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Keiichiro Ono
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Cytoscape 2.8: new features for data integration and network visualization
ME Smoot, K Ono, J Ruscheinski, PL Wang, T Ideker
Bioinformatics 27 (3), 431-432, 2011
50182011
Integration of biological networks and gene expression data using Cytoscape
MS Cline, M Smoot, E Cerami, A Kuchinsky, N Landys, C Workman, ...
Nature protocols 2 (10), 2366-2382, 2007
27312007
A travel guide to Cytoscape plugins
R Saito, ME Smoot, K Ono, J Ruscheinski, PL Wang, S Lotia, AR Pico, ...
Nature methods 9 (11), 1069-1076, 2012
14892012
Functional genomic screen for modulators of ciliogenesis and cilium length
J Kim, JE Lee, S Heynen-Genel, E Suyama, K Ono, KY Lee, T Ideker, ...
Nature 464 (7291), 1048-1051, 2010
5602010
Using deep learning to model the hierarchical structure and function of a cell
J Ma, MK Yu, S Fong, K Ono, E Sage, B Demchak, R Sharan, T Ideker
Nature methods 15 (4), 290-298, 2018
3792018
PSICQUIC and PSISCORE: accessing and scoring molecular interactions
B Aranda, H Blankenburg, S Kerrien, FSL Brinkman, A Ceol, E Chautard, ...
Nature methods 8 (7), 528-529, 2011
3142011
NDEx, the network data exchange
D Pratt, J Chen, D Welker, R Rivas, R Pillich, V Rynkov, K Ono, C Miello, ...
Cell systems 1 (4), 302-305, 2015
2452015
A new reference implementation of the PSICQUIC web service
N del-Toro, M Dumousseau, S Orchard, RC Jimenez, E Galeota, ...
Nucleic acids research 41 (W1), W601-W606, 2013
1132013
CyREST: turbocharging Cytoscape access for external tools via a RESTful API
K Ono, T Muetze, G Kolishovski, P Shannon, B Demchak
F1000Research 4, 2015
922015
KEGGscape: a Cytoscape app for pathway data integration
K Nishida, K Ono, S Kanaya, K Takahashi
F1000Research 3, 2014
792014
The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows
T Katayama, K Arakawa, M Nakao, K Ono, KF Aoki-Kinoshita, ...
Journal of biomedical semantics 1, 1-19, 2010
542010
Landscape of protein–protein interactions in Drosophila immune deficiency signaling during bacterial challenge
H Fukuyama, Y Verdier, Y Guan, C Makino-Okamura, V Shilova, X Liu, ...
Proceedings of the National Academy of Sciences 110 (26), 10717-10722, 2013
522013
PiNGO: a Cytoscape plugin to find candidate genes in biological networks
M Smoot, K Ono, T Ideker, S Maere
Bioinformatics 27 (7), 1030-1031, 2011
512011
The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies
T Katayama, MD Wilkinson, G Micklem, S Kawashima, A Yamaguchi, ...
Journal of biomedical semantics 4, 1-17, 2013
492013
Cytoscape tools for the web age: D3. js and Cytoscape. js exporters
K Ono, B Demchak, T Ideker
F1000Research 3, 2014
442014
Systems biology analysis reveals role of MDM2 in diabetic nephropathy
R Saito, A Rocanin-Arjo, YH You, M Darshi, B Van Espen, S Miyamoto, ...
JCI insight 1 (17), 2016
402016
Interpretation of cancer mutations using a multiscale map of protein systems
F Zheng, MR Kelly, DJ Ramms, ML Heintschel, K Tao, B Tutuncuoglu, ...
Science 374 (6563), eabf3067, 2021
372021
Active interaction mapping reveals the hierarchical organization of autophagy
MH Kramer, JC Farre, K Mitra, MK Yu, K Ono, B Demchak, K Licon, ...
Molecular cell 65 (4), 761-774. e5, 2017
372017
Evidence mining and novelty assessment of protein–protein interactions with the ConsensusPathDB plugin for Cytoscape
K Pentchev, K Ono, R Herwig, T Ideker, A Kamburov
Bioinformatics 26 (21), 2796-2797, 2010
332010
cyNeo4j: connecting Neo4j and Cytoscape
G Summer, T Kelder, K Ono, M Radonjic, S Heymans, B Demchak
Bioinformatics 31 (23), 3868-3869, 2015
322015
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Articles 1–20