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Results: 1 to 20 of 29


Development of a toxicogenomics signature for genotoxicity using a dose-optimization and informatics strategy in human cells.

Li HH, Hyduke DR, Chen R, Heard P, Yauk CL, Aubrecht J, Fornace AJ Jr.

Environ Mol Mutagen. 2015 Mar 2. doi: 10.1002/em.21941. [Epub ahead of print]


Integration of metabolic activation with a predictive toxicogenomics signature to classify genotoxic versus nongenotoxic chemicals in human TK6 cells.

Buick JK, Moffat I, Williams A, Swartz CD, Recio L, Hyduke DR, Li HH, Fornace AJ Jr, Aubrecht J, Yauk CL.

Environ Mol Mutagen. 2015 Mar 2. doi: 10.1002/em.21940. [Epub ahead of print]


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.

Moffat I, Chepelev NL, Labib S, Bourdon-Lacombe J, Kuo B, Buick JK, Lemieux F, Williams A, Halappanavar S, Malik AI, Luijten M, Aubrecht J, Hyduke DR, Fornace AJ Jr, Swartz CD, Recio L, Yauk CL.

Crit Rev Toxicol. 2015 Jan;45(1):1-43. doi: 10.3109/10408444.2014.973934.


A systems approach to predict oncometabolites via context-specific genome-scale metabolic networks.

Nam H, Campodonico M, Bordbar A, Hyduke DR, Kim S, Zielinski DC, Palsson BO.

PLoS Comput Biol. 2014 Sep 18;10(9):e1003837. doi: 10.1371/journal.pcbi.1003837. eCollection 2014 Sep.


Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction.

O'Brien EJ, Lerman JA, Chang RL, Hyduke DR, Palsson BØ.

Mol Syst Biol. 2013 Oct 1;9:693. doi: 10.1038/msb.2013.52.


GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data.

Schmidt BJ, Ebrahim A, Metz TO, Adkins JN, Palsson BØ, Hyduke DR.

Bioinformatics. 2013 Nov 15;29(22):2900-8. doi: 10.1093/bioinformatics/btt493. Epub 2013 Aug 23.


COBRApy: COnstraints-Based Reconstruction and Analysis for Python.

Ebrahim A, Lerman JA, Palsson BO, Hyduke DR.

BMC Syst Biol. 2013 Aug 8;7:74. doi: 10.1186/1752-0509-7-74.


Identifying radiation exposure biomarkers from mouse blood transcriptome.

Hyduke DR, Laiakis EC, Li HH, Fornace AJ Jr.

Int J Bioinform Res Appl. 2013;9(4):365-85. doi: 10.1504/IJBRA.2013.054701.


Salmonella modulates metabolism during growth under conditions that induce expression of virulence genes.

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, Adkins JN.

Mol Biosyst. 2013 Jun;9(6):1522-34. doi: 10.1039/c3mb25598k. Epub 2013 Apr 5.


Analysis of omics data with genome-scale models of metabolism.

Hyduke DR, Lewis NE, Palsson BØ.

Mol Biosyst. 2013 Feb 2;9(2):167-74. doi: 10.1039/c2mb25453k. Epub 2012 Dec 18. Review.


Exposure to ionizing radiation induced persistent gene expression changes in mouse mammary gland.

Datta K, Hyduke DR, Suman S, Moon BH, Johnson MD, Fornace AJ Jr.

Radiat Oncol. 2012 Dec 5;7:205. doi: 10.1186/1748-717X-7-205.


In silico method for modelling metabolism and gene product expression at genome scale.

Lerman JA, Hyduke DR, Latif H, Portnoy VA, Lewis NE, Orth JD, Schrimpe-Rutledge AC, Smith RD, Adkins JN, Zengler K, Palsson BO.

Nat Commun. 2012 Jul 3;3:929. doi: 10.1038/ncomms1928.


Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation.

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.

Mol Syst Biol. 2012 Jun 26;8:558. doi: 10.1038/msb.2012.21.


An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92.

Charusanti P, Chauhan S, McAteer K, Lerman JA, Hyduke DR, Motin VL, Ansong C, Adkins JN, Palsson BO.

BMC Syst Biol. 2011 Oct 13;5:163. doi: 10.1186/1752-0509-5-163.


Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0.

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.

Nat Protoc. 2011 Aug 4;6(9):1290-307. doi: 10.1038/nprot.2011.308.


Technologies and approaches to elucidate and model the virulence program of salmonella.

McDermott JE, Yoon H, Nakayasu ES, Metz TO, Hyduke DR, Kidwai AS, Palsson BO, Adkins JN, Heffron F.

Front Microbiol. 2011 Jun 2;2:121. doi: 10.3389/fmicb.2011.00121. eCollection 2011.


A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2.

Thiele I, Hyduke DR, Steeb B, Fankam G, Allen DK, Bazzani S, Charusanti P, Chen FC, Fleming RM, Hsiung CA, De Keersmaecker SC, Liao YC, Marchal K, Mo ML, Özdemir E, Raghunathan A, Reed JL, Shin SI, Sigurbjörnsdóttir S, Steinmann J, Sudarsan S, Swainston N, Thijs IM, Zengler K, Palsson BO, Adkins JN, Bumann D.

BMC Syst Biol. 2011 Jan 18;5:8. doi: 10.1186/1752-0509-5-8.


Trimming of mammalian transcriptional networks using network component analysis.

Tran LM, Hyduke DR, Liao JC.

BMC Bioinformatics. 2010 Oct 13;11:511. doi: 10.1186/1471-2105-11-511.


Towards genome-scale signalling network reconstructions.

Hyduke DR, Palsson BØ.

Nat Rev Genet. 2010 Apr;11(4):297-307. doi: 10.1038/nrg2750. Review.

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