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Volume 7 Supplement 1

First International Conference on Phylogenomics


Edited by Hervé Philippe, Mathieu Blanchette

First International Conference on Phylogenomics. Go to conference site.

Sainte-Adèle, Québec, Canada15-19 March, 2006

  1. 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...

    Authors: Hervé Philippe and Mathieu Blanchette
    Citation: BMC Evolutionary Biology 2007 7(Suppl 1):S1
  2. 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 ...

    Authors: Béatrice Roure, Naiara Rodriguez-Ezpeleta and Hervé Philippe
    Citation: BMC Evolutionary Biology 2007 7(Suppl 1):S2
  3. 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...

    Authors: Nicolas Lartillot, Henner Brinkmann and Hervé Philippe
    Citation: BMC Evolutionary Biology 2007 7(Suppl 1):S4
  4. 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...

    Authors: Le Bao, Hong Gu, Katherine A Dunn and Joseph P Bielawski
    Citation: BMC Evolutionary Biology 2007 7(Suppl 1):S5
  5. 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...

    Authors: Huai-Chun Wang and Donal A Hickey
    Citation: BMC Evolutionary Biology 2007 7(Suppl 1):S6
  6. 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...

    Authors: Iñaki Comas, Andrés Moya and Fernando González-Candelas
    Citation: BMC Evolutionary Biology 2007 7(Suppl 1):S7
  7. 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...

    Authors: Pradeep Reddy Marri, Weilong Hao and G Brian Golding
    Citation: BMC Evolutionary Biology 2007 7(Suppl 1):S8
  8. 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...

    Authors: Hui Chen and Mathieu Blanchette
    Citation: BMC Evolutionary Biology 2007 7(Suppl 1):S9
  9. 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...

    Authors: Karin S Dorman
    Citation: BMC Evolutionary Biology 2007 7(Suppl 1):S10
  10. 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...

    Authors: Cameron J Weadick and Belinda SW Chang
    Citation: BMC Evolutionary Biology 2007 7(Suppl 1):S11
  11. 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...

    Authors: Nandini Krishnamurthy, Duncan Brown and Kimmen Sjölander
    Citation: BMC Evolutionary Biology 2007 7(Suppl 1):S12
  12. 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...

    Authors: Michael D Woodhams, Peter F Stadler, David Penny and Lesley J Collins
    Citation: BMC Evolutionary Biology 2007 7(Suppl 1):S13
  13. 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...

    Authors: Zhaolei Zhang, Andy Wing Chun Pang and Mark Gerstein
    Citation: BMC Evolutionary Biology 2007 7(Suppl 1):S14
  14. 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...

    Authors: Brandon Smith, Hung Fang, Youlian Pan, P Roy Walker, A Fazel Famili and Marianna Sikorska
    Citation: BMC Evolutionary Biology 2007 7(Suppl 1):S15

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