Daniel R. Hyduke, Ph. D

Dr. D.R. Hyduke - CV - The openCOBRA Project


2006 Ph.D. Chemical Engineering University of California, Los Angeles Advisor: James C. Liao

1999 B.S. Chemical Engineering Michigan State University


  1. Hyduke DR, Laiakis EC, Li HH, Fornace Jr. AJ. Identifying radiation exposure biomarkers from mouse blood transcriptome. Int J Bioinform Res Appl (In Press)
  2. Hyduke DR✝, Lewis NE, Palsson BO. Analysis of omics data with genome-scale models of metabolism. Mol. BioSyst. (DOI:10.1039/C2MB25453K). ✝Corresponding Author
  3. Datta K, Hyduke DR, Suman S, Moon BH, Johnson M, Fornace AJ Jr. 2012 Exposure to ionizing radiation induced persistent gene expression changes in mouse mammary gland. Radiation Oncology 7:205
  4. Ansong C, Deatherage BL, Hyduke DR, Schmidt B, McDermott JE, Jones MB, Chauhan S, Charusanti P, Kim YM, Nakayasu ES, Li J, Kidwai A, Niemann G, Brown RN, Metz TO, McAteer K, Heffron F, Peterson SN, Motin V, Palsson BO, Smith RD, Adkins JN. 2012 Studying Salmonellae and Yersiniae Host-Pathogen Interactions Using Integrated 'Omics and Modeling. Curr Top Microbiol Immunol (DOI: 10.1007/82_2012_247).
  5. Lerman JA*, Hyduke DR*, Latif H, Portnoy VA, Lewis NE, Orth JD, Schrimpe-Rutledge AC, Smith RD, Adkins JN, Zengler K, Palsson BO. 2012 In silico method for modelling metabolism and gene product expression at genome scale. Nature Communications 3:929. *Equal Contributor.
  6. Bordbar A, Mo ML, Nakayasu ES, Schrimpe-Rutledge AC, Kim YM, Metz TO, Jones MB, Frank BC, Peterson SN, Hyduke DR, Adkins JN, Palsson BO. 2012 Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation. Molecular Systems Biology 8:558.
  7. Laiakis EC, Hyduke DR, Fornace Jr AJ 2012 Comparison of Mouse Urinary Metabolic Profiles after Exposure to the Inflammatory Stressors γ Radiation and Lipopolysaccharide. Radiation Research 177(2):187-99.
  8. McDermott JE, Braun P, Bonneau R, Hyduke DR 2012 Modeling host-pathogen interactions: computational biology and bioinformatics for infectious disease research. Pac Symp Biocomput 17:283-6.
  9. Charusanti P, Chauhan S, McAteer K, Lerman JA, Hyduke DR, Motin VL, Ansong C, Adkins JN, Palsson BØ. 2011 An Experimentally-Supported Genome-Scale Metabolic Network Reconstruction for Yersinia pestis CO92. BMC Sys Bio 5:163.
  10. Schellenberger J, Que R, Fleming RMT, Thiele I, Orth JD, Feist AM, Zielinski DC, Bordbar A, Lewis NE, Rahmanian S, Kang J, Hyduke DR, Palsson BØ. 2011 Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nature Protocols 6:1290-1307.
  11. McDermott JE, Yoon H, Nakayasu E, Metz TO, Hyduke DR, Kidwai AS, Palsson BØ, Adkins JN, Heffron F. 2011 Technologies and approaches to elucidate and model the virulence program of Salmonella Front Cell Infect Microbio 2(121):1-14.
  12. Hyduke DR, Amundson SA, Fornace Jr. AJ. Complexity of Stress Signaling and Responses. R. A. Bradshaw, and E. A. Dennis (eds.), Regulation of Organelle and Cell Compartment Signaling: Cell Signaling Collection. Academic Press, 2011.
  13. Thiele I*, Hyduke DR*, Steeb B, Fankam G, Allen DK, Bazzani S, Charusanti P, Chen FC, Fleming RMT, Hala D, Hsiung CA, de Keersmaecker S, Liao YC, Marchal K, Mo ML, Özdemir E, Raghunathan A, Reed JL, Shin SI, Sigurbjörnsdóttir S, Steinman J, Swainston N, Thijs I, Zengler K, Palsson BØ, Adkins JN, Bumann D 2011 A community effort towards a knowledge-base and mathematical model of human pathogen Salmonella Typhimurium LT2. BMC Sys Bio 5:8 *Equal contributor.
  14. Tran LM, Hyduke DR, Liao JC 2010 Trimming of Mammalian Transcriptional Networks using Network Component Analysis BMC Bioinformatics 11(1):511
  15. Hyduke DR, Palsson BØ 2010 Towards Genome Scale Signaling Network Reconstructions. Nature Reviews Genetics 11:297-307.
  16. Park H, Suy S, Danner M, Dailey V, Zhang Y, Li HH, Hyduke DR, Collins B, Gagnon G, Kallakury B, Kumar D, Brown M, Fornace AJ Jr., Dristchilo A, Collins S 2009 AMP-Activated Protein Kinase Promotes Human Prostate Cancer Cell Growth and Survival. Molecular Cancer Therapeutics 8(4):733-41.
  17. Jarboe LR, Hyduke DR, Liao JC 2009 Systems Approaches to Unraveling Nitric Oxide Response Networks in Prokaryotes. Nitric Oxide: Biology and Pathobiology, 2nd Ed., Ch. 4, pp. 103-36.
  18. Hyduke DR, Amundson SA, Fornace AJ Jr 2009 Complexity of Stress Signaling and Responses. Handbook of Cell Signaling, 2nd Ed., Vol. 3, Ch. 257, pp. 2107-25.
  19. Jarboe LR*, Hyduke DR*, Tran LM, Chou KJY, Liao JC 2008 Determination of S-nitrosoglutathione targets and response networks in Escherichia coli using integrated biochemical and systems analysis. J. Biol. Chem. 283(8):5148-57. *Equal contributor.
  20. Hyduke DR*, Jarboe LR*, Tran LM, Chou KJY, Liao JC 2007 Integrated network analysis identifies nitric oxide response networks and dihydroxyacid dehydratase as a crucial target in Escherichia coli. Proc. Natl. Acad. Sci. USA 104(20):8484-8489. *Equal contributor.
  21. Hyduke DR, Liao JC. 2005 Analysis of nitric oxide donor effectiveness in resistance vessels. Am. J. Physiol. Heart. Circ. Physiol. 288:H2390-9.
  22. Han TH, Qamirani E, Nelson AG, Hyduke DR, Chaudhuri G, Kuo L, Liao JC. 2003 Regulation of nitric oxide consumption by hypoxic red blood cells. Proc. Natl. Acad. Sci. USA 100(21):12504-12509.
  23. Hyduke DR, Rohlin L, Kao KC, Liao JC. 2003 A software package for cDNA microarray data normalization and assessing confidence intervals. OMICS 7(3):227-234.
  24. Joshi MS, Ferguson TB Jr, Han TH, Hyduke DR, Liao JC, Rassaf T, Bryan N, Feelisch M, Lancaster JR Jr. 2002 Nitric oxide is consumed, rather than conserved, by reaction with oxyhemoglobin under physiological conditions. Proc. Natl. Acad. Sci. USA 99(16):10341-10346.
  25. Han TH, Hyduke DR, Vaughn MW, Fukuto JM, Liao JC. 2002 Nitric oxide reaction with red blood cells and hemoglobin under heterogeneous conditions. Proc. Natl. Acad. Sci. USA 99(11):7763-7768.
  26. Huang KT, Han TH, Hyduke DR, Vaughn MW, Van Herle H, Hein TW, Zhang C, Kuo L, Liao JC. 2001 Modulation of nitric oxide bioavailability by erythrocytes. Proc. Natl. Acad. Sci. USA 98(20):11771-11776.
  27. Dombrowski RJ, Lastoskie CM, Hyduke DR. 2001 The Horvath-Kawazoe method revisited. Colloids and Surfaces A 187: 23-39.
  28. Dombrowski RJ, Hyduke DR, Lastoskie CM. 2000 Pore size analysis of activated carbons from argon and nitrogen porosimetry using density functional theory. Langmuir 16 (11): 5041-5050.

Email Address: hyduke at ucsd.edu

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