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Citations per year

Number of citations per year for the bioinformatics software tool NetMatch
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NetMatch specifications

Information


Unique identifier OMICS_19358
Name NetMatch
Alternative name NetMatchStar
Software type Package/Module
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Windows
Programming languages Java
Computer skills Medium
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Rosalba Giugno

Publications for NetMatch

NetMatch citations

 (7)
library_books

Inferring miRNA sponge co regulation of protein protein interactions in human breast cancer

2017
BMC Bioinformatics
PMCID: 5423010
PMID: 28482794
DOI: 10.1186/s12859-017-1672-2

[…] a common protein that is a party of a PPI.To search for miRSCoPPI motifs, we firstly integrate BRCA-related miRNA sponge interactions, PPIs, and lncRNA-target interactions into a network. We use the NetMatchStar plugin [] in Cytoscape [] to search the integrated network for the two types of miRScoPPI motifs. Finally, we merge the identified miRSCoPPI motifs to obtain the BRCA-related miRSCoPPI ne […]

library_books

Systems biology approaches for advancing the discovery of effective drug combinations

2015
J Cheminform
PMCID: 4348553
PMID: 25741385
DOI: 10.1186/s13321-015-0055-9

[…] topology can be a useful strategy in prioritizing drug combinations to test experimentally. Networks exported into Cytoscape [], a open source software platform for network visualization, can use the Netmatch plug-in [] to quickly search for motifs of interest. […]

library_books

Novel Factors in the Pathogenesis of Psoriasis and Potential Drug Candidates Are Found with Systems Biology Approach

2013
PLoS One
PMCID: 3841158
PMID: 24303025
DOI: 10.1371/journal.pone.0080751

[…] tworks in which a motif occurred more often than in the input network, divided by total number of random networks. was used as cutoff. Respective sub-networks of enriched motifs were identified with NetMatch Cytoscape plugin. jActiveModules and ClusterONE were used for network module and protein complex detection. ClusterONE analysis was carried out with minimum cluster size of 3 with unweighted […]

library_books

RMOD: A Tool for Regulatory Motif Detection in Signaling Network

2013
PLoS One
PMCID: 3710000
PMID: 23874612
DOI: 10.1371/journal.pone.0068407

[…] occur repeatedly within the network. For instance, the mFinder , MAVisto , FANMOD , SNAVI , and CytoKavosh detect motifs that recur in the network much more often than expected in a random network; NetMatch searches only for network motifs that match a user-defined query graph. In addition, the NetDS , a Cytoscape plugin, was recently developed to analyze a limited size of feedback and feedforw […]

library_books

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

2011
BMC Bioinformatics
PMCID: 3236843
PMID: 22166047
DOI: 10.1186/1471-2105-12-S10-S20

[…] information difficult. Several bioinformatic toolkits have been developed to extract biological interactions from public databases for well-studied model organisms. For example, BioNetBuilder [,] and NetMatch [] are Cytoscape [] plug-ins for retrieving, integrating, visualization and analysis of known biological networks. However, these programs cannot be applied to species that have no or limited […]

library_books

NetGrep: fast network schema searches in interactomes

2008
Genome Biol
PMCID: 2592716
PMID: 18801179
DOI: 10.1186/gb-2008-9-9-r138

[…] ding linear paths in a network. MOTUS [] is designed for non-topology constrained subgraph searches in metabolic networks. Qnet [] is restricted to tree queries and utilizes only sequence similarity. NetMatch [], extending ideas of GraphGrep [], allows users to search for subgraphs within the Cytoscape [] environment and can be used for simple schema queries. SAGA [] is a subgraph matching tool fo […]


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NetMatch institution(s)
Department of Math and Computer Science, University of Catania, Catania, Italy; Department of Computer Science, University of Verona, Verona, Italy; The Donnelly Centre, University of Toronto, Toronto, ON, Canada; Department of Computer Science, Courant Institute of Mathematical Sciences, New York University, New York, NY, USA; Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy

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