Now showing items 1-20 of 37

    • 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 ...
    • 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 ...
    • 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 ...
    • 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 ...
    • A framework for complexity management in graph visualization 

      Doğrusöz, Uğur; Genç, Burkay (Springer, Berlin, Heidelberg, 2002)
      We present a comprehensive framework for development of complexity management techniques in graph visualization tools. The presented architecture is capable of managing multiple associated graphs with navigation links and ...
    • Graph drawing contest report 

      Doğrusöz, Uğur; Duncan, C. A.; Gutwenger, C.; Sander, G. (Springer, 2009-09)
      This report describes the 15th Annual Graph Drawing Contest, held in conjunction with the 2008 Graph Drawing Symposium in Heraklion, Crete, Greece. The purpose of the contest is to monitor and challenge the current state ...
    • Hydra: Detecting fraud in financial transactions via graph based representation and visual analysis 

      Canbaz, Yusuf Sait; Doğrusöz, Uğur; Çeliksoy, M.; Güngör, F.; Kurban, K. (IEEE, 2020)
      In this paper, we describe a web based tool named Hydra for analyzing financial transaction data with the aim to detect or verify fraudulent activities via visual analysis and graph based querying. Hydra exclusively uses ...
    • A layout algorithm for signaling pathways 

      Genç, Burkay; Doğrusöz, Uğur (Elsevier, 2006-01-20)
      Visualization is crucial to the effective analysis of biological pathways. A poorly laid out pathway confuses the user, while a well laid out one improves the user's comprehension of the underlying biological phenomenon. ...
    • A layout algorithm for undirected compound graphs 

      Doğrusöz, Uğur; Giral, Erhan; Çetintaş, Ahmet; Civril, Ali; Demir, Emek (Elsevier, 2009-03-15)
      We present an algorithm for the layout of undirected compound graphs, relaxing restrictions of previously known algorithms in regards to topology and geometry. The algorithm is based on the traditional force-directed layout ...