BOOL-AN: A method for comparative sequence analysis and phylogenetic reconstruction [PDF]
, 2009 A novel discrete mathematical approach is proposed as an additional tool for molecular systematics which does not require prior statistical assumptions concerning the evolutionary process.
Ari, Eszter +4 more
core +1 more source
Phylogenetic Analysis of Cell Types using Histone Modifications
, 2013 In cell differentiation, a cell of a less specialized type becomes one of a more specialized type, even though all cells have the same genome. Transcription factors and epigenetic marks like histone modifications can play a significant role in the ...
Bucher, Philipp +3 more
core +1 more source
MISSEL: a method to identify a large number of small species-specific genomic subsequences and its application to viruses classification [PDF]
, 2016 Continuous improvements in next generation sequencing technologies led to ever-increasing collections of genomic sequences, which have not been easily characterized by biologists, and whose analysis requires huge computational effort.
Babakir Mina, Muhammed +10 more
core +2 more sources
Nucleic Acids Research, 2014 The emergence of new sequencing technologies has facilitated the use of bacterial whole genome alignments for evolutionary studies and outbreak analyses.
N. Croucher +7 more
semanticscholar +1 more source
SICLE: A high-throughput tool for extracting evolutionary relationships from phylogenetic trees
, 2016 We present the phylogeny analysis software SICLE (Sister Clade Extractor), an easy-to-use, high- throughput tool to describe the nearest neighbors to a node of interest in a phylogenetic tree as well as the support value for the relationship.
DeBlasio, Dan, Wiscaver, Jennifer
core +2 more sources
Complete Genome Sequence of a Putative Densovirus of the Asian Citrus Psyllid, Diaphorina citri. [PDF]
, 2016 Here, we report the complete genome sequence of a putative densovirus of the Asian citrus psyllid, Diaphorina citri Diaphorina citri densovirus (DcDNV) was originally identified through metagenomics, and here, we obtained the complete nucleotide sequence
Falk, Bryce W +2 more
core +1 more source
Geogenomic segregation and temporal trends of human pathogenic Escherichia coli o157:H7, Washington, USA, 2005-2014 [PDF]
, 2018 The often-noted and persistent increased incidence of Escherichia coli O157:H7 infections in rural areas is not well understood. We used a cohort of E.
Besser, Thomas E +8 more
core +2 more sources
Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10
Virus Evolution, 2018 The Bayesian Evolutionary Analysis by Sampling Trees (BEAST) software package has become a primary tool for Bayesian phylogenetic and phylodynamic inference from genetic sequence data.
M. Suchard +5 more
semanticscholar +1 more source
Microbial exopolysaccharide production by polyextremophiles in the adaptation to multiple extremes
FEBS Letters, EarlyView.Polyextremophiles are microorganisms that endure multiple extreme conditions by various adaptation strategies that also include the production of exopolysaccharides (EPSs). This review provides an integrated perspective on EPS biosynthesis, function, and regulation in these organisms, emphasizing their critical role in survival and highlighting their ...
Tracey M Gloster, Ebru Toksoy Öner
wiley +1 more source
The Prevalence and Impact of Model Violations in Phylogenetic Analysis
Genome Biology and Evolution, 2019 In phylogenetic inference, we commonly use models of substitution which assume that sequence evolution is stationary, reversible, and homogeneous (SRH).
Suha Naser-Khdour +4 more
semanticscholar +1 more source