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Items: 1 to 20 of 95


Prediction of evolutionarily conserved interologs in Mus musculus.

Yellaboina S, Dudekula DB, Ko MSh.

BMC Genomics. 2008 Oct 8;9:465. doi: 10.1186/1471-2164-9-465.


3D-interologs: an evolution database of physical protein- protein interactions across multiple genomes.

Lo YS, Chen YC, Yang JM.

BMC Genomics. 2010 Dec 1;11 Suppl 3:S7. doi: 10.1186/1471-2164-11-S3-S7.


Improving the specificity of high-throughput ortholog prediction.

Fulton DL, Li YY, Laird MR, Horsman BG, Roche FM, Brinkman FS.

BMC Bioinformatics. 2006 May 28;7:270.


Prediction of protein-protein interactions using distant conservation of sequence patterns and structure relationships.

Espadaler J, Romero-Isart O, Jackson RM, Oliva B.

Bioinformatics. 2005 Aug 15;21(16):3360-8.


Mycobacterium tuberculosis and Clostridium difficille interactomes: demonstration of rapid development of computational system for bacterial interactome prediction.

Ananthasubramanian S, Metri R, Khetan A, Gupta A, Handen A, Chandra N, Ganapathiraju M.

Microb Inform Exp. 2012 Mar 21;2:4. doi: 10.1186/2042-5783-2-4.


Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs.

Yu H, Luscombe NM, Lu HX, Zhu X, Xia Y, Han JD, Bertin N, Chung S, Vidal M, Gerstein M.

Genome Res. 2004 Jun;14(6):1107-18.


Automatic annotation of experimentally derived, evolutionarily conserved post-translational modifications onto multiple genomes.

Sridhara V, Marchler-Bauer A, Bryant SH, Geer LY.

Database (Oxford). 2011 May 13;2011:bar019. doi: 10.1093/database/bar019.


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. doi: 10.1186/1471-2164-9-461.


Comparative analysis and assessment of M. tuberculosis H37Rv protein-protein interaction datasets.

Zhou H, Wong L.

BMC Genomics. 2011 Nov 30;12 Suppl 3:S20. doi: 10.1186/1471-2164-12-S3-S20.


Mulan: multiple-sequence local alignment and visualization for studying function and evolution.

Ovcharenko I, Loots GG, Giardine BM, Hou M, Ma J, Hardison RC, Stubbs L, Miller W.

Genome Res. 2005 Jan;15(1):184-94.


PAIR: the predicted Arabidopsis interactome resource.

Lin M, Shen X, Chen X.

Nucleic Acids Res. 2011 Jan;39(Database issue):D1134-40. doi: 10.1093/nar/gkq938.


Using shared genomic synteny and shared protein functions to enhance the identification of orthologous gene pairs.

Zheng XH, Lu F, Wang ZY, Zhong F, Hoover J, Mural R.

Bioinformatics. 2005 Mar;21(6):703-10.


DAPID: a 3D-domain annotated protein-protein interaction database.

Chen YC, Chen HC, Yang JM.

Genome Inform. 2006;17(2):206-15.


A database of phylogenetically atypical genes in archaeal and bacterial genomes, identified using the DarkHorse algorithm.

Podell S, Gaasterland T, Allen EE.

BMC Bioinformatics. 2008 Oct 7;9:419. doi: 10.1186/1471-2105-9-419.


Comparative analysis of function and interaction of transcription factors in nematodes: extensive conservation of orthology coupled to rapid sequence evolution.

Haerty W, Artieri C, Khezri N, Singh RS, Gupta BP.

BMC Genomics. 2008 Aug 27;9:399. doi: 10.1186/1471-2164-9-399.


A critical assessment of Mus musculus gene function prediction using integrated genomic evidence.

Peña-Castillo L, Tasan M, Myers CL, Lee H, Joshi T, Zhang C, Guan Y, Leone M, Pagnani A, Kim WK, Krumpelman C, Tian W, Obozinski G, Qi Y, Mostafavi S, Lin GN, Berriz GF, Gibbons FD, Lanckriet G, Qiu J, Grant C, Barutcuoglu Z, Hill DP, Warde-Farley D, Grouios C, Ray D, Blake JA, Deng M, Jordan MI, Noble WS, Morris Q, Klein-Seetharaman J, Bar-Joseph Z, Chen T, Sun F, Troyanskaya OG, Marcotte EM, Xu D, Hughes TR, Roth FP.

Genome Biol. 2008;9 Suppl 1:S2. doi: 10.1186/gb-2008-9-s1-s2.

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