PubMed

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. Epub 2006 Jun 8.PMID: 16762047 [PubMed - indexed for MEDLINE]Related articlesFree article

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.PMID: 18000002 [PubMed - indexed for MEDLINE]Related articlesFree article

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.PMID: 16381927 [PubMed - indexed for MEDLINE]Related articlesFree article

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. Epub 2008 Sep 11.PMID: 18786976 [PubMed - indexed for MEDLINE]Related articlesFree article

Mining protein networks for synthetic genetic interactions.

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

BMC Bioinformatics. 2008 Oct 9;9:426.PMID: 18844977 [PubMed - indexed for MEDLINE]Related articlesFree article

Filtering high-throughput protein-protein interaction data using a combination of genomic features.

Patil A, Nakamura H.

BMC Bioinformatics. 2005 Apr 18;6:100.PMID: 15833142 [PubMed - indexed for MEDLINE]Related articlesFree article

Beyond synexpression relationships: local clustering of time-shifted and inverted gene expression profiles identifies new, biologically relevant interactions.

Qian J, Dolled-Filhart M, Lin J, Yu H, Gerstein M.

J Mol Biol. 2001 Dec 14;314(5):1053-66.PMID: 11743722 [PubMed - indexed for MEDLINE]Related articles

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.PMID: 20093466 [PubMed - indexed for MEDLINE]Related articles

False positive reduction in protein-protein interaction predictions using gene ontology annotations.

Mahdavi MA, Lin YH.

BMC Bioinformatics. 2007 Jul 23;8:262.PMID: 17645798 [PubMed - indexed for MEDLINE]Related articlesFree article

Stratus not altocumulus: a new view of the yeast protein interaction network.

Batada NN, Reguly T, Breitkreutz A, Boucher L, Breitkreutz BJ, Hurst LD, Tyers M.

PLoS Biol. 2006 Oct;4(10):e317.PMID: 16984220 [PubMed - indexed for MEDLINE]Related articlesFree article

DroID: the Drosophila Interactions Database, a comprehensive resource for annotated gene and protein interactions.

Yu J, Pacifico S, Liu G, Finley RL Jr.

BMC Genomics. 2008 Oct 7;9:461.PMID: 18840285 [PubMed - indexed for MEDLINE]Related articlesFree article

Finding friends and enemies in an enemies-only network: a graph diffusion kernel for predicting novel genetic interactions and co-complex membership from yeast genetic interactions.

Qi Y, Suhail Y, Lin YY, Boeke JD, Bader JS.

Genome Res. 2008 Dec;18(12):1991-2004. Epub 2008 Oct 2.PMID: 18832443 [PubMed - indexed for MEDLINE]Related articlesFree article

Automatic extraction of gene ontology annotation and its correlation with clusters in protein networks.

Daraselia N, Yuryev A, Egorov S, Mazo I, Ispolatov I.

BMC Bioinformatics. 2007 Jul 10;8:243.PMID: 17620146 [PubMed - indexed for MEDLINE]Related articlesFree article

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.PMID: 17982175 [PubMed - indexed for MEDLINE]Related articlesFree article

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. Epub 2009 Nov 11.PMID: 19906697 [PubMed - indexed for MEDLINE]Related articlesFree article

Effect of dataset selection on the topological interpretation of protein interaction networks.

Hakes L, Robertson DL, Oliver SG.

BMC Genomics. 2005 Sep 20;6:131.PMID: 16174296 [PubMed - indexed for MEDLINE]Related articlesFree article

Global mapping of the yeast genetic interaction network.

Tong AH, Lesage G, Bader GD, Ding H, Xu H, Xin X, Young J, Berriz GF, Brost RL, Chang M, Chen Y, Cheng X, Chua G, Friesen H, Goldberg DS, Haynes J, Humphries C, He G, Hussein S, Ke L, Krogan N, Li Z, Levinson JN, Lu H, Ménard P, Munyana C, Parsons AB, Ryan O, Tonikian R, Roberts T, Sdicu AM, Shapiro J, Sheikh B, Suter B, Wong SL, Zhang LV, Zhu H, Burd CG, Munro S, Sander C, Rine J, Greenblatt J, Peter M, Bretscher A, Bell G, Roth FP, Brown GW, Andrews B, Bussey H, Boone C.

Science. 2004 Feb 6;303(5659):808-13.PMID: 14764870 [PubMed - indexed for MEDLINE]Related articlesFree article

Information flow analysis of interactome networks.

Missiuro PV, Liu K, Zou L, Ross BC, Zhao G, Liu JS, Ge H.

PLoS Comput Biol. 2009 Apr;5(4):e1000350. Epub 2009 Apr 10.PMID: 19503817 [PubMed - indexed for MEDLINE]Related articlesFree article

Exploration of the omics evidence landscape: adding qualitative labels to predicted protein-protein interactions.

van Noort V, Snel B, Huynen MA.

Genome Biol. 2007;8(9):R197.PMID: 17880677 [PubMed - indexed for MEDLINE]Related articlesFree article

PIPE: a protein-protein interaction prediction engine based on the re-occurring short polypeptide sequences between known interacting protein pairs.

Pitre S, Dehne F, Chan A, Cheetham J, Duong A, Emili A, Gebbia M, Greenblatt J, Jessulat M, Krogan N, Luo X, Golshani A.

BMC Bioinformatics. 2006 Jul 27;7:365.PMID: 16872538 [PubMed - indexed for MEDLINE]Related articlesFree article