Format
Sort by
Items per page

Send to

Choose Destination

Links from PubMed

Items: 19

1.

PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways.

Mi H, Guo N, Kejariwal A, Thomas PD.

Nucleic Acids Res. 2007 Jan;35(Database issue):D247-52. Epub 2006 Nov 27.

2.

cPath: open source software for collecting, storing, and querying biological pathways.

Cerami EG, Bader GD, Gross BE, Sander C.

BMC Bioinformatics. 2006 Nov 13;7:497.

3.

Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project.

Hucka M, Finney A, Bornstein BJ, Keating SM, Shapiro BE, Matthews J, Kovitz BL, Schilstra MJ, Funahashi A, Doyle JC, Kitano H.

Syst Biol (Stevenage). 2004 Jun;1(1):41-53. Review.

PMID:
17052114
4.

Supporting the SBML layout extension.

Deckard A, Bergmann FT, Sauro HM.

Bioinformatics. 2006 Dec 1;22(23):2966-7. Epub 2006 Oct 11.

PMID:
17038346
5.

A comprehensive map of the toll-like receptor signaling network.

Oda K, Kitano H.

Mol Syst Biol. 2006;2:2006.0015. Epub 2006 Apr 18. Review.

6.

Escalating model sizes and complexities call for standardized forms of representation.

Hucka M, Finney A.

Mol Syst Biol. 2005;1:2005.0011. Epub 2005 May 25. No abstract available.

7.

A comprehensive pathway map of epidermal growth factor receptor signaling.

Oda K, Matsuoka Y, Funahashi A, Kitano H.

Mol Syst Biol. 2005;1:2005.0010. Epub 2005 May 25.

8.

Using process diagrams for the graphical representation of biological networks.

Kitano H, Funahashi A, Matsuoka Y, Oda K.

Nat Biotechnol. 2005 Aug;23(8):961-6.

PMID:
16082367
9.

Text mining for metabolic pathways, signaling cascades, and protein networks.

Hoffmann R, Krallinger M, Andres E, Tamames J, Blaschke C, Valencia A.

Sci STKE. 2005 May 10;2005(283):pe21. Review.

PMID:
15886388
10.

Reactome: a knowledgebase of biological pathways.

Joshi-Tope G, Gillespie M, Vastrik I, D'Eustachio P, Schmidt E, de Bono B, Jassal B, Gopinath GR, Wu GR, Matthews L, Lewis S, Birney E, Stein L.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D428-32.

11.

The Genome Knowledgebase: a resource for biologists and bioinformaticists.

Joshi-Tope G, Vastrik I, Gopinath GR, Matthews L, Schmidt E, Gillespie M, D'Eustachio P, Jassal B, Lewis S, Wu G, Birney E, Stein L.

Cold Spring Harb Symp Quant Biol. 2003;68:237-43. No abstract available.

PMID:
15338623
12.

Pathway databases.

Schaefer CF.

Ann N Y Acad Sci. 2004 May;1020:77-91. Review.

PMID:
15208185
13.

Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration.

Sauro HM, Hucka M, Finney A, Wellock C, Bolouri H, Doyle J, Kitano H.

OMICS. 2003 Winter;7(4):355-72.

PMID:
14683609
14.

Systems biology markup language: Level 2 and beyond.

Finney A, Hucka M.

Biochem Soc Trans. 2003 Dec;31(Pt 6):1472-3.

PMID:
14641091
15.

Cytoscape: a software environment for integrated models of biomolecular interaction networks.

Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T.

Genome Res. 2003 Nov;13(11):2498-504.

16.

Systems biology: understanding cells.

Nurse P.

Nature. 2003 Aug 21;424(6951):883. No abstract available.

PMID:
12931164
17.

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.

Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, Cuellar AA, Dronov S, Gilles ED, Ginkel M, Gor V, Goryanin II, Hedley WJ, Hodgman TC, Hofmeyr JH, Hunter PJ, Juty NS, Kasberger JL, Kremling A, Kummer U, Le Novère N, Loew LM, Lucio D, Mendes P, Minch E, Mjolsness ED, Nakayama Y, Nelson MR, Nielsen PF, Sakurada T, Schaff JC, Shapiro BE, Shimizu TS, Spence HD, Stelling J, Takahashi K, Tomita M, Wagner J, Wang J; SBML Forum.

Bioinformatics. 2003 Mar 1;19(4):524-31.

PMID:
12611808
18.

Systems biology: a brief overview.

Kitano H.

Science. 2002 Mar 1;295(5560):1662-4. Review.

PMID:
11872829
19.

A new approach to decoding life: systems biology.

Ideker T, Galitski T, Hood L.

Annu Rev Genomics Hum Genet. 2001;2:343-72. Review.

PMID:
11701654

Supplemental Content

Support Center