Keiichiro Ono

NDEx, the Network Data Exchange.

Published in Cell Systems

The Cytoscape app article collection.

Published in F1000Research

As a network visualization and analysis platform, Cytoscape relies on apps to provide domain-specific features and functions. There are many resources available to support Cytoscape app development and distribution, including the Cytoscape App Store and an online "cookbook" for app developers. This article collection is another resource to help res...

A travel guide to Cytoscape plugins.

Published in Nature Methods

Cytoscape is open-source software for integration, visualization and analysis of biological networks. It can be extended through Cytoscape plugins, enabling a broad community of scientists to contribute useful features. This growth has occurred organically through the independent efforts of diverse authors, yielding a powerful but heterogeneous set...

cyNeo4j: connecting Neo4j and Cytoscape.

Published in Bioinformatics

Cytoscape tools for the web age: D3.js and Cytoscape.js exporters.

Published in F1000Research

In this paper we present new data export modules for Cytoscape 3 that can generate network files for Cytoscape.js and D3.js. Cytoscape.js exporter is implemented as a core feature of Cytoscape 3, and D3.js exporter is available as a Cytoscape 3 app. These modules enable users to seamlessly export network and table data sets generated in Cytoscape t...

NeXO Web: the NeXO ontology database and visualization platform.

Published in Nucleic Acids Research

The Network-extracted Ontology (NeXO) is a gene ontology inferred directly from large-scale molecular networks. While most ontologies are constructed through manual expert curation, NeXO uses a principled computational approach which integrates evidence from hundreds of thousands of individual gene and protein interactions to construct a global hie...

Landscape of protein-protein interactions in Drosophila immune deficiency signaling during bacterial challenge.

Published in Proceedings of the National Academy of Sciences

The Drosophila defense against pathogens largely relies on the activation of two signaling pathways: immune deficiency (IMD) and Toll. The IMD pathway is triggered mainly by Gram-negative bacteria, whereas the Toll pathway responds predominantly to Gram-positive bacteria and fungi. The activation of these pathways leads to the rapid induction of nu...

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

Published in Bioinformatics

Cytoscape 2.8: new features for data integration and network visualization.

Published in Bioinformatics

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

Published in Bioinformatics

Ideker is corresponding author) Integration of Biological Networks and Gene Expression Data using Cytoscape

Published in Nature Protocols

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

Published in Nature Protocols

To take full advantage of high-throughput genetic and physical interaction mapping projects, the raw interactions must first be assembled into models of cell structure and function. PanGIA (for physical and genetic interaction alignment) is a plug-in for the bioinformatics platform Cytoscape, designed to integrate physical and genetic interactions ...

Functional genomic screen for modulators of ciliogenesis and cilium length.

Published in Nature

Primary cilia are evolutionarily conserved cellular organelles that organize diverse signalling pathways. Defects in the formation or function of primary cilia are associated with a spectrum of human diseases and developmental abnormalities. Genetic screens in model organisms have discovered core machineries of cilium assembly and maintenance. Howe...