Now showing items 1-20 of 44

    • Abstract 207: the cBioPortal for cancer genomics 

      Gao, J.; Mazor, T.; de Bruijn, I.; Abeshouse, A.; Baiceanu, D.; Erkoç, Z.; Gross, B.; Higgins, D.; Jagannathan, P. K.; Kalletla, K.; Kumari, Priti; Kundra, R.; Li, X.; Lindsay, J.; Lisman, A.; Lukasse, P.; Madala, D.; Madupuri, R.; Ochoa, A.; Plantalech, O.; Quach, J.; Rodenburg, S.; Satravada, A.; Schaeffer, F.; Sheridan, R.; Sikina, L.; Sümer, S. O.; Sun, Y.; van Dijk, P.; van Nierop, P.; Wang, A.; Wilson, M.; Zhang, H.; Zhao, G.; van Hagen, S.; van Bochove, K.; Doğrusöz, Uğur; Heath, A.; Resnick, A.; Pugh, T. J.; Sander, C.; Cerami, E.; Schultz, N. (American Association for Cancer Research (AACR), 2021)
      The cBioPortal for Cancer Genomics is an open-source software platform that enables interactive, exploratory analysis of large-scale cancer genomics data sets with a user-friendly interface. It integrates genomic and ...
    • Algorithms for effective querying of compound graph-based pathway databases 

      Doğrusöz, Uğur; Çetintaş, Ahmet; Demir, Emek; Babur, Özgün (BioMed Central Ltd., 2009-11-16)
      Background: Graph-based pathway ontologies and databases are widely used to represent data about cellular processes. This representation makes it possible to programmatically integrate cellular networks and to investigate ...
    • Algorithms for layout of disconnected graphs 

      Doğrusöz, Uğur (Elsevier, 2000)
      We present efficient algorithms for the layout of disconnected objects in a graph (isolated nodes and components) for a specified aspect ratio. These linear and near-linear algorithms are based on alternate-bisection and ...
    • Analyzing causal relationships in proteomic profiles using CausalPath 

      Luna, A.; Siper, M. C.; Korkut, A.; Durupinar, F.; Aslan, J. E.; Sander, C.; Demir, E.; Babur, O.; Doğrusöz, Uğur (Cell Press, 2021-12-17)
      CausalPath (causalpath.org) evaluates proteomic measurements against prior knowledge of biological pathways and infers causality between changes in measured features, such as global protein and phospho-protein levels. It ...
    • The BioPAX community standard for pathway data sharing 

      Demir, Emek; Cary, M. P.; Paley, S.; Fukuda, K.; Lemer, C.; Vastrik, I.; Wu, G.; D'Eustachio, P.; Schaefer, C.; Luciano, J.; Schacherer, F.; Martinez-Flores, I.; Hu, Z.; Jimenez-Jacinto, V.; Joshi-Tope, G.; Kandasamy, K.; Lopez-Fuentes, A. C.; Mi, H.; Pichler, E.; Rodchenkov, I.; Splendiani, A.; Tkachev, S.; Zucker, J.; Gopinath, G.; Rajasimha, H.; Ramakrishnan, R.; Shah, I.; Syed, M.; Anwar, N.; Babur, Özgün; Blinov, M.; Brauner, E.; Corwin, D.; Donaldson, S.; Gibbons, F.; Goldberg, R.; Hornbeck, P.; Luna, A.; Murray-Rust, P.; Neumann, E.; Reubenacker, O.; Samwald, M.; Iersel, Martijn van; Wimalaratne, S.; Allen, K.; Braun, B.; Whirl-Carrillo, M.; Cheung, Kei-Hoi; Dahlquist, K.; Finney, A.; Gillespie, M.; Glass, E.; Gong, L.; Haw, R.; Honig, M.; Hubaut, O.; Kane, D.; Krupa, S.; Kutmon, M.; Leonard, J.; Marks, D.; Merberg, D.; Petri, V.; Pico, A.; Ravenscroft, D.; Ren, L.; Shah, N.; Sunshine, M.; Tang R.; Whaley, R.; Letovksy, S.; Buetow, K. H.; Rzhetsky, A.; Schachter, V.; Sobral, B. S.; Doğrusöz, Uğur; McWeeney, S.; Aladjem, M.; Birney, E.; Collado-Vides, J.; Goto, S.; Hucka, M.; Novère, Nicolas Le; Maltsev, N.; Pandey, A.; Thomas, P.; Wingender, E.; Karp, P. D.; Sander, C.; Bader, G. D. (Nature Publishing Group, 2010-09)
      Biological Pathway Exchange (BioPAX) is a standard language to represent biological pathways at the molecular and cellular level and to facilitate the exchange of pathway data. The rapid growth of the volume of pathway ...
    • Causal interactions from proteomic profiles: Molecular data meet pathway knowledge 

      Babur, Ö.; Luna, A.; Korkut, A.; Durupınar, F.; Siper, M. C.; Doğrusöz, Uğur; Jacome, A. S. V.; Peckner, R.; Christiansen, K. E.; Jaffe, J.D; Spellman, P.T.; Aslan, J. E.; Sander, C.; Demir, E. (Cell Press, 2021-06)
      We present a computational method to infer causal mechanisms in cell biology by analyzing changes in high-throughput proteomic profiles on the background of prior knowledge captured in biochemical reaction knowledge bases. ...
    • The cBioPortal for cancer genomics and its application in precision oncology 

      Gao, J.; Lindsay, J.; Watt, S.; Doğrusöz, Uğur; Lukasse, P.; Abeshouse, A.; Chen, H.; Bruijn, I.; Gross, B.; Li, D.; Kundra, R.; Heins, Z.; Reis-Filho, J.; Sumer, O.; Sun, Y.; Wang, J.; Wang, Q.; Zhang, H.; Kumari, P.; Şahin, Mehmet Furkan; Ridder, S.; Schaeffer, F.; Bochove, K.; Pugh, T.; Sander, C.; Cerami, E.; Schultz, N.; Bahçeci, İstemi (American Association for Cancer Research, 2016)
      Abstract The cBioPortal for Cancer Genomics provides intuitive visualization and analysis of complex cancer genomics data. The public site (http://cbioportal.org/) is accessed by more than 1,500 researchers per day, and ...
    • cd2sbgnml: Bidirectional conversion between CellDesigner and SBGN formats 

      Balaur, I.; Roy, L.; Mazein, A.; Karaca, S. Gökberk; Doğrusöz, Uğur; Barillot, E.; Zinovyev, A. (Oxford University Press, 2020-01)
      Motivation: CellDesigner is a well-established biological map editor used in many large-scale scientific efforts. However, the interoperability between the Systems Biology Graphical Notation (SBGN) Markup Language (SBGNML) ...
    • ChiBE: interactive visualization and manipulation of BioPAX pathway models 

      Babur, Özgün; Doğrusöz, Uğur; Demir, Emek; Sander, C. (Oxford University Press, 2010-02-01)
      SUMMARY: Representing models of cellular processes or pathways in a graphically rich form facilitates interpretation of biological observations and generation of new hypotheses. Solving biological problems using large ...
    • Collaborative workspaces for pathway curation 

      Durupınar-Babur, F.; Siper, Metin Can; Doğrusöz, Uğur; Bahceci, İstemi; Babur, O.; Demir, E. (CEUR-WS, 2016-08)
      We present a web based visual biocuration workspace, focusing on curating detailed mechanistic pathways. It was designed as a flexible platform where multiple humans, NLP and AI agents can collaborate in real-time on a ...
    • Combinatorial pattern matching: 15th annual symposium, CPM 2004 Istanbul, Turkey, july 5-7, 2004 proceedings 

      Şahinalp, S. C.; Muthukrishnan, S.; Doğrusöz, Uğur (Springer, Berlin, Heidelberg, 2004)
    • Community-driven roadmap for integrated disease maps 

      Ostaszewski, M.; Gebel, S.; Kuperstein, I.; Mazein, A.; Zinovyev, A.; Doğrusöz, Uğur; Hasenauer, J.; Fleming, R. M. T.; Novere, N. L.; Gawron, P.; Ligon, T.; Niarakis, A.; Nickerson, D.; Weindl, D.; Balling, R.; Barillot, E.; Auffray, C.; Schneider, R. (Oxford University Press, 2018)
      The Disease Maps Project builds on a network of scientific and clinical groups that exchange best practices, share information and develop systems biomedicine tools. The project aims for an integrated, highly curated and ...
    • A compound graph layout algorithm for biological pathways 

      Doğrusöz, Uğur; Giral, Erhan; Çetintaş, Ahmet; Çivril, Ali; Demir, Emek (Springer, Berlin, Heidelberg, 2004-09-10)
      We present a new compound graph layout algorithm based on traditional force-directed layout scheme with extensions for nesting and other application-specific constraints. The algorithm has been successfully implemented ...
    • A constrained, force-directed layout algorithm for biological pathways 

      Genç, Burkay; Doğrusöz, Uğur (Springer, Berlin, Heidelberg, 2004-09)
      We present a new elegant algorithm for layout of biological signaling pathways. It uses a force-directed layout scheme, taking into account directional and regional constraints enforced by different molecular interaction ...
    • CoSEP: a compound spring embedder layout algorithm with support for ports 

      Okka, Alihan; Doğrusöz, Uğur; Balcı, Hasan (Sage Publications, 2021-07-01)
      This paper describes a new automatic layout algorithm named CoSEP for compound graphs with port constraints. The algorithm works by extending the physical model of a previous algorithm named CoSE by defining additional ...
    • Disconnected graph layout and the polyomino packing approach 

      Freivalds, K.; Doğrusöz, Uğur; Kikusts, P. (Springer, Berlin, Heidelberg, 2002)
      We review existing algorithms and present a new approach for layout of disconnected graphs. The new approach is based on polyomino representation of components as opposed to rectangles. The parameters of our algorithm and ...
    • Discovering modulators of gene expression 

      Babur, Özgün; Demir, Emek; Gönen, M.; Sander, C.; Doğrusöz, Uğur (Oxford University Press, 2010-09-01)
      Proteins that modulate the activity of transcription factors, often called modulators, play a critical role in creating tissue- and context-specific gene expression responses to the signals cells receive. GEM (Gene Expression ...
    • Edge labeling in the graph layout toolkit 

      Doğrusöz, Uğur; Kakoulis, K. G.; Madden, B.; Tollis, I. G. (Springer, Berlin, Heidelberg, 1998)
      The Graph Layout Toolkit is a family of portable graph drawing and layout libraries designed for integration into graphical user interface application programs. When visualizing graphs, it becomes essential to communicate ...
    • Efficient methods and readily customizable libraries for managing complexity of large networks 

      Doğrusöz, Uğur; Karaçelik, Alper; Safarli, İlkin; Balcı, Hasan; Dervishi, Leonard; Siper, Metin Can (Public Library of Science, 2018)
      Background One common problem in visualizing real-life networks, including biological pathways, is the large size of these networks. Often times, users find themselves facing slow, non-scaling operations due to network ...
    • fCoSE: A fast compound graph layout algorithm with constraint support 

      Balcı, Hasan; Doğrusöz, Uğur (IEEE, 2021-07-07)
      Visual analysis of relational information is vital in most real-life analytics applications. Automatic layout is a key requirement for effective visual display of such information. This paper introduces a new layout algorithm ...