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Alignment of molecular networks by integer quadratic programming
Zhenping, Li; Zhang, Shihua; Wang, Yong; Zhang, Xiang-Sun; Chen, Luonan
Source PublicationBIOINFORMATICS
AbstractMotivation: With more and more data on molecular networks (e.g. protein interaction networks, gene regulatory networks and metabolic networks) available, the discovery of conserved patterns or signaling pathways by comparing various kinds of networks among different species or within a species becomes an increasingly important problem. However, most of the conventional approaches either restrict comparative analysis to special structures, such as pathways, or adopt heuristic algorithms due to computational burden. Results: In this article, to find the conserved substructures, we develop an efficient algorithm for aligning molecular networks based on both molecule similarity and architecture similarity, by using integer quadratic programming (IQP). Such an IQP can be relaxed into the corresponding quadratic programming (QP) which almost always ensures an integer solution, thereby making molecular network alignment tractable without any approximation. The proposed framework is very flexible and can be applied to many kinds of molecular networks including weighted and unweighted, directed and undirected networks with or without loops.
WOS Research AreaBiochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Computer Science ; Mathematical & Computational Biology ; Mathematics
WOS SubjectBiochemical Research Methods ; Biotechnology & Applied Microbiology ; Computer Science, Interdisciplinary Applications ; Mathematical & Computational Biology ; Statistics & Probability
WOS IDWOS:000248620400008
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Document Type期刊论文
Corresponding AuthorZhenping, Li
Affiliation1.Beijing Wuzi Univ, Beijing 101149, Peoples R China
2.Chinese Acad Sci, Acad Math & Syst Sci, Beijing 100080, Peoples R China
3.Chinese Acad Sci, Grad Univ, Beijing 100049, Peoples R China
4.Shanghai Univ, Inst Syst Biol, Shanghai 200444, Peoples R China
5.Osaka Sangyo Univ, Osaka 5748530, Japan
6.JST, ERATO Aihara Complex Modelling Project, Tokyo 1538530, Japan
7.Univ Tokyo, Inst Ind Sci, Tokyo 1538505, Japan
Recommended Citation
GB/T 7714
Zhenping, Li,Zhang, Shihua,Wang, Yong,et al. Alignment of molecular networks by integer quadratic programming[J]. BIOINFORMATICS,2007,23(13):1631-1639.
APA Zhenping, Li,Zhang, Shihua,Wang, Yong,Zhang, Xiang-Sun,&Chen, Luonan.(2007).Alignment of molecular networks by integer quadratic programming.BIOINFORMATICS,23(13),1631-1639.
MLA Zhenping, Li,et al."Alignment of molecular networks by integer quadratic programming".BIOINFORMATICS 23.13(2007):1631-1639.
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