Literature DB >> 21478195

CyClus3D: a Cytoscape plugin for clustering network motifs in integrated networks.

Pieter Audenaert1, Thomas Van Parys, Florian Brondel, Mario Pickavet, Piet Demeester, Yves Van de Peer, Tom Michoel.   

Abstract

SUMMARY: Network motifs in integrated molecular networks represent functional relationships between distinct data types. They aggregate to form dense topological structures corresponding to functional modules which cannot be detected by traditional graph clustering algorithms. We developed CyClus3D, a Cytoscape plugin for clustering composite three-node network motifs using a 3D spectral clustering algorithm. AVAILABILITY: Via the Cytoscape plugin manager or http://bioinformatics.psb.ugent.be/software/details/CyClus3D.

Mesh：

Year:  2011        PMID： 21478195     DOI： 10.1093/bioinformatics/btr182

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


  8 in total

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Authors:  Grant R Cramer; Kaoru Urano; Serge Delrot; Mario Pezzotti; Kazuo Shinozaki
Journal:  BMC Plant Biol       Date:  2011-11-17       Impact factor: 4.215

2.  FunMod: a Cytoscape plugin for identifying functional modules in undirected protein-protein networks.

Authors:  Massimo Natale; Alfredo Benso; Stefano Di Carlo; Elisa Ficarra
Journal:  Genomics Proteomics Bioinformatics       Date:  2014-08-19       Impact factor: 7.691

3.  Identification of Novel Breast Cancer Subtype-Specific Biomarkers by Integrating Genomics Analysis of DNA Copy Number Aberrations and miRNA-mRNA Dual Expression Profiling.

Authors:  Dongguo Li; Hong Xia; Zhen-ya Li; Lin Hua; Lin Li
Journal:  Biomed Res Int       Date:  2015-04-15       Impact factor: 3.411

4.  A Single Human-Relevant Fast Food Meal Rapidly Reorganizes Metabolomic and Transcriptomic Signatures in a Gut Microbiota-Dependent Manner.

Authors:  Lucas J Osborn; Danny Orabi; Maryam Goudzari; Naseer Sangwan; Rakhee Banerjee; Amanda L Brown; Anagha Kadam; Anthony D Gromovsky; Pranavi Linga; Gail A M Cresci; Tytus D Mak; Belinda B Willard; Jan Claesen; J Mark Brown
Journal:  Immunometabolism       Date:  2021-09-18

5.  The index-based subgraph matching algorithm (ISMA): fast subgraph enumeration in large networks using optimized search trees.

Authors:  Sofie Demeyer; Tom Michoel; Jan Fostier; Pieter Audenaert; Mario Pickavet; Piet Demeester
Journal:  PLoS One       Date:  2013-04-19       Impact factor: 3.240

6.  Integration of interactive, multi-scale network navigation approach with Cytoscape for functional genomics in the big data era.

Authors:  Thanet Praneenararat; Toshihisa Takagi; Wataru Iwasaki
Journal:  BMC Genomics       Date:  2012-12-13       Impact factor: 3.969

7.  Inferring microRNA and transcription factor regulatory networks in heterogeneous data.

Authors:  Thuc D Le; Lin Liu; Bing Liu; Anna Tsykin; Gregory J Goodall; Kenji Satou; Jiuyong Li
Journal:  BMC Bioinformatics       Date:  2013-03-11       Impact factor: 3.169

8.  yApoptosis: yeast apoptosis database.

Authors:  Kwanjeera Wanichthanarak; Marija Cvijovic; Andrea Molt; Dina Petranovic
Journal:  Database (Oxford)       Date:  2013-09-29       Impact factor: 3.451
  8 in total

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