danielhyduke at gmail.com
Ph.D. Chemical Engineering, University of California, Los Angeles, CA, 2006
Thesis: Nitric Oxide Chemical Biology in a Systems Biology Context
Advisor: James C. Liao, Ph.D.
B.S. Chemical Engineering, Michigan State University, East Lansing, MI 1999
2011-2012 Seed Award from the San Diego Center for Systems Biology, one of the NIGMS-funded National Centers for Systems Biology
2006-2008 National Institutes of Health Ruth L. Kirschstein National Research Service Award – CA009078
2006/2007 Outstanding Ph.D. – Department of Chemical & Biomolecular Engineering, University of California, Los Angeles
2003-2004 National Science Foundation Integrative Graduate Education and Research Traineeship Bioinformatics Fellow – DGE9987641
2011 Jan 3-7 Co-Chair Systems Biology of Host-Pathogen Interactions in Hawaii
2010-Present The openCOBRA Project
2008-Present Systems Biology for EnteroPathogens Center
2013-Present Assistant Professor
Department of Biological Engineering, Utah State University
2011-2013 Project Scientist
2008-2011 Postdoctoral Scholar
Department of Bioenginering, University of California, San Diego
Mentor: Bernhard Ø. Palsson, Ph.D.
2006-2008 Postdoctoral Fellow
Department of Biochemistry and Molecular & Cellular Biology, Georgetown University
Department of Genetics & Complex Diseases, Harvard School of Public Health
Mentor: Al J. Fornace, Jr., M.D.
1999-2006 Graduate Research Assistant, Department of Chemical & Biomolecular Engineering, University of California, Los Angeles
Advisor: James C. Liao, Ph.D.
Investigation of nitric oxide delivery, reactions, and transport in the cardiovascular system.
Systems biology approach to unravel E. coli's responses to reactive nitrogen oxide species.
2000-2004 Teaching Associate, Department of Chemical & Biomolecular Engineering, University of California, Los Angeles
Molecular Biotechnology for Engineers, Chemical Engineering Laboratory I & II
1997-1999 Teaching Assistant, Department of Mathematics, Michigan State University
Precalculus, Calculus I & II
1997-1999 Undergraduate Research Assistant, Department of Chemical Engineering, Michigan State University.
Advisor: Christian M. Lastoskie, Ph. D.
Density Functional Theory Modeling of Adsorption of Methane, Argon, and Carbon Dioxide onto Activated Carbon.
1996-1997 Undergraduate Research Assistant, Department of Civil Engineering, Division of Engineering Research, Michigan State University
- Hyduke DR✝, Laiakis EC, Li HH, Fornace Jr. AJ. Identifying radiation exposure biomarkers from mouse blood transcriptome. Int J Bioinform Res Appl (In Press) ✝Corresponding Author
- Kim YM, Schmidt BJ, Kidwai AS, Jones MB, Deatherage-Kaiser BL, Brewer HM, Mitchell HD, Palsson BO, McDermott JE, Heffron F, Smith RD, Peterson SN, Ansong CK, Hyduke DR, Metz TO, Adkins JN. 2013 Salmonella Modulates Metabolism During Growth under Conditions that Induce Expression of Virulence Genes. Molecular BioSystems. 9:1522-34.
- 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 363:21-41.
- Hyduke DR✝, Lewis NE, Palsson BO. 2013 Analysis of omics data with genome-scale models of metabolism. Mol. BioSyst. 9:167-74. ✝Corresponding Author
- 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
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- Tran LM, Hyduke DR, Liao JC 2010 Trimming of Mammalian Transcriptional Networks using Network Component Analysis BMC Bioinformatics 11(1):511.
- Hyduke DR, Palsson BØ 2010 Towards Genome Scale Signaling Network Reconstructions. Nature Reviews Genetics 11:297-307.
- 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.
- 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.
- 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.
- 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.
- 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.
- Hyduke DR, Liao JC. 2005 Analysis of nitric oxide donor effectiveness in resistance vessels. Am. J. Physiol. Heart. Circ. Physiol. 288:H2390-9.
- 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.
- 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.
- 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.
- 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.
- 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.
- Dombrowski RJ, Lastoskie CM, Hyduke DR. 2001 The Horvath-Kawazoe method revisited. Colloids and Surfaces A 187: 23-39.
- 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.
- Hyduke DR*. 2012 Combining omics data with genome-scale models of metabolism and macromolecular expression. Mass Spectrometry Special Interest Group. 20th Annual International Conference on Intelligent Systems for Molecular Biology. *Invited speaker.
- Hyduke DR, Law GL, Waters KM, McDermott JE, Anderson GA, Owens T, Green R, Ansong C, Metz TO, SmithRD, Systems Virology Center, Katze MG, Center for Systems Biology of Enteropathogens, Adkins JN 2012 Systems Biology Resources for Infectious Disease Research of Enteropathogens, Influenza, and Severe Acute Respiratory Syndrome Associated Coronavirus. American Society for Microbiology 112th General Meeting.
- Lerman JA, Hyduke DR, Latif H, Portnoy VA, Lewis NE, Orth JD, Schrimpe-Rutledge AC, Smith RD, Adkins JN, Zengler K, Palsson BØ 2011 Quantitative genome-scale simulation of molecular biology and metabolism 5th IECA Conference
- Hyduke DR 2011 Virtual transcriptomes with real results: quantitative simulation of molecular biology. San Diego Center for Systems Biology Weekly Meeting.
- Hyduke DR. 2011 The Biology of M/E: Genome-Scale Modeling of Metabolism and Expression. UCSD Complex Networks Seminar
- Hyduke DR*. 2010 Genome-Scale Metabolic Network Reconstructions. NSF Engineering Research Center for Biorenewable Chemicals Webinar Series. *Invited speaker
- Datta K, Johnson MD, Hyduke DR, Trani D, Kallakury B, Doiron K, Forance AJ Jr. 2010 Sustained activation of proliferative pathways and increased mammary gland tumorigenesis with gamma radiation: A mouse model study. Proc Am Ass Can Res Ann Meet 51:318
- Hyduke DR*. 2010 Reconstruction of Genome-Scale Signaling Networks Foundain Mérieux - Systems Biology and Immune Response. *Invited speaker.
- Hyduke DR, Li HH, Park HU, Collins SP, Aubrecht J, Fornace AJ Jr 2008 A Network Based Approach for the Identification of Stress Responses In Lead Compound Transcriptome Profiles AIChE Annual Meeting
- Fornace AJ, Li HH, Hyduke DR, Aubrecht J 2008 Toward agent-specific signatures: Pathway analysis of molecular responses to stress with a systems biology approach Environmental and Molecular Mutagenesis 49(7):518
- Hyduke DR, Jarboe LR, Tran LM, Chou KJY Liao JC. 2007 Integrated Network Analysis Implicates IlvD as the Focal Point for the NO-Induced Stringent Response. ASM General Meeting
- Hyduke DR, Jarboe LR, Tran LM, Liao JC. 2006 Chemogenomic Deduction of Escherichia coli’s Nitric oxide Response Network. AIChE Annual Meeting
- Hyduke DR and Liao JC. 2006 Modeling Delivery of Supplemental Nitric Oxide in Resistance Vessels. AIChE Annual Meeting
- Han TH, Hyduke DR, Fukuto JM, Liao JC, Vaughn MW. 2004 Nitric oxide reaction networks in the vasculature. Abstracts of Papers of the American Chemical Society 227: U49-U49
- Han TH, Huang KT, Hyduke DR, Vaughn MW, van Herle H, Hein TW, Zhang CH, Kuo L, Liao JC. 2002 Modulation of nitric oxide bioavailability by erythrocytes. FASEB Journal 16 (5): A913-A913
- Huang KT, Han TH, Hyduke DR, van Herle H, Vaughn MW, Liao JC. 2002 Modulation of nitric oxide bioavailability by erythrocytes. Nitric Oxide: Biology and Chemistry 6(4):402
- Hyduke DR, Han TH, Liao JC. 2002 Flux dependent reactions of nitric oxide with oxygenated hemoglobin. FASEB Journal 16 (5): A913-A914
- Joshi MS, Ferguson TB Jr., Han TH, Hyduke DR, Liao JC, Rassaf T, Bryan N, Feelish M, Lancaster JR Jr. 2002 Nitric oxide is consumed, rather than conserved, by reaction with oxyhemoglobin under physiological conditions. Nitric Oxide: Biology and Chemistry 6(4):407-408
- METHOD FOR IN SILICO MODELING OF GENE PRODUCT EXPRESSION AND METABOLISM. U.S. Provisional Application Serial No. 61/644,924 filed on May 9, 2012, Daniel Robert Hyduke, Joshua A. Lerman, and Bernhard O. Palsson