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Items: 1 to 20 of 72

1.

NetGrep: fast network schema searches in interactomes.

Banks E, Nabieva E, Peterson R, Singh M.

Genome Biol. 2008;9(9):R138. doi: 10.1186/gb-2008-9-9-r138. Epub 2008 Sep 18.

2.

Organization of physical interactomes as uncovered by network schemas.

Banks E, Nabieva E, Chazelle B, Singh M.

PLoS Comput Biol. 2008 Oct;4(10):e1000203. doi: 10.1371/journal.pcbi.1000203. Epub 2008 Oct 24.

3.

SPIDer: Saccharomyces protein-protein interaction database.

Wu X, Zhu L, Guo J, Fu C, Zhou H, Dong D, Li Z, Zhang DY, Lin K.

BMC Bioinformatics. 2006 Dec 18;7 Suppl 5:S16.

4.

INTEGRATOR: interactive graphical search of large protein interactomes over the Web.

Chang AN, McDermott J, Frazier Z, Guerquin M, Samudrala R.

BMC Bioinformatics. 2006 Mar 16;7:146.

5.

NatalieQ: a web server for protein-protein interaction network querying.

El-Kebir M, Brandt BW, Heringa J, Klau GW.

BMC Syst Biol. 2014 Apr 1;8:40. doi: 10.1186/1752-0509-8-40.

6.

Predicting the interactome of Xanthomonas oryzae pathovar oryzae for target selection and DB service.

Kim JG, Park D, Kim BC, Cho SW, Kim YT, Park YJ, Cho HJ, Park H, Kim KB, Yoon KO, Park SJ, Lee BM, Bhak J.

BMC Bioinformatics. 2008 Jan 24;9:41. doi: 10.1186/1471-2105-9-41.

7.

Protein complex prediction via verifying and reconstructing the topology of domain-domain interactions.

Ozawa Y, Saito R, Fujimori S, Kashima H, Ishizaka M, Yanagawa H, Miyamoto-Sato E, Tomita M.

BMC Bioinformatics. 2010 Jun 28;11:350. doi: 10.1186/1471-2105-11-350.

8.

Decomposing protein networks into domain-domain interactions.

Albrecht M, Huthmacher C, Tosatto SC, Lengauer T.

Bioinformatics. 2005 Sep 1;21 Suppl 2:ii220-1.

PMID:
16204107
9.

Comparative interactomics analysis of protein family interaction networks using PSIMAP (protein structural interactome map).

Park D, Lee S, Bolser D, Schroeder M, Lappe M, Oh D, Bhak J.

Bioinformatics. 2005 Aug 1;21(15):3234-40. Epub 2005 May 24.

PMID:
15914543
10.

Knowledge-guided inference of domain-domain interactions from incomplete protein-protein interaction networks.

Liu M, Chen XW, Jothi R.

Bioinformatics. 2009 Oct 1;25(19):2492-9. doi: 10.1093/bioinformatics/btp480. Epub 2009 Aug 10.

11.

Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps.

Nabieva E, Jim K, Agarwal A, Chazelle B, Singh M.

Bioinformatics. 2005 Jun;21 Suppl 1:i302-10.

PMID:
15961472
12.

Predicting interactions in protein networks by completing defective cliques.

Yu H, Paccanaro A, Trifonov V, Gerstein M.

Bioinformatics. 2006 Apr 1;22(7):823-9. Epub 2006 Feb 2.

PMID:
16455753
13.

SiPAN: simultaneous prediction and alignment of protein-protein interaction networks.

Alkan F, Erten C.

Bioinformatics. 2015 Jul 15;31(14):2356-63. doi: 10.1093/bioinformatics/btv160. Epub 2015 Mar 18.

PMID:
25788620
14.

A database and tool, IM Browser, for exploring and integrating emerging gene and protein interaction data for Drosophila.

Pacifico S, Liu G, Guest S, Parrish JR, Fotouhi F, Finley RL Jr.

BMC Bioinformatics. 2006 Apr 7;7:195.

15.

Topology-free querying of protein interaction networks.

Bruckner S, H├╝ffner F, Karp RM, Shamir R, Sharan R.

J Comput Biol. 2010 Mar;17(3):237-52. doi: 10.1089/cmb.2009.0170.

PMID:
20377443
16.

Context-specific protein network miner--an online system for exploring context-specific protein interaction networks from the literature.

Chowdhary R, Tan SL, Zhang J, Karnik S, Bajic VB, Liu JS.

PLoS One. 2012;7(4):e34480. doi: 10.1371/journal.pone.0034480. Epub 2012 Apr 6.

17.

An enhanced Java graph applet interface for visualizing interactomes.

Chang AN, McDermott J, Samudrala R.

Bioinformatics. 2005 Apr 15;21(8):1741-2. Epub 2004 Dec 21.

PMID:
15613388
18.

PathBLAST: a tool for alignment of protein interaction networks.

Kelley BP, Yuan B, Lewitter F, Sharan R, Stockwell BR, Ideker T.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W83-8.

19.

Discovering motif pairs at interaction sites from protein sequences on a proteome-wide scale.

Li H, Li J, Wong L.

Bioinformatics. 2006 Apr 15;22(8):989-96. Epub 2006 Jan 29.

PMID:
16446278
20.

RESQUE: network reduction using semi-Markov random walk scores for efficient querying of biological networks.

Sahraeian SM, Yoon BJ.

Bioinformatics. 2012 Aug 15;28(16):2129-36. doi: 10.1093/bioinformatics/bts341. Epub 2012 Jun 23.

PMID:
22730436

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