Volume 7 Supplement 1
Edited by Hervé Philippe, Mathieu Blanchette
First International Conference on Phylogenomics. Go to conference site.
Sainte-Adèle, Québec, Canada15-19 March, 2006
The First Phylogenomics Conference was held in Ste-Adèle (Québec, Canada) in March 2006. Selected papers appear in this special issue of BMC Evolutionary Biology. Here, we give an introduction to the field and pr...
Phylogenetic analyses based on datasets rich in both genes and species (phylogenomics) are becoming a standard approach to resolve evolutionary questions. However, several difficulties are associated with the ...
Most studies inferring species phylogenies use sequences from single copy genes or sets of orthologs culled from gene families. For taxa such as plants, with very high levels of gene duplication in their nucle...
Thanks to the large amount of signal contained in genome-wide sequence alignments, phylogenomic analyses are converging towards highly supported trees. However, high statistical support does not imply that the...
Models of codon evolution have proven useful for investigating the strength and direction of natural selection. In some cases, a priori biological knowledge has been used successfully to model heterogeneous evolu...
Synonymous codon usage varies widely between genomes, and also between genes within genomes. Although there is now a large body of data on variations in codon usage, it is still not clear if the observed patte...
A comprehensive evolutionary analysis of bacterial genomes implies to identify the hallmark of vertical and non-vertical signals and to discriminate them from the presence of mere phylogenetic noise. In this r...
Bacterial genomes develop new mechanisms to tide them over the imposing conditions they encounter during the course of their evolution. Acquisition of new genes by lateral gene transfer may be one of the domin...
Comparative genomics approaches, where orthologous DNA regions are compared and inter-species conserved regions are identified, have proven extremely powerful for identifying non-coding regulatory regions loca...
The rate of evolution varies spatially along genomes and temporally in time. The presence of evolutionary rate variation is an informative signal that often marks functional regions of genomes and historical s...
The diversity of visual systems in fish has long been of interest for evolutionary biologists and neurophysiologists, and has recently begun to attract the attention of molecular evolutionary geneticists. Seve...
Function prediction by transfer of annotation from the top database hit in a homology search has been shown to be prone to systematic error. Phylogenomic analysis reduces these errors by inferring protein func...
Within eukaryotes there is a complex cascade of RNA-based macromolecules that process other RNA molecules, especially mRNA, tRNA and rRNA. An example is RNase MRP processing ribosomal RNA (rRNA) in ribosome bi...
Widespread transcription activities in the human genome were recently observed in high-resolution tiling array experiments, which revealed many novel transcripts that are outside of the boundaries of known pro...
Transcription factors regulate gene expression by interacting with their specific DNA binding sites. Some transcription factors, particularly those involved in transcription initiation, always bind close to tr...
We report an analysis of a protein network of functionally linked proteins, identified from a phylogenetic statistical analysis of complete eukaryotic genomes. Phylogenetic methods identify pairs of proteins t...
For BMC Evolutionary Biology (former title)
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