DCA for genome-wide epistasis analysis: the statistical genetics perspective
文献类型：期刊论文
| 作者 | Gao, CY; Cecconi, F4,6; Vulpiani, A4,6,7; Zhou, HJ ; Aurell, E1,5,8,9
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| 刊名 | PHYSICAL BIOLOGY
 |
| 出版日期 | 2019 |
| 卷号 | 16期号:2页码:26002 |
| ISSN号 | 1478-3967 |
| 关键词 | DIRECT-COUPLING ANALYSIS PROTEIN-STRUCTURE CONTACTS HIV IDENTIFICATION RECOMBINATION LINKAGE LANDSCAPE INFERENCE MODEL |
| DOI | 10.1088/1478-3975/aafbe0 |
| 英文摘要 | 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. |
| 学科主题 | Biochemistry & Molecular Biology ; Biophysics |
| 语种 | 英语 |
| 源URL | [http://ir.itp.ac.cn/handle/311006/23476]  |
| 专题 | 理论物理研究所_理论物理所1978-2010年知识产出 计算平台成果 |
| 作者单位 | 1.KTH Royal Inst Technol, Dept Computat Biol, SE-10044 Stockholm, Sweden 2.PSL Res Univ, Lab Phys Chim Theor, UMR CNRS Gulliver 7083, ESPCI, 10 Rue Vauquelin, F-75231 Paris, France 3.Chinese Acad Sci, Inst Theoret Phys, Key Lab Theoret Phys, Beijing 100190, Peoples R China 4.Univ Chinese Acad Sci, Sch Phys Sci, Beijing 100049, Peoples R China 5.Aalto Univ, Dept Comp Sci, FIN-00076 Aalto, Finland 6.Sapienza Univ Roma, CNR ISC, Ple Moro 2, I-00185 Rome, Italy 7.Sapienza Univ Roma, Dipartimento Fis, Ple Moro 2, I-00185 Rome, Italy 8.Accademia Lincei, Ctr Interdisciplinare B Segre, Rome, Italy 9.Aalto Univ, Dept Appl Phys, FIN-00076 Aalto, Finland |
| 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. |
入库方式： OAI收割
来源：理论物理研究所
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