Christopher S Henry

Summary

Affiliation: Argonne National Laboratory
Country: USA

Publications

  1. pmc iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations
    Christopher S Henry
    Mathematics and Computer Science Department, Argonne National Laboratory, S, Cass Avenue, Argonne, IL 60439, USA
    Genome Biol 10:R69. 2009
  2. doi request reprint High-throughput generation, optimization and analysis of genome-scale metabolic models
    Christopher S Henry
    Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA
    Nat Biotechnol 28:977-82. 2010
  3. doi request reprint Connecting genotype to phenotype in the era of high-throughput sequencing
    Christopher S Henry
    Argonne National Laboratory, Argonne, IL 60439, USA
    Biochim Biophys Acta 1810:967-77. 2011
  4. pmc Systematic identification and analysis of frequent gene fusion events in metabolic pathways
    Christopher S Henry
    Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
    BMC Genomics 17:473. 2016
  5. pmc Microbial Community Metabolic Modeling: A Community Data-Driven Network Reconstruction
    Christopher S Henry
    Division of Mathematics and Computer Science, Argonne National Laboratory, Argonne, Illinois
    J Cell Physiol 231:2339-45. 2016
  6. pmc Reconstruction of the Regulatory Network for Bacillus subtilis and Reconciliation with Gene Expression Data
    José P Faria
    Computation Institute, University of ChicagoChicago, IL, USA Computing, Environment and Life Sciences, Argonne National LaboratoryArgonne, IL, USA Centre of Biological Engineering, University of MinhoBraga, Portugal
    Front Microbiol 7:275. 2016
  7. pmc Modeling central metabolism and energy biosynthesis across microbial life
    Janaka N Edirisinghe
    Mathematics and Computer Science Department, Argonne National Laboratory, S Cass Avenue, Argonne, IL, 60439, USA
    BMC Genomics 17:568. 2016
  8. pmc Building the repertoire of dispensable chromosome regions in Bacillus subtilis entails major refinement of cognate large-scale metabolic model
    Kosei Tanaka
    INRA, UMR 1319 Micalis, AgroParisTech, UMR Micalis, Jouy en Josas F 78350, France
    Nucleic Acids Res 41:687-99. 2013
  9. doi request reprint Cover Image, Volume 231, Number 11, November 2016
    Christopher S Henry
    Division of Mathematics and Computer Science, Argonne National Laboratory, Argonne, Illinois
    J Cell Physiol 231:i. 2016
  10. pmc Computing and Applying Atomic Regulons to Understand Gene Expression and Regulation
    José P Faria
    Computation Institute, University of ChicagoChicago, IL, USA Computing, Environment and Life Sciences, Argonne National LaboratoryArgonne, IL, USA Centre of Biological Engineering, University of Minho, Campus de GualtarBraga, Portugal Mathematics and Computer Science Division, Argonne National LaboratoryArgonne, IL, USA
    Front Microbiol 7:1819. 2016

Collaborators

Detail Information

Publications14

  1. pmc iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations
    Christopher S Henry
    Mathematics and Computer Science Department, Argonne National Laboratory, S, Cass Avenue, Argonne, IL 60439, USA
    Genome Biol 10:R69. 2009
    ..subtilis 168 called iBsu1103. This new model is based on the annotated B. subtilis 168 genome generated by the SEED, one of the most up-to-date and accurate annotations of B. subtilis 168 available...
  2. doi request reprint High-throughput generation, optimization and analysis of genome-scale metabolic models
    Christopher S Henry
    Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA
    Nat Biotechnol 28:977-82. 2010
    ..Twenty-two of the models were validated against available gene essentiality and Biolog data, with the average model accuracy determined to be 66% before optimization and 87% after optimization...
  3. doi request reprint Connecting genotype to phenotype in the era of high-throughput sequencing
    Christopher S Henry
    Argonne National Laboratory, Argonne, IL 60439, USA
    Biochim Biophys Acta 1810:967-77. 2011
    ....
  4. pmc Systematic identification and analysis of frequent gene fusion events in metabolic pathways
    Christopher S Henry
    Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
    BMC Genomics 17:473. 2016
    ..The availability of a large fusion dataset would help probe functional associations and enable systematic analysis of where and why fusion events occur...
  5. pmc Microbial Community Metabolic Modeling: A Community Data-Driven Network Reconstruction
    Christopher S Henry
    Division of Mathematics and Computer Science, Argonne National Laboratory, Argonne, Illinois
    J Cell Physiol 231:2339-45. 2016
    ..J. Cell. Physiol. 231: 2339-2345, 2016. © 2016 Wiley Periodicals, Inc. ..
  6. pmc Reconstruction of the Regulatory Network for Bacillus subtilis and Reconciliation with Gene Expression Data
    José P Faria
    Computation Institute, University of ChicagoChicago, IL, USA Computing, Environment and Life Sciences, Argonne National LaboratoryArgonne, IL, USA Centre of Biological Engineering, University of MinhoBraga, Portugal
    Front Microbiol 7:275. 2016
    ..During this process, we were also able to infer novel stimuli for hypothetical genes by exploring the genome expression metadata relating to experimental conditions, gaining insights into novel biology. ..
  7. pmc Modeling central metabolism and energy biosynthesis across microbial life
    Janaka N Edirisinghe
    Mathematics and Computer Science Department, Argonne National Laboratory, S Cass Avenue, Argonne, IL, 60439, USA
    BMC Genomics 17:568. 2016
    ....
  8. pmc Building the repertoire of dispensable chromosome regions in Bacillus subtilis entails major refinement of cognate large-scale metabolic model
    Kosei Tanaka
    INRA, UMR 1319 Micalis, AgroParisTech, UMR Micalis, Jouy en Josas F 78350, France
    Nucleic Acids Res 41:687-99. 2013
    ..The iBsu1103V2 model has improved considerably at predicting loss of viability, and many insights gained from the model revisions have been integrated into the Model SEED to improve reconstruction of other microbial models...
  9. doi request reprint Cover Image, Volume 231, Number 11, November 2016
    Christopher S Henry
    Division of Mathematics and Computer Science, Argonne National Laboratory, Argonne, Illinois
    J Cell Physiol 231:i. 2016
    ..Imaged by PNNL scientist, William B. Chrisler. ..
  10. pmc Computing and Applying Atomic Regulons to Understand Gene Expression and Regulation
    José P Faria
    Computation Institute, University of ChicagoChicago, IL, USA Computing, Environment and Life Sciences, Argonne National LaboratoryArgonne, IL, USA Centre of Biological Engineering, University of Minho, Campus de GualtarBraga, Portugal Mathematics and Computer Science Division, Argonne National LaboratoryArgonne, IL, USA
    Front Microbiol 7:1819. 2016
    ....
  11. doi request reprint Plant B vitamin pathways and their compartmentation: a guide for the perplexed
    Svetlana Gerdes
    Mathematics and Computer Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439 USA
    J Exp Bot 63:5379-95. 2012
    ..The SEED-encoded B vitamin pathway collection is a publicly available, expertly curated, one-stop resource for metabolic reconstruction and modeling...
  12. doi request reprint Discovery and analysis of novel metabolic pathways for the biosynthesis of industrial chemicals: 3-hydroxypropanoate
    Christopher S Henry
    Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
    Biotechnol Bioeng 106:462-73. 2010
    ..Examination of the optimal pathways for the biosynthesis of these 28 compounds in E. coli revealed pyruvate and succinate to be ideal intermediates for achieving high product yields from glucose...
  13. pmc Thermodynamics-based metabolic flux analysis
    Christopher S Henry
    Department of Chemical and Biological Engineering, McCormick School of Engineering and Applied Sciences, Northwestern University, Evanston, Illinois, USA
    Biophys J 92:1792-805. 2007
    ..Further, we find that the NAD/NADH and NADP/NADPH ratios maintained in the cell are close to the minimum feasible ratio and maximum feasible ratio, respectively...
  14. pmc Genome-scale thermodynamic analysis of Escherichia coli metabolism
    Christopher S Henry
    Department of Chemical and Biological Engineering, McCormick School of Engineering and Applied Sciences, Northwestern University, Evanston, Illinois, USA
    Biophys J 90:1453-61. 2006
    ..The methodologies and results discussed can be used to facilitate the refinement of the feasible ranges for cellular parameters such as species concentrations and reaction rate constants...