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Searching the protein interaction space through the MINT database.
Chatr-Aryamontri A, Zanzoni A, Ceol A, Cesareni G. Chatr-Aryamontri A, et al. Methods Mol Biol. 2008;484:305-17. doi: 10.1007/978-1-59745-398-1_20. Methods Mol Biol. 2008. PMID: 18592188
The BioGRID interaction database: 2017 update.
Chatr-Aryamontri A, Oughtred R, Boucher L, Rust J, Chang C, Kolas NK, O'Donnell L, Oster S, Theesfeld C, Sellam A, Stark C, Breitkreutz BJ, Dolinski K, Tyers M. Chatr-Aryamontri A, et al. Nucleic Acids Res. 2017 Jan 4;45(D1):D369-D379. doi: 10.1093/nar/gkw1102. Epub 2016 Dec 14. Nucleic Acids Res. 2017. PMID: 27980099 Free PMC article.
The BioGRID interaction database: 2015 update.
Chatr-Aryamontri A, Breitkreutz BJ, Oughtred R, Boucher L, Heinicke S, Chen D, Stark C, Breitkreutz A, Kolas N, O'Donnell L, Reguly T, Nixon J, Ramage L, Winter A, Sellam A, Chang C, Hirschman J, Theesfeld C, Rust J, Livstone MS, Dolinski K, Tyers M. Chatr-Aryamontri A, et al. Nucleic Acids Res. 2015 Jan;43(Database issue):D470-8. doi: 10.1093/nar/gku1204. Epub 2014 Nov 26. Nucleic Acids Res. 2015. PMID: 25428363 Free PMC article.
Protein interaction data curation: the International Molecular Exchange (IMEx) consortium.
Orchard S, Kerrien S, Abbani S, Aranda B, Bhate J, Bidwell S, Bridge A, Briganti L, Brinkman FS, Cesareni G, Chatr-aryamontri A, Chautard E, Chen C, Dumousseau M, Goll J, Hancock RE, Hannick LI, Jurisica I, Khadake J, Lynn DJ, Mahadevan U, Perfetto L, Raghunath A, Ricard-Blum S, Roechert B, Salwinski L, Stümpflen V, Tyers M, Uetz P, Xenarios I, Hermjakob H. Orchard S, et al. Nat Methods. 2012 Apr;9(4):345-50. doi: 10.1038/nmeth.1931. Nat Methods. 2012. PMID: 22453911 Free PMC article.
How to link ontologies and protein-protein interactions to literature: text-mining approaches and the BioCreative experience.
Krallinger M, Leitner F, Vazquez M, Salgado D, Marcelle C, Tyers M, Valencia A, Chatr-aryamontri A. Krallinger M, et al. Database (Oxford). 2012 Mar 21;2012:bas017. doi: 10.1093/database/bas017. Print 2012. Database (Oxford). 2012. PMID: 22438567 Free PMC article.
The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text.
Krallinger M, Vazquez M, Leitner F, Salgado D, Chatr-Aryamontri A, Winter A, Perfetto L, Briganti L, Licata L, Iannuccelli M, Castagnoli L, Cesareni G, Tyers M, Schneider G, Rinaldi F, Leaman R, Gonzalez G, Matos S, Kim S, Wilbur WJ, Rocha L, Shatkay H, Tendulkar AV, Agarwal S, Liu F, Wang X, Rak R, Noto K, Elkan C, Lu Z, Dogan RI, Fontaine JF, Andrade-Navarro MA, Valencia A. Krallinger M, et al. BMC Bioinformatics. 2011 Oct 3;12 Suppl 8(Suppl 8):S3. doi: 10.1186/1471-2105-12-S8-S3. BMC Bioinformatics. 2011. PMID: 22151929 Free PMC article.
Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions.
Kerrien S, Orchard S, Montecchi-Palazzi L, Aranda B, Quinn AF, Vinod N, Bader GD, Xenarios I, Wojcik J, Sherman D, Tyers M, Salama JJ, Moore S, Ceol A, Chatr-Aryamontri A, Oesterheld M, Stümpflen V, Salwinski L, Nerothin J, Cerami E, Cusick ME, Vidal M, Gilson M, Armstrong J, Woollard P, Hogue C, Eisenberg D, Cesareni G, Apweiler R, Hermjakob H. Kerrien S, et al. BMC Biol. 2007 Oct 9;5:44. doi: 10.1186/1741-7007-5-44. BMC Biol. 2007. PMID: 17925023 Free PMC article.
The minimum information required for reporting a molecular interaction experiment (MIMIx).
Orchard S, Salwinski L, Kerrien S, Montecchi-Palazzi L, Oesterheld M, Stümpflen V, Ceol A, Chatr-aryamontri A, Armstrong J, Woollard P, Salama JJ, Moore S, Wojcik J, Bader GD, Vidal M, Cusick ME, Gerstein M, Gavin AC, Superti-Furga G, Greenblatt J, Bader J, Uetz P, Tyers M, Legrain P, Fields S, Mulder N, Gilson M, Niepmann M, Burgoon L, De Las Rivas J, Prieto C, Perreau VM, Hogue C, Mewes HW, Apweiler R, Xenarios I, Eisenberg D, Cesareni G, Hermjakob H. Orchard S, et al. Nat Biotechnol. 2007 Aug;25(8):894-8. doi: 10.1038/nbt1324. Nat Biotechnol. 2007. PMID: 17687370 Review.
Identification of new substrates of the protein-tyrosine phosphatase PTP1B by Bayesian integration of proteome evidence.
Ferrari E, Tinti M, Costa S, Corallino S, Nardozza AP, Chatraryamontri A, Ceol A, Cesareni G, Castagnoli L. Ferrari E, et al. J Biol Chem. 2011 Feb 11;286(6):4173-85. doi: 10.1074/jbc.M110.157420. Epub 2010 Dec 1. J Biol Chem. 2011. PMID: 21123182 Free PMC article.
MINT, the molecular interaction database: 2009 update.
Ceol A, Chatr Aryamontri A, Licata L, Peluso D, Briganti L, Perfetto L, Castagnoli L, Cesareni G. Ceol A, et al. Nucleic Acids Res. 2010 Jan;38(Database issue):D532-9. doi: 10.1093/nar/gkp983. Epub 2009 Nov 6. Nucleic Acids Res. 2010. PMID: 19897547 Free PMC article.
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