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Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae.

Reguly T, Breitkreutz A, Boucher L, Breitkreutz BJ, Hon GC, Myers CL, Parsons A, Friesen H, Oughtred R, Tong A, Stark C, Ho Y, Botstein D, Andrews B, Boone C, Troyanskya OG, Ideker T, Dolinski K, Batada NN, Tyers M.

J Biol. 2006;5(4):11. doi: 10.1186/jbiol36. Epub 2006 Jun 8.


The BioGRID Interaction Database: 2008 update.

Breitkreutz BJ, Stark C, Reguly T, Boucher L, Breitkreutz A, Livstone M, Oughtred R, Lackner DH, Bähler J, Wood V, Dolinski K, Tyers M.

Nucleic Acids Res. 2008 Jan;36(Database issue):D637-40. Epub 2007 Nov 13.


The BioGRID Interaction Database: 2011 update.

Stark C, Breitkreutz BJ, Chatr-Aryamontri A, Boucher L, Oughtred R, Livstone MS, Nixon J, Van Auken K, Wang X, Shi X, Reguly T, Rust JM, Winter A, Dolinski K, Tyers M.

Nucleic Acids Res. 2011 Jan;39(Database issue):D698-704. doi: 10.1093/nar/gkq1116. Epub 2010 Nov 11.


BioGRID: a general repository for interaction datasets.

Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D535-9.


The BioGRID interaction database: 2013 update.

Chatr-Aryamontri A, Breitkreutz BJ, Heinicke S, Boucher L, Winter A, Stark C, Nixon J, Ramage L, Kolas N, O'Donnell L, Reguly T, Breitkreutz A, Sellam A, Chen D, Chang C, Rust J, Livstone M, Oughtred R, Dolinski K, Tyers M.

Nucleic Acids Res. 2013 Jan;41(Database issue):D816-23. doi: 10.1093/nar/gks1158. Epub 2012 Nov 30.


BioGRID: A Resource for Studying Biological Interactions in Yeast.

Oughtred R, Chatr-aryamontri A, Breitkreutz BJ, Chang CS, Rust JM, Theesfeld CL, Heinicke S, Breitkreutz A, Chen D, Hirschman J, Kolas N, Livstone MS, Nixon J, O'Donnell L, Ramage L, Winter A, Reguly T, Sellam A, Stark C, Boucher L, Dolinski K, Tyers M.

Cold Spring Harb Protoc. 2016 Jan 4;2016(1):pdb.top080754. doi: 10.1101/pdb.top080754.


Is newer better?--evaluating the effects of data curation on integrated analyses in Saccharomyces cerevisiae.

James K, Wipat A, Hallinan J.

Integr Biol (Camb). 2012 Jul;4(7):715-27. doi: 10.1039/c2ib00123c. Epub 2012 Apr 23.


New insights into protein-protein interaction data lead to increased estimates of the S. cerevisiae interactome size.

Sambourg L, Thierry-Mieg N.

BMC Bioinformatics. 2010 Dec 21;11:605. doi: 10.1186/1471-2105-11-605.


Reconstruction of the yeast protein-protein interaction network involved in nutrient sensing and global metabolic regulation.

Nandy SK, Jouhten P, Nielsen J.

BMC Syst Biol. 2010 May 25;4:68. doi: 10.1186/1752-0509-4-68.


MPI-LIT: a literature-curated dataset of microbial binary protein--protein interactions.

Rajagopala SV, Goll J, Gowda ND, Sunil KC, Titz B, Mukherjee A, Mary SS, Raviswaran N, Poojari CS, Ramachandra S, Shtivelband S, Blazie SM, Hofmann J, Uetz P.

Bioinformatics. 2008 Nov 15;24(22):2622-7. doi: 10.1093/bioinformatics/btn481. Epub 2008 Sep 11.


Mining protein networks for synthetic genetic interactions.

Paladugu SR, Zhao S, Ray A, Raval A.

BMC Bioinformatics. 2008 Oct 9;9:426. doi: 10.1186/1471-2105-9-426.


The genetic landscape of a cell.

Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear ED, Sevier CS, Ding H, Koh JL, Toufighi K, Mostafavi S, Prinz J, St Onge RP, VanderSluis B, Makhnevych T, Vizeacoumar FJ, Alizadeh S, Bahr S, Brost RL, Chen Y, Cokol M, Deshpande R, Li Z, Lin ZY, Liang W, Marback M, Paw J, San Luis BJ, Shuteriqi E, Tong AH, van Dyk N, Wallace IM, Whitney JA, Weirauch MT, Zhong G, Zhu H, Houry WA, Brudno M, Ragibizadeh S, Papp B, Pál C, Roth FP, Giaever G, Nislow C, Troyanskaya OG, Bussey H, Bader GD, Gingras AC, Morris QD, Kim PM, Kaiser CA, Myers CL, Andrews BJ, Boone C.

Science. 2010 Jan 22;327(5964):425-31. doi: 10.1126/science.1180823.


Saccharomyces genome database provides new regulation data.

Costanzo MC, Engel SR, Wong ED, Lloyd P, Karra K, Chan ET, Weng S, Paskov KM, Roe GR, Binkley G, Hitz BC, Cherry JM.

Nucleic Acids Res. 2014 Jan;42(Database issue):D717-25. doi: 10.1093/nar/gkt1158. Epub 2013 Nov 21.


Functional annotations for the Saccharomyces cerevisiae genome: the knowns and the known unknowns.

Christie KR, Hong EL, Cherry JM.

Trends Microbiol. 2009 Jul;17(7):286-94. doi: 10.1016/j.tim.2009.04.005. Epub 2009 Jul 2. Review.


Gene Ontology annotations at SGD: new data sources and annotation methods.

Hong EL, Balakrishnan R, Dong Q, Christie KR, Park J, Binkley G, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Krieger CJ, Livstone MS, Miyasato SR, Nash RS, Oughtred R, Skrzypek MS, Weng S, Wong ED, Zhu KK, Dolinski K, Botstein D, Cherry JM.

Nucleic Acids Res. 2008 Jan;36(Database issue):D577-81. Epub 2007 Nov 3.


Curated protein information in the Saccharomyces genome database.

Hellerstedt ST, Nash RS, Weng S, Paskov KM, Wong ED, Karra K, Engel SR, Cherry JM.

Database (Oxford). 2017 Jan 1;2017(1). doi: 10.1093/database/bax011.


Saccharomyces Genome Database provides mutant phenotype data.

Engel SR, Balakrishnan R, Binkley G, Christie KR, Costanzo MC, Dwight SS, Fisk DG, Hirschman JE, Hitz BC, Hong EL, Krieger CJ, Livstone MS, Miyasato SR, Nash R, Oughtred R, Park J, Skrzypek MS, Weng S, Wong ED, Dolinski K, Botstein D, Cherry JM.

Nucleic Acids Res. 2010 Jan;38(Database issue):D433-6. doi: 10.1093/nar/gkp917. Epub 2009 Nov 11.


Inference of gene interaction networks using conserved subsequential patterns from multiple time course gene expression datasets.

Liu Q, Song R, Li J.

BMC Genomics. 2015;16 Suppl 12:S4. doi: 10.1186/1471-2164-16-S12-S4. Epub 2015 Dec 9.


The yeast noncoding RNA interaction network.

Panni S, Prakash A, Bateman A, Orchard S.

RNA. 2017 Oct;23(10):1479-1492. doi: 10.1261/rna.060996.117. Epub 2017 Jul 12.

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