Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal von Gao, Jianjiong, Aksoy, Bülent Arman, Dogrusoz, Ugur, Dresdner, Gideon, Gross, Benjamin, Sumer, S Onur, Sun, Yichao, Jacobsen, Anders, Sinha, Rileen, Larsson, Erik, Cerami, Ethan, Sander, Chris, Schultz, Nikolaus

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SyBLaRS: A web service for laying out, rendering and mining biological maps in SBGN, SBML and more von Balci, Hasan, Dogrusoz, Ugur, Ozgul, Yusuf Ziya, Atayev, Perman

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Pathway Commons 2019 Update: integration, analysis and exploration of pathway data von Rodchenkov, Igor, Babur, Ozgun, Luna, Augustin, Aksoy, Bulent Arman, Wong, Jeffrey V, Fong, Dylan, Franz, Max, Siper, Metin Can, Cheung, Manfred, Wrana, Michael, Mistry, Harsh, Mosier, Logan, Dlin, Jonah, Wen, Qizhi, O’Callaghan, Caitlin, Li, Wanxin, Elder, Geoffrey, Smith, Peter T, Dallago, Christian, Cerami, Ethan, Gross, Benjamin, Dogrusoz, Ugur, Demir, Emek, Bader, Gary D, Sander, Chris

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The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data von Cerami, Ethan, Gao, Jianjiong, Dogrusoz, Ugur, Gross, Benjamin E, Sumer, Selcuk Onur, Aksoy, Bülent Arman, Jacobsen, Anders, Byrne, Caitlin J, Heuer, Michael L, Larsson, Erik, Antipin, Yevgeniy, Reva, Boris, Goldberg, Arthur P, Sander, Chris, Schultz, Nikolaus

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The BioPAX community standard for pathway data sharing von Bader, Gary D, Demir, Emek, Cary, Michael P, Paley, Suzanne, Fukuda, Ken, Lemer, Christian, Vastrik, Imre, Wu, Guanming, D'Eustachio, Peter, Schaefer, Carl, Luciano, Joanne, Schacherer, Frank, Martinez-Flores, Irma, Hu, Zhenjun, Jimenez-Jacinto, Veronica, Joshi-Tope, Geeta, Kandasamy, Kumaran, Lopez-Fuentes, Alejandra C, Mi, Huaiyu, Pichler, Elgar, Rodchenkov, Igor, Splendiani, Andrea, Tkachev, Sasha, Zucker, Jeremy, Gopinath, Gopal, Rajasimha, Harsha, Ramakrishnan, Ranjani, Shah, Imran, Syed, Mustafa, Anwar, Nadia, Babur, Özgün, Blinov, Michael, Brauner, Erik, Corwin, Dan, Donaldson, Sylva, Gibbons, Frank, Goldberg, Robert, Hornbeck, Peter, Luna, Augustin, Murray-Rust, Peter, Neumann, Eric, Reubenacker, Oliver, Samwald, Matthias, van Iersel, Martijn, Wimalaratne, Sarala, Allen, Keith, Braun, Burk, Whirl-Carrillo, Michelle, Cheung, Kei-Hoi, Dahlquist, Kam, Finney, Andrew, Gillespie, Marc, Glass, Elizabeth, Gong, Li, Haw, Robin, Honig, Michael, Hubaut, Olivier, Kane, David, Krupa, Shiva, Kutmon, Martina, Leonard, Julie, Marks, Debbie, Merberg, David, Petri, Victoria, Pico, Alex, Ravenscroft, Dean, Ren, Liya, Shah, Nigam, Sunshine, Margot, Tang, Rebecca, Whaley, Ryan, Letovksy, Stan, Buetow, Kenneth H, Rzhetsky, Andrey, Schachter, Vincent, Sobral, Bruno S, Dogrusoz, Ugur, McWeeney, Shannon, Aladjem, Mirit, Birney, Ewan, Collado-Vides, Julio, Goto, Susumu, Hucka, Michael, Novère, Nicolas Le, Maltsev, Natalia, Pandey, Akhilesh, Thomas, Paul, Wingender, Edgar, Karp, Peter D, Sander, Chris

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CoSEP: A compound spring embedder layout algorithm with support for ports von Okka, Alihan, Dogrusoz, Ugur, Balci, Hasan

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Efficient methods and readily customizable libraries for managing complexity of large networks von Dogrusoz, Ugur, Karacelik, Alper, Safarli, Ilkin, Balci, Hasan, Dervishi, Leonard, Siper, Metin Can

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SBGNViz: A Tool for Visualization and Complexity Management of SBGN Process Description Maps von Sari, Mecit, Bahceci, Istemi, Dogrusoz, Ugur, Sumer, Selcuk Onur, Aksoy, Bülent Arman, Babur, Özgün, Demir, Emek

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fCoSE: A Fast Compound Graph Layout Algorithm with Constraint Support von Balci, Hasan, Dogrusoz, Ugur

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Causal interactions from proteomic profiles: Molecular data meet pathway knowledge von Babur, Özgün, Luna, Augustin, Korkut, Anil, Durupinar, Funda, Siper, Metin Can, Dogrusoz, Ugur, Vaca Jacome, Alvaro Sebastian, Peckner, Ryan, Christianson, Karen E., Jaffe, Jacob D., Spellman, Paul T., Aslan, Joseph E., Sander, Chris, Demir, Emek

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Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0 von Rougny, Adrien, Touré, Vasundra, Moodie, Stuart, Balaur, Irina, Czauderna, Tobias, Borlinghaus, Hanna, Dogrusoz, Ugur, Mazein, Alexander, Dräger, Andreas, Blinov, Michael L, Villéger, Alice, Haw, Robin, Demir, Emek, Mi, Huaiyu, Sorokin, Anatoly, Schreiber, Falk, Luna, Augustin

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Algorithms for effective querying of compound graph-based pathway databases von Dogrusoz, Ugur, Cetintas, Ahmet, Demir, Emek, Babur, Ozgun

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Software support for SBGN maps: SBGN-ML and LibSBGN von van Iersel, Martijn P, Villéger, Alice C, Czauderna, Tobias, Boyd, Sarah E, Bergmann, Frank T, Luna, Augustin, Demir, Emek, Sorokin, Anatoly, Dogrusoz, Ugur, Matsuoka, Yukiko, Funahashi, Akira, Aladjem, Mirit I, Mi, Huaiyu, Moodie, Stuart L, Kitano, Hiroaki, Le Novère, Nicolas, Schreiber, Falk

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A guide for developing comprehensive systems biology maps of disease mechanisms: planning, construction and maintenance von Mazein, Alexander, Acencio, Marcio Luis, Balaur, Irina, Rougny, Adrien, Welter, Danielle, Niarakis, Anna, Ramirez Ardila, Diana, Dogrusoz, Ugur, Gawron, Piotr, Satagopam, Venkata, Gu, Wei, Kremer, Andreas, Schneider, Reinhard, Ostaszewski, Marek

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Systems biology graphical notation markup language (SBGNML) version 0.3 von Bergmann, Frank T., Czauderna, Tobias, Dogrusoz, Ugur, Rougny, Adrien, Dräger, Andreas, Touré, Vasundra, Mazein, Alexander, Blinov, Michael L., Luna, Augustin

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Analyzing causal relationships in proteomic profiles using CausalPath von Luna, Augustin, Siper, Metin Can, Korkut, Anil, Durupinar, Funda, Dogrusoz, Ugur, Aslan, Joseph E., Sander, Chris, Demir, Emek, Babur, Ozgun

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Combinatorial Pattern Matching: 15th Annual Symposium, CPM 2004, Istanbul, Turkey, July 5-7, 2004, Proceedings von Sahinalp, Suleyman C, Muthukrishnan, S, Dogrusoz, Ugur

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An algorithm for automated layout of process description maps drawn in SBGN von Genc, Begum, Dogrusoz, Ugur

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Abstract 5277: The cBioPortal for cancer genomics and its application in precision oncology von Gao, Jianjiong, Lindsay, James, Watt, Stuart, Bahceci, Istemi, Lukasse, Pieter, Abeshouse, Adam, Chen, Hsiao-Wei, de Bruijn, Ino, Gross, Benjamin, Li, Dong, Kundra, Ritika, Heins, Zachary, Reis-Filho, Jorge, Sumer, Onur, Sun, Yichao, Wang, Jiaojiao, Wang, Qingguo, Zhang, Hongxin, Kumari, Priti, Sahin, M. Furkan, de Ridder, Sander, Schaeffer, Fedde, van Bochove, Kees, Dogrusoz, Ugur, Pugh, Trevor, Sander, Chris, Cerami, Ethan, Schultz, Nikolaus

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Oncogenic Signaling Pathways in The Cancer Genome Atlas von Chatila, Walid K., Luna, Augustin, Kantheti, Havish S., Daian, Foysal, Shmulevich, Ilya, Greene, Casey S., Iavarone, Antonio, Tward, Aaron D., Meyerson, Matthew, Sofia, Heidi J., Zenklusen, Jean C., Pihl, Todd, Meier, Sam, Noble, Michael S., Kramer, Roger, Hegde, Apurva M., Li, Jun, Rao, Arvind, Abeshouse, Adam, Schultz, Nikolaus, Taylor, Barry S., Stuart, Joshua M., Wong, Christopher K., Parker, Joel S., Carlsen, Rebecca, Tam, Angela, Gabriel, Stacey B., Ha, Gavin, Schumacher, Steven E., Maglinte, Dennis T., Balu, Saianand, Skelly, Tara, Laird, Peter W., Lewis, Lora, Muzny, Donna, Santibanez, Jireh, Wang, Min, Morris, Scott, Shelton, Candace, Gerken, Mark, Costello, Tony, Reis, Rui M., Scapulatempo-Neto, Cristovam, Singh, Rosy, Duffy, Elizabeth R., Setdikova, Galiya, Devine, Karen, Ostrom, Quinn T., Deyarmin, Brenda, Kvecher, Leonid, Mural, Richard J., Latour, Mathieu, Lacombe, Louis, Lipp, Eric, Marks, Jeffrey, Pickens, Alan, Shin, Dong M., Zhang, Hongzheng, Calatozzolo, Chiara, Cuzzubbo, Stefania, Kycler, Witold, Giné, Eva, Beuschlein, Felix, Borad, Mitesh, Chandan, Vishal, Farnell, Michael, Torbenson, Michael, Logothetis, Christopher, Rice, David, Jakrot, Valerie, Mann, Graham, Moncrieff, Marc, Doruc, Serghei, Bartlett, John, Parfitt, Jeremy, Bifulco, Carlo, Hayward, Nicholas, Grazi, Gianluca, Marino, Mirella, Naska, Theresa, Borgia, Jeffrey A., Pool, Mark, Gaudio, Eugenio, Bell, Sue, Hilty, Joe, Sexton, Katherine C., Asa, Sylvia L., Schlomm, Thorsten, Prados, Michael, Smith-McCune, Karen, Bossler, Aaron, Moxley, Katherine, Carlotti, Carlos Gilberto, Swisher, Elizabeth, Korst, Robert, Rathmell, W. Kimryn, Heath, Sharon, Aredes, Natália D., Mariamidze, Armaz, Van Allen, Eliezer M.

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