Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

    We have a manual that explains all the features 

Record number 403956
Title SLIDER: A Generic Metaheuristic for the Discovery of Correlated Motifs in Protein-Protein Interaction Networks
Author(s) Boyen, P.; Dyck, D. van; Neven, F.; Ham, R.C.H.J. van; Dijk, A.D.J. van
Source IEEE/ACM Transactions on Computational Biology and Bioinformatics 8 (2011)5. - ISSN 1545-5963 - p. 1344 - 1357.
Department(s) Bioinformatics
PRI BIOS Applied Bioinformatics
Biometris (WU MAT)
Publication type Refereed Article in a scientific journal
Publication year 2011
Keyword(s) sequences - scale - pairs
Abstract Correlated motif mining (CMM) is the problem of finding overrepresented pairs of patterns, called motifs, in sequences of interacting proteins. Algorithmic solutions for CMM thereby provide a computational method for predicting binding sites for protein interaction. In this paper, we adopt a motif-driven approach where the support of candidate motif pairs is evaluated in the network. We experimentally establish the superiority of the Chi-square-based support measure over other support measures. Furthermore, we obtain that CMM is an NP-hard problem for a large class of support measures (including Chi-square) and reformulate the search for correlated motifs as a combinatorial optimization problem. We then present the generic metaheuristic SLIDER which uses steepest ascent with a neighborhood function based on sliding motifs and employs the Chi-square-based support measure. We show that SLIDER outperforms existing motif-driven CMM methods and scales to large protein-protein interaction networks. The SLIDER-implementation and the data used in the experiments are available on
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