homeostasis. ..
  19. pmc Regulation of yeast pyruvate kinase by ultrasensitive allostery independent of phosphorylation
    Yi Fan Xu
    Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
    Mol Cell 48:52-62. 2012
    ..Thus, while yeast pyruvate kinase is covalently modified in response to glucose availability, its activity is controlled almost exclusively by ultrasensitive allostery...
  20. pmc Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli
    Bryson D Bennett
    Department of Chemistry and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
    Nat Chem Biol 5:593-9. 2009
    ..The data and analyses presented here highlight the ability to identify organizing metabolic principles from systems-level absolute metabolite concentration data...
  21. pmc Liquid chromatography-high resolution mass spectrometry analysis of fatty acid metabolism
    Jurre J Kamphorst
    Lewis Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
    Anal Chem 83:9114-22. 2011
    ..This LC/MS method and associated isotope tracer techniques should be broadly applicable to investigating fatty acid metabolism...
  22. pmc Coordinated concentration changes of transcripts and metabolites in Saccharomyces cerevisiae
    Patrick H Bradley
    Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
    PLoS Comput Biol 5:e1000270. 2009
    ....
  23. doi request reprint Descriptor-free molecular discovery in large libraries by adaptive substituent reordering
    Scott R McAllister
    Department of Chemical Engineering, Princeton University, Princeton, NJ 08544, USA
    Bioorg Med Chem Lett 18:5967-70. 2008
    ....
  24. pmc Systems-level metabolic flux profiling identifies fatty acid synthesis as a target for antiviral therapy
    Joshua Munger
    Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, New Jersey 08544, USA
    Nat Biotechnol 26:1179-86. 2008
    ..These results show that fatty acid synthesis is essential for the replication of two divergent enveloped viruses and that systems-level metabolic flux profiling can identify metabolic targets for antiviral therapy...
  25. pmc Divergent effects of human cytomegalovirus and herpes simplex virus-1 on cellular metabolism
    Livia Vastag
    Department of Chemistry, Princeton University, Princeton, New Jersey, United States of America
    PLoS Pathog 7:e1002124. 2011
    ..Although our results confirm that this is a robust target for HSV-1, therapeutic interventions at other points in metabolism might prove more effective for treatment of HCMV...
  26. pmc Absolute quantitation of intracellular metabolite concentrations by an isotope ratio-based approach
    Bryson D Bennett
    Department of Chemistry and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
    Nat Protoc 3:1299-311. 2008
    ..It enables absolute quantitation of several dozen metabolites over approximately 1 week of work...
  27. pmc Survival of starving yeast is correlated with oxidative stress response and nonrespiratory mitochondrial function
    Allegra A Petti
    Lewis Sigler Institute for Integrative Genomics and Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
    Proc Natl Acad Sci U S A 108:E1089-98. 2011
    ....
  28. pmc A domino effect in antifolate drug action in Escherichia coli
    Yun Kyung Kwon
    Department of Chemistry and Lewis Sigler Institute for Integrative Genomics, Carl Icahn Laboratory, Princeton University, Washington Road, Princeton, New Jersey 08544, USA
    Nat Chem Biol 4:602-8. 2008
    ..These results highlight the potential for quantitative analysis of cellular metabolism to reveal mechanisms of drug action...
  29. pmc Metabolomic analysis via reversed-phase ion-pairing liquid chromatography coupled to a stand alone orbitrap mass spectrometer
    Wenyun Lu
    Lewis Sigler Institute for Integrative Genomics and Department of Chemistry Princeton University, Princeton, New Jersey 08544, USA
    Anal Chem 82:3212-21. 2010
    ..These examples demonstrate the suitability of the present method for quantitative metabolomics, fluxomics, and discovery metabolite profiling...
  30. pmc Herpes simplex virus 1 infection activates poly(ADP-ribose) polymerase and triggers the degradation of poly(ADP-ribose) glycohydrolase
    Sarah L Grady
    Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
    J Virol 86:8259-68. 2012
    ....
  31. doi request reprint Absence of detectable arsenate in DNA from arsenate-grown GFAJ-1 cells
    Marshall Louis Reaves
    Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
    Science 337:470-3. 2012
    ..Furthermore, mass spectrometry showed that this DNA contains only trace amounts of free arsenate and no detectable covalently bound arsenate...
  32. doi request reprint LC-MS data processing with MAVEN: a metabolomic analysis and visualization engine
    Michelle F Clasquin
    Department of Chemistry and Integrative Genomics, Carl Icahn Laboratory, Princeton, New Jersey, USA
    Curr Protoc Bioinformatics . 2012
    ..Together, these instructions describe a workflow that allows efficient processing of raw LC-MS data into a form ready for biological analysis...
  33. pmc Human kinome profiling identifies a requirement for AMP-activated protein kinase during human cytomegalovirus infection
    Laura J Terry
    Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
    Proc Natl Acad Sci U S A 109:3071-6. 2012
    ..We propose that HCMV requires AMPK or related activity for viral replication and reprogramming of cellular metabolism...
  34. pmc Achieving optimal growth through product feedback inhibition in metabolism
    Sidhartha Goyal
    Department of Physics, Princeton University, Princeton, New Jersey, USA
    PLoS Comput Biol 6:e1000802. 2010
    ....
  35. pmc Characteristic phenotypes associated with ptsN-null mutants in Escherichia coli K-12 are absent in strains with functional ilvG
    Marshall Louis Reaves
    Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
    J Bacteriol 193:4576-81. 2011
    ..We conclude that the ptsN gene product does not regulate organic nitrogen source utilization as previously proposed...
  36. pmc Branched tricarboxylic acid metabolism in Plasmodium falciparum
    Kellen L Olszewski
    Department of Molecular Biology and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
    Nature 466:774-8. 2010
    ..These results significantly clarify our understanding of the Plasmodium metabolic network and highlight the ability of altered variants of central carbon metabolism to arise in response to unique environments...
  37. pmc Diverse metabolic model parameters generate similar methionine cycle dynamics
    Matthew Piazza
    Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
    J Theor Biol 251:628-39. 2008
    ....
  38. pmc The Vibrio cholerae quorum-sensing autoinducer CAI-1: analysis of the biosynthetic enzyme CqsA
    Robert C Kelly
    Department of Molecular Biology, Princeton University, New Jersey, USA
    Nat Chem Biol 5:891-5. 2009
    ..cholerae responds to amino-CAI-1 as well as CAI-1, whereas other CAI-1 variants do not elicit a quorum-sensing response. Thus, both CAI-1 and amino-CAI-1 have potential as lead molecules in the development of an anticholera treatment...
  39. doi request reprint Mass spectrometry-based metabolomics of yeast
    Christopher A Crutchfield
    Lewis Sigler Institute for Integrative Genomics, Department of Chemistry, Princeton University, Princeton, New Jersey, USA
    Methods Enzymol 470:393-426. 2010
    ..Throughout, we highlight interdependencies between the steps that are relevant to developing an integrated workflow which effectively leverages LC-MS to reveal yeast biology...
  40. ncbi request reprint Separation and quantitation of water soluble cellular metabolites by hydrophilic interaction chromatography-tandem mass spectrometry
    Sunil U Bajad
    Lewis Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
    J Chromatogr A 1125:76-88. 2006
    ..When applied to extracts of Escherichia coli grown in [12C]- versus [13C]glucose, the method reveals appropriate 12C- and 13C-peaks for 79 different metabolites...
  41. pmc Identifying decomposition products in extracts of cellular metabolites
    Elizabeth Kimball
    Department of Chemistry and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08542, USA
    Anal Biochem 358:273-80. 2006
    ..For extraction of E. coli with methanol:water, cold temperature and a high methanol fraction minimize artifacts due to metabolite decomposition...
  42. pmc Isotope ratio-based profiling of microbial folates
    Wenyun Lu
    Department of Chemistry and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
    J Am Soc Mass Spectrom 18:898-909. 2007
    ..This finding highlights the potential for analysis of the full spectrum of cellular folates by MS/MS to unveil novel biological phenomena...
  43. pmc Antifolate-induced depletion of intracellular glycine and purines inhibits thymineless death in E. coli
    Yun Kyung Kwon
    Department of Chemistry and Lewis Sigler Institute for Integrative Genomics, Princeton University, New Jersey 08544, USA
    ACS Chem Biol 5:787-95. 2010
    ..Thus, E. coli has dual systems for surviving folate depletion and avoiding thymineless death: a short-term response based on sensing of amino acids and a long-term response based on sensing of nucleotides...
  44. pmc Analytical strategies for LC-MS-based targeted metabolomics
    Wenyun Lu
    Lewis Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
    J Chromatogr B Analyt Technol Biomed Life Sci 871:236-42. 2008
    ..We suggest that both are viable solutions, with MRM preferred when targeting a more limited number of analytes, and full scan preferred for its potential ability to bridge targeted and untargeted metabolomics...
  45. pmc Synaptic vesicle-like lipidome of human cytomegalovirus virions reveals a role for SNARE machinery in virion egress
    Sean T H Liu
    Department of Molecular Biology, Lewis Thomas Laboratory, University, Princeton, NJ 08544, USA
    Proc Natl Acad Sci U S A 108:12869-74. 2011
    ..We propose that cytomegalovirus capsids acquire their envelope by budding into vesicles with a lipid composition similar to that of synaptic vesicles, which subsequently fuse with the plasma membrane to release virions from the cell...
  46. ncbi request reprint Kinetic flux profiling of nitrogen assimilation in Escherichia coli
    Jie Yuan
    Department of Chemistry and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
    Nat Chem Biol 2:529-30. 2006
    ..Fluxes measured on the basis of the kinetics of nitrogen assimilation in exponentially growing E. coli agree well with those fluxes predicted to allow optimal biomass production...
  47. pmc Metabolomics in systems microbiology
    Marshall Louis Reaves
    Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
    Curr Opin Biotechnol 22:17-25. 2011
    ..We also indicate enduring challenges concerning unstable and low abundance compounds, subcellular compartmentalization, and quantitative amalgamation of different data types...
  48. doi request reprint Control of nitromethane photoionization efficiency with shaped femtosecond pulses
    Jonathan Roslund
    Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
    J Chem Phys 134:154301. 2011
    ..Finally, the discovered pulse shape is demonstrated to interact with the molecular system in a coherent fashion as assessed from the asymmetry between the response to the optimal field and its time-reversed counterpart...
  49. doi request reprint Resolution of strongly competitive product channels with optimal dynamic discrimination: application to flavins
    Jonathan Roslund
    Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
    J Chem Phys 134:034511. 2011
    ..The successful implementation of ODD on quantum systems of such high complexity bodes well for the future development of the field and the use of ODD techniques in a variety of demanding practical applications...
  50. ncbi request reprint Mutagenic evidence for the optimal control of evolutionary dynamics
    Raj Chakrabarti
    Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
    Phys Rev Lett 100:258103. 2008
    ..Optimal control theory explains a striking pattern of extremization in the redox potentials of electron transport proteins, assuming only that their fitness measure is a control objective functional with bounded controls...
  51. ncbi request reprint Topology of the quantum control landscape for observables
    Michael Hsieh
    Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
    J Chem Phys 130:104109. 2009
    ..The implications of the landscape topology for practical quantum control efforts are discussed, including in the context of nonideal operating conditions...
  52. ncbi request reprint Accelerated monotonic convergence of optimal control over quantum dynamics
    Tak San Ho
    Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
    Phys Rev E Stat Nonlin Soft Matter Phys 82:026703. 2010
    ....
  53. pmc RpoS proteolysis is controlled directly by ATP levels in Escherichia coli
    Celeste N Peterson
    Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
    Genes Dev 26:548-53. 2012
    ..In vitro reconstitution assays directly demonstrate that ClpXP fails to degrade RpoS, but not other proteins, at low ATP hydrolysis rates. These data suggest that cellular ATP levels directly control RpoS stability...
  54. pmc Remodeling of the metabolome during early frog development
    Livia Vastag
    Carl Icahn Laboratory, Department of Chemistry and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
    PLoS ONE 6:e16881. 2011
    ....
  55. pmc Autophagy and metabolism
    Joshua D Rabinowitz
    Department of Chemistry and Lewis Sigler Institute for Integrative Genomics, 241 Carl Icahn Laboratory, Washington Road, Princeton University, Princeton, NJ 08544, USA
    Science 330:1344-8. 2010
    ..A powerful promoter of metabolic homeostasis at both the cellular and whole-animal level, autophagy prevents degenerative diseases. It does have a downside, however--cancer cells exploit it to survive in nutrient-poor tumors...
  56. pmc Riboneogenesis in yeast
    Michelle F Clasquin
    Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton NJ 08544, USA
    Cell 145:969-80. 2011
    ..Flux through SHB17 increases when ribose demand is high relative to demand for NADPH, including during ribosome biogenesis in metabolically synchronized yeast cells...
  57. ncbi request reprint A high-performance liquid chromatography-tandem mass spectrometry method for quantitation of nitrogen-containing intracellular metabolites
    Wenyun Lu
    Lewis Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
    J Am Soc Mass Spectrom 17:37-50. 2006
    ....
  58. pmc Differentiating metabolites formed from de novo synthesis versus macromolecule decomposition
    Jie Yuan
    Department of Chemistry and Lewis Sigler Institute for Integrative Genomics, 241 Carl Icahn Laboratory, Princeton University, Princeton, NJ 08542, USA
    J Am Chem Soc 129:9294-5. 2007
  59. pmc Quorum sensing controls biofilm formation in Vibrio cholerae through modulation of cyclic di-GMP levels and repression of vpsT
    Christopher M Waters
    Department of Molecular Biology, Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
    J Bacteriol 190:2527-36. 2008
    ..cholerae integrates information about the vicinal bacterial community contained in extracellular QS autoinducers with the intracellular environmental information encoded in c-di-GMP to control biofilm formation...
  60. pmc Saturated very long chain fatty acids are required for the production of infectious human cytomegalovirus progeny
    Emre Koyuncu
    Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
    PLoS Pathog 9:e1003333. 2013
    ..These results reveal a dependence of cytomegalovirus on very long chain fatty acid metabolism...
  61. pmc Regulatory and metabolic rewiring during laboratory evolution of ethanol tolerance in E. coli
    Hani Goodarzi
    Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
    Mol Syst Biol 6:378. 2010
    ..Remarkably, these laboratory-evolved strains, by and large, follow the same adaptive paths as inferred from our coarse-grained search of the fitness landscape...
  62. pmc Ammonium toxicity and potassium limitation in yeast
    David C Hess
    Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
    PLoS Biol 4:e351. 2006
    ..The amounts of amino acids excreted increased in relation to the severity of growth impairment by ammonium, suggesting that amino acid excretion is used by yeast for ammonium detoxification...
  63. pmc Dynamics of the cellular metabolome during human cytomegalovirus infection
    Joshua Munger
    Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
    PLoS Pathog 2:e132. 2006
    ....
  64. doi request reprint Metabolomic analysis and visualization engine for LC-MS data
    Eugene Melamud
    Department of Chemistry and Integrative Genomics, Carl Icahn Laboratory, Princeton, New Jersey 08544, USA
    Anal Chem 82:9818-26. 2010
    ..These tools enable animating series of pathway graphs, e.g., to show propagation of labeled forms through a metabolic network. MAVEN is released under an open source license at http://maven.princeton.edu...
  65. ncbi request reprint Calcium blocks formation of apoptosome by preventing nucleotide exchange in Apaf-1
    Qing Bao
    Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ 08544, USA
    Mol Cell 25:181-92. 2007
    ..Consequently, calcium blocks the ability of Apaf-1 to activate caspase-9. These observations suggest an important role of calcium homeostasis on the Apaf-1-dependent apoptotic pathway...
  66. pmc Optimizing genetic circuits by global sensitivity analysis
    Xiao Jiang Feng
    Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
    Biophys J 87:2195-202. 2004
    ....
  67. pmc Itaconic acid is a mammalian metabolite induced during macrophage activation
    Cheryl L Strelko
    Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, USA
    J Am Chem Soc 133:16386-9. 2011
    ..Our results highlight a previously unidentified biosynthetic pathway related to TCA cycle metabolism in mammalian cells and a novel metabolite that likely plays a role in macrophage-based immune response...
  68. ncbi request reprint Efficient chemical kinetic modeling through neural network maps
    Neil Shenvi
    Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
    J Chem Phys 120:9942-51. 2004
    ..RPN kinetic modeling has a broad range of applications, including kinetic parameter inversion, simulation of reactor dynamics, and atmospheric modeling...
  69. ncbi request reprint Optimal deep brain stimulation of the subthalamic nucleus--a computational study
    Xiao Jiang Feng
    Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
    J Comput Neurosci 23:265-82. 2007
    ..Such alternative DBS inputs could potentially be identified, guided by the model-free learning algorithm, in experimental or eventual clinical settings...
  70. ncbi request reprint Maximal use of minimal libraries through the adaptive substituent reordering algorithm
    Fan Liang
    Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
    J Phys Chem B 109:5842-54. 2005
    ..The enhanced algorithm is tested on copolymer and transition metal complex libraries, and the results demonstrate the capability of the algorithm to accurately interpolate various properties of both molecular libraries...
  71. ncbi request reprint Random sampling-high dimensional model representation (RS-HDMR) and orthogonality of its different order component functions
    Genyuan Li
    Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
    J Phys Chem A 110:2474-85. 2006
    ..An integrated exposure and dose model as well as ionospheric electron density determined from measured ionosonde data are used as test cases, which show that the new method has better accuracy than the prior one...
  72. ncbi request reprint Identification of biological microparticles using ultrafast depletion spectroscopy
    Francois Courvoisier
    GAP Biophotonics, University of Geneva, 20, rue de l Ecole de Medecine, 1211, Geneva 4, Switzerland
    Faraday Discuss 137:37-49; discussion 99-113. 2008
    ..Further improvement is required to allow the discrimination of one pathogenic among other non-pathogenic micro-organisms. This improved selectivity may be reached with optimal coherent control experiments, as discussed in the paper...
  73. ncbi request reprint Closed-loop learning control of bio-networks
    Jason Ku
    Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
    J Comput Biol 11:642-59. 2004
    ....
  74. doi request reprint Incoherent control of quantum systems with wavefunction-controllable subspaces via quantum reinforcement learning
    Daoyi Dong
    Institute of Systems Science, AMSS, Chinese Academy of Sciences, Beijing 100190, China
    IEEE Trans Syst Man Cybern B Cybern 38:957-62. 2008
    ..This incoherent control scheme provides an alternative quantum engineering strategy for locally controllable quantum systems...

Research Grants6

  1. Migraine Headache Treatment by Drug Aerosol Inhalation
    Joshua Rabinowitz; Fiscal Year: 2004
    ..Accomplishment of the goals of Phase II will lead directly to human clinical testing of a commercially viable device that could improve the lives of millions of people every year. ..
  2. Metabolomics of the Virus-host Cell Interaction
    Joshua Rabinowitz; Fiscal Year: 2007
    ..Such pathways, once identified, will be attractive new targets for antiviral therapy. ..
  3. Metabolomics of the Virus-host Cell Interaction
    Joshua D Rabinowitz; Fiscal Year: 2010
    ..Such pathways, once identified, will be attractive new targets for antiviral therapy. ..