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1.
2.

Network-based prediction of human tissue-specific metabolism.

Shlomi T, Cabili MN, Herrgård MJ, Palsson BØ, Ruppin E.

Nat Biotechnol. 2008 Sep;26(9):1003-10. doi: 10.1038/nbt.1487.

PMID:
18711341
3.

A survey on methods for modeling and analyzing integrated biological networks.

Tenazinha N, Vinga S.

IEEE/ACM Trans Comput Biol Bioinform. 2011 Jul-Aug;8(4):943-58. doi: 10.1109/TCBB.2010.117. Review.

PMID:
21116043
4.

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

Becker SA, Feist AM, Mo ML, Hannum G, Palsson BØ, Herrgard MJ.

Nat Protoc. 2007;2(3):727-38.

PMID:
17406635
5.

Mathematical formalisms based on approximated kinetic representations for modeling genetic and metabolic pathways.

Alves R, Vilaprinyo E, Hernádez-Bermejo B, Sorribas A.

Biotechnol Genet Eng Rev. 2008;25:1-40. Review.

PMID:
21412348
6.
7.

Genome-scale constraint-based modeling of Geobacter metallireducens.

Sun J, Sayyar B, Butler JE, Pharkya P, Fahland TR, Famili I, Schilling CH, Lovley DR, Mahadevan R.

BMC Syst Biol. 2009 Jan 28;3:15. doi: 10.1186/1752-0509-3-15.

8.

Genome-scale metabolic networks.

Terzer M, Maynard ND, Covert MW, Stelling J.

Wiley Interdiscip Rev Syst Biol Med. 2009 Nov-Dec;1(3):285-97. doi: 10.1002/wsbm.37. Review.

PMID:
20835998
9.

Towards kinetic modeling of global metabolic networks: Methylobacterium extorquens AM1 growth as validation.

Ao P, Lee LW, Lidstrom ME, Yin L, Zhu X.

Sheng Wu Gong Cheng Xue Bao. 2008 Jun;24(6):980-94.

PMID:
18807980
10.

Comparing methods for metabolic network analysis and an application to metabolic engineering.

Tomar N, De RK.

Gene. 2013 May 25;521(1):1-14. doi: 10.1016/j.gene.2013.03.017. Epub 2013 Mar 26. Review.

PMID:
23537990
11.

Extraction of elementary rate constants from global network analysis of E. coli central metabolism.

Zhao J, Ridgway D, Broderick G, Kovalenko A, Ellison M.

BMC Syst Biol. 2008 May 7;2:41. doi: 10.1186/1752-0509-2-41.

12.

Prediction of microbial growth rate versus biomass yield by a metabolic network with kinetic parameters.

Adadi R, Volkmer B, Milo R, Heinemann M, Shlomi T.

PLoS Comput Biol. 2012;8(7):e1002575. doi: 10.1371/journal.pcbi.1002575. Epub 2012 Jul 5.

13.

Metabolic reconstruction, constraint-based analysis and game theory to probe genome-scale metabolic networks.

Ruppin E, Papin JA, de Figueiredo LF, Schuster S.

Curr Opin Biotechnol. 2010 Aug;21(4):502-10. doi: 10.1016/j.copbio.2010.07.002. Epub 2010 Aug 6. Review.

PMID:
20692823
14.

From genomes to in silico cells via metabolic networks.

Borodina I, Nielsen J.

Curr Opin Biotechnol. 2005 Jun;16(3):350-5. Review.

PMID:
15961036
15.

Predicting gene essentiality using genome-scale in silico models.

Joyce AR, Palsson BØ.

Methods Mol Biol. 2008;416:433-57. doi: 10.1007/978-1-59745-321-9_30.

PMID:
18392986
16.

Mining, modeling, and evaluation of subnetworks from large biomolecular networks and its comparison study.

Hu X, Ng M, Wu FX, Sokhansanj BA.

IEEE Trans Inf Technol Biomed. 2009 Mar;13(2):184-94. doi: 10.1109/TITB.2008.2007649.

PMID:
19272861
17.

Filling kinetic gaps: dynamic modeling of metabolism where detailed kinetic information is lacking.

Resendis-Antonio O.

PLoS One. 2009;4(3):e4967. doi: 10.1371/journal.pone.0004967. Epub 2009 Mar 23.

18.

Genome-scale modeling and in silico analysis of mouse cell metabolic network.

Selvarasu S, Karimi IA, Ghim GH, Lee DY.

Mol Biosyst. 2010 Jan;6(1):152-61. doi: 10.1039/b912865d. Epub 2009 Sep 2.

PMID:
20024077
19.

Direct coupling of a genome-scale microbial in silico model and a groundwater reactive transport model.

Fang Y, Scheibe TD, Mahadevan R, Garg S, Long PE, Lovley DR.

J Contam Hydrol. 2011 Mar 25;122(1-4):96-103. doi: 10.1016/j.jconhyd.2010.11.007. Epub 2010 Nov 28.

PMID:
21172725
20.

Flux-sum analysis: a metabolite-centric approach for understanding the metabolic network.

Chung BK, Lee DY.

BMC Syst Biol. 2009 Dec 19;3:117. doi: 10.1186/1752-0509-3-117.

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