Gregory N Stephanopoulos

Summary

Affiliation: Massachusetts Institute of Technology
Country: USA

Publications

  1. ncbi request reprint Metabolic and transcriptional patterns accompanying glutamine depletion and repletion in mouse hepatoma cells: a model for physiological regulatory networks
    Matthew S Wong
    Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
    Physiol Genomics 16:247-55. 2004
  2. ncbi request reprint Challenges in engineering microbes for biofuels production
    Gregory Stephanopoulos
    Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Science 315:801-4. 2007
  3. pmc NTFD--a stand-alone application for the non-targeted detection of stable isotope-labeled compounds in GC/MS data
    Karsten Hiller
    Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L 4362 Esch Belval, Luxembourg
    Bioinformatics 29:1226-8. 2013
  4. pmc Ketogenic essential amino acids modulate lipid synthetic pathways and prevent hepatic steatosis in mice
    Yasushi Noguchi
    Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
    PLoS ONE 5:e12057. 2010
  5. pmc Enhancing solubility of deoxyxylulose phosphate pathway enzymes for microbial isoprenoid production
    Kang Zhou
    Chemical and Pharmaceutical Engineering, Singapore MIT Alliance, 4 Engineering Drive 3, Singapore, Singapore
    Microb Cell Fact 11:148. 2012
  6. pmc Incremental parameter estimation of kinetic metabolic network models
    Gengjie Jia
    Chemical and Pharmaceutical Engineering, Singapore MIT Alliance, Singapore 117576, Singapore
    BMC Syst Biol 6:142. 2012
  7. doi request reprint Synthetic biology and metabolic engineering
    Gregory Stephanopoulos
    Department of Chemical Engineering, Massachusetts Institute of Technology, Building 56 Room 469C, 77 Massachusetts Ave, Cambridge, MA 02139, USA
    ACS Synth Biol 1:514-25. 2012
  8. pmc Novel reference genes for quantifying transcriptional responses of Escherichia coli to protein overexpression by quantitative PCR
    Kang Zhou
    Chemical and Pharmaceutical Engineering, Singapore MIT Alliance, 4 Engineering Drive 3, Singapore
    BMC Mol Biol 12:18. 2011
  9. pmc Assessment of heterologous butyrate and butanol pathway activity by measurement of intracellular pathway intermediates in recombinant Escherichia coli
    Curt R Fischer
    Department of Chemical Engineering, Massachusetts Institute of Technology, Room 56 469, Cambridge, MA 02139, USA
    Appl Microbiol Biotechnol 88:265-75. 2010
  10. ncbi request reprint Exploiting biological complexity for strain improvement through systems biology
    Gregory Stephanopoulos
    Department of Chemical Engineering, Massachusetts Institute of Technology, Room 56 469, Cambridge, MA 02139, USA
    Nat Biotechnol 22:1261-7. 2004

Collaborators

Detail Information

Publications32

  1. ncbi request reprint Metabolic and transcriptional patterns accompanying glutamine depletion and repletion in mouse hepatoma cells: a model for physiological regulatory networks
    Matthew S Wong
    Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
    Physiol Genomics 16:247-55. 2004
    ..In conclusion, this model may be useful as a prototype physiological regulatory network where gene expression profiles are analyzed in concert with changes in cell function...
  2. ncbi request reprint Challenges in engineering microbes for biofuels production
    Gregory Stephanopoulos
    Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Science 315:801-4. 2007
    ..There is justified optimism that the full potential of biofuel production from cellulosic biomass will be obtainable in the next 10 to 15 years...
  3. pmc NTFD--a stand-alone application for the non-targeted detection of stable isotope-labeled compounds in GC/MS data
    Karsten Hiller
    Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L 4362 Esch Belval, Luxembourg
    Bioinformatics 29:1226-8. 2013
    ..These data provide information on relative fluxes in a metabolic network. The graphical user interface allows users to import GC/MS data in netCDF format and export all information into a tab-separated format...
  4. pmc Ketogenic essential amino acids modulate lipid synthetic pathways and prevent hepatic steatosis in mice
    Yasushi Noguchi
    Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
    PLoS ONE 5:e12057. 2010
    ..Although dietary ketogenic essential amino acid (KAA) content modifies accumulation of hepatic lipids, the molecular interactions between KAAs and lipid metabolism are yet to be fully elucidated...
  5. pmc Enhancing solubility of deoxyxylulose phosphate pathway enzymes for microbial isoprenoid production
    Kang Zhou
    Chemical and Pharmaceutical Engineering, Singapore MIT Alliance, 4 Engineering Drive 3, Singapore, Singapore
    Microb Cell Fact 11:148. 2012
    ..This study examined the solubility of over-expressed homologous enzymes of the deoxyxylulose phosphate pathway (DXP) and the impact of inclusion body formation on metabolic engineering of microbes...
  6. pmc Incremental parameter estimation of kinetic metabolic network models
    Gengjie Jia
    Chemical and Pharmaceutical Engineering, Singapore MIT Alliance, Singapore 117576, Singapore
    BMC Syst Biol 6:142. 2012
    ..Unfortunately, the associated computational requirement often becomes prohibitively high due to the large number of parameters and the lack of complete parameter identifiability (i.e. not all parameters can be uniquely identified)...
  7. doi request reprint Synthetic biology and metabolic engineering
    Gregory Stephanopoulos
    Department of Chemical Engineering, Massachusetts Institute of Technology, Building 56 Room 469C, 77 Massachusetts Ave, Cambridge, MA 02139, USA
    ACS Synth Biol 1:514-25. 2012
    ....
  8. pmc Novel reference genes for quantifying transcriptional responses of Escherichia coli to protein overexpression by quantitative PCR
    Kang Zhou
    Chemical and Pharmaceutical Engineering, Singapore MIT Alliance, 4 Engineering Drive 3, Singapore
    BMC Mol Biol 12:18. 2011
    ..The objective of this study is to identify a set of reliable reference genes for transcription analysis in recombinant protein over-expression studies in E. coli...
  9. pmc Assessment of heterologous butyrate and butanol pathway activity by measurement of intracellular pathway intermediates in recombinant Escherichia coli
    Curt R Fischer
    Department of Chemical Engineering, Massachusetts Institute of Technology, Room 56 469, Cambridge, MA 02139, USA
    Appl Microbiol Biotechnol 88:265-75. 2010
    ..Our thermodynamic interpretation of pool size measurements is applicable to the analysis of other metabolic pathways...
  10. ncbi request reprint Exploiting biological complexity for strain improvement through systems biology
    Gregory Stephanopoulos
    Department of Chemical Engineering, Massachusetts Institute of Technology, Room 56 469, Cambridge, MA 02139, USA
    Nat Biotechnol 22:1261-7. 2004
    ....
  11. ncbi request reprint Engineering metabolism and product formation in Corynebacterium glutamicum by coordinated gene overexpression
    Mattheos A G Koffas
    Department of Chemical Engineering, Massachusetts Institute of Technology, Room 56 469 77, Cambridge, MA 02139, USA
    Metab Eng 5:32-41. 2003
    ..This can be achieved either by external, gene expression inducing, controls or controls responding to the physiological cellular state...
  12. ncbi request reprint Determination of minimum sample size and discriminatory expression patterns in microarray data
    Daehee Hwang
    Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Bioinformatics 18:1184-93. 2002
    ..It is therefore important to provide a method for the determination of the minimum number of microarrays required to separate, with statistical reliability, distinct disease states or other physiological differences...
  13. ncbi request reprint Mapping physiological states from microarray expression measurements
    Gregory Stephanopoulos
    Department of Chemical Engineering, Massachusetts Institute of Technology, Room 56 469, Cambridge 02139, USA
    Bioinformatics 18:1054-63. 2002
    ..Such methods should be robust and maintain biological interpretability...
  14. ncbi request reprint After a decade of progress, an expanded role for metabolic engineering
    G Stephanopoulos
    Department of Chemical Engineering, MIT Room 56 469, Cambridge, MA 02139, USA
    Adv Biochem Eng Biotechnol 73:1-8. 2001
    ..To facilitate the burgeoning scientific exchange in this area on a more regular and convenient basis, a new conference series was launched in 1996 followed by a new journal in 1999...
  15. ncbi request reprint A generic motif discovery algorithm for sequential data
    Kyle L Jensen
    Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Bioinformatics 22:21-8. 2006
    ..However, previous methods have been unable to combine exhaustive search with complex motif representations and are each typically only applicable to a certain class of problems...
  16. ncbi request reprint Systematic identification of conserved metabolites in GC/MS data for metabolomics and biomarker discovery
    Mark P Styczynski
    Department of Chemical Engineering, Massachusetts Institute of Technology, Room 56 469c, Cambridge, Massachusetts 02139, USA
    Anal Chem 79:966-73. 2007
    ..By systematically cataloguing conserved metabolite peaks prior to data analysis methods, our approach broadens the scope of metabolomics and facilitates biomarker discovery...
  17. ncbi request reprint Metabolic engineering
    M Koffas
    Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
    Annu Rev Biomed Eng 1:535-57. 1999
    ..In this article we review basic concepts of metabolic engineering and provide examples of applications in the production of primary and secondary metabolites, improving cellular properties, and biomedical engineering...
  18. ncbi request reprint Expanding the metabolic engineering toolbox: more options to engineer cells
    Keith E Tyo
    Department of Chemical Engineering, Massachusetts Institute of Technology, Room 56 469, Cambridge, MA 02139, USA
    Trends Biotechnol 25:132-7. 2007
    ....
  19. ncbi request reprint An extension and novel solution to the (l,d)-motif challenge problem
    Mark P Styczynski
    Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
    Genome Inform 15:63-71. 2004
    ..We demonstrate the performance of the algorithm on publicly available datasets and show that the algorithm deterministically enumerates the optimal motifs...
  20. ncbi request reprint Optimization of protein fusion partner length for maximizing in vitro translation of peptides
    Christopher R Loose
    Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
    Biotechnol Prog 23:444-51. 2007
    ..This trend was verified using two fusion partners with different amino acid sequences. Furthermore, protease inhibitors were used to confirm that proteases were responsible for limiting accumulation of peptides below the optimal length...
  21. ncbi request reprint De Novo metabolic engineering and the promise of synthetic DNA
    Daniel Klein-Marcuschamer
    Bioinformatics and Metabolic Engineering Laboratory, Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
    Adv Biochem Eng Biotechnol 120:101-31. 2010
    ..The possibilities that arise with the use of synthetic oligonucleotides will be delineated herein...
  22. pmc High-throughput screen for poly-3-hydroxybutyrate in Escherichia coli and Synechocystis sp. strain PCC6803
    Keith E Tyo
    Department of Chemical Engineering, MIT 56 469, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
    Appl Environ Microbiol 72:3412-7. 2006
    ..coli using fluorescence-activated cell sorting to identify mutants with increased PHB-accumulating properties...
  23. doi request reprint Controlling the release of peptide antimicrobial agents from surfaces
    Anita Shukla
    Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
    Biomaterials 31:2348-57. 2010
    ..These films provide the level of control over drug loading and release kinetics required in medically relevant applications including coatings for implant materials and bandages, while eliminating susceptibility to bacterial resistance...
  24. ncbi request reprint Elucidation of cellular metabolism via metabolomics and stable-isotope assisted metabolomics
    Karsten Hiller
    Massachusetts Institute of Technology, Department of Chemical Engineering, 77 Massachusetts Ave, 56 439, Cambridge, MA 02140, USA
    Curr Pharm Biotechnol 12:1075-86. 2011
    ....
  25. doi request reprint Tracking cellular metabolomics in lipoapoptosis- and steatosis-developing liver cells
    Yasushi Noguchi
    Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Mol Biosyst 7:1409-19. 2011
    ..Thus, our data suggest that abnormal PPP fluxes, in addition to increased adenosine levels, might be related to the decoupling of glycolysis and the resulting lipoapoptotic phenotype...
  26. ncbi request reprint Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli
    Hal Alper
    Department of Chemical Engineering, Massachusetts Institute of Technology, Room 56 469, 77 Massachusetts Ave, Cambridge, MA 02139, USA
    Metab Eng 7:155-64. 2005
    ..For the case of lycopene biosynthesis, the so identified knockout targets yielded a triple knockout construct that exhibited a nearly 40% increase over an engineered, high producing parental strain...
  27. ncbi request reprint Rapamycin reduces hybridoma cell death and enhances monoclonal antibody production
    R R Balcarcel
    Department of Chemical Engineering, Massachusetts Institute of Technology, Room 56-469, Cambridge, Massachusetts 02139, USA
    Biotechnol Bioeng 76:1-10. 2001
    ....
  28. ncbi request reprint Mining of biological data I: identifying discriminating features via mean hypothesis testing
    R T Kamimura
    Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02319, USA
    Metab Eng 2:218-27. 2000
    ..We present here the method for identifying discriminating features in data via mean hypothesis testing along with results from the analysis of case studies from industrial fermentations..
  29. ncbi request reprint Identification of optimal classification functions for biological sample and state discrimination from metabolic profiling data
    Kyongbum Lee
    Chemical and Biological Engineering, Tufts University, Medford, MA 02155, USA
    Bioinformatics 20:959-69. 2004
    ..To this end, we develop a novel set of computational tools by integrating regression optimization, stepwise variable selection and cross-validation algorithms...
  30. ncbi request reprint Profiling of dynamic changes in hypermetabolic livers
    Kyongbum Lee
    Shriners Burns Hospital and Center for Engineering in Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
    Biotechnol Bioeng 83:400-15. 2003
    ....
  31. ncbi request reprint Application of multivariate analysis to optimize function of cultured hepatocytes
    Christina Chan
    Department of Chemical Engineering and Material Science, Michigan State University, East Lansing, Michigan 48824, USA
    Biotechnol Prog 19:580-98. 2003
    ..This study illustrates a framework for optimizing hepatic function and a possibility of identifying potential targets for improving hepatic functions...
  32. pmc Thermodynamic and kinetic characterization of antisense oligodeoxynucleotide binding to a structured mRNA
    S Patrick Walton
    Center for Engineering in Medicine Surgical Services, Massachusetts General Hospital, Harvard Medical School and Shriners Burns Hospital, Boston, Massachusetts 02114, USA
    Biophys J 82:366-77. 2002
    ..Implications for the rational design of effective antisense reagents are discussed...

Research Grants11

  1. LINKING GENOMICS TO FUNCTION VIA METABOLIC PHENOTYPING
    Gregory Stephanopoulos; Fiscal Year: 2000
    ..As such, it holds the promise of identifying most, if not all points in metabolism affected by the action of drugs or genetic modifications thus guiding future programs of drug development and gene therapy. ..
  2. Elucidating modulators of hepatic metabolism by quantitative flux analysis
    Gregory Stephanopoulos; Fiscal Year: 2010
    ..Ultimately, we aspire to establish flux quantification as an indispenable tool in biomedical research. ..
  3. Metabolic Engineering for Microbial Taxol Biosynthesis
    Gregory Stephanopoulos; Fiscal Year: 2010
    ..Additionally, a heterologous taxol biosynthetic pathway would drastically expand the opportunities of biosynthesizing a vast diversity of taxol derivatives with greater efficacy and broader anticancer properties. ..
  4. Elucidating modulators of hepatic metabolism by quantitative flux analysis
    Gregory Stephanopoulos; Fiscal Year: 2009
    ..Ultimately, we aspire to establish flux quantification as an indispenable tool in biomedical research. ..
  5. Metabolic Engineering for Microbial Taxol Biosynthesis
    Gregory Stephanopoulos; Fiscal Year: 2009
    ..Additionally, a heterologous taxol biosynthetic pathway would drastically expand the opportunities of biosynthesizing a vast diversity of taxol derivatives with greater efficacy and broader anticancer properties. ..
  6. Elucidating modulators of hepatic metabolism by quantitative flux analysis
    Gregory Stephanopoulos; Fiscal Year: 2008
    ..Ultimately, we aspire to establish flux quantification as an indispenable tool in biomedical research. ..
  7. Elucidating modulators of hepatic metabolism by quantitative flux analysis
    Gregory Stephanopoulos; Fiscal Year: 2007
    ..Ultimately, we aspire to establish flux quantification as an indispensable tool in biomedical research. [unreadable] [unreadable] [unreadable]..
  8. Elucidating modulators of hepatic metabolism by quantitative flux analysis
    Gregory Stephanopoulos; Fiscal Year: 2006
    ..Ultimately, we aspire to establish flux quantification as an indispensable tool in biomedical research. [unreadable] [unreadable] [unreadable]..
  9. LINKING GENOMICS TO FUNCTION VIA METABOLIC PHENOTYPING
    Gregory Stephanopoulos; Fiscal Year: 2002
    ..As such, it holds the promise of identifying most, if not all points in metabolism affected by the action of drugs or genetic modifications thus guiding future programs of drug development and gene therapy. ..
  10. LINKING GENOMICS TO FUNCTION VIA METABOLIC PHENOTYPING
    Gregory Stephanopoulos; Fiscal Year: 2001
    ..As such, it holds the promise of identifying most, if not all points in metabolism affected by the action of drugs or genetic modifications thus guiding future programs of drug development and gene therapy. ..
  11. Metabolic Engineering for Microbial Taxol Biosynthesis
    Gregory Stephanopoulos; Fiscal Year: 2010
    ..Additionally, a heterologous taxol biosynthetic pathway would drastically expand the opportunities of biosynthesizing a vast diversity of taxol derivatives with greater efficacy and broader anticancer properties. ..