Now showing items 1-6 of 6

    • Algorithms for effective querying of compound graph-based pathway databases 

      Dogrusoz, U.; Cetintas, A.; Demir, E.; Babur, O. (BioMed Central Ltd., 2009)
      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 ...
    • The BioPAX community standard for pathway data sharing 

      Demir, E.; 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, Ö.; 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.; Dogrusoz, U.; 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)
      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 ...
    • A compound graph layout algorithm for biological pathways 

      Doğrusöz, Uğur; Giral, Erhan; Çetintaş, Ahmet; Çivril, Ali; Demir, Emek (Springer, Berlin, Heidelberg, 2004)
      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 ...
    • Data and model driven hybrid approach to activity scoring of cyclic pathways 

      Işık, Z.; Atalay V.; Aykanat, Cevdet; Çetin-Atalay, Rengül (Springer, Dordrecht, 2010)
      Analysis of large scale -omics data based on a single tool remains inefficient to reveal molecular basis of cellular events. Therefore, data integration from multiple heterogeneous sources is highly desirable and required. ...
    • A layout algorithm for undirected compound graphs 

      Dogrusoz, U.; Giral, E.; Cetintas, A.; Civril, A.; Demir, E. (Elsevier Inc., 2009-03)
      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 ...
    • A signal transduction score flow algorithm for cyclic cellular pathway analysis, which combines transcriptome and ChIP-seq data 

      Isik, Z.; Ersahin, T.; Atalay, V.; Aykanat, C.; Cetin Atalay, R. (Royal Society of Chemistry, 2012)
      Determination of cell signalling behaviour is crucial for understanding the physiological response to a specific stimulus or drug treatment. Current approaches for large-scale data analysis do not effectively incorporate ...