Self-organizing map approaches for the haplotype assembly problem

doi:10.1016/j.matcom.2009.01.021

CSpace > 应用数学研究所

	Self-organizing map approaches for the haplotype assembly problem
	Wu, Ling-Yun1 ; Li, Zhenping 2; Wang, Rui-Sheng 3; Zhang, Xiang-Sun1 ; Chen, Luonan 4
	2009-06-01
发表期刊	MATHEMATICS AND COMPUTERS IN SIMULATION
ISSN	0378-4754
卷号	79 期号:10 页码:3026-3037
摘要	Haplotype assembly is to reconstruct a pair of haplotypes from SNP values observed in a set of individual DNA fragments. In this paper, we focus on studying minimum error correction (MEC) model for the haplotype assembly problem and explore self-organizing map (SOM) methods for this problem. Specifically, haplotype assembly by MEC is formulated into an integer linear programming model. Since the MEC problem is NP-hard and thus cannot be solved exactly within acceptable running time for large-scale instances, we investigate the ability of classical SOMs to solve the haplotype assembly problem with MEC model. Then, aiming to overcome the limits of classical SOW a novel SOM approach is proposed for the problem. Extensive computational experiments on both synthesized and real datasets show that the new SOM-based algorithm can efficiently reconstruct haplotype pairs in a very high accuracy under realistic parameter settings. Comparison with previous methods also confirms the superior performance of the new SOM approach. (C) 2009 IMACS. Published by Elsevier B.V. All rights reserved.
关键词	SNP Haplotype assembly Minimum error correction Self-organizing maps Neural network
DOI	10.1016/j.matcom.2009.01.021
语种	英语
资助项目	Academic Human Resources Development in Institutions of Higher Learning ; National Natural Science Foundation of China[10631070] ; National Natural Science Foundation of China[60503004] ; National Natural Science Foundation of China[60873205] ; Foundation of Beijing Wuzi University ; Beijing Natural Science Foundation[1092011] ; JSPS-NSFC Scientific Cooperation Program[10711140116]
WOS研究方向	Computer Science ; Mathematics
WOS类目	Computer Science, Interdisciplinary Applications ; Computer Science, Software Engineering ; Mathematics, Applied
WOS记录号	WOS:000267312200005
出版者	ELSEVIER SCIENCE BV
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/7911
专题	应用数学研究所
通讯作者	Zhang, Xiang-Sun
作者单位	1.Chinese Acad Sci, Acad Math & Syst Sci, Beijing 100080, Peoples R China 2.Beijing Wuzi Univ, Sch Informat, Beijing 101149, Peoples R China 3.Renmin Univ China, Dept Math, Beijing 100872, Peoples R China 4.Osaka Sangyo Univ, Dept Elect Engn & Elect, Osaka 5748530, Japan
推荐引用方式 GB/T 7714	Wu, Ling-Yun,Li, Zhenping,Wang, Rui-Sheng,et al. Self-organizing map approaches for the haplotype assembly problem[J]. MATHEMATICS AND COMPUTERS IN SIMULATION,2009,79(10):3026-3037.
APA	Wu, Ling-Yun,Li, Zhenping,Wang, Rui-Sheng,Zhang, Xiang-Sun,&Chen, Luonan.(2009).Self-organizing map approaches for the haplotype assembly problem.MATHEMATICS AND COMPUTERS IN SIMULATION,79(10),3026-3037.
MLA	Wu, Ling-Yun,et al."Self-organizing map approaches for the haplotype assembly problem".MATHEMATICS AND COMPUTERS IN SIMULATION 79.10(2009):3026-3037.