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A novel algorithm to reconstruct phylogenies using gene sequences and expression data
Department of Mathematics, Uppsala University, Uppsala, Sweden.
Computer Laboratory , University of Cambridge, Cambridge, Un ited Kingdom.
2014 (English)In: International Proceedings of Chemical, Biological & Environmental Engineering; Environment, Energy and Biotechnology III, 2014, Vol. 70, p. 8-12Conference paper, Published paper (Refereed)
Abstract [en]

Phylogenies based on single loci should be viewed with caution and the best approach for obtaining robust trees is to examine numerous loci across the genome. It often happens that for the same set of species trees derived from different genes are in conflict between each other. There are several methods that combine information from different genes in order to infer the species tree. One novel approach is to use informationfrom different -omics. Here we describe a phylogenetic method based on an Ornstein–Uhlenbeck process that combines sequence and gene expression data. We test our method on genes belonging to the histidine biosynthetic operon. We found that the method provides interesting insights into selection pressures and adaptive hypotheses concerning gene expression levels.

Place, publisher, year, edition, pages
2014. Vol. 70, p. 8-12
National Category
Bioinformatics (Computational Biology) Evolutionary Biology Probability Theory and Statistics
Research subject
Bioinformatics; Mathematical Statistics; Statistics
Identifiers
URN: urn:nbn:se:liu:diva-140853OAI: oai:DiVA.org:liu-140853DiVA, id: diva2:1141002
Conference
3rd International Conference on Environment Energy and Biotechnology, (ICEEB 2014), 9th to 10th June 2014, Bangkok, Thailand
Note

Svenska institutet supported this work through their Östersjösamarbetet scholarship program.

Available from: 2014-11-12 Created: 2017-09-13 Last updated: 2018-01-13Bibliographically approved

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CiteExportLink to record
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Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
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  • 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