| 1. |
- Bartoszek, Krzysztof, 1984-, et al.
(författare)
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A novel algorithm to reconstruct phylogenies using gene sequences and expression data
- 2014
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Ingår i: International Proceedings of Chemical, Biological & Environmental Engineering; Environment, Energy and Biotechnology III. ; , s. 8-12
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Konferensbidrag (refereegranskat)abstract
- 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.
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| 2. |
- Bartoszek, Krzysztof, 1984-, et al.
(författare)
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Influenza differentiation and evolution
- 2010
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Ingår i: Acta Physica Polonica B Proceedings Supplement. ; 3:2, s. 417-452
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Konferensbidrag (refereegranskat)abstract
- The aim of the study is to do a very wide analysis of HA, NA and M influenza gene segments to find short nucleotide regions,which differentiate between strains (i.e. H1, H2, ... e.t.c.), hosts, geographic regions, time when sequence was found and combination of time and region using a simple methodology. Finding regions differentiating between strains has as its goal the construction of a Luminex microarray which will allow quick and efficient strain recognition. Discovery for the other splitting factors could shed lighton structures significant for host specificity and on the history of influenza evolution. A large number of places in the HA, NA and M gene segments were found that can differentiate between hosts, regions, time and combination of time and region. Also very good differentiation between different Hx strains can be seen.We link one of our findings to a proposed stochastic model of creation of viral phylogenetic trees.
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