Hyduke DR - Search Results

1

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

Hyduke DR, Lewis NE, Palsson BØ. Hyduke DR, et al. Mol Biosyst. 2013 Feb 2;9(2):167-74. doi: 10.1039/c2mb25453k. Epub 2012 Dec 18. Mol Biosyst. 2013. PMID: 23247105 Free PMC article. Review.

2

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. Ebrahim A, et al. Mol Syst Biol. 2015 Oct 14;11(10):831. doi: 10.15252/msb.20156157. Mol Syst Biol. 2015. PMID: 26467284 Free PMC article. No abstract available.

3

Towards genome-scale signalling network reconstructions.

Hyduke DR, Palsson BØ. Hyduke DR, et al. Nat Rev Genet. 2010 Apr;11(4):297-307. doi: 10.1038/nrg2750. Nat Rev Genet. 2010. PMID: 20177425 Review.

4

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. Bordbar A, et al. Among authors: hyduke dr. Mol Syst Biol. 2012 Jun 26;8:558. doi: 10.1038/msb.2012.21. Mol Syst Biol. 2012. PMID: 22735334 Free PMC article.

5

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. Lerman JA, et al. Among authors: hyduke dr. Nat Commun. 2012 Jul 3;3:929. doi: 10.1038/ncomms1928. Nat Commun. 2012. PMID: 22760628 Free PMC article.

6

COBRApy: COnstraints-Based Reconstruction and Analysis for Python.

Ebrahim A, Lerman JA, Palsson BO, Hyduke DR. Ebrahim A, et al. Among authors: hyduke dr. BMC Syst Biol. 2013 Aug 8;7:74. doi: 10.1186/1752-0509-7-74. BMC Syst Biol. 2013. PMID: 23927696 Free PMC article.

7

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. O'Brien EJ, et al. Among authors: hyduke dr. Mol Syst Biol. 2013 Oct 1;9:693. doi: 10.1038/msb.2013.52. Mol Syst Biol. 2013. PMID: 24084808 Free PMC article.

8

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. Schellenberger J, et al. Among authors: hyduke dr. Nat Protoc. 2011 Aug 4;6(9):1290-307. doi: 10.1038/nprot.2011.308. Nat Protoc. 2011. PMID: 21886097 Free PMC article.

9

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. Charusanti P, et al. Among authors: hyduke dr. BMC Syst Biol. 2011 Oct 13;5:163. doi: 10.1186/1752-0509-5-163. BMC Syst Biol. 2011. PMID: 21995956 Free PMC article.

10

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. Kim YM, et al. Among authors: hyduke dr. Mol Biosyst. 2013 Jun;9(6):1522-34. doi: 10.1039/c3mb25598k. Epub 2013 Apr 5. Mol Biosyst. 2013. PMID: 23559334 Free PMC article.

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