A travel guide to Cytoscape plugins (Q29788355)

24 June 2017

title

A travel guide to Cytoscape plugins (English)

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24 June 2017

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7

Alexander R Pico

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Gary D. Bader

object named as

Gary D Bader

8

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Trey Ideker

9

object named as

Trey Ideker

1 reference

24 June 2017

3

Keiichiro Ono

1 reference

24 June 2017

6

Samad Lotia

1 reference

24 June 2017

Rintaro Saito

1

1 reference

24 June 2017

Michael E Smoot

2

1 reference

24 June 2017

Johannes Ruscheinski

4

1 reference

24 June 2017

Peng-Liang Wang

5

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24 June 2017

publication date

6 November 2012

1 reference

24 June 2017

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24 June 2017

volume

9

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24 June 2017

issue

11

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24 June 2017

page(s)

1069-1076

1 reference

describes a project that uses

24 June 2017

2 references

9 June 2022

https://europepmc.org/search?query=(METHODS:'Cytoscape')

based on heuristic

inferred from PubMed Central ID database lookup

cites work

The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services

1 reference

Integration of biological networks and gene expression data using Cytoscape

6 May 2017

1 reference

Cytoscape: a software environment for integrated models of biomolecular interaction networks

6 May 2017

1 reference

The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data

6 May 2017

1 reference

The BioPAX community standard for pathway data sharing

6 May 2017

1 reference

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models

6 May 2017

1 reference

The BioGRID Interaction Database: 2011 update

6 May 2017

1 reference

Integrating and annotating the interactome using the MiMI plugin for cytoscape

6 May 2017

1 reference

PSICQUIC and PSISCORE: accessing and scoring molecular interactions

6 May 2017

1 reference

Metscape: a Cytoscape plug-in for visualizing and interpreting metabolomic data in the context of human metabolic networks

6 May 2017

1 reference

KEGG: kyoto encyclopedia of genes and genomes

6 May 2017

1 reference

WikiPathways: pathway editing for the people

6 May 2017

1 reference

Pathway Commons, a web resource for biological pathway data

6 May 2017

1 reference

Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders

6 May 2017

1 reference

High-throughput generation, optimization and analysis of genome-scale metabolic models

6 May 2017

1 reference

Lethality and centrality in protein networks

6 May 2017

1 reference

An efficient algorithm for large-scale detection of protein families

6 May 2017

1 reference

An automated method for finding molecular complexes in large protein interaction networks

6 May 2017

1 reference

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles

6 May 2017

1 reference

BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks

6 May 2017

1 reference

Gene ontology: tool for the unification of biology

6 May 2017

1 reference

ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks

6 May 2017

1 reference

Network-based classification of breast cancer metastasis

6 May 2017

1 reference

Discovering regulatory and signalling circuits in molecular interaction networks

6 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649846

Which clustering algorithm is better for predicting protein complexes?

12 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649846

clusterMaker: a multi-algorithm clustering plugin for Cytoscape

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649846

iCTNet: a Cytoscape plugin to produce and analyze integrative complex traits networks

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649846

Assembling global maps of cellular function through integrative analysis of physical and genetic networks

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649846

MINE: Module Identification in Networks

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649846

WordCloud: a Cytoscape plugin to create a visual semantic summary of networks

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649846

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649846

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649846

ExprEssence--revealing the essence of differential experimental data in the context of an interaction/regulation net-work

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649846

Enrichment map: a network-based method for gene-set enrichment visualization and interpretation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649846

OmicsAnalyzer: a Cytoscape plug-in suite for modeling omics data

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649846

GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649846

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649846

Glioblastoma-specific protein interaction network identifies PP1A and CSK21 as connecting molecules between cell cycle-associated genes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649846

AltAnalyze and DomainGraph: analyzing and visualizing exon expression data

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649846

Computational approaches for detecting protein complexes from protein interaction networks: a survey

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649846

NeMo: Network Module identification in Cytoscape

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649846

How to visually interpret biological data using networks

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649846

Analyzing biological network parameters with CentiScaPe

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649846

BioQuali Cytoscape plugin: analysing the global consistency of regulatory networks

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649846

BioMart Central Portal--unified access to biological data

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649846

Literature-curated protein interaction datasets.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649846

FERN - a Java framework for stochastic simulation and evaluation of reaction networks

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649846

VistaClara: an expression browser plug-in for Cytoscape

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649846

Characterization of the mouse pancreatic islet proteome and comparative analysis with other mouse tissues

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649846

NetAtlas: a Cytoscape plugin to examine signaling networks based on tissue gene expression

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649846

The Edinburgh human metabolic network reconstruction and its functional analysis

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649846

CABIN: collective analysis of biological interaction networks

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649846

Clustering by passing messages between data points

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649846

The Gaggle: an open-source software system for integrating bioinformatics software and data sources

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649846

Modularized learning of genetic interaction networks from biological annotations and mRNA expression data

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649846

Comprehensive cluster analysis with Transitivity Clustering

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649846

Analyzing and visualizing residue networks of protein structures

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649846

MODEVO: exploring modularity and evolution of protein interaction networks.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649846

PerturbationAnalyzer: a tool for investigating the effects of concentration perturbation on protein interaction networks.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649846

Exploring biological networks with Cytoscape software

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649846

Computing topological parameters of biological networks.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649846

APID2NET: unified interactome graphic analyzer

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649846

structureViz: linking Cytoscape and UCSF Chimera.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649846

An architecture for biological information extraction and representation

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649846

KeyPathwayMiner: Detecting Case-Specific Biological Pathways Using Expression Data

26 November 2018

1 reference

inferred from DOI database lookup

7 January 2021

based on heuristic

Identifiers

DOI

10.1038/NMETH.2212

1 reference

Dimensions Publication ID

24 June 2017

1026331197

0 references

OpenCitations bibliographic resource ID

660804

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

660804

1 reference