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    Keiichiro Ono

    TitleProgrammer Analyst 4
    SchoolUniversity of California, San Diego
    DepartmentMedicine
    Address9500 Gilman Drive #0688
    CA La Jolla 92093
    Phone858-822-4705
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      Collapse Bibliographic 
      Collapse Publications
      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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      1. Kramer MH, Farré JC, Mitra K, Yu MK, Ono K, Demchak B, Licon K, Flagg M, Balakrishnan R, Cherry JM, Subramani S, Ideker T. Active Interaction Mapping Reveals the Hierarchical Organization of Autophagy. Mol Cell. 2017 Jan 23. PMID: 28132844.
        View in: PubMed
      2. Saito R, Rocanin-Arjo A, You YH, Darshi M, Van Espen B, Miyamoto S, Pham J, Pu M, Romoli S, Natarajan L, Ju W, Kretzler M, Nelson R, Ono K, Thomasova D, Mulay SR, Ideker T, D'Agati V, Beyret E, Belmonte JC, Anders HJ, Sharma K. Systems biology analysis reveals role of MDM2 in diabetic nephropathy. JCI Insight. 2016 Oct 20; 1(17):e87877. PMID: 27777973.
        View in: PubMed
      3. Pratt D, Chen J, Welker D, Rivas R, Pillich R, Rynkov V, Ono K, Miello C, Hicks L, Szalma S, Stojmirovic A, Dobrin R, Braxenthaler M, Kuentzer J, Demchak B, Ideker T. NDEx, the Network Data Exchange. Cell Syst. 2015 Oct 28; 1(4):302-305. PMID: 26594663.
        View in: PubMed
      4. Summer G, Kelder T, Ono K, Radonjic M, Heymans S, Demchak B. cyNeo4j: connecting Neo4j and Cytoscape. Bioinformatics. 2015 Dec 01; 31(23):3868-9. PMID: 26272981; PMCID: PMC4653389.
      5. Ono K, Muetze T, Kolishovski G, Shannon P, Demchak B. CyREST: Turbocharging Cytoscape Access for External Tools via a RESTful API. F1000Res. 2015; 4:478. PMID: 26672762; PMCID: PMC4670004.
      6. Nishida K, Ono K, Kanaya S, Takahashi K. KEGGscape: a Cytoscape app for pathway data integration. F1000Res. 2014; 3:144. PMID: 25177485; PMCID: PMC4141640.
      7. Ono K, Demchak B, Ideker T. Cytoscape tools for the web age: D3.js and Cytoscape.js exporters. F1000Res. 2014; 3:143. PMID: 25520778.
        View in: PubMed
      8. Pico AR, Bader GD, Demchak B, Guitart Pla O, Hull T, Longabaugh W, Lopes C, Lotia S, Molenaar P, Montojo J, Morris JH, Ono K, Schwikowski B, Welker D, Ideker T. The Cytoscape app article collection. F1000Res. 2014; 3:138. PMID: 25580224.
        View in: PubMed
      9. Dutkowski J, Ono K, Kramer M, Yu M, Pratt D, Demchak B, Ideker T. NeXO Web: the NeXO ontology database and visualization platform. Nucleic Acids Res. 2014 Jan 1; 42(1):D1269-74. PMID: 24271398.
        View in: PubMed
      10. del-Toro N, Dumousseau M, Orchard S, Jimenez RC, Galeota E, Launay G, Goll J, Breuer K, Ono K, Salwinski L, Hermjakob H. A new reference implementation of the PSICQUIC web service. Nucleic Acids Res. 2013 Jul; 41(Web Server issue):W601-6. PMID: 23671334; PMCID: PMC3977660.
      11. Saito R, Smoot ME, Ono K, Ruscheinski J, Wang PL, Lotia S, Pico AR, Bader GD, Ideker T. A travel guide to Cytoscape plugins. Nat Methods. 2012 Nov; 9(11):1069-76. PMID: 23132118.
        View in: PubMed
      12. Aranda B, Blankenburg H, Kerrien S, Brinkman FS, Ceol A, Chautard E, Dana JM, De Las Rivas J, Dumousseau M, Galeota E, Gaulton A, Goll J, Hancock RE, Isserlin R, Jimenez RC, Kerssemakers J, Khadake J, Lynn DJ, Michaut M, O'Kelly G, Ono K, Orchard S, Prieto C, Razick S, Rigina O, Salwinski L, Simonovic M, Velankar S, Winter A, Wu G, Bader GD, Cesareni G, Donaldson IM, Eisenberg D, Kleywegt GJ, Overington J, Ricard-Blum S, Tyers M, Albrecht M, Hermjakob H. PSICQUIC and PSISCORE: accessing and scoring molecular interactions. Nat Methods. 2011 Jun 29; 8(7):528-9. PMID: 21716279; NIHMSID: NIHMS345023.
        View in: PubMed
      13. Smoot M, Ono K, Ideker T, Maere S. PiNGO: a Cytoscape plugin to find candidate genes in biological networks. Bioinformatics. 2011 Apr 1; 27(7):1030-1. PMID: 21278188.
        View in: PubMed
      14. Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T. Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics. 2011 Feb 1; 27(3):431-2. PMID: 21149340.
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      15. Pentchev K, Ono K, Herwig R, Ideker T, Kamburov A. Evidence mining and novelty assessment of protein-protein interactions with the ConsensusPathDB plugin for Cytoscape. Bioinformatics. 2010 Nov 1; 26(21):2796-7. PMID: 20847220.
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      16. Kim J, Lee JE, Heynen-Genel S, Suyama E, Ono K, Lee K, Ideker T, Aza-Blanc P, Gleeson JG. Functional genomic screen for modulators of ciliogenesis and cilium length. Nature. 2010 Apr 15; 464(7291):1048-51. PMID: 20393563.
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      17. Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, Hanspers K, Isserlin R, Kelley R, Killcoyne S, Lotia S, Maere S, Morris J, Ono K, Pavlovic V, Pico AR, Vailaya A, Wang PL, Adler A, Conklin BR, Hood L, Kuiper M, Sander C, Schmulevich I, Schwikowski B, Warner GJ, Ideker T, Bader GD. Integration of biological networks and gene expression data using Cytoscape. Nat Protoc. 2007; 2(10):2366-82. PMID: 17947979.
        View in: PubMed