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Results: 1 to 20 of 72

1.

NetPath: a public resource of curated signal transduction pathways.

Kandasamy K, Mohan SS, Raju R, Keerthikumar S, Kumar GS, Venugopal AK, Telikicherla D, Navarro JD, Mathivanan S, Pecquet C, Gollapudi SK, Tattikota SG, Mohan S, Padhukasahasram H, Subbannayya Y, Goel R, Jacob HK, Zhong J, Sekhar R, Nanjappa V, Balakrishnan L, Subbaiah R, Ramachandra YL, Rahiman BA, Prasad TS, Lin JX, Houtman JC, Desiderio S, Renauld JC, Constantinescu SN, Ohara O, Hirano T, Kubo M, Singh S, Khatri P, Draghici S, Bader GD, Sander C, Leonard WJ, Pandey A.

Genome Biol. 2010 Jan 12;11(1):R3. doi: 10.1186/gb-2010-11-1-r3.

PMID:
20067622
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

NetSlim: high-confidence curated signaling maps.

Raju R, Nanjappa V, Balakrishnan L, Radhakrishnan A, Thomas JK, Sharma J, Tian M, Palapetta SM, Subbannayya T, Sekhar NR, Muthusamy B, Goel R, Subbannayya Y, Telikicherla D, Bhattacharjee M, Pinto SM, Syed N, Srikanth MS, Sathe GJ, Ahmad S, Chavan SN, Kumar GS, Marimuthu A, Prasad TS, Harsha HC, Rahiman BA, Ohara O, Bader GD, Sujatha Mohan S, Schiemann WP, Pandey A.

Database (Oxford). 2011 Sep 29;2011:bar032. doi: 10.1093/database/bar032. Print 2011.

PMID:
21959865
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Integrating Omics data for signaling pathways, interactome reconstruction, and functional analysis.

Tieri P, de la Fuente A, Termanini A, Franceschi C.

Methods Mol Biol. 2011;719:415-33. doi: 10.1007/978-1-61779-027-0_19.

PMID:
21370095
[PubMed - indexed for MEDLINE]
4.

InnateDB: facilitating systems-level analyses of the mammalian innate immune response.

Lynn DJ, Winsor GL, Chan C, Richard N, Laird MR, Barsky A, Gardy JL, Roche FM, Chan TH, Shah N, Lo R, Naseer M, Que J, Yau M, Acab M, Tulpan D, Whiteside MD, Chikatamarla A, Mah B, Munzner T, Hokamp K, Hancock RE, Brinkman FS.

Mol Syst Biol. 2008;4:218. doi: 10.1038/msb.2008.55. Epub 2008 Sep 2.

PMID:
18766178
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

MILANO--custom annotation of microarray results using automatic literature searches.

Rubinstein R, Simon I.

BMC Bioinformatics. 2005 Jan 20;6:12.

PMID:
15661078
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

A comprehensive curated resource for follicle stimulating hormone signaling.

Telikicherla D, Ambekar A, Palapetta SM, Dwivedi SB, Raju R, Sharma J, Prasad TsK, Ramachandra Y, Mohan SS, Maharudraiah J, Mukherjee S, Pandey A.

BMC Res Notes. 2011 Oct 13;4:408. doi: 10.1186/1756-0500-4-408.

PMID:
21996254
[PubMed]
Free PMC Article
7.

Human Protein Reference Database--2009 update.

Keshava Prasad TS, Goel R, Kandasamy K, Keerthikumar S, Kumar S, Mathivanan S, Telikicherla D, Raju R, Shafreen B, Venugopal A, Balakrishnan L, Marimuthu A, Banerjee S, Somanathan DS, Sebastian A, Rani S, Ray S, Harrys Kishore CJ, Kanth S, Ahmed M, Kashyap MK, Mohmood R, Ramachandra YL, Krishna V, Rahiman BA, Mohan S, Ranganathan P, Ramabadran S, Chaerkady R, Pandey A.

Nucleic Acids Res. 2009 Jan;37(Database issue):D767-72. doi: 10.1093/nar/gkn892. Epub 2008 Nov 6.

PMID:
18988627
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Modeling cell signaling networks.

Eungdamrong NJ, Iyengar R.

Biol Cell. 2004 Jun;96(5):355-62. Review.

PMID:
15207904
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

INOH: ontology-based highly structured database of signal transduction pathways.

Yamamoto S, Sakai N, Nakamura H, Fukagawa H, Fukuda K, Takagi T.

Database (Oxford). 2011 Nov 26;2011:bar052. doi: 10.1093/database/bar052. Print 2011.

PMID:
22120663
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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.

PMID:
17101041
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Associations between HIV and human pathways revealed by protein-protein interactions and correlated gene expression profiles.

Chen KC, Wang TY, Chan CH.

PLoS One. 2012;7(3):e34240. doi: 10.1371/journal.pone.0034240. Epub 2012 Mar 27.

PMID:
22479575
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Automated modelling of signal transduction networks.

Steffen M, Petti A, Aach J, D'haeseleer P, Church G.

BMC Bioinformatics. 2002 Nov 1;3:34.

PMID:
12413400
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Reactome knowledgebase of human biological pathways and processes.

D'Eustachio P.

Methods Mol Biol. 2011;694:49-61. doi: 10.1007/978-1-60761-977-2_4.

PMID:
21082427
[PubMed - indexed for MEDLINE]
14.

Bioinformatics and cellular signaling.

Papin J, Subramaniam S.

Curr Opin Biotechnol. 2004 Feb;15(1):78-81. Review.

PMID:
15102471
[PubMed - indexed for MEDLINE]
15.

Atlas - a data warehouse for integrative bioinformatics.

Shah SP, Huang Y, Xu T, Yuen MM, Ling J, Ouellette BF.

BMC Bioinformatics. 2005 Feb 21;6:34.

PMID:
15723693
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Bioinformatics analyses for signal transduction networks.

Liu W, Li D, Zhu Y, He F.

Sci China C Life Sci. 2008 Nov;51(11):994-1002. doi: 10.1007/s11427-008-0134-5. Epub 2008 Nov 7.

PMID:
18989642
[PubMed - indexed for MEDLINE]
17.

SPIKE: a database of highly curated human signaling pathways.

Paz A, Brownstein Z, Ber Y, Bialik S, David E, Sagir D, Ulitsky I, Elkon R, Kimchi A, Avraham KB, Shiloh Y, Shamir R.

Nucleic Acids Res. 2011 Jan;39(Database issue):D793-9. doi: 10.1093/nar/gkq1167. Epub 2010 Nov 19.

PMID:
21097778
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Biological information: making it accessible and integrated (and trying to make sense of it).

Hubbard T.

Bioinformatics. 2002;18 Suppl 2:S140.

PMID:
12385995
[PubMed - indexed for MEDLINE]
Free Article
19.

Extending signaling pathways with protein-interaction networks. Application to apoptosis.

Planas-Iglesias J, Guney E, García-García J, Robertson KA, Raza S, Freeman TC, Ghazal P, Oliva B.

OMICS. 2012 May;16(5):245-56. doi: 10.1089/omi.2011.0130. Epub 2012 Mar 2.

PMID:
22385281
[PubMed - indexed for MEDLINE]
20.

The mEPN scheme: an intuitive and flexible graphical system for rendering biological pathways.

Freeman TC, Raza S, Theocharidis A, Ghazal P.

BMC Syst Biol. 2010 May 17;4:65. doi: 10.1186/1752-0509-4-65.

PMID:
20478018
[PubMed - indexed for MEDLINE]
Free PMC Article

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