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Items: 1 to 20 of 112

1.

ETAscape: analyzing protein networks to predict enzymatic function and substrates in Cytoscape.

Bachman BJ, Venner E, Lua RC, Erdin S, Lichtarge O.

Bioinformatics. 2012 Aug 15;28(16):2186-8. doi: 10.1093/bioinformatics/bts331.

2.

Evolutionary Trace Annotation Server: automated enzyme function prediction in protein structures using 3D templates.

Ward RM, Venner E, Daines B, Murray S, Erdin S, Kristensen DM, Lichtarge O.

Bioinformatics. 2009 Jun 1;25(11):1426-7. doi: 10.1093/bioinformatics/btp160.

3.

Accurate protein structure annotation through competitive diffusion of enzymatic functions over a network of local evolutionary similarities.

Venner E, Lisewski AM, Erdin S, Ward RM, Amin SR, Lichtarge O.

PLoS One. 2010 Dec 13;5(12):e14286. doi: 10.1371/journal.pone.0014286.

4.

Function prediction from networks of local evolutionary similarity in protein structure.

Erdin S, Venner E, Lisewski AM, Lichtarge O.

BMC Bioinformatics. 2013;14 Suppl 3:S6. doi: 10.1186/1471-2105-14-S3-S6.

5.

Evolutionary trace annotation of protein function in the structural proteome.

Erdin S, Ward RM, Venner E, Lichtarge O.

J Mol Biol. 2010 Mar 12;396(5):1451-73. doi: 10.1016/j.jmb.2009.12.037.

6.

Integrating and annotating the interactome using the MiMI plugin for cytoscape.

Gao J, Ade AS, Tarcea VG, Weymouth TE, Mirel BR, Jagadish HV, States DJ.

Bioinformatics. 2009 Jan 1;25(1):137-8. doi: 10.1093/bioinformatics/btn501.

7.

GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop.

Montojo J, Zuberi K, Rodriguez H, Kazi F, Wright G, Donaldson SL, Morris Q, Bader GD.

Bioinformatics. 2010 Nov 15;26(22):2927-8. doi: 10.1093/bioinformatics/btq562.

8.

GALANT: a Cytoscape plugin for visualizing data as functional landscapes projected onto biological networks.

Camilo E, Bovolenta LA, Acencio ML, Rybarczyk-Filho JL, Castro MA, Moreira JC, Lemke N.

Bioinformatics. 2013 Oct 1;29(19):2505-6. doi: 10.1093/bioinformatics/btt377.

PMID:
23894138
9.

NOA: a cytoscape plugin for network ontology analysis.

Zhang C, Wang J, Hanspers K, Xu D, Chen L, Pico AR.

Bioinformatics. 2013 Aug 15;29(16):2066-7. doi: 10.1093/bioinformatics/btt334.

10.

Mosaic: making biological sense of complex networks.

Zhang C, Hanspers K, Kuchinsky A, Salomonis N, Xu D, Pico AR.

Bioinformatics. 2012 Jul 15;28(14):1943-4. doi: 10.1093/bioinformatics/bts278.

11.

ET viewer: an application for predicting and visualizing functional sites in protein structures.

Morgan DH, Kristensen DM, Mittelman D, Lichtarge O.

Bioinformatics. 2006 Aug 15;22(16):2049-50.

PMID:
16809388
12.

PiNGO: a Cytoscape plugin to find candidate genes in biological networks.

Smoot M, Ono K, Ideker T, Maere S.

Bioinformatics. 2011 Apr 1;27(7):1030-1. doi: 10.1093/bioinformatics/btr045.

13.

Integration of biological networks and gene expression data using Cytoscape.

Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, Hanspers K, Isserlin R, Kelley R, Killcoyne S, Lotia S, Maere S, Morris J, Ono K, Pavlovic V, Pico AR, Vailaya A, Wang PL, Adler A, Conklin BR, Hood L, Kuiper M, Sander C, Schmulevich I, Schwikowski B, Warner GJ, Ideker T, Bader GD.

Nat Protoc. 2007;2(10):2366-82.

14.

OrthoNets: simultaneous visual analysis of orthologs and their interaction neighborhoods across different organisms.

Hao Y, Merkoulovitch A, Vlasblom J, Pu S, Turinsky AL, Roudeva D, Turner B, Greenblatt J, Wodak SJ.

Bioinformatics. 2011 Mar 15;27(6):883-4. doi: 10.1093/bioinformatics/btr035.

15.

VIRGO: computational prediction of gene functions.

Massjouni N, Rivera CG, Murali TM.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W340-4.

16.

Evidence mining and novelty assessment of protein-protein interactions with the ConsensusPathDB plugin for Cytoscape.

Pentchev K, Ono K, Herwig R, Ideker T, Kamburov A.

Bioinformatics. 2010 Nov 1;26(21):2796-7. doi: 10.1093/bioinformatics/btq522.

17.

Cytoscape 2.8: new features for data integration and network visualization.

Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T.

Bioinformatics. 2011 Feb 1;27(3):431-2. doi: 10.1093/bioinformatics/btq675.

18.

SpotXplore: a Cytoscape plugin for visual exploration of hotspot expression in gene regulatory networks.

Westenberg MA, Roerdink JB, Kuipers OP, van Hijum SA.

Bioinformatics. 2010 Nov 15;26(22):2922-3. doi: 10.1093/bioinformatics/btq535.

19.

ReNE: a cytoscape plugin for regulatory network enhancement.

Politano G, Benso A, Savino A, Di Carlo S.

PLoS One. 2014 Dec 26;9(12):e115585. doi: 10.1371/journal.pone.0115585.

20.

Prediction and experimental validation of enzyme substrate specificity in protein structures.

Amin SR, Erdin S, Ward RM, Lua RC, Lichtarge O.

Proc Natl Acad Sci U S A. 2013 Nov 5;110(45):E4195-202. doi: 10.1073/pnas.1305162110.

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