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Items: 1 to 20 of 291

1.

Temporal logic patterns for querying dynamic models of cellular interaction networks.

Monteiro PT, Ropers D, Mateescu R, Freitas AT, de Jong H.

Bioinformatics. 2008 Aug 15;24(16):i227-33. doi: 10.1093/bioinformatics/btn275.

PMID:
18689830
2.

GenePro: a Cytoscape plug-in for advanced visualization and analysis of interaction networks.

Vlasblom J, Wu S, Pu S, Superina M, Liu G, Orsi C, Wodak SJ.

Bioinformatics. 2006 Sep 1;22(17):2178-9.

PMID:
16921162
3.

An efficient algorithm for detecting frequent subgraphs in biological networks.

Koyut├╝rk M, Grama A, Szpankowski W.

Bioinformatics. 2004 Aug 4;20 Suppl 1:i200-7.

PMID:
15262800
4.

Fitting a geometric graph to a protein-protein interaction network.

Higham DJ, Rasajski M, Przulj N.

Bioinformatics. 2008 Apr 15;24(8):1093-9. doi: 10.1093/bioinformatics/btn079. Epub 2008 Mar 14.

PMID:
18344248
5.

MMG: a probabilistic tool to identify submodules of metabolic pathways.

Sanguinetti G, Noirel J, Wright PC.

Bioinformatics. 2008 Apr 15;24(8):1078-84. doi: 10.1093/bioinformatics/btn066. Epub 2008 Feb 21.

PMID:
18292114
6.

Validation of qualitative models of genetic regulatory networks by model checking: analysis of the nutritional stress response in Escherichia coli.

Batt G, Ropers D, de Jong H, Geiselmann J, Mateescu R, Page M, Schneider D.

Bioinformatics. 2005 Jun;21 Suppl 1:i19-28.

PMID:
15961457
7.

Artificial gene networks for objective comparison of analysis algorithms.

Mendes P, Sha W, Ye K.

Bioinformatics. 2003 Oct;19 Suppl 2:ii122-9.

PMID:
14534181
8.

Reduced modeling of signal transduction - a modular approach.

Koschorreck M, Conzelmann H, Ebert S, Ederer M, Gilles ED.

BMC Bioinformatics. 2007 Sep 13;8:336.

9.

ProtNet: a tool for stochastic simulations of protein interaction networks dynamics.

Bernaschi M, Castiglione F, Ferranti A, Gavrila C, Tinti M, Cesareni G.

BMC Bioinformatics. 2007 Mar 8;8 Suppl 1:S4.

10.

A global pathway crosstalk network.

Li Y, Agarwal P, Rajagopalan D.

Bioinformatics. 2008 Jun 15;24(12):1442-7. doi: 10.1093/bioinformatics/btn200. Epub 2008 Apr 23.

PMID:
18434343
11.

COPASI--a COmplex PAthway SImulator.

Hoops S, Sahle S, Gauges R, Lee C, Pahle J, Simus N, Singhal M, Xu L, Mendes P, Kummer U.

Bioinformatics. 2006 Dec 15;22(24):3067-74. Epub 2006 Oct 10.

PMID:
17032683
12.

Supervised reconstruction of biological networks with local models.

Bleakley K, Biau G, Vert JP.

Bioinformatics. 2007 Jul 1;23(13):i57-65.

PMID:
17646345
13.

A query language for biological networks.

Leser U.

Bioinformatics. 2005 Sep 1;21 Suppl 2:ii33-9.

PMID:
16204121
14.

Validating module network learning algorithms using simulated data.

Michoel T, Maere S, Bonnet E, Joshi A, Saeys Y, Van den Bulcke T, Van Leemput K, van Remortel P, Kuiper M, Marchal K, Van de Peer Y.

BMC Bioinformatics. 2007 May 3;8 Suppl 2:S5.

15.

Detection of local community structures in complex dynamic networks with random walks.

Thakur GS, Tiwari R, Thai MT, Chen SS, Dress AW.

IET Syst Biol. 2009 Jul;3(4):266-78. doi: 10.1049/iet-syb.2007.0061.

PMID:
19640165
16.

Design and implementation of a tool for translating SBML into the biochemical stochastic pi-calculus.

Eccher C, Priami C.

Bioinformatics. 2006 Dec 15;22(24):3075-81. Epub 2006 Oct 17.

PMID:
17046974
17.

APID2NET: unified interactome graphic analyzer.

Hernandez-Toro J, Prieto C, De las Rivas J.

Bioinformatics. 2007 Sep 15;23(18):2495-7. Epub 2007 Jul 21.

PMID:
17644818
18.

Edge-based scoring and searching method for identifying condition-responsive protein-protein interaction sub-network.

Guo Z, Wang L, Li Y, Gong X, Yao C, Ma W, Wang D, Li Y, Zhu J, Zhang M, Yang D, Rao S, Wang J.

Bioinformatics. 2007 Aug 15;23(16):2121-8. Epub 2007 Jun 1. Erratum in: Bioinformatics. 2009 Jun 15;25(12):1574. Wang, Lei [added]; Rao, Shaoqi [added].

PMID:
17545181
19.

Learning kernels from biological networks by maximizing entropy.

Tsuda K, Noble WS.

Bioinformatics. 2004 Aug 4;20 Suppl 1:i326-33.

PMID:
15262816
20.

Efficient estimation of graphlet frequency distributions in protein-protein interaction networks.

Przulj N, Corneil DG, Jurisica I.

Bioinformatics. 2006 Apr 15;22(8):974-80. Epub 2006 Feb 1.

PMID:
16452112

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