| 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 | 5205 | 2011 |
| 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 | 2824 | 2007 |
| 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 | 1579 | 2012 |
| 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 | 574 | 2010 |
| 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 | 423 | 2018 |
| 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 | 323 | 2011 |
| 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 | 266 | 2015 |
| 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 | 119 | 2013 |
| CyREST: turbocharging Cytoscape access for external tools via a RESTful API K Ono, T Muetze, G Kolishovski, P Shannon, B Demchak F1000Research 4, 478, 2015 | 96 | 2015 |
| KEGGscape: a Cytoscape app for pathway data integration K Nishida, K Ono, S Kanaya, K Takahashi F1000Research 3, 144, 2014 | 91 | 2014 |
| 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 | 61 | 2021 |
| 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 | 56 | 2011 |
| 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 | 55 | 2010 |
| 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 | 52 | 2013 |
| 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 | 49 | 2013 |
| Cytoscape tools for the web age: D3. js and Cytoscape. js exporters K Ono, B Demchak, T Ideker F1000Research 3, 143, 2014 | 47 | 2014 |
| 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), e87877, 2016 | 43 | 2016 |
| 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 | 37 | 2017 |
| cyNeo4j: connecting Neo4j and Cytoscape G Summer, T Kelder, K Ono, M Radonjic, S Heymans, B Demchak Bioinformatics 31 (23), 3868-3869, 2015 | 34 | 2015 |
| 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 | 33 | 2010 |
Trey IdekerUniversity of California San DiegoPatvirtintas el. paštas ucsd.edu
