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F1000 research, ISSN 2046-1402, 08/2018, Volume 7, pp. 725 - 725
Identifier Mapping, the association of terms across disparate taxonomies and databases, is a common hurdle in bioinformatics workflows. The app for Cytoscape... 
Journal Article
F1000 research, ISSN 2046-1402, 07/2016, Volume 5, pp. 1717 - 1717
Networks often contain regions of tightly connected nodes, or clusters, that highlight their shared relationships. An effective way to create a visual summary... 
Bioinformatics
Journal Article
PloS one, ISSN 1932-6203, 06/2014, Volume 9, Issue 6, pp. e100040 - e100040
Journal Article
F1000 research, ISSN 2046-1402, 05/2018, Volume 7, p. 563
Residue interaction networks (RINs) have been shown to be relevant representations of the tertiary or quaternary structures of proteins, in particular thanks... 
Centrality analysis | Automation | Cytoscape | Rinspector | Flexibility prediction | Residue interaction network | Protein structure | Structure ensemble
Journal Article
F1000 research, ISSN 2046-1402, 2018, Volume 7, pp. 800 - 800
Cytoscape is the premiere platform for interactive analysis, integration and visualization of network data. While Cytoscape itself delivers much basic... 
App | Network Biology | Automation | Cytoscape | Network Visualization | Network Analysis | Bioinformatics | Computer Science
Journal Article
F1000 research, ISSN 2046-1402, 06/2018, Volume 7, p. 823
Adjacency matrices are useful for storing pairwise interaction data, such as correlations between gene pairs in a pathway or similarities between genes and... 
Cytoscape | REST | Microservice | Reproducibility | Workflow | Adjacency | Interoperability | Names | Automation | Researchers | Graph representations
Journal Article
F1000 research, ISSN 2046-1402, 08/2018, Volume 7, p. 823
Adjacency matrices are useful for storing pairwise interaction data, such as correlations between gene pairs in a pathway or similarities between genes and... 
Index Medicus
Journal Article
F1000 research, ISSN 2046-1402, 05/2018, Volume 7, pp. 531 - 531
Pathway- and network-based approaches project seemingly unrelated genes onto the context of pathways and networks, enhancing the analysis power that cannot be... 
Cytoscape | ReactomeFIViz | Pathway and network | Reactome | CyREST
Journal Article
F1000 research, ISSN 2046-1402, 05/2018, Volume 6, pp. 2120 - 2120
Motivation: Many biologists are discouraged from using network simulation tools because these require manual, often tedious network construction. This... 
Bioinformatics | Genomics | KEGG | Cytoscape | Simulation | Gene expression | Biological network | BioNSi
Journal Article
F1000 research, ISSN 2046-1402, 12/2017, Volume 6, p. 2120
Motivation: Many biologists are discouraged from using network simulation tools because these require manual, often tedious network construction. This... 
Bioinformatics | Genomics
Journal Article
F1000 research, ISSN 2046-1402, 11/2017, Volume 5, p. 2524
Biological networks are becoming a fundamental tool for the investigation of high-throughput data in several fields of biology and biotechnology. With the... 
Bioinformatics | Genomics | Protein Chemistry & Proteomics | Network randomisation | Cytoscape | Network generation | Random networks | Network analysis | Biotechnology | Software | Algorithms | Statistical analysis | Experiments
Journal Article
F1000 research, ISSN 2046-1402, 12/2019, Volume 8, pp. 1774 - 1774
RCy3 is an R package in Bioconductor that communicates with Cytoscape via its REST API, providing access to the full feature set of Cytoscape from within the R... 
Visualization | Automation | Layouts | User interface | Biology | Default | Open source software | Index Medicus
Journal Article
Journal of proteome research, ISSN 1535-3893, 02/2019, Volume 18, Issue 2, pp. 623 - 632
Journal Article
F1000 research, ISSN 2046-1402, 06/2018, Volume 7, p. 743
Here, we present an update of the open-source CyTargetLinker app for Cytoscape (http://apps.cytoscape.org/apps/cytargetlinker) that introduces new automation... 
Reproducibility of Results | Molecular Sequence Annotation | Software
Journal Article
F1000Research, ISSN 2046-1402, 2017, Volume 6, pp. 58 - 58
PathLinker is a graph-theoretic algorithm for reconstructing the interactions in a signaling pathway of interest. It efficiently computes multiple short paths... 
Bioinformatics | Signaling pathways | PathLinker | Cytoscape | Protein interaction networks | K-shortest paths | Pathway reconstruction
Journal Article
Journal Article