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D. Hyduke · SciRah

Researcher profile · Semantic Scholar

D. Hyduke

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D. Hyduke — researcher profile on SciRah

h-index: 31
Works: 47
Citations: 6,971

Most-cited papers

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0
Jan Schellenberger, Richard A. Que, R. Fleming, I. Thiele +9 more
2007Nature Protocols1,782 citations Open access
Semantic Scholar
COBRApy: COnstraints-Based Reconstruction and Analysis for Python
A. Ebrahim, J. Lerman, B. Palsson, D. Hyduke
2013BMC Systems Biology1,302 citations Open access
Semantic Scholar
Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction
Edward J. O'Brien, J. Lerman, Roger L. Chang, D. Hyduke +1 more
2013Molecular Systems Biology504 citations Open access
Semantic Scholar
In silico method for modelling metabolism and gene product expression at genome scale
J. Lerman, D. Hyduke, Haythem Latif, Vasiliy Portnoy +7 more
2012Nature Communications287 citations Open access
Semantic Scholar
SBML Level 3: an extensible format for the exchange and reuse of biological models
Sarah M. Keating, D. Waltemath, Matthias König, Feng-Kai Zhang +137 more
2020Molecular Systems Biology269 citations Open access
Semantic Scholar
Nitric oxide is consumed, rather than conserved, by reaction with oxyhemoglobin under physiological conditions
M. Joshi, T. Ferguson, T. H. Han, D. Hyduke +5 more
2002Proceedings of the National Academy of Sciences of the United States of America211 citations Open access
Semantic Scholar
AMP-Activated Protein Kinase Promotes Human Prostate Cancer Cell Growth and Survival
H. U. Park, S. Suy, M. Danner, V. Dailey +11 more
2009Molecular Cancer Therapeutics200 citations Open access
Semantic Scholar
Analysis of omics data with genome-scale models of metabolism
D. Hyduke, Nathan E. Lewis, B. Palsson
2012Molecular Biosystems191 citations Open access
Semantic Scholar
Modulation of nitric oxide bioavailability by erythrocytes
Kuang‐Tse Huang, T. H. Han, D. Hyduke, Mark W Vaughn +5 more
2001Proceedings of the National Academy of Sciences of the United States of America184 citations Open access
Semantic Scholar
Integrated network analysis identifies nitric oxide response networks and dihydroxyacid dehydratase as a crucial target in Escherichia coli
D. Hyduke, L. Jarboe, Linh M. Tran, Katherine J. Chou +1 more
2007Proceedings of the National Academy of Sciences of the United States of America163 citations Open access
Semantic Scholar
Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation
A. Bordbar, Monica L. Mo, E. Nakayasu, Alexandra C Schrimpe-Rutledge +9 more
2012Molecular Systems Biology161 citations Open access
Semantic Scholar
A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2
I. Thiele, D. Hyduke, Benjamin Steeb, Guy Fankam +23 more
2011BMC Systems Biology161 citations Open access
Semantic Scholar
Comparison of toxicogenomics and traditional approaches to inform mode of action and points of departure in human health risk assessment of benzo[a]pyrene in drinking water
I. Moffat, N. Chepelev, S. Labib, J. Bourdon-Lacombe +13 more
2015Critical Reviews in Toxicology137 citations Open access
Semantic Scholar
GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data
B. Schmidt, A. Ebrahim, T. Metz, J. Adkins +2 more
2013Bioinform.137 citations Open access
Semantic Scholar
Towards genome-scale signalling-network reconstructions
D. Hyduke, B. Palsson
2010Nature reviews genetics133 citations
Semantic Scholar
Pore size analysis of activated carbons from argon and nitrogen porosimetry using density functional theory
Robert J. Dombrowski, D. Hyduke, C. Lastoskie
2000113 citations
Semantic Scholar
Nitric oxide reaction with red blood cells and hemoglobin under heterogeneous conditions
T. H. Han, D. Hyduke, Mark W Vaughn, J. Fukuto +1 more
2002Proceedings of the National Academy of Sciences of the United States of America106 citations Open access
Semantic Scholar
Development and validation of a high-throughput transcriptomic biomarker to address 21st century genetic toxicology needs
Heng-Hong Li, Ren-Xiang Chen, D. Hyduke, Andrew Williams +6 more
2017Proceedings of the National Academy of Sciences of the United States of America89 citations Open access
Semantic Scholar
Development of a toxicogenomics signature for genotoxicity using a dose-optimization and informatics strategy in human cells
Heng-Hong Li, D. Hyduke, Ren-Xiang Chen, P. Heard +3 more
2015Environmental and Molecular Mutagenesis88 citations Open access
Semantic Scholar
The Horvath–Kawazoe method revisited
Robert J. Dombrowski, C. Lastoskie, D. Hyduke
200176 citations
Semantic Scholar
A Systems Approach to Predict Oncometabolites via Context-Specific Genome-Scale Metabolic Networks
Hojung Nam, M. Campodonico, A. Bordbar, D. Hyduke +3 more
2014PLoS Comput. Biol.68 citations Open access
Semantic Scholar
Do genome-scale models need exact solvers or clearer standards?
A. Ebrahim, E. Almaas, Eugen Bauer, A. Bordbar +37 more
2015Molecular Systems Biology66 citations Open access
Semantic Scholar
Regulation of nitric oxide consumption by hypoxic red blood cells
T. H. Han, Erion Qamirani, Allyson G. Nelson, D. Hyduke +3 more
2003Proceedings of the National Academy of Sciences of the United States of America59 citations Open access
Semantic Scholar
Salmonella Modulates Metabolism during Growth under Conditions that Induce Expression of Virulence Genes
Young-Mo Kim, B. Schmidt, Afshan S. Kidwai, Marcus B. Jones +12 more
2013Molecular Biosystems56 citations Open access
Semantic Scholar
Comparison of Mouse Urinary Metabolic Profiles after Exposure to the Inflammatory Stressors γ Radiation and Lipopolysaccharide
E. Laiakis, D. Hyduke, A. Fornace
2011Radiation Research54 citations Open access
Semantic Scholar
Integration of metabolic activation with a predictive toxicogenomics signature to classify genotoxic versus nongenotoxic chemicals in human TK6 cells
Julie K. Buick, I. Moffat, Andrew Williams, C. Swartz +6 more
2015Environmental and Molecular Mutagenesis52 citations Open access
Semantic Scholar
An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92
Pep Charusanti, Sadhana Chauhan, K. Mcateer, J. Lerman +5 more
2011BMC Systems Biology46 citations Open access
Semantic Scholar
Determination of the Escherichia coli S-Nitrosoglutathione Response Network Using Integrated Biochemical and Systems Analysis*
L. Jarboe, D. Hyduke, Linh M. Tran, Katherine J. Chou +1 more
2008Journal of Biological Chemistry43 citations Open access
Semantic Scholar
TGx-DDI, a Transcriptomic Biomarker for Genotoxicity Hazard Assessment of Pharmaceuticals and Environmental Chemicals
Heng-Hong Li, C. Yauk, Ren-Xiang Chen, D. Hyduke +6 more
2019Frontiers in Big Data41 citations Open access
Semantic Scholar
COBRA Toolbox 2.0
D. Hyduke, Jan Schellenberger, Richard A. Que, R. Fleming +9 more
201139 citations Open access
Semantic Scholar
Exposure to ionizing radiation induced persistent gene expression changes in mouse mammary gland
Kamal Datta, D. Hyduke, S. Suman, Bo-Hyun Moon +2 more
2012Radiation Oncology33 citations Open access
Semantic Scholar
Technologies and Approaches to Elucidate and Model the Virulence Program of Salmonella
J. Mcdermott, Hyunjin Yoon, E. Nakayasu, T. Metz +5 more
2011Front. Microbio.26 citations Open access
Semantic Scholar
Trimming of mammalian transcriptional networks using network component analysis
Linh M. Tran, D. Hyduke, J. Liao
2010BMC Bioinformatics20 citations Open access
Semantic Scholar
A Software Package for cDNA Microarray Data Normalization and Assessing Confidence Intervals
D. Hyduke, L. Rohlin, Katy C. Kao, J. Liao
2003Omics19 citations
Semantic Scholar
A predictive toxicogenomics signature to classify genotoxic versus non-genotoxic chemicals in human TK6 cells
Andrew Williams, Julie K. Buick, I. Moffat, C. Swartz +6 more
2015Data in Brief17 citations Open access
Semantic Scholar
Identifying radiation exposure biomarkers from mouse blood transcriptome
D. Hyduke, E. Laiakis, Heng-Hong Li, A. Fornace
2013International Journal of Bioinformatics Research and Applications13 citations Open access
Semantic Scholar
Studying Salmonellae and Yersiniae Host–Pathogen Interactions Using Integrated ‘Omics and Modeling
C. Ansong, B. Deatherage, D. Hyduke, B. Schmidt +18 more
2012Current Topics in Microbiology and Immunology11 citations Open access
Semantic Scholar
Analysis of nitric oxide donor effectiveness in resistance vessels.
D. Hyduke, J. Liao
2005American Journal of Physiology. Heart and Circulatory Physiology9 citations
Semantic Scholar
Systems Approaches to Unraveling Nitric Oxide Response Networks in Prokaryotes
L. Jarboe, D. Hyduke, J. Liao
20108 citations
Semantic Scholar
Complexity of Stress Signaling
D. Hyduke, S. Amundson, A. Fornace
20102 citations
Semantic Scholar
Exposure to ionizing radiation induced persistent gene expression changes in mouse mammary gland
Kamal Datta, D. Hyduke, S. Suman, Bo-Hyun Moon +2 more
2012Radiation Oncology1 citations Open access
Semantic Scholar
Identification of aberrant pathway and network activity from high-throughput data.
P. Braun, D. Hyduke
2011Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing1 citations
Semantic Scholar
vesselsof nitric oxide donor effectiveness in resistance
D. Hyduke, J. Liao
20160 citations
Semantic Scholar
Developing omics-based approaches for short-and long-term space radiation risk assessment Posted : 8 / 5 / 2014
Kamal Datta, S. Suman, D. Hyduke, J. Shay +1 more
20140 citations
Semantic Scholar
Session introduction
J. Mcdermott, P. Braun, Richard Bonneau, D. Hyduke
2011Pacific Symposium on Biocomputing0 citations
Semantic Scholar
Abstract 1323: Sustained activation of proliferative pathways and increased mammary gland tumorigenesis with γ radiation: A mouse model study
Kamal Datta, M. Johnson, D. Hyduke, D. Trani +3 more
20100 citations
Semantic Scholar
Identification of escherichia coli’s reactive nitrogen oxide species sensing circuits
D. Hyduke, L. Jarboe, Linh M. Tran, J. Liao
20060 citations
Semantic Scholar

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