RSTrace+: Reviewer suggestion using software artifact traceability graphs von Sülün, Emre, Tüzün, Eray, Doğrusöz, Uğur

Volltext

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

Volltext

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

Volltext

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

Volltext

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

Volltext

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

Volltext

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

Volltext

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

Volltext

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

Volltext

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

Volltext

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

Volltext

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

Volltext

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

Volltext

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

Volltext

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

Volltext

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

Volltext

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

Volltext

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

Volltext

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

Volltext

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

Volltext