An efficient network querying method based on conditional random fields

doi:10.1093/bioinformatics/btr524

CSpace > 应用数学研究所

	An efficient network querying method based on conditional random fields
	Huang, Qiang; Wu, Ling-Yun; Zhang, Xiang-Sun
	2011-11-15
发表期刊	BIOINFORMATICS
ISSN	1367-4803
卷号	27 期号:22 页码:3173-3178
摘要	Motivation: A large amount of biomolecular network data for multiple species have been generated by high-throughput experimental techniques, including undirected and directed networks such as protein-protein interaction networks, gene regulatory networks and metabolic networks. There are many conserved functionally similar modules and pathways among multiple biomolecular networks in different species; therefore, it is important to analyze the similarity between the biomolecular networks. Network querying approaches aim at efficiently discovering the similar subnetworks among different species. However, many existing methods only partially solve this problem. Results: In this article, a novel approach for network querying problem based on conditional random fields (CRFs) model is presented, which can handle both undirected and directed networks, acyclic and cyclic networks and any number of insertions/deletions. The CRF method is fast and can query pathways in a large network in seconds using a PC. To evaluate the CRF method, extensive computational experiments are conducted on the simulated and real data, and the results are compared with the existing network querying methods. All results show that the CRF method is very useful and efficient to find the conserved functionally similar modules and pathways in multiple biomolecular networks.
DOI	10.1093/bioinformatics/btr524
语种	英语
资助项目	National Natural Science Foundation of China[60970091] ; National Natural Science Foundation of China[60873205] ; Chinese Academy of Sciences[kjcx-yw-s7]
WOS研究方向	Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Computer Science ; Mathematical & Computational Biology ; Mathematics
WOS类目	Biochemical Research Methods ; Biotechnology & Applied Microbiology ; Computer Science, Interdisciplinary Applications ; Mathematical & Computational Biology ; Statistics & Probability
WOS记录号	WOS:000296637500014
出版者	OXFORD UNIV PRESS
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/12451
专题	应用数学研究所
通讯作者	Wu, Ling-Yun
作者单位	Chinese Acad Sci, Natl Ctr Math & Interdisciplinary Sci, Acad Math & Syst Sci, Beijing 100190, Peoples R China
推荐引用方式 GB/T 7714	Huang, Qiang,Wu, Ling-Yun,Zhang, Xiang-Sun. An efficient network querying method based on conditional random fields[J]. BIOINFORMATICS,2011,27(22):3173-3178.
APA	Huang, Qiang,Wu, Ling-Yun,&Zhang, Xiang-Sun.(2011).An efficient network querying method based on conditional random fields.BIOINFORMATICS,27(22),3173-3178.
MLA	Huang, Qiang,et al."An efficient network querying method based on conditional random fields".BIOINFORMATICS 27.22(2011):3173-3178.