Christopher D Herring

Summary

Publications

  1. ncbi An evaluation of Comparative Genome Sequencing (CGS) by comparing two previously-sequenced bacterial genomes
    Christopher D Herring
    Department of Bioengineering, University of California San Diego, La Jolla, USA
    BMC Genomics 8:274. 2007
  2. ncbi Systems approach to refining genome annotation
    Jennifer L Reed
    Department of Bioengineering, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0412, USA
    Proc Natl Acad Sci U S A 103:17480-4. 2006
  3. ncbi The global transcriptional regulatory network for metabolism in Escherichia coli exhibits few dominant functional states
    Christian L Barrett
    Bioengineering Department, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0412, USA
    Proc Natl Acad Sci U S A 102:19103-8. 2005
  4. ncbi Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale
    Christopher D Herring
    Department of Bioengineering, University of California, San Diego, California 92093, USA
    Nat Genet 38:1406-12. 2006
  5. ncbi Marker removal system for Thermoanaerobacterium saccharolyticum and development of a markerless ethanologen
    A Joe Shaw
    Mascoma Corporation, 67 Etna Rd, Lebanon, NH 03766, USA
    Appl Environ Microbiol 77:2534-6. 2011
  6. ncbi Immobilization of Escherichia coli RNA polymerase and location of binding sites by use of chromatin immunoprecipitation and microarrays
    Christopher D Herring
    Department of Engineering, UC San Diego Bioengineering, 9500 Gilman Drive, Dept 0412, La Jolla, CA 92093-0412, USA
    J Bacteriol 187:6166-74. 2005
  7. ncbi In silico design and adaptive evolution of Escherichia coli for production of lactic acid
    Stephen S Fong
    Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0412, USA
    Biotechnol Bioeng 91:643-8. 2005
  8. ncbi Introduction of conditional lethal amber mutations in Escherichia coli
    Christopher D Herring
    Mascoma Corporation, Lebanon, NH, USA
    Methods Mol Biol 416:323-34. 2008
  9. ncbi Global transcriptional effects of a suppressor tRNA and the inactivation of the regulator frmR
    Christopher D Herring
    Laboratory of Genetics, University of Wisconsin Madison, 445 Henry Mall, Madison, WI 53706, USA
    J Bacteriol 186:6714-20. 2004
  10. ncbi Conditional lethal amber mutations in essential Escherichia coli genes
    Christopher D Herring
    Laboratory of Genetics, University of Wisconsin Madison, 445 Henry Mall, Madison, WI 53706, USA
    J Bacteriol 186:2673-81. 2004

Collaborators

Detail Information

Publications12

  1. ncbi An evaluation of Comparative Genome Sequencing (CGS) by comparing two previously-sequenced bacterial genomes
    Christopher D Herring
    Department of Bioengineering, University of California San Diego, La Jolla, USA
    BMC Genomics 8:274. 2007
    ..It is critical though to know the accuracy of the technique used, and to establish confidence that all of the mutations were detected...
  2. ncbi Systems approach to refining genome annotation
    Jennifer L Reed
    Department of Bioengineering, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0412, USA
    Proc Natl Acad Sci U S A 103:17480-4. 2006
    ..This study thus demonstrates the use of systems analysis to discover metabolic and transport functions and their genetic basis by a combination of experimental and computational approaches...
  3. ncbi The global transcriptional regulatory network for metabolism in Escherichia coli exhibits few dominant functional states
    Christian L Barrett
    Bioengineering Department, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0412, USA
    Proc Natl Acad Sci U S A 102:19103-8. 2005
    ....
  4. ncbi Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale
    Christopher D Herring
    Department of Bioengineering, University of California, San Diego, California 92093, USA
    Nat Genet 38:1406-12. 2006
    ..The success of this new genome-scale approach indicates that real-time evolution studies will now be practical in a wide variety of contexts...
  5. ncbi Marker removal system for Thermoanaerobacterium saccharolyticum and development of a markerless ethanologen
    A Joe Shaw
    Mascoma Corporation, 67 Etna Rd, Lebanon, NH 03766, USA
    Appl Environ Microbiol 77:2534-6. 2011
    ..The pta- and ack-based haloacetate selective strategy was subsequently used to create strain M0355, a markerless ?ldh ?pta ?ack strain that produces ethanol at a high yield...
  6. ncbi Immobilization of Escherichia coli RNA polymerase and location of binding sites by use of chromatin immunoprecipitation and microarrays
    Christopher D Herring
    Department of Engineering, UC San Diego Bioengineering, 9500 Gilman Drive, Dept 0412, La Jolla, CA 92093-0412, USA
    J Bacteriol 187:6166-74. 2005
    ..This map of RNA polymerase binding sites represents a foundation for studies of transcription factors in E. coli and an important evaluation of the chIP-chip technique...
  7. ncbi In silico design and adaptive evolution of Escherichia coli for production of lactic acid
    Stephen S Fong
    Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0412, USA
    Biotechnol Bioeng 91:643-8. 2005
    ..Strains grown on 2 g/L glucose at 37 degrees C showed lactate titers ranging from 0.87 to 1.75 g/L and secretion rates that were directly coupled to growth rates...
  8. ncbi Introduction of conditional lethal amber mutations in Escherichia coli
    Christopher D Herring
    Mascoma Corporation, Lebanon, NH, USA
    Methods Mol Biol 416:323-34. 2008
    ..The mutants then depend upon expression of a suppressor transfer RNA (tRNA) for survival, which is expressed under control of the arabinose promoter on a high-copy-number plasmid...
  9. ncbi Global transcriptional effects of a suppressor tRNA and the inactivation of the regulator frmR
    Christopher D Herring
    Laboratory of Genetics, University of Wisconsin Madison, 445 Henry Mall, Madison, WI 53706, USA
    J Bacteriol 186:6714-20. 2004
    ..The operon was shown to be induced by formaldehyde, and the genes have been renamed frmR, frmA, and frmB, respectively...
  10. ncbi Conditional lethal amber mutations in essential Escherichia coli genes
    Christopher D Herring
    Laboratory of Genetics, University of Wisconsin Madison, 445 Henry Mall, Madison, WI 53706, USA
    J Bacteriol 186:2673-81. 2004
    ..Such experiments may inexpensively provide valuable information for the identification and prioritization of targets for antibiotic development...
  11. ncbi Gene replacement without selection: regulated suppression of amber mutations in Escherichia coli
    Christopher D Herring
    Laboratory of Genetics, University of Wisconsin Madison, 445 Henry Mall, Madison, WI 53706, USA
    Gene 311:153-63. 2003
    ..To compliment this approach we developed an arabinose inducible amber suppressor tRNA. Controlled expression mediated by the suppressor was demonstrated for the lacZ and xylA amber mutants...
  12. ncbi Engineering a reduced Escherichia coli genome
    Vitaliy Kolisnychenko
    Institute of Biochemistry, Biological Research Center, H-6701 Szeged, Hungary
    Genome Res 12:640-7. 2002
    ....