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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Acetates
D. Amador-Noguez, Brasg, I. A., Feng, X. - J., Roquet, N., and Rabinowitz, J. D., “Metabolome remodeling during the acidogenic-solventogenic transition in Clostridium acetobutylicum.”, Appl Environ Microbiol, vol. 77, no. 22, pp. 7984-97, 2011.
Acetone
D. Amador-Noguez, Brasg, I. A., Feng, X. - J., Roquet, N., and Rabinowitz, J. D., “Metabolome remodeling during the acidogenic-solventogenic transition in Clostridium acetobutylicum.”, Appl Environ Microbiol, vol. 77, no. 22, pp. 7984-97, 2011.
Adenosine Triphosphate
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.
Aging
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.
Algorithms
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.
Amino Acids
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.
Aminohydrolases
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.
Ammonia
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.
Animals
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.
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.
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.
Bacteria
M. Louis Reaves and Rabinowitz, J. D., “Metabolomics in systems microbiology.”, Curr Opin Biotechnol, vol. 22, no. 1, pp. 17-25, 2011.
Biocatalysis
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.
Butanols
D. Amador-Noguez, Brasg, I. A., Feng, X. - J., Roquet, N., and Rabinowitz, J. D., “Metabolome remodeling during the acidogenic-solventogenic transition in Clostridium acetobutylicum.”, Appl Environ Microbiol, vol. 77, no. 22, pp. 7984-97, 2011.
Butyrates
D. Amador-Noguez, Brasg, I. A., Feng, X. - J., Roquet, N., and Rabinowitz, J. D., “Metabolome remodeling during the acidogenic-solventogenic transition in Clostridium acetobutylicum.”, Appl Environ Microbiol, vol. 77, no. 22, pp. 7984-97, 2011.
Carbon Cycle
M. Louis Reaves and Rabinowitz, J. D., “Metabolomics in systems microbiology.”, Curr Opin Biotechnol, vol. 22, no. 1, pp. 17-25, 2011.
Carbon Radioisotopes
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.
Carrier Proteins
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.
Catalytic Domain
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.
Cell Compartmentation
M. Louis Reaves and Rabinowitz, J. D., “Metabolomics in systems microbiology.”, Curr Opin Biotechnol, vol. 22, no. 1, pp. 17-25, 2011.
Cell Line
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.
Cell Proliferation
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.
Cells, Cultured
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.
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.
Chromatography, High Pressure Liquid
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.
C. Jang, Chen, L., and Rabinowitz, J. D., “Metabolomics and Isotope Tracing.”, Cell, vol. 173, no. 4, pp. 822-837, 2018.
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.
Chromatography, Liquid
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.
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.
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.
Chromatography, Reverse-Phase
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.
Clostridium acetobutylicum
D. Amador-Noguez, Brasg, I. A., Feng, X. - J., Roquet, N., and Rabinowitz, J. D., “Metabolome remodeling during the acidogenic-solventogenic transition in Clostridium acetobutylicum.”, Appl Environ Microbiol, vol. 77, no. 22, pp. 7984-97, 2011.
Codon
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.
Computer Simulation
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.
Cytosol
D. Amador-Noguez, Brasg, I. A., Feng, X. - J., Roquet, N., and Rabinowitz, J. D., “Metabolome remodeling during the acidogenic-solventogenic transition in Clostridium acetobutylicum.”, Appl Environ Microbiol, vol. 77, no. 22, pp. 7984-97, 2011.
Electron Transport
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.
Energy Metabolism
D. Amador-Noguez, Brasg, I. A., Feng, X. - J., Roquet, N., and Rabinowitz, J. D., “Metabolome remodeling during the acidogenic-solventogenic transition in Clostridium acetobutylicum.”, Appl Environ Microbiol, vol. 77, no. 22, pp. 7984-97, 2011.
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.
Escherichia coli
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.
Ethanol
D. Amador-Noguez, Brasg, I. A., Feng, X. - J., Roquet, N., and Rabinowitz, J. D., “Metabolome remodeling during the acidogenic-solventogenic transition in Clostridium acetobutylicum.”, Appl Environ Microbiol, vol. 77, no. 22, pp. 7984-97, 2011.
Fermentation
D. Amador-Noguez, Brasg, I. A., Feng, X. - J., Roquet, N., and Rabinowitz, J. D., “Metabolome remodeling during the acidogenic-solventogenic transition in Clostridium acetobutylicum.”, Appl Environ Microbiol, vol. 77, no. 22, pp. 7984-97, 2011.
Fibroblasts
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.
Folic Acid
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.
Folic Acid Antagonists
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.
Gas Chromatography-Mass Spectrometry
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.
Gene Expression Regulation, Bacterial
D. Amador-Noguez, Brasg, I. A., Feng, X. - J., Roquet, N., and Rabinowitz, J. D., “Metabolome remodeling during the acidogenic-solventogenic transition in Clostridium acetobutylicum.”, Appl Environ Microbiol, vol. 77, no. 22, pp. 7984-97, 2011.
Genetic Techniques
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.
Glutamine
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.
Glutathione
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.
Glycine Hydroxymethyltransferase
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.
Glycolysis
C. Jang, Chen, L., and Rabinowitz, J. D., “Metabolomics and Isotope Tracing.”, Cell, vol. 173, no. 4, pp. 822-837, 2018.
GTP-Binding Proteins
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.
Guanosine
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.
Guidelines as Topic
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.
HCT116 Cells
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.
HEK293 Cells
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.
Homeostasis
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.
M. Louis Reaves and Rabinowitz, J. D., “Metabolomics in systems microbiology.”, Curr Opin Biotechnol, vol. 22, no. 1, pp. 17-25, 2011.
Humans
C. Jang, Chen, L., and Rabinowitz, J. D., “Metabolomics and Isotope Tracing.”, Cell, vol. 173, no. 4, pp. 822-837, 2018.
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.
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.
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.
Immunity, Innate
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.
Indoleamine-Pyrrole 2,3,-Dioxygenase
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.
Inflammation
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.
Isotope Labeling
C. Jang, Chen, L., and Rabinowitz, J. D., “Metabolomics and Isotope Tracing.”, Cell, vol. 173, no. 4, pp. 822-837, 2018.
Ketoglutaric Acids
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.
Kinetics
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.
Kynurenine
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.
Leucine
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.
Liquid Phase Microextraction
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.
Lysine
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.
Macrophages
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.
Magnetic Resonance Spectroscopy
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.
Mass Spectrometry
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.
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.
M. Louis Reaves and Rabinowitz, J. D., “Metabolomics in systems microbiology.”, Curr Opin Biotechnol, vol. 22, no. 1, pp. 17-25, 2011.
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.
C. Jang, Chen, L., and Rabinowitz, J. D., “Metabolomics and Isotope Tracing.”, Cell, vol. 173, no. 4, pp. 822-837, 2018.
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.
Metabolic Networks and Pathways
M. Louis Reaves and Rabinowitz, J. D., “Metabolomics in systems microbiology.”, Curr Opin Biotechnol, vol. 22, no. 1, pp. 17-25, 2011.
Metabolome
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.
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.
D. Amador-Noguez, Brasg, I. A., Feng, X. - J., Roquet, N., and Rabinowitz, J. D., “Metabolome remodeling during the acidogenic-solventogenic transition in Clostridium acetobutylicum.”, Appl Environ Microbiol, vol. 77, no. 22, pp. 7984-97, 2011.
C. Jang, Chen, L., and Rabinowitz, J. D., “Metabolomics and Isotope Tracing.”, Cell, vol. 173, no. 4, pp. 822-837, 2018.
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.
Metabolomics
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.
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.
M. Louis Reaves and Rabinowitz, J. D., “Metabolomics in systems microbiology.”, Curr Opin Biotechnol, vol. 22, no. 1, pp. 17-25, 2011.
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.
C. Jang, Chen, L., and Rabinowitz, J. D., “Metabolomics and Isotope Tracing.”, Cell, vol. 173, no. 4, pp. 822-837, 2018.
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.
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.
Methylation
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.
Methylenetetrahydrofolate Dehydrogenase (NADP)
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.
Mice
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.
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.
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.
Mice, Inbred C57BL
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.
Mice, Knockout
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.
Mitochondria
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.
C. Jang, Chen, L., and Rabinowitz, J. D., “Metabolomics and Isotope Tracing.”, Cell, vol. 173, no. 4, pp. 822-837, 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.
Models, Biological
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.
M. Louis Reaves and Rabinowitz, J. D., “Metabolomics in systems microbiology.”, Curr Opin Biotechnol, vol. 22, no. 1, pp. 17-25, 2011.
Models, Genetic
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.
Multifunctional Enzymes
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.
Multiprotein Complexes
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.
Mutation
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.
NAD
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.
NADP
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.
Naphthyridines
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.
Nitrogen
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.
Oxidative Phosphorylation
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.
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.
Pentosyltransferases
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.
Phagocytosis
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.
Pinocytosis
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.
Principal Component Analysis
C. Jang, Chen, L., and Rabinowitz, J. D., “Metabolomics and Isotope Tracing.”, Cell, vol. 173, no. 4, pp. 822-837, 2018.
Protein Biosynthesis
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.
Protein Kinase Inhibitors
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.
Protein Stability
M. Louis Reaves and Rabinowitz, J. D., “Metabolomics in systems microbiology.”, Curr Opin Biotechnol, vol. 22, no. 1, pp. 17-25, 2011.
Proteins
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.
M. Louis Reaves and Rabinowitz, J. D., “Metabolomics in systems microbiology.”, Curr Opin Biotechnol, vol. 22, no. 1, pp. 17-25, 2011.
Proteolysis
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.
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.
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.
Quaternary Ammonium Compounds
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.
Ribosomes
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.
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.
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
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.
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.
Signal Transduction
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.
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.
Software
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.
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.
Spectrometry, Mass, Electrospray Ionization
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.
Systems Biology
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.
M. Louis Reaves and Rabinowitz, J. D., “Metabolomics in systems microbiology.”, Curr Opin Biotechnol, vol. 22, no. 1, pp. 17-25, 2011.
Tetrahydrofolates
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.
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
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.
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.
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.
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.
Yeasts
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.