References of "Vakati, Sudheer"
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See detailExploring biological interaction networks with tailored weighted quasi-bicliques.
Chang, Wen-Chieh; Vakati, Sudheer; Krause, Roland UL et al

in BMC Bioinformatics (2012), 13 Suppl 10

BACKGROUND: Biological networks provide fundamental insights into the functional characterization of genes and their products, the characterization of DNA-protein interactions, the identification of ... [more ▼]

BACKGROUND: Biological networks provide fundamental insights into the functional characterization of genes and their products, the characterization of DNA-protein interactions, the identification of regulatory mechanisms, and other biological tasks. Due to the experimental and biological complexity, their computational exploitation faces many algorithmic challenges. RESULTS: We introduce novel weighted quasi-biclique problems to identify functional modules in biological networks when represented by bipartite graphs. In difference to previous quasi-biclique problems, we include biological interaction levels by using edge-weighted quasi-bicliques. While we prove that our problems are NP-hard, we also describe IP formulations to compute exact solutions for moderately sized networks. CONCLUSIONS: We verify the effectiveness of our IP solutions using both simulation and empirical data. The simulation shows high quasi-biclique recall rates, and the empirical data corroborate the abilities of our weighted quasi-bicliques in extracting features and recovering missing interactions from biological networks. [less ▲]

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