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2020 – today
- 2023
[j9]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:
NDEx IQuery: a multi-method network gene set analysis leveraging the Network Data Exchange. Bioinform. 39(3) (2023)
2010 – 2019
- 2018
- [i5]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, Benno Schwikowski, Piet Molenaar, Trey Ideker:
The Cytoscape Automation app article collection. F1000Research 7: 800 (2018) - 2015
- [j8]Georg Summer, Thomas Kelder, Keiichiro Ono, Marijana Radonjic, Stephane Heymans, Barry Demchak:
cyNeo4j: connecting Neo4j and Cytoscape. Bioinform. 31(23): 3868-3869 (2015) - [i4]Keiichiro Ono, Tanja Muetze, Georgi Kolishovski, Paul Shannon, Barry Demchak:
CyREST: Turbocharging Cytoscape Access for External Tools via a RESTful API. F1000Research 4: 478 (2015) - 2014
- [j7]Janusz Dutkowski, Keiichiro Ono, Michael Kramer, Michael Yu, Dexter Pratt, Barry Demchak, Trey Ideker:
NeXO Web: the NeXO ontology database and visualization platform. Nucleic Acids Res. 42(Database-Issue): 1269-1274 (2014) - [i3]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, Benno Schwikowski, David Welker, Trey Ideker:
The Cytoscape app article collection. F1000Research 3: 138 (2014) - [i2]Keiichiro Ono, Barry Demchak, Trey Ideker:
Cytoscape tools for the web age: D3.js and Cytoscape.js exporters. F1000Research 3: 143 (2014) - [i1]Kozo Nishida, Keiichiro Ono, Shigehiko Kanaya, Koichi Takahashi:
KEGGscape: a Cytoscape app for pathway data integration. F1000Research 3: 144 (2014) - 2013
- [j6]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:
A new reference implementation of the PSICQUIC web service. Nucleic Acids Res. 41(Webserver-Issue): 601-606 (2013) - 2011
- [j5]Michael E. Smoot, Keiichiro Ono, Johannes Ruscheinski, Peng-Liang Wang, Trey Ideker:
Cytoscape 2.8: new features for data integration and network visualization. Bioinform. 27(3): 431-432 (2011) - [j4]Michael E. Smoot, Keiichiro Ono, Trey Ideker, Steven Maere:
PiNGO: a Cytoscape plugin to find candidate genes in biological networks. Bioinform. 27(7): 1030-1031 (2011) - [j3]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, Kazuharu Arakawa, Bruno Aranda, Raoul Jean Pierre Bonnal, José María Fernández, Takatomo Fujisawa, Paul M. K. Gordon, Naohisa Goto, Syed Haider, Todd W. Harris, Takashi Hatakeyama, Isaac Ho, Masumi Itoh, Arek Kasprzyk, Nobuhiro Kido, Young-Joo Kim, Akira R. Kinjo, Fumikazu Konishi, Yulia Kovarskaya, Gregory Von Kuster, Alberto Labarga, Vachiranee Limviphuvadh, E. Luke McCarthy, Yasukazu Nakamura, Yunsun Nam, Kozo Nishida, Kunihiro Nishimura, Tatsuya Nishizawa, Soichi Ogishima, Tom Oinn, Shinobu Okamoto, Shujiro Okuda, Keiichiro Ono, Kazuki Oshita, Keun-Joon Park, Nicholas H. Putnam, Martin Senger, Jessica Severin, Yasumasa Shigemoto, Hideaki Sugawara, James Taylor, Oswaldo Trelles, Chisato Yamasaki, Riu Yamashita, Noriyuki Satoh, Toshihisa Takagi:
The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications. J. Biomed. Semant. 2: 4 (2011) - 2010
- [j2]Konstantin Pentchev, Keiichiro Ono, Ralf Herwig, Trey Ideker, Atanas Kamburov:
Evidence mining and novelty assessment of protein-protein interactions with the ConsensusPathDB plugin for Cytoscape. Bioinform. 26(21): 2796-2797 (2010) - [j1]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, Raoul Jean Pierre Bonnal, Richard M. Bruskiewich, Jan Christian Bryne, José María Fernández, Akira Funahashi, Paul M. K. Gordon, Naohisa Goto, Andreas Groscurth, Alex Gutteridge, Richard C. G. Holland, Yoshinobu Kano, Edward A. Kawas, Arnaud Kerhornou, Eri Kibukawa, Akira R. Kinjo, Michael Kuhn, Hilmar Lapp, Heikki Lehväslaiho, Hiroyuki Nakamura, Yasukazu Nakamura, Tatsuya Nishizawa, Chikashi Nobata, Tamotsu Noguchi, Thomas M. Oinn, Shinobu Okamoto, Stuart Owen, Evangelos Pafilis, Matthew R. Pocock, Pjotr Prins, René Ranzinger, Florian Reisinger, Lukasz Salwínski, Mark J. Schreiber, Martin Senger, Yasumasa Shigemoto, Daron M. Standley, Hideaki Sugawara, Toshiyuki Tashiro, Oswaldo Trelles, Rutger A. Vos, Mark D. Wilkinson, William S. York, Christian M. Zmasek, Kiyoshi Asai, Toshihisa Takagi:
The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. J. Biomed. Semant. 1: 8 (2010)
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