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

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

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

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

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

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

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

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

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

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

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

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

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

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