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Signaling gateway molecule pages--a data model perspective.

Dinasarapu AR, Saunders B, Ozerlat I, Azam K, Subramaniam S.

Bioinformatics. 2011 Jun 15;27(12):1736-8. doi: 10.1093/bioinformatics/btr190. Epub 2011 Apr 19.


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.


Qualitative translation of relations from BioPAX to SBML qual.

Büchel F, Wrzodek C, Mittag F, Dräger A, Eichner J, Rodriguez N, Le Novère N, Zell A.

Bioinformatics. 2012 Oct 15;28(20):2648-53. doi: 10.1093/bioinformatics/bts508. Epub 2012 Aug 24.


SIGNOR: a database of causal relationships between biological entities.

Perfetto L, Briganti L, Calderone A, Cerquone Perpetuini A, Iannuccelli M, Langone F, Licata L, Marinkovic M, Mattioni A, Pavlidou T, Peluso D, Petrilli LL, Pirrò S, Posca D, Santonico E, Silvestri A, Spada F, Castagnoli L, Cesareni G.

Nucleic Acids Res. 2016 Jan 4;44(D1):D548-54. doi: 10.1093/nar/gkv1048. Epub 2015 Oct 13.


Allosteric conformational barcodes direct signaling in the cell.

Nussinov R, Ma B, Tsai CJ, Csermely P.

Structure. 2013 Sep 3;21(9):1509-21. doi: 10.1016/j.str.2013.06.002. Review.


PID: the Pathway Interaction Database.

Schaefer CF, Anthony K, Krupa S, Buchoff J, Day M, Hannay T, Buetow KH.

Nucleic Acids Res. 2009 Jan;37(Database issue):D674-9. doi: 10.1093/nar/gkn653. Epub 2008 Oct 2.


PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse.

Hornbeck PV, Kornhauser JM, Tkachev S, Zhang B, Skrzypek E, Murray B, Latham V, Sullivan M.

Nucleic Acids Res. 2012 Jan;40(Database issue):D261-70. doi: 10.1093/nar/gkr1122. Epub 2011 Dec 1.


Modeling of cell signaling pathways in macrophages by semantic networks.

Hsing M, Bellenson JL, Shankey C, Cherkasov A.

BMC Bioinformatics. 2004 Oct 19;5:156.


JXP4BIGI: a generalized, Java XML-based approach for biological information gathering and integration.

Huang Y, Ni T, Zhou L, Su S.

Bioinformatics. 2003 Dec 12;19(18):2351-8.


SACS--self-maintaining database of antibody crystal structure information.

Allcorn LC, Martin AC.

Bioinformatics. 2002 Jan;18(1):175-81.


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.


PDTD: a web-accessible protein database for drug target identification.

Gao Z, Li H, Zhang H, Liu X, Kang L, Luo X, Zhu W, Chen K, Wang X, Jiang H.

BMC Bioinformatics. 2008 Feb 19;9:104. doi: 10.1186/1471-2105-9-104.


Unique intracellular trafficking processes associated with neural cell adhesion molecule and its intracellular signaling.

Chen Y, Tang BL.

Cell Commun Adhes. 2010 Aug;17(4-6):69-74. doi: 10.3109/15419061.2010.549976. Epub 2011 Jan 19.


hiPathDB: a human-integrated pathway database with facile visualization.

Yu N, Seo J, Rho K, Jang Y, Park J, Kim WK, Lee S.

Nucleic Acids Res. 2012 Jan;40(Database issue):D797-802. doi: 10.1093/nar/gkr1127. Epub 2011 Nov 28.


Bioinformatics and cellular signaling.

Papin J, Subramaniam S.

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


SBRML: a markup language for associating systems biology data with models.

Dada JO, Spasić I, Paton NW, Mendes P.

Bioinformatics. 2010 Apr 1;26(7):932-8. doi: 10.1093/bioinformatics/btq069. Epub 2010 Feb 21.


Cleavage of the signaling mucin Msb2 by the aspartyl protease Yps1 is required for MAPK activation in yeast.

Vadaie N, Dionne H, Akajagbor DS, Nickerson SR, Krysan DJ, Cullen PJ.

J Cell Biol. 2008 Jun 30;181(7):1073-81. doi: 10.1083/jcb.200704079.

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