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http://hdl.handle.net/1942/12110
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DC Field | Value | Language |
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dc.contributor.author | BOYEN, Peter | - |
dc.contributor.author | VAN DYCK, Dries | - |
dc.contributor.author | NEVEN, Frank | - |
dc.contributor.author | van Ham, Roeland C. H. J. | - |
dc.contributor.author | van Dijk, Aalt D. J. | - |
dc.date.accessioned | 2011-08-17T10:32:18Z | - |
dc.date.available | NO_RESTRICTION | - |
dc.date.available | 2011-08-17T10:32:18Z | - |
dc.date.issued | 2011 | - |
dc.identifier.citation | IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, 8(5). p. 1344-1357 | - |
dc.identifier.issn | 1545-5963 | - |
dc.identifier.uri | http://hdl.handle.net/1942/12110 | - |
dc.description.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 http://bioinformatics.uhasselt.be. | - |
dc.description.sponsorship | Peter Boyen is funded by a PhD grant of the Institute for the Promotion of Innovation through Science and Technology in Flanders (IWT-Vlaanderen). Aalt D.J. van Dijk is supported by an NWO (Netherlands Organisation for Scientific Research) VENI grant (863.08.027). This research is supported by the BioRange programme (SP 2.3.1) of the Netherlands Bioinformatics Centre (NBIC), which is supported through the Netherlands Genomics Initiative (NGI) and the Research Programme of the Research Foundation Flanders (FWO) (G030607). This work was also sponsored by the BiG Grid project for the use of computing and storage facilities, with financial support from NWO. The present paper is the extended full version of [5]. | - |
dc.language.iso | en | - |
dc.publisher | IEEE COMPUTER SOC | - |
dc.subject.other | Graphs and networks; biology and genetics | - |
dc.title | SLIDER: A Generic Metaheuristic for the Discovery of Correlated Motifs in Protein-Protein Interaction Networks | - |
dc.type | Journal Contribution | - |
dc.identifier.epage | 1357 | - |
dc.identifier.issue | 5 | - |
dc.identifier.spage | 1344 | - |
dc.identifier.volume | 8 | - |
local.format.pages | 14 | - |
local.bibliographicCitation.jcat | A1 | - |
dc.description.notes | [Boyen, P; Van Dyck, D; Neven, F] Hasselt Univ, B-3590 Diepenbeek, Belgium [Boyen, P; Van Dyck, D; Neven, F] Transnatl Univ Limburg, B-3590 Diepenbeek, Belgium [van Dijk, ADJ] Wageningen Univ & Res Ctr, Bioinformat Grp, NL-6708 PB Wageningen, Netherlands peter.boyen@uhasselt.be; dries.vandyck@uhasselt.be; frank.neven@uhasselt.be; roeland.vanham@wur.nl; aaltjan.vandijk@wur.nl | - |
local.type.refereed | Refereed | - |
local.type.specified | Article | - |
dc.bibliographicCitation.oldjcat | A1 | - |
dc.identifier.doi | 10.1109/TCBB.2011.17 | - |
dc.identifier.isi | 000292681800016 | - |
item.contributor | BOYEN, Peter | - |
item.contributor | VAN DYCK, Dries | - |
item.contributor | NEVEN, Frank | - |
item.contributor | van Ham, Roeland C. H. J. | - |
item.contributor | van Dijk, Aalt D. J. | - |
item.accessRights | Open Access | - |
item.fullcitation | BOYEN, Peter; VAN DYCK, Dries; NEVEN, Frank; van Ham, Roeland C. H. J. & van Dijk, Aalt D. J. (2011) SLIDER: A Generic Metaheuristic for the Discovery of Correlated Motifs in Protein-Protein Interaction Networks. In: IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, 8(5). p. 1344-1357. | - |
item.fulltext | With Fulltext | - |
item.validation | ecoom 2012 | - |
crisitem.journal.issn | 1545-5963 | - |
crisitem.journal.eissn | 1557-9964 | - |
Appears in Collections: | Research publications |
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File | Description | Size | Format | |
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preprint.pdf | Non Peer-reviewed author version | 1.2 MB | Adobe PDF | View/Open |
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