Evidence mining and novelty assessment of protein-protein interactions with the ConsensusPathDB plugin for Cytoscape. - Konstantin Pentchev; Keiichiro Ono; Ralf Herwig; Trey Ideker; Atanas Kamburov (Bioinform., 2010)

The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. - Toshiaki Katayama; Kazuharu Arakawa; Mitsuteru Nakao; Keiichiro Ono; Kiyoko F. Aoki-Kinoshita; Yasunori Yamamoto; Atsuko Yamaguchi; Shuichi Kawashima; Hong-Woo Chun; Jan Aerts; Bruno Aranda; Lord H. Barboza; et al. (J. Biomed. Semant., 2010)

PiNGO: a Cytoscape plugin to find candidate genes in biological networks. - Michael E. Smoot; Keiichiro Ono; Trey Ideker; Steven Maere (Bioinform., 2011)

Cytoscape 2.8: new features for data integration and network visualization. - Michael E. Smoot; Keiichiro Ono; Johannes Ruscheinski; Peng-Liang Wang; Trey Ideker (Bioinform., 2011)

The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications. - Toshiaki Katayama; Mark D. Wilkinson; Rutger A. Vos; Takeshi Kawashima; Shuichi Kawashima; Mitsuteru Nakao; Yasunori Yamamoto; Hong-Woo Chun; Atsuko Yamaguchi; Shin Kawano; Jan Aerts; Kiyoko F. Aoki-Kinoshita; et al. (J. Biomed. Semant., 2011)

A new reference implementation of the PSICQUIC web service. - Noemi del-Toro; Marine Dumousseau; Sandra E. Orchard; Rafael C. Jiménez; Eugenia Galeota; Guillaume Launay; Johannes Goll; Karin Breuer; Keiichiro Ono; Lukasz Salwínski; Henning Hermjakob (Nucleic Acids Res., 2013)

KEGGscape: a Cytoscape app for pathway data integration. - Kozo Nishida; Keiichiro Ono; Shigehiko Kanaya; Koichi Takahashi (F1000Research, 2014)

Cytoscape tools for the web age: D3.js and Cytoscape.js exporters. - Keiichiro Ono; Barry Demchak; Trey Ideker (F1000Research, 2014)

The Cytoscape app article collection. - Alexander R. Pico; Gary D. Bader; Barry Demchak; Oriol Guitart Pla; Timothy Hull; William J. R. Longabaugh; Christian Tannus Lopes; Samad Lotia; Piet Molenaar; Jason Montojo; John H. Morris; Keiichiro Ono; et al. (F1000Research, 2014)

NeXO Web: the NeXO ontology database and visualization platform. - Janusz Dutkowski; Keiichiro Ono; Michael Kramer; Michael Yu; Dexter Pratt; Barry Demchak; Trey Ideker (Nucleic Acids Res., 2014)

cyNeo4j: connecting Neo4j and Cytoscape. - Georg Summer; Thomas Kelder; Keiichiro Ono; Marijana Radonjic; Stephane Heymans; Barry Demchak (Bioinform., 2015)

CyREST: Turbocharging Cytoscape Access for External Tools via a RESTful API. - Keiichiro Ono; Tanja Muetze; Georgi Kolishovski; Paul Shannon; Barry Demchak (F1000Research, 2015)

The Cytoscape Automation app article collection. - Barry Demchak; David Otasek; Alexander R. Pico; Gary D. Bader; Keiichiro Ono; Brett Settle; Eric Sage; John H. Morris; William J. R. Longabaugh; Christian Tannus Lopes; Michael Kucera; Adam Treister; et al. (F1000Research, 2018)

NDEx IQuery: a multi-method network gene set analysis leveraging the Network Data Exchange. - Rudolf T. Pillich; Jing Chen; Christopher Churas; Dylan Fong; Benjamin M. Gyori; Trey Ideker; Klas Karis; Sophie N. Liu; Keiichiro Ono; Alexander R. Pico; Dexter Pratt (Bioinform., 2023)