Now showing items 1-3 of 3

    • 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 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 ...
    • 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 ...