Alignment of molecular networks by integer quadratic programming

doi:10.1093/bioinformatics/btm156

CORC > 数学与系统科学研究院 > 中国科学院数学与系统科学研究院 > 应用数学研究所

	Alignment of molecular networks by integer quadratic programming
	Zhenping, Li ; Zhang, Shihua ; Wang, Yong ; Zhang, Xiang-Sun; Chen, Luonan
刊名	BIOINFORMATICS
	2007-07-01
卷号	23 期号:13 页码:1631-1639
ISSN号	1367-4803
DOI	10.1093/bioinformatics/btm156
英文摘要	Motivation: 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研究方向	Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Computer Science ; Mathematical & Computational Biology ; Mathematics
语种	英语
出版者	OXFORD UNIV PRESS
WOS记录号	WOS:000248620400008
内容类型	期刊论文
源URL	[http://ir.amss.ac.cn/handle/2S8OKBNM/4255]
专题	应用数学研究所
通讯作者	Zhenping, Li
作者单位	1.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
推荐引用方式 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.