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Items: 1 to 20 of 89

1.

The Alpha Project: a model system for systems biology research.

Yu RC, Resnekov O, Abola AP, Andrews SS, Benjamin KR, Bruck J, Burbulis IE, Colman-Lerner A, Endy D, Gordon A, Holl M, Lok L, Pesce CG, Serra E, Smith RD, Thomson TM, Tsong AE, Brent R.

IET Syst Biol. 2008 Sep;2(5):222-33. doi: 10.1049/iet-syb:20080127. Review.

2.

Integrated analysis of multiple data sources reveals modular structure of biological networks.

Lu H, Shi B, Wu G, Zhang Y, Zhu X, Zhang Z, Liu C, Zhao Y, Wu T, Wang J, Chen R.

Biochem Biophys Res Commun. 2006 Jun 23;345(1):302-9. Epub 2006 Apr 27.

PMID:
16690033
3.

Characterization of degree frequency distribution in protein interaction networks.

Romano SA, Eguia MC.

Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Mar;71(3 Pt 1):031901. Epub 2005 Mar 3.

PMID:
15903453
4.

Dynamic simulation of protein complex formation on a genomic scale.

Beyer A, Wilhelm T.

Bioinformatics. 2005 Apr 15;21(8):1610-6. Epub 2004 Dec 14.

PMID:
15598828
5.

Scaffold number in yeast signaling system sets tradeoff between system output and dynamic range.

Thomson TM, Benjamin KR, Bush A, Love T, Pincus D, Resnekov O, Yu RC, Gordon A, Colman-Lerner A, Endy D, Brent R.

Proc Natl Acad Sci U S A. 2011 Dec 13;108(50):20265-70. doi: 10.1073/pnas.1004042108. Epub 2011 Nov 23.

6.

Towards a genome-scale kinetic model of cellular metabolism.

Smallbone K, Simeonidis E, Swainston N, Mendes P.

BMC Syst Biol. 2010 Jan 28;4:6. doi: 10.1186/1752-0509-4-6.

7.

Inferring network interactions within a cell.

Carter GW.

Brief Bioinform. 2005 Dec;6(4):380-9. Review.

PMID:
16420736
8.

Modeling interactome: scale-free or geometric?

Przulj N, Corneil DG, Jurisica I.

Bioinformatics. 2004 Dec 12;20(18):3508-15. Epub 2004 Jul 29.

PMID:
15284103
9.

Application of Petri net based analysis techniques to signal transduction pathways.

Sackmann A, Heiner M, Koch I.

BMC Bioinformatics. 2006 Nov 2;7:482.

10.

Discover true association rates in multi-protein complex proteomics data sets.

Shen C, Li L, Chen JY.

Proc IEEE Comput Syst Bioinform Conf. 2005:167-74.

PMID:
16447974
11.

Bioinformatics, multiscale modeling and the IUPS Physiome Project.

Hunter PJ, Crampin EJ, Nielsen PM.

Brief Bioinform. 2008 Jul;9(4):333-43. doi: 10.1093/bib/bbn024. Epub 2008 May 13.

PMID:
18477639
12.
13.

Genome-scale analysis of Saccharomyces cerevisiae metabolism and ethanol production in fed-batch culture.

Hjersted JL, Henson MA, Mahadevan R.

Biotechnol Bioeng. 2007 Aug 1;97(5):1190-204.

PMID:
17243146
14.

Yeast pheromone pathway modeling using Petri nets.

Majumdar A, Scott SD, Deogun JS, Harris S.

BMC Bioinformatics. 2014;15 Suppl 7:S13. doi: 10.1186/1471-2105-15-S7-S13. Epub 2014 May 28.

15.

Joint learning of gene functions--a Bayesian network model approach.

Deng X, Geng H, Ali HH.

J Bioinform Comput Biol. 2006 Apr;4(2):217-39.

PMID:
16819781
16.
17.

Systematic planning of genome-scale experiments in poorly studied species.

Guan Y, Dunham M, Caudy A, Troyanskaya O.

PLoS Comput Biol. 2010 Mar 5;6(3):e1000698. doi: 10.1371/journal.pcbi.1000698.

18.

Information flow in interaction networks II: channels, path lengths, and potentials.

Stojmirović A, Yu YK.

J Comput Biol. 2012 Apr;19(4):379-403. doi: 10.1089/cmb.2010.0228. Epub 2012 Mar 12.

19.

Systematic interpretation of genetic interactions using protein networks.

Kelley R, Ideker T.

Nat Biotechnol. 2005 May;23(5):561-6.

20.

Genome-wide system analysis reveals stable yet flexible network dynamics in yeast.

Gustafsson M, Hörnquist M, Björkegren J, Tegnér J.

IET Syst Biol. 2009 Jul;3(4):219-28. doi: 10.1049/iet-syb.2008.0112.

PMID:
19640161

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