Knowledge Management System of Institute of Theoretical Physics, CAS
Gao, CY; Cecconi, F2,3; Vulpiani, A2,3,4; Zhou, HJ; Aurell, E5,6,7,8 | |
DCA for genome-wide epistasis analysis: the statistical genetics perspective | |
发表期刊 | PHYSICAL BIOLOGY |
语种 | 英语 |
关键词 | DIRECT-COUPLING ANALYSIS PROTEIN-STRUCTURE CONTACTS HIV IDENTIFICATION RECOMBINATION LINKAGE LANDSCAPE INFERENCE MODEL |
摘要 | Direct coupling analysis (DCA) is a now widely used method to leverage statistical information from many similar biological systems to draw meaningful conclusions on each system separately. DCA has been applied with great success to sequences of homologous proteins, and also more recently to whole-genome population-wide sequencing data. We here argue that the use of DCA on the genome scale is contingent on fundamental issues of population genetics. DCA can be expected to yield meaningful results when a population is in the quasi-linkage equilibrium (QLE) phase studied by Kimura and others, but not, for instance, in a phase of clonal competition. We discuss how the exponential (Potts model) distributions emerge in QLE, and compare couplings to correlations obtained in a study of about 3000 genomes of the human pathogen Streptococcus pneumoniae. |
2019 | |
ISSN | 1478-3967 |
卷号 | 16期号:2页码:26002 |
学科领域 | Biochemistry & Molecular Biology ; Biophysics |
学科门类 | Biochemistry & Molecular Biology ; Biophysics |
DOI | 10.1088/1478-3975/aafbe0 |
收录类别 | SCIE |
引用统计 | |
文献类型 | 期刊论文 |
条目标识符 | http://ir.itp.ac.cn/handle/311006/23476 |
专题 | SCI期刊论文 计算平台成果 |
作者单位 | 1.Chinese Acad Sci, Inst Theoret Phys, Key Lab Theoret Phys, Beijing 100190, Peoples R China 2.Univ Chinese Acad Sci, Sch Phys Sci, Beijing 100049, Peoples R China 3.Sapienza Univ Roma, CNR ISC, Ple Moro 2, I-00185 Rome, Italy 4.Sapienza Univ Roma, Dipartimento Fis, Ple Moro 2, I-00185 Rome, Italy 5.Accademia Lincei, Ctr Interdisciplinare B Segre, Rome, Italy 6.KTH Royal Inst Technol, Dept Computat Biol, SE-10044 Stockholm, Sweden 7.Aalto Univ, Dept Appl Phys, FIN-00076 Aalto, Finland 8.Aalto Univ, Dept Comp Sci, FIN-00076 Aalto, Finland 9.PSL Res Univ, Lab Phys Chim Theor, UMR CNRS Gulliver 7083, ESPCI, 10 Rue Vauquelin, F-75231 Paris, France |
推荐引用方式 GB/T 7714 | Gao, CY,Cecconi, F,Vulpiani, A,et al. DCA for genome-wide epistasis analysis: the statistical genetics perspective[J]. PHYSICAL BIOLOGY,2019,16(2):26002. |
APA | Gao, CY,Cecconi, F,Vulpiani, A,Zhou, HJ,&Aurell, E.(2019).DCA for genome-wide epistasis analysis: the statistical genetics perspective.PHYSICAL BIOLOGY,16(2),26002. |
MLA | Gao, CY,et al."DCA for genome-wide epistasis analysis: the statistical genetics perspective".PHYSICAL BIOLOGY 16.2(2019):26002. |
条目包含的文件 | ||||||
文件名称/大小 | 文献类型 | 版本类型 | 开放类型 | 使用许可 | ||
DCA for genome-wide (1652KB) | 期刊论文 | 作者接受稿 | 开放获取 | CC BY-NC-SA | 请求全文 |
除非特别说明,本系统中所有内容都受版权保护,并保留所有权利。
修改评论