Browsing by Author "Aladaǧ, Ahmet Emre"

Now showing items 1-3 of 3

  • An integrated model for visualizing biclusters from gene expression data and PPI networks 

    Authors:Aladaǧ, Ahmet Emre; Erten, Cesim; Sözdinler, Melih
    Publisher and Date:(2010)
    We provide a model to integrate the visualization of biclusters extracted from gene expresion data and the underlying PPI networks. Such an integration conveys the biologically relevant interconnection between these two structures inferred from biological experiments. We model the reliabilities of the structures using directed graphs with vertex and edge weights. The resulting graphs are drawn using appropriate weighted modifications of the algorithms necessary for the layered drawings of directed ...

  • Reliability-Oriented bioinformatic networks visualization 

    Authors:Aladaǧ, Ahmet Emre; Erten, Cesim; Sözdinler, Melih
    Publisher and Date:(Oxford University Press, 2011)
    We present our protein-protein interaction (PPI) network visualization system RobinViz (reliability-oriented bioinformatic networks visualization). Clustering the PPI network based on gene ontology (GO) annotations or biclustered gene expression data providing a clustered visualization model based on a central/peripheral duality computing layouts with algorithms specialized for interaction reliabilities represented as weights completely automated data acquisition processing are notable features ...

  • SPINAL: scalable protein interaction network alignment 

    Authors:Aladaǧ, Ahmet Emre; Erten, Cesim
    Publisher and Date:(Oxford University Press, 2013)
    Motivation: Given protein-protein interaction (PPI) networks of a pair of species a pairwise global alignment corresponds to a one-to-one mapping between their proteins. Based on the presupposition that such a mapping provides pairs of functionally orthologous proteins accurately the results of the alignment may then be used in comparative systems biology problems such as function prediction/verification or construction of evolutionary relationships. Results: We show that the problem is NP-hard ...