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Items: 33


Development and validation of a high-throughput transcriptomic biomarker to address 21st century genetic toxicology needs.

Li HH, Chen R, Hyduke DR, Williams A, Frötschl R, Ellinger-Ziegelbauer H, O'Lone R, Yauk CL, Aubrecht J, Fornace AJ Jr.

Proc Natl Acad Sci U S A. 2017 Dec 19;114(51):E10881-E10889. doi: 10.1073/pnas.1714109114. Epub 2017 Dec 4.


Do genome-scale models need exact solvers or clearer standards?

Ebrahim A, Almaas E, Bauer E, Bordbar A, Burgard AP, Chang RL, Dräger A, Famili I, Feist AM, Fleming RM, Fong SS, Hatzimanikatis V, Herrgård MJ, Holder A, Hucka M, Hyduke D, Jamshidi N, Lee SY, Le Novère N, Lerman JA, Lewis NE, Ma D, Mahadevan R, Maranas C, Nagarajan H, Navid A, Nielsen J, Nielsen LK, Nogales J, Noronha A, Pal C, Palsson BO, Papin JA, Patil KR, Price ND, Reed JL, Saunders M, Senger RS, Sonnenschein N, Sun Y, Thiele I.

Mol Syst Biol. 2015 Oct 14;11(10):831. doi: 10.15252/msb.20156157. No abstract available.


A predictive toxicogenomics signature to classify genotoxic versus non-genotoxic chemicals in human TK6 cells.

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

Data Brief. 2015 Aug 24;5:77-83. doi: 10.1016/j.dib.2015.08.013. eCollection 2015 Dec.


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 Jul;56(6):505-19. doi: 10.1002/em.21941. Epub 2015 Mar 2.


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 Jul;56(6):520-34. doi: 10.1002/em.21940. Epub 2015 Mar 2.


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 N, Labib S, Bourdon-Lacombe J, Kuo B, Buick JK, Lemieux F, Williams A, Halappanavar S, Malik A, 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. Review.


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.


Studying Salmonellae and Yersiniae host-pathogen interactions using integrated 'omics and modeling.

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, McAteer K, Heffron F, Peterson SN, Motin V, Palsson BO, Smith RD, Adkins JN.

Curr Top Microbiol Immunol. 2013;363:21-41. doi: 10.1007/82_2012_247. Review.


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.


AMP-activated protein kinase promotes human prostate cancer cell growth and survival.

Park HU, Suy S, Danner M, Dailey V, Zhang Y, Li H, Hyduke DR, Collins BT, Gagnon G, Kallakury B, Kumar D, Brown ML, Fornace A, Dritschilo A, Collins SP.

Mol Cancer Ther. 2009 Apr;8(4):733-41. doi: 10.1158/1535-7163.MCT-08-0631.


Determination of the Escherichia coli S-nitrosoglutathione response network using integrated biochemical and systems analysis.

Jarboe LR, Hyduke DR, Tran LM, Chou KJ, Liao JC.

J Biol Chem. 2008 Feb 22;283(8):5148-57. Epub 2007 Dec 10.


Integrated network analysis identifies nitric oxide response networks and dihydroxyacid dehydratase as a crucial target in Escherichia coli.

Hyduke DR, Jarboe LR, Tran LM, Chou KJ, Liao JC.

Proc Natl Acad Sci U S A. 2007 May 15;104(20):8484-9. Epub 2007 May 9.


Analysis of nitric oxide donor effectiveness in resistance vessels.

Hyduke DR, Liao JC.

Am J Physiol Heart Circ Physiol. 2005 May;288(5):H2390-9. Epub 2005 Jan 14.


A software package for cDNA microarray data normalization and assessing confidence intervals.

Hyduke DR, Rohlin L, Kao KC, Liao JC.

OMICS. 2003 Fall;7(3):227-34.


Regulation of nitric oxide consumption by hypoxic red blood cells.

Han TH, Qamirani E, Nelson AG, Hyduke DR, Chaudhuri G, Kuo L, Liao JC.

Proc Natl Acad Sci U S A. 2003 Oct 14;100(21):12504-9. Epub 2003 Oct 1.


Nitric oxide is consumed, rather than conserved, by reaction with oxyhemoglobin under physiological conditions.

Joshi MS, Ferguson TB Jr, Han TH, Hyduke DR, Liao JC, Rassaf T, Bryan N, Feelisch M, Lancaster JR Jr.

Proc Natl Acad Sci U S A. 2002 Aug 6;99(16):10341-6. Epub 2002 Jul 17.


Nitric oxide reaction with red blood cells and hemoglobin under heterogeneous conditions.

Han TH, Hyduke DR, Vaughn MW, Fukuto JM, Liao JC.

Proc Natl Acad Sci U S A. 2002 May 28;99(11):7763-8. Erratum in: Proc Natl Acad Sci U S A 2002 Jul 23;99(15):10227.


Modulation of nitric oxide bioavailability by erythrocytes.

Huang KT, Han TH, Hyduke DR, Vaughn MW, Van Herle H, Hein TW, Zhang C, Kuo L, Liao JC.

Proc Natl Acad Sci U S A. 2001 Sep 25;98(20):11771-6.

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