Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
DCA for genome-wide epistasis analysis: the statistical genetics perspective
Chinese Acad Sci, Inst Theoret Phys, Key Lab Theoret Phys, Beijing 100190, Peoples R China.;Univ Chinese Acad Sci, Sch Phys Sci, Beijing 100049, Peoples R China..
Sapienza Univ Roma, CNR ISC, Ple Moro 2, I-00185 Rome, Italy.;Sapienza Univ Roma, Dipartimento Fis, Ple Moro 2, I-00185 Rome, Italy..
Sapienza Univ Roma, CNR ISC, Ple Moro 2, I-00185 Rome, Italy.;Sapienza Univ Roma, Dipartimento Fis, Ple Moro 2, I-00185 Rome, Italy.;Accademia Lincei, Ctr Interdisciplinare B Segre, Rome, Italy..
Chinese Acad Sci, Inst Theoret Phys, Key Lab Theoret Phys, Beijing 100190, Peoples R China.;Univ Chinese Acad Sci, Sch Phys Sci, Beijing 100049, Peoples R China..
Show others and affiliations
2019 (English)In: Physical Biology, ISSN 1478-3967, E-ISSN 1478-3975, Vol. 16, no 2, article id 026002Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
IOP PUBLISHING LTD , 2019. Vol. 16, no 2, article id 026002
Keywords [en]
direct coupling analysis, genome-scale, quasi-linkage equilibrium
National Category
Biological Sciences
Identifiers
URN: urn:nbn:se:kth:diva-244087DOI: 10.1088/1478-3975/aafbe0ISI: 000457186800001PubMedID: 30605896Scopus ID: 2-s2.0-85060569494OAI: oai:DiVA.org:kth-244087DiVA, id: diva2:1289909
Note

QC 20190219

Available from: 2019-02-19 Created: 2019-02-19 Last updated: 2019-02-19Bibliographically approved

Open Access in DiVA

No full text in DiVA

Other links

Publisher's full textPubMedScopus

Authority records BETA

Aurell, Erik

Search in DiVA

By author/editor
Aurell, Erik
By organisation
Computational Science and Technology (CST)
In the same journal
Physical Biology
Biological Sciences

Search outside of DiVA

GoogleGoogle Scholar

doi
pubmed
urn-nbn

Altmetric score

doi
pubmed
urn-nbn
Total: 86 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf