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List of works by Keiichiro Ono

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Integration of biological networks and gene expression data using Cytoscape

scientific article (publication date: 2007)
A travel guide to Cytoscape plugins

scientific article
Functional genomic screen for modulators of ciliogenesis and cilium length

scientific article
PSICQUIC and PSISCORE: accessing and scoring molecular interactions

scientific article (publication date: 29 June 2011)
NDEx, the Network Data Exchange

scientific article
Using deep learning to model the hierarchical structure and function of a cell

scientific article published on 5 March 2018
CyREST: Turbocharging Cytoscape Access for External Tools via a RESTful API.

scientific article published on 5 August 2015
A new reference implementation of the PSICQUIC web service

scientific article published on 13 May 2013
KEGGscape: a Cytoscape app for pathway data integration

scientific article published on January 1, 2014
The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*

scientific article (publication date: 21 August 2010)
PiNGO: a Cytoscape plugin to find candidate genes in biological networks.

scientific article
The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies

scientific article (publication date: 11 February 2013)
Evidence mining and novelty assessment of protein-protein interactions with the ConsensusPathDB plugin for Cytoscape

scientific article
The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications

scientific article
Active Interaction Mapping Reveals the Hierarchical Organization of Autophagy

scientific article published on 23 January 2017
Systems biology analysis reveals role of MDM2 in diabetic nephropathy

scientific article (publication date: 20 October 2016)
Cytoscape tools for the web age: D3.js and Cytoscape.js exporters

scientific article published on July 2014
NeXO Web: the NeXO ontology database and visualization platform.

scientific article
cyNeo4j: connecting Neo4j and Cytoscape

scientific article published on 12 August 2015
The Cytoscape app article collection.

scientific article published on July 2014
DDOT: A Swiss Army Knife for Investigating Data-Driven Biological Ontologies

scientific article published on 13 March 2019
The Cytoscape Automation app article collection

scientific article
NDEx: Accessing Network Models and Streamlining Network Biology Workflows

Interpretation of cancer mutations using a multiscale map of protein systems

scientific article published on 01 October 2021
NDEx IQuery: a multi-method network gene set analysis leveraging the Network Data Exchange

scientific article published in 2023

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