Now showing items 1-5 of 5

    • 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 ...
    • 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 ...
    • PATIKAmad: putting microarray data into pathway context 

      Babur, Özgün; Colak, Recep; Demir, Emek; Doğrusöz, Uğur (Wiley - V C H Verlag GmbH & Co. KGaA, 2008-06)
      High-throughput experiments, most significantly DNA microarrays, provide us with system-scale profiles. Connecting these data with existing biological networks poses a formidable challenge to uncover facts about a cell's ...
    • VISIBIOweb: visualization and layout services for BioPAX pathway models 

      Dilek, Alptuğ; Belviranlı, Mehmet E.; Doğrusöz, Uğur (Oxford University Press, 2010-06-01)
      With recent advancements in techniques for cellular data acquisition, information on cellular processes has been increasing at a dramatic rate. Visualization is critical to analyzing and interpreting complex information; ...