Daniel R Hyduke

Summary

Affiliation: University of California
Country: USA

Publications

  1. doi request reprint Identifying radiation exposure biomarkers from mouse blood transcriptome
    Daniel R Hyduke
    Department of Biochemistry and Molecular and Cellular Biology, and Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
    Int J Bioinform Res Appl 9:365-85. 2013
  2. pmc Analysis of omics data with genome-scale models of metabolism
    Daniel R Hyduke
    Department of Bioengineering, University of California San Diego, La Jolla, CA 92093 0412, USA
    Mol Biosyst 9:167-74. 2013
  3. doi request reprint Towards genome-scale signalling network reconstructions
    Daniel R Hyduke
    Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093 0412, USA
    Nat Rev Genet 11:297-307. 2010
  4. pmc Comparison of mouse urinary metabolic profiles after exposure to the inflammatory stressors γ radiation and lipopolysaccharide
    Evagelia C Laiakis
    Department of Biochemistry and Molecular and Cellular Biology, Georgetown University, Washington, DC 20057, USA
    Radiat Res 177:187-99. 2012
  5. pmc GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data
    Brian J Schmidt
    Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093 0412, USA and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
    Bioinformatics 29:2900-8. 2013
  6. pmc In silico method for modelling metabolism and gene product expression at genome scale
    Joshua A Lerman
    Department of Bioengineering, University of California San Diego, PFBH Room 419, 9500 Gliman Drive, La Jolla, California 92093 0412, USA
    Nat Commun 3:929. 2012
  7. pmc COBRApy: COnstraints-Based Reconstruction and Analysis for Python
    Ali Ebrahim
    Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive MC0412, La Jolla, CA 92093 0412, USA
    BMC Syst Biol 7:74. 2013
  8. pmc Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction
    Edward J O'Brien
    Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
    Mol Syst Biol 9:693. 2013
  9. pmc An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92
    Pep Charusanti
    Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
    BMC Syst Biol 5:163. 2011
  10. pmc Exposure to ionizing radiation induced persistent gene expression changes in mouse mammary gland
    Kamal Datta
    Department of Biochemistry and Molecular and Cellular Biology, Georgetown University, 3970 Reservoir Rd, Washington, DC, NW 20057 1468, USA
    Radiat Oncol 7:205. 2012

Collaborators

Detail Information

Publications10

  1. doi request reprint Identifying radiation exposure biomarkers from mouse blood transcriptome
    Daniel R Hyduke
    Department of Biochemistry and Molecular and Cellular Biology, and Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
    Int J Bioinform Res Appl 9:365-85. 2013
    ..We used this dataset with the Random Forest algorithm to correctly classify independently generated data and to identify putative metabolite biomarkers for radiation exposure. ..
  2. pmc Analysis of omics data with genome-scale models of metabolism
    Daniel R Hyduke
    Department of Bioengineering, University of California San Diego, La Jolla, CA 92093 0412, USA
    Mol Biosyst 9:167-74. 2013
    ..This improvement is largely due to knowledge bases providing a validated biological context for interpreting the data...
  3. doi request reprint Towards genome-scale signalling network reconstructions
    Daniel R Hyduke
    Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093 0412, USA
    Nat Rev Genet 11:297-307. 2010
    ....
  4. pmc Comparison of mouse urinary metabolic profiles after exposure to the inflammatory stressors γ radiation and lipopolysaccharide
    Evagelia C Laiakis
    Department of Biochemistry and Molecular and Cellular Biology, Georgetown University, Washington, DC 20057, USA
    Radiat Res 177:187-99. 2012
    ..It can also provide quick and reliable assessment of medical conditions in a mass casualty radiological scenario and aid in effective triaging...
  5. pmc GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data
    Brian J Schmidt
    Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093 0412, USA and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
    Bioinformatics 29:2900-8. 2013
    ..However, few practical methods for integrating metabolomics data with other omics data sources into genome-scale models of metabolism have been developed...
  6. pmc In silico method for modelling metabolism and gene product expression at genome scale
    Joshua A Lerman
    Department of Bioengineering, University of California San Diego, PFBH Room 419, 9500 Gliman Drive, La Jolla, California 92093 0412, USA
    Nat Commun 3:929. 2012
    ....
  7. pmc COBRApy: COnstraints-Based Reconstruction and Analysis for Python
    Ali Ebrahim
    Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive MC0412, La Jolla, CA 92093 0412, USA
    BMC Syst Biol 7:74. 2013
    ..The openCOBRA Project is a community effort to promote constraints-based research through the distribution of freely available software...
  8. pmc Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction
    Edward J O'Brien
    Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
    Mol Syst Biol 9:693. 2013
    ..Our results unify many existing principles developed to describe bacterial growth...
  9. pmc An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92
    Pep Charusanti
    Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
    BMC Syst Biol 5:163. 2011
    ..Metabolism in Y. pestis displays remarkable flexibility and robustness, allowing the bacterium to proliferate in both warm-blooded mammalian hosts and cold-blooded insect vectors such as fleas...
  10. pmc Exposure to ionizing radiation induced persistent gene expression changes in mouse mammary gland
    Kamal Datta
    Department of Biochemistry and Molecular and Cellular Biology, Georgetown University, 3970 Reservoir Rd, Washington, DC, NW 20057 1468, USA
    Radiat Oncol 7:205. 2012
    ..We undertook this study to delineate radiation-induced persistent alterations in gene expression in mouse mammary glands 2-month after radiation exposure...