Now showing items 1-6 of 6

    • Clustering protein-protein interactions based on conversed domain similarities 

      Ayaz, Aslı (Bilkent University, 2004)
      Protein interactions govern most cellular processes, including signal transduction, transcriptional regulation and metabolism. Saccharomyces ceravisae is estimated to have 16,000 protein interactions. Appereantly only a ...
    • Microarray data analysis and pathway activity inference in PATIKA 

      Babur, Özgün; Demir, Emek; Ayaz, Aslı; Doğrusöz, Uğur; Sakarya, Onur (ISCB Org, 2004)
      Pathway activity inference attempts to infer differential activity of cellular networks, given a qualitative state - transition model of the network and an expression profile of RNA molecules. We present an efficient ...
    • An ontology for collaborative construction and analysis of cellular pathways 

      Demir, Emek; Babur, Özgün; Doğrusöz, Uğur; Gürsoy, Atilla; Ayaz, Aslı; Güleşır, Gürcan; Nişancı, Gürkan; Çetin Atalay, Rengül (Oxford University Press, 2004-02-12)
      Motivation: As the scientific curiosity in genome studies shifts toward identification of functions of the genomes in large scale, data produced about cellular processes at molecular level has been accumulating with an ...
    • Pathway activity inference using microarray data 

      Babur, Özgün; Demir, Emek; Ayaz, Aslı; Doğrusöz, Uğur; Sakarya, Onur (Bilkent Center for Bioinformatics (BCBI), 2004)
      Motivation: Microarray technology provides cell-scale expression data; however, analyzing this data is notoriously difficult. It is becoming clear that system-oriented methods are needed in order to best interpret this ...
    • PATIKA: An informatics infrastructure for cellular networks 

      Aksay, Çağrı; Ayaz, Aslı; Babur, Özgün; Bilgin, C.; Çetintaş, Ahmet; Çivril, Ali; Çolak, Recep; Çözen, G.; Demir, Emek; Doğrusöz, Uğur; Erson, Zeynep; Gerdaneri, Ozan; Giral, Erhan; Güleşır, Gürcan; Nişancı, Gürkan; Sakarya, O.; Yıldırım, Hilmi (ISCB Org, 2004)
      The PATIKA Project aims for an informatics infrastructure to cope with the inherently complex cellular pathway data and provides software tools with sophisticated visualization technology around a central database using ...
    • PATIKAweb: a Web service for querying, visualizing and analyzing a graph-based pathway database 

      Aksay, Çağrı; Arık, Fatma; Ataer, Esra; Ayaz, Aslı; Babur, Özgün; Belviranlı, Mehmet E.; Çetintaş, Ahmet; Çolak, Recep; Çözen, G.; Demir, Emek; Dilek, Alptuğ; Doğrusöz, Uğur; Giral, Erhan; Kaya, Engin; Küçük, Evren; Tekin, A. S.; Yıldırım, Hilmi; Erson, Zeynep (ISCB Org, 2005-06)
      PATIKAweb provides a Web service for retrieving and analyzing biological pathways in PATIKA database, which currently contains data integrated from popular public pathway databases like Reactome. It features a user-friendly ...