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Results: 1 to 20 of 230

1.

Installing a local copy of the Reactome Web site and database.

Vastrik I.

Curr Protoc Bioinformatics. 2008 Mar;Chapter 9:Unit 9.10. doi: 10.1002/0471250953.bi0910s21.

PMID:
18428688
[PubMed - indexed for MEDLINE]
2.

Using the Reactome database.

Stein LD.

Curr Protoc Bioinformatics. 2004 Oct;Chapter 8:Unit 8.7. doi: 10.1002/0471250953.bi0807s7.

PMID:
18428737
[PubMed - indexed for MEDLINE]
3.

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.

PMID:
15608231
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

PATIKAweb: a Web interface for analyzing biological pathways through advanced querying and visualization.

Dogrusoz U, Erson EZ, Giral E, Demir E, Babur O, Cetintas A, Colak R.

Bioinformatics. 2006 Feb 1;22(3):374-5. Epub 2005 Nov 15.

PMID:
16287939
[PubMed - indexed for MEDLINE]
Free Article
5.

Searching, viewing, and visualizing data in the Biomolecular Interaction Network Database (BIND).

Willis RC, Hogue CW.

Curr Protoc Bioinformatics. 2006 Jan;Chapter 8:Unit 8.9. doi: 10.1002/0471250953.bi0809s12.

PMID:
18428770
[PubMed - indexed for MEDLINE]
6.

Searching the MINT database for protein interaction information.

Cesareni G, Chatr-aryamontri A, Licata L, Ceol A.

Curr Protoc Bioinformatics. 2008 Jun;Chapter 8:Unit 8.5. doi: 10.1002/0471250953.bi0805s22. Review.

PMID:
18551417
[PubMed - indexed for MEDLINE]
7.

IntAct--open source resource for molecular interaction data.

Kerrien S, Alam-Faruque Y, Aranda B, Bancarz I, Bridge A, Derow C, Dimmer E, Feuermann M, Friedrichsen A, Huntley R, Kohler C, Khadake J, Leroy C, Liban A, Lieftink C, Montecchi-Palazzi L, Orchard S, Risse J, Robbe K, Roechert B, Thorneycroft D, Zhang Y, Apweiler R, Hermjakob H.

Nucleic Acids Res. 2007 Jan;35(Database issue):D561-5. Epub 2006 Dec 1.

PMID:
17145710
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Online predicted human interaction database.

Brown KR, Jurisica I.

Bioinformatics. 2005 May 1;21(9):2076-82. Epub 2005 Jan 18.

PMID:
15657099
[PubMed - indexed for MEDLINE]
Free Article
9.

Human protein reference database--2006 update.

Mishra GR, Suresh M, Kumaran K, Kannabiran N, Suresh S, Bala P, Shivakumar K, Anuradha N, Reddy R, Raghavan TM, Menon S, Hanumanthu G, Gupta M, Upendran S, Gupta S, Mahesh M, Jacob B, Mathew P, Chatterjee P, Arun KS, Sharma S, Chandrika KN, Deshpande N, Palvankar K, Raghavnath R, Krishnakanth R, Karathia H, Rekha B, Nayak R, Vishnupriya G, Kumar HG, Nagini M, Kumar GS, Jose R, Deepthi P, Mohan SS, Gandhi TK, Harsha HC, Deshpande KS, Sarker M, Prasad TS, Pandey A.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D411-4.

PMID:
16381900
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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
[PubMed - indexed for MEDLINE]
Free Article
11.

Predicting the interactome of Xanthomonas oryzae pathovar oryzae for target selection and DB service.

Kim JG, Park D, Kim BC, Cho SW, Kim YT, Park YJ, Cho HJ, Park H, Kim KB, Yoon KO, Park SJ, Lee BM, Bhak J.

BMC Bioinformatics. 2008 Jan 24;9:41. doi: 10.1186/1471-2105-9-41.

PMID:
18215330
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

POINT: a database for the prediction of protein-protein interactions based on the orthologous interactome.

Huang TW, Tien AC, Huang WS, Lee YC, Peng CL, Tseng HH, Kao CY, Huang CY.

Bioinformatics. 2004 Nov 22;20(17):3273-6. Epub 2004 Jun 24.

PMID:
15217821
[PubMed - indexed for MEDLINE]
Free Article
13.

Reactome pathway analysis to enrich biological discovery in proteomics data sets.

Haw R, Hermjakob H, D'Eustachio P, Stein L.

Proteomics. 2011 Sep;11(18):3598-613. doi: 10.1002/pmic.201100066.

PMID:
21751369
[PubMed - indexed for MEDLINE]
14.

The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases.

Côté RG, Jones P, Martens L, Kerrien S, Reisinger F, Lin Q, Leinonen R, Apweiler R, Hermjakob H.

BMC Bioinformatics. 2007 Oct 18;8:401.

PMID:
17945017
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

PathAligner: metabolic pathway retrieval and alignment.

Chen M, Hofestädt R.

Appl Bioinformatics. 2004;3(4):241-52.

PMID:
15702955
[PubMed - indexed for MEDLINE]
16.

soaPDB: a web application for searching the Protein Data Bank, organizing results, and receiving automatic email alerts.

Lesburg CA, Duca JS.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W252-4. doi: 10.1093/nar/gkn270. Epub 2008 May 16.

PMID:
18487276
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

The Molecule Pages database.

Saunders B, Lyon S, Day M, Riley B, Chenette E, Subramaniam S, Vadivelu I.

Nucleic Acids Res. 2008 Jan;36(Database issue):D700-6. Epub 2007 Oct 26. Erratum in: Nucleic Acids Res.2008 Apr;36(7): 2457.

PMID:
17965093
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

MedicCyc: a biochemical pathway database for Medicago truncatula.

Urbanczyk-Wochniak E, Sumner LW.

Bioinformatics. 2007 Jun 1;23(11):1418-23. Epub 2007 Mar 7.

PMID:
17344243
[PubMed - indexed for MEDLINE]
Free Article
19.

Presenting and exploring biological pathways with PathVisio.

van Iersel MP, Kelder T, Pico AR, Hanspers K, Coort S, Conklin BR, Evelo C.

BMC Bioinformatics. 2008 Sep 25;9:399. doi: 10.1186/1471-2105-9-399.

PMID:
18817533
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Genome Projector: zoomable genome map with multiple views.

Arakawa K, Tamaki S, Kono N, Kido N, Ikegami K, Ogawa R, Tomita M.

BMC Bioinformatics. 2009 Jan 23;10:31. doi: 10.1186/1471-2105-10-31.

PMID:
19166610
[PubMed - indexed for MEDLINE]
Free PMC Article

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