Using deep learning to model the hierarchical structure and function of a cell von Ma, Jianzhu, Yu, Michael Ku, Fong, Samson, Ono, Keiichiro, Sage, Eric, Demchak, Barry, Sharan, Roded, Ideker, Trey

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Cytoscape 2.8: new features for data integration and network visualization von SMOOT, Michael E, ONO, Keiichiro, RUSCHEINSKI, Johannes, WANG, Peng-Liang, IDEKER, Trey

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Functional genomic screen for modulators of ciliogenesis and cilium length von Gleeson, Joseph G, Kim, Joon, Lee, Ji Eun, Heynen-Genel, Susanne, Suyama, Eigo, Ono, Keiichiro, Lee, KiYoung, Ideker, Trey, Aza-Blanc, Pedro

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Integration of biological networks and gene expression data using Cytoscape von Ideker, Trey, Cline, Melissa S, Smoot, Michael, Cerami, Ethan, Kuchinsky, Allan, Landys, Nerius, Workman, Chris, Christmas, Rowan, Avila-Campilo, Iliana, Creech, Michael, Gross, Benjamin, Hanspers, Kristina, Isserlin, Ruth, Kelley, Ryan, Killcoyne, Sarah, Lotia, Samad, Maere, Steven, Morris, John, Ono, Keiichiro, Pavlovic, Vuk, Pico, Alexander R, Vailaya, Aditya, Wang, Peng-Liang, Adler, Annette, Conklin, Bruce R, Hood, Leroy, Kuiper, Martin, Sander, Chris, Schmulevich, Ilya, Schwikowski, Benno, Warner, Guy J, Bader, Gary D

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PSICQUIC and PSISCORE: accessing and scoring molecular interactions von Aranda, Bruno, Blankenburg, Hagen, Kerrien, Samuel, Brinkman, Fiona S L, Ceol, Arnaud, Chautard, Emilie, Dana, Jose M, De Las Rivas, Javier, Dumousseau, Marine, Galeota, Eugenia, Gaulton, Anna, Goll, Johannes, Hancock, Robert E W, Isserlin, Ruth, Jimenez, Rafael C, Kerssemakers, Jules, Khadake, Jyoti, Lynn, David J, Michaut, Magali, O'Kelly, Gavin, Ono, Keiichiro, Orchard, Sandra, Prieto, Carlos, Razick, Sabry, Rigina, Olga, Salwinski, Lukasz, Simonovic, Milan, Velankar, Sameer, Winter, Andrew, Wu, Guanming, Bader, Gary D, Cesareni, Gianni, Donaldson, Ian M, Eisenberg, David, Kleywegt, Gerard J, Overington, John, Ricard-Blum, Sylvie, Tyers, Mike, Albrecht, Mario, Hermjakob, Henning

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KEGGscape: a Cytoscape app for pathway data integration [version 1; peer review: 1 approved, 2 approved with reservations] von Nishida, Kozo, Ono, Keiichiro, Kanaya, Shigehiko, Takahashi, Koichi

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CyREST: Turbocharging Cytoscape Access for External Tools via a RESTful API von Ono, Keiichiro, Muetze, Tanja, Kolishovski, Georgi, Shannon, Paul, Demchak, Barry

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Active Interaction Mapping Reveals the Hierarchical Organization of Autophagy von Kramer, Michael H., Farré, Jean-Claude, Mitra, Koyel, Yu, Michael Ku, Ono, Keiichiro, Demchak, Barry, Licon, Katherine, Flagg, Mitchell, Balakrishnan, Rama, Cherry, J. Michael, Subramani, Suresh, Ideker, Trey

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The Cytoscape Automation app article collection [version 1; peer review: not peer reviewed] von Demchak, Barry, Otasek, David, Pico, Alexander R, Bader, Gary D, Ono, Keiichiro, Settle, Brett, Sage, Eric, Morris, John H, Longabaugh, William, Lopes, Christian, Kucera, Michael, Treister, Adam, Schwikowski, Benno, Molenaar, Piet, Ideker, Trey

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A new reference implementation of the PSICQUIC web service von del-Toro, Noemi, Dumousseau, Marine, Orchard, Sandra, Jimenez, Rafael C., Galeota, Eugenia, Launay, Guillaume, Goll, Johannes, Breuer, Karin, Ono, Keiichiro, Salwinski, Lukasz, Hermjakob, Henning

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The Cytoscape app article collection [version 1; peer review: not peer reviewed] von Pico, Alexander R, Bader, Gary D, Demchak, Barry, Guitart Pla, Oriol, Hull, Timothy, Longabaugh, William, Lopes, Christian, Lotia, Samad, Molenaar, Piet, Montojo, Jason, Morris, John H, Ono, Keiichiro, Schwikowski, Benno, Welker, David, Ideker, Trey

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Abstract 3206: IQuery: A tool aggregating multiple gene set analysis methods, based on networks and pathways in a community-driven public data repository von Pratt, Dexter R., Ono, Keiichiro, Liu, Sophie, Chen, Jing, Churas, Christopher

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

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cyNeo4j: connecting Neo4j and Cytoscape von Summer, Georg, Kelder, Thomas, Ono, Keiichiro, Radonjic, Marijana, Heymans, Stephane, Demchak, Barry

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NDEx, the Network Data Exchange von Pratt, Dexter, Chen, Jing, Welker, David, Rivas, Ricardo, Pillich, Rudolf, Rynkov, Vladimir, Ono, Keiichiro, Miello, Carol, Hicks, Lyndon, Szalma, Sandor, Stojmirovic, Aleksandar, Dobrin, Radu, Braxenthaler, Michael, Kuentzer, Jan, Demchak, Barry, Ideker, Trey

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A new reference implementation of the PSICQUIC web service von del-Toro, Noemi, Dumousseau, Marine, Orchard, Sandra, Jimenez, Rafael C, Galeota, Eugenia, Launay, Guillaume, Goll, Johannes, Breuer, Karin, Ono, Keiichiro, Salwinski, Lukasz, Hermjakob, Henning

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Abstract PR14: A multiscale map of recurrently mutated systems in cancer von Zheng, Fan, Ono, Keiichiro, Silva, Erica, Swaney, Danielle, Kim, Minkyu, Shangguan, Julia, Pratt, Dexter, Nan, Xiaolin, Krogan, Nevan, Ideker, Trey

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Interpretation of cancer mutations using a multiscale map of protein systems von Zheng, Fan, Kelly, Marcus R., Ramms, Dana J., Heintschel, Marissa L., Tao, Kai, Tutuncuoglu, Beril, Lee, John J., Ono, Keiichiro, Foussard, Helene, Chen, Michael, Herrington, Kari A., Silva, Erica, Liu, Sophie N., Chen, Jing, Churas, Christopher, Wilson, Nicholas, Kratz, Anton, Pillich, Rudolf T., Patel, Devin N., Park, Jisoo, Kuenzi, Brent, Yu, Michael K., Licon, Katherine, Pratt, Dexter, Kreisberg, Jason F., Kim, Minkyu, Swaney, Danielle L., Nan, Xiaolin, Fraley, Stephanie, Gutkind, J. Silvio, Krogan, Nevan J., Ideker, Trey

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NDEx: Accessing Network Models and Streamlining Network Biology Workflows von Pillich, Rudolf T., Chen, Jing, Churas, Christopher, Liu, Sophie, Ono, Keiichiro, Otasek, David, Pratt, Dexter

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Abstract 1317: Multi-scale mapping of the physical and functional architecture of the cancer cell von Zheng, Fan, Yu, Michael K., Kim, Minkyu, Ono, Keiichiro, Flagg, Mitchell, Kreisberg, Jason F., Krogan, Nevan, Ideker, Trey

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