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Literature DB >> 17277332

NetMatch: a Cytoscape plugin for searching biological networks.

A Ferro¹, R Giugno, G Pigola, A Pulvirenti, D Skripin, G D Bader, D Shasha.

Abstract

UNLABELLED: NetMatch is a Cytoscape plugin which allows searching biological networks for subcomponents matching a given query. Queries may be approximate in the sense that certain parts of the subgraph-query may be left unspecified. To make the query creation process easy, a drawing tool is provided. Cytoscape is a bioinformatics software platform for the visualization and analysis of biological networks. AVAILABILITY: The full package, a tutorial and associated examples are available at the following web sites: http://alpha.dmi.unict.it/~ctnyu/netmatch.html, http://baderlab.org/Software/NetMatch.

Entities: Species

Mesh：

Year: 2007 PMID： 17277332 DOI： 10.1093/bioinformatics/btm032

Source DB: PubMed Journal: Bioinformatics ISSN： 1367-4803 Impact factor: 6.937

Keyword Cloud
Cited

22 in total

1. Integration of biological networks and gene expression data using Cytoscape.

Authors: Melissa S Cline; Michael Smoot; Ethan Cerami; Allan Kuchinsky; Nerius Landys; Chris Workman; Rowan Christmas; Iliana Avila-Campilo; Michael Creech; Benjamin Gross; Kristina Hanspers; Ruth Isserlin; Ryan Kelley; Sarah Killcoyne; Samad Lotia; Steven Maere; John Morris; Keiichiro Ono; Vuk Pavlovic; Alexander R Pico; Aditya Vailaya; Peng-Liang Wang; Annette Adler; Bruce R Conklin; Leroy Hood; Martin Kuiper; Chris Sander; Ilya Schmulevich; Benno Schwikowski; Guy J Warner; Trey Ideker; Gary D Bader
Journal: Nat Protoc Date: 2007 Impact factor: 13.491

Review 2. Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review.

Authors: Peter Csermely; Tamás Korcsmáros; Huba J M Kiss; Gábor London; Ruth Nussinov
Journal: Pharmacol Ther Date: 2013-02-04 Impact factor: 12.310

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

Authors: Jing Gao; Alex S Ade; V Glenn Tarcea; Terry E Weymouth; Barbara R Mirel; H V Jagadish; David J States
Journal: Bioinformatics Date: 2008-09-23 Impact factor: 6.937

4. CySBGN: a Cytoscape plug-in to integrate SBGN maps.

Authors: Emanuel Gonçalves; Martijn van Iersel; Julio Saez-Rodriguez
Journal: BMC Bioinformatics Date: 2013-01-16 Impact factor: 3.169

5. RINQ: Reference-based Indexing for Network Queries.

Authors: Günhan Gülsoy; Tamer Kahveci
Journal: Bioinformatics Date: 2011-07-01 Impact factor: 6.937

6. RefNetBuilder: a platform for construction of integrated reference gene regulatory networks from expressed sequence tags.

Authors: Ying Li; Ping Gong; Edward J Perkins; Chaoyang Zhang; Nan Wang
Journal: BMC Bioinformatics Date: 2011-10-18 Impact factor: 3.169

NetMatch: a Cytoscape plugin for searching biological networks.

1. Integration of biological networks and gene expression data using Cytoscape.

Review 2. Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review.

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

4. CySBGN: a Cytoscape plug-in to integrate SBGN maps.

5. RINQ: Reference-based Indexing for Network Queries.

6. RefNetBuilder: a platform for construction of integrated reference gene regulatory networks from expressed sequence tags.

7. NetGrep: fast network schema searches in interactomes.

8. A subgraph isomorphism algorithm and its application to biochemical data.

9. Organization of physical interactomes as uncovered by network schemas.

10. Biomolecular network querying: a promising approach in systems biology.