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Results: 1 to 20 of 25

1.

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.

PMID:
24084808
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

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.

PMID:
23975765
[PubMed - indexed for MEDLINE]
3.

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.

PMID:
23927696
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

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.

PMID:
23797995
[PubMed - indexed for MEDLINE]
5.

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.

PMID:
23559334
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

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.

PMID:
23247105
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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.

PMID:
23216862
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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.

PMID:
22760628
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

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.

PMID:
22735334
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Comparison of mouse urinary metabolic profiles after exposure to the inflammatory stressors γ radiation and lipopolysaccharide.

Laiakis EC, Hyduke DR, Fornace AJ.

Radiat Res. 2012 Feb;177(2):187-99. Epub 2011 Nov 30.

PMID:
22128784
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

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.

PMID:
21995956
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

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.

PMID:
21886097
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

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.

PMID:
21687430
[PubMed]
Free PMC Article
14.

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.

PMID:
21244678
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

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.

PMID:
20942926
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Towards genome-scale signalling network reconstructions.

Hyduke DR, Palsson BØ.

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

PMID:
20177425
[PubMed - indexed for MEDLINE]
17.

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.

PMID:
19372545
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

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.

PMID:
18070885
[PubMed - indexed for MEDLINE]
Free Article
19.

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.

PMID:
17494765
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

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.

PMID:
15653763
[PubMed - indexed for MEDLINE]
Free Article

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