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Author Details

Keiichiro Ono
university of california san diego
0000-0003-4042-3748
2007
29
17
Trey Ideker (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
36882166NDEx IQuery: a multi-method network gene set analysis leveraging the Network Data Exchange.Bioinformatics2023
37220749A multi-scale map of protein assemblies in the DNA damage response.Cell Syst2023
34992246Deep distributed computing to reconstruct extremely large lineage trees.Nat Biotechnol2022
34570431NDEx: Accessing Network Models and Streamlining Network Biology Workflows.Curr Protoc2021
34591613Interpretation of cancer mutations using a multiscale map of protein systems.Science2021
30878356DDOT: A Swiss Army Knife for Investigating Data-Driven Biological Ontologies.Cell Syst2019
29505029Using deep learning to model the hierarchical structure and function of a cell.Nat Methods2018
29983926The Cytoscape Automation app article collection.F1000Res2018
28132844Active Interaction Mapping Reveals the Hierarchical Organization of Autophagy.Mol Cell2017
27777973Systems biology analysis reveals role of MDM2 in diabetic nephropathy.JCI Insight2016
26672762CyREST: Turbocharging Cytoscape Access for External Tools via a RESTful API.F1000Res2015
26272981cyNeo4j: connecting Neo4j and Cytoscape.Bioinformatics2015
26594663NDEx, the Network Data Exchange.Cell Syst2015
24271398NeXO Web: the NeXO ontology database and visualization platform.Nucleic Acids Res2014
25580224The Cytoscape app article collection.F1000Res2014
25177485KEGGscape: a Cytoscape app for pathway data integration.F1000Res2014
23398680The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies.J Biomed Semantics2013
23671334A new reference implementation of the PSICQUIC web service.Nucleic Acids Res2013
23132118A travel guide to Cytoscape plugins.Nat Methods2012
21278188PiNGO: a Cytoscape plugin to find candidate genes in biological networks.Bioinformatics2011
21806842The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications.J Biomed Semantics2011
21886098Assembling global maps of cellular function through integrative analysis of physical and genetic networks.Nat Protoc2011
21716279PSICQUIC and PSISCORE: accessing and scoring molecular interactions.Nat Methods2011
21149340Cytoscape 2.8: new features for data integration and network visualization.Bioinformatics2011
20393563Functional genomic screen for modulators of ciliogenesis and cilium length.Nature2010
20727200The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*.J Biomed Semantics2010
20847220Evidence mining and novelty assessment of protein-protein interactions with the ConsensusPathDB plugin for Cytoscape.Bioinformatics2010
17577547Malignant calcifying epithelial odontogenic tumor of the mandible: report of a case with pulmonary metastasis showing remarkable response to platinum derivatives.Oral Surg Oral Med Oral Pathol Oral Radiol Endod2007
17947979Integration of biological networks and gene expression data using Cytoscape.Nat Protoc2007
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Collaborators

Trey Ideker (CM4AI)
University of California San Diego
Co-authored papers 19
Barry Demchak
University of California
Co-authored papers 9
Dexter Pratt (CM4AI)
UC San Diego
Co-authored papers 8
Michael Ku Yu
University of California San Diego
Co-authored papers 5
Gary D Bader
University of Toronto
Co-authored papers 5
Michael Smoot
University of California
Co-authored papers 5
Pengliang Wang
Sun Yat-sen Memorial Hospital, Sun Yat-sen University
Co-authored papers 4
Rudolf T Pillich
University of California San Diego
Co-authored papers 4
Alexander R Pico
Institute of Data Science and Biotechnology, Gladstone Institutes
Co-authored papers 4
Bruno Aranda
European Bioinformatics Institute
Co-authored papers 4
Johannes Ruscheinski
Co-authored papers 3
Rutger A Vos
Naturalis Biodiversity Center
Co-authored papers 3
Mark D Wilkinson
Universidad Politecnica de Madrid (UPM)
Co-authored papers 3
Raoul J P Bonnal
National Institute for Molecular Genetics "Romeo ed Enrica Invernizzi"
Co-authored papers 3
Samad Lotia
Gladstone Institutes
Co-authored papers 3
Kozo Nishida
Japan Science and Technology Agency
Co-authored papers 3
Christopher Churas (CM4AI)
University of California San Diego
Co-authored papers 3
Benno Schwikowski
Center for Bioinformatics, Institut Pasteur CNRS
Co-authored papers 3
Katherine Licon
University of California San Diego
Co-authored papers 3
John H Morris
University of California san francisco
Co-authored papers 3
Shuichi Kawashima
Database Center for Life Science, Joint Support-Center for Data Science Research
Co-authored papers 3
Toshiaki Katayama
Database Center for Life Science
Co-authored papers 3
Jan Aerts
Co-authored papers 3
Fan Zheng
University of California San Diego
Co-authored papers 3
Lukasz Salwinski
university of california los angeles
Co-authored papers 3
Yasunori Yamamoto
Database Center for Life Science, Joint Support-Center for Data Science Research
Co-authored papers 3
Martin Senger
DKFZ - German Cancer Research Center
Co-authored papers 2
David Otasek
University of California San Diego
Co-authored papers 2
Kiyoko F Aoki-Kinoshita
Co-authored papers 2
Soichi Ogishima
Tohoku University Graduate School of Medicine
Co-authored papers 2
Release 1.2