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Daniel R. Hyduke, Ph.D. - Publications

Affiliations: 
2006 University of California, Los Angeles, Los Angeles, CA 
Area:
Chemical and Biomolecular Engineering
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27 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2015 Williams A, Buick JK, Moffat I, Swartz CD, Recio L, Hyduke DR, Li HH, Fornace AJ, Aubrecht J, Yauk CL. A predictive toxicogenomics signature to classify genotoxic versus non-genotoxic chemicals in human TK6 cells. Data in Brief. 5: 77-83. PMID 26425668 DOI: 10.1016/J.Dib.2015.08.013  0.353
2015 Li HH, Hyduke DR, Chen R, Heard P, Yauk CL, Aubrecht J, Fornace AJ. Development of a toxicogenomics signature for genotoxicity using a dose-optimization and informatics strategy in human cells. Environmental and Molecular Mutagenesis. 56: 505-19. PMID 25733355 DOI: 10.1002/Em.21941  0.321
2015 Buick JK, Moffat I, Williams A, Swartz CD, Recio L, Hyduke DR, Li HH, Fornace AJ, Aubrecht J, Yauk CL. Integration of metabolic activation with a predictive toxicogenomics signature to classify genotoxic versus nongenotoxic chemicals in human TK6 cells. Environmental and Molecular Mutagenesis. 56: 520-34. PMID 25733247 DOI: 10.1002/Em.21940  0.328
2014 Nam H, Campodonico M, Bordbar A, Hyduke DR, Kim S, Zielinski DC, Palsson BO. A systems approach to predict oncometabolites via context-specific genome-scale metabolic networks. Plos Computational Biology. 10: e1003837. PMID 25232952 DOI: 10.1371/Journal.Pcbi.1003837  0.317
2013 O'Brien EJ, Lerman JA, Chang RL, Hyduke DR, Palsson BØ. Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction. Molecular Systems Biology. 9: 693. PMID 24084808 DOI: 10.1038/Msb.2013.52  0.322
2013 Schmidt BJ, Ebrahim A, Metz TO, Adkins JN, Palsson BØ, Hyduke DR. GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data. Bioinformatics (Oxford, England). 29: 2900-8. PMID 23975765 DOI: 10.1093/Bioinformatics/Btt493  0.362
2013 Ebrahim A, Lerman JA, Palsson BO, Hyduke DR. COBRApy: COnstraints-Based Reconstruction and Analysis for Python. Bmc Systems Biology. 7: 74. PMID 23927696 DOI: 10.1186/1752-0509-7-74  0.351
2013 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 C, Hyduke DR, Metz TO, et al. Salmonella modulates metabolism during growth under conditions that induce expression of virulence genes. Molecular Biosystems. 9: 1522-34. PMID 23559334 DOI: 10.1039/C3Mb25598K  0.384
2013 Hyduke DR, Lewis NE, Palsson BØ. Analysis of omics data with genome-scale models of metabolism. Molecular Biosystems. 9: 167-74. PMID 23247105 DOI: 10.1039/C2Mb25453K  0.322
2012 Ansong C, Deatherage BL, Hyduke D, Schmidt B, McDermott JE, Jones MB, Chauhan S, Charusanti P, Kim YM, Nakayasu ES, Li J, Kidwai A, Niemann G, Brown RN, Metz TO, et al. Studying Salmonellae and Yersiniae Host–Pathogen Interactions Using Integrated ‘Omics and Modeling Current Topics in Microbiology and Immunology. 363: 21-41. PMID 22886542 DOI: 10.1007/82-2012-247  0.316
2012 Lerman JA, Hyduke DR, Latif H, Portnoy VA, Lewis NE, Orth JD, Schrimpe-Rutledge AC, Smith RD, Adkins JN, Zengler K, Palsson BO. In silico method for modelling metabolism and gene product expression at genome scale. Nature Communications. 3: 929. PMID 22760628 DOI: 10.1038/Ncomms1928  0.337
2012 Bordbar A, Mo ML, Nakayasu ES, Schrimpe-Rutledge AC, Kim YM, Metz TO, Jones MB, Frank BC, Smith RD, Peterson SN, Hyduke DR, Adkins JN, Palsson BO. Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation. Molecular Systems Biology. 8: 558. PMID 22735334 DOI: 10.1038/Msb.2012.21  0.34
2011 Charusanti P, Chauhan S, McAteer K, Lerman JA, Hyduke DR, Motin VL, Ansong C, Adkins JN, Palsson BO. An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92. Bmc Systems Biology. 5: 163. PMID 21995956 DOI: 10.1186/1752-0509-5-163  0.338
2011 Schellenberger J, Que R, Fleming RM, Thiele I, Orth JD, Feist AM, Zielinski DC, Bordbar A, Lewis NE, Rahmanian S, Kang J, Hyduke DR, Palsson BØ. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nature Protocols. 6: 1290-307. PMID 21886097 DOI: 10.1038/Nprot.2011.308  0.315
2011 McDermott JE, Yoon H, Nakayasu ES, Metz TO, Hyduke DR, Kidwai AS, Palsson BO, Adkins JN, Heffron F. Technologies and approaches to elucidate and model the virulence program of salmonella. Frontiers in Microbiology. 2: 121. PMID 21687430 DOI: 10.3389/Fmicb.2011.00121  0.407
2010 Tran LM, Hyduke DR, Liao JC. Trimming of mammalian transcriptional networks using network component analysis. Bmc Bioinformatics. 11: 511. PMID 20942926 DOI: 10.1186/1471-2105-11-511  0.64
2010 Hyduke DR, Palsson BØ. Towards genome-scale signalling network reconstructions. Nature Reviews. Genetics. 11: 297-307. PMID 20177425 DOI: 10.1038/Nrg2750  0.322
2010 Jarboe LR, Hyduke DR, Liao JC. Systems Approaches to Unraveling Nitric Oxide Response Networks in Prokaryotes Nitric Oxide. 103-136. DOI: 10.1016/B978-0-12-373866-0.00004-6  0.672
2008 Jarboe LR, Hyduke DR, Tran LM, Chou KJ, Liao JC. Determination of the Escherichia coli S-nitrosoglutathione response network using integrated biochemical and systems analysis. The Journal of Biological Chemistry. 283: 5148-57. PMID 18070885 DOI: 10.1074/Jbc.M706018200  0.725
2007 Hyduke DR, Jarboe LR, Tran LM, Chou KJ, Liao JC. Integrated network analysis identifies nitric oxide response networks and dihydroxyacid dehydratase as a crucial target in Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America. 104: 8484-9. PMID 17494765 DOI: 10.1073/Pnas.0610888104  0.719
2005 Hyduke DR, Liao JC. Analysis of nitric oxide donor effectiveness in resistance vessels. American Journal of Physiology. Heart and Circulatory Physiology. 288: H2390-9. PMID 15653763 DOI: 10.1152/Ajpheart.00990.2004  0.494
2005 Jarboe LR, Hyduke D, Tran LM, Liao JC. Chemogenomic analysis of signaling pathways for reactive nitrogen oxide species in escherichia coli Aiche Annual Meeting, Conference Proceedings. 10384.  0.659
2003 Hyduke DR, Rohlin L, Kao KC, Liao JC. A software package for cDNA microarray data normalization and assessing confidence intervals. Omics : a Journal of Integrative Biology. 7: 227-34. PMID 14583113 DOI: 10.1089/153623103322452369  0.667
2003 Han TH, Qamirani E, Nelson AG, Hyduke DR, Chaudhuri G, Kuo L, Liao JC. Regulation of nitric oxide consumption by hypoxic red blood cells. Proceedings of the National Academy of Sciences of the United States of America. 100: 12504-9. PMID 14523233 DOI: 10.1073/Pnas.2133409100  0.596
2002 Joshi MS, Ferguson TB, Han TH, Hyduke DR, Liao JC, Rassaf T, Bryan N, Feelisch M, Lancaster JR. Nitric oxide is consumed, rather than conserved, by reaction with oxyhemoglobin under physiological conditions. Proceedings of the National Academy of Sciences of the United States of America. 99: 10341-6. PMID 12124398 DOI: 10.1073/Pnas.152149699  0.591
2002 Han TH, Hyduke DR, Vaughn MW, Fukuto JM, Liao JC. Nitric oxide reaction with red blood cells and hemoglobin under heterogeneous conditions. Proceedings of the National Academy of Sciences of the United States of America. 99: 7763-8. PMID 12032357 DOI: 10.1073/Pnas.122118299  0.602
2001 Huang KT, Han TH, Hyduke DR, Vaughn MW, Van Herle H, Hein TW, Zhang C, Kuo L, Liao JC. Modulation of nitric oxide bioavailability by erythrocytes. Proceedings of the National Academy of Sciences of the United States of America. 98: 11771-6. PMID 11573011 DOI: 10.1073/Pnas.201276698  0.589
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