Evolutionary Bioinformatics

  title={Evolutionary Bioinformatics},
  author={Donald R. Forsdyke},
  booktitle={Cambridge International Law Journal},
  • D. Forsdyke
  • Published in
    Cambridge International Law…
    15 June 2006
  • Biology
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Intelligent Strategies for Pathway Mining

shape, 32 activation, 2, 41, 86 activator, 8 indicates that the shape of the TSP increases the likelihood of TSP activation in the response of an activator.

Freshwater Metaviromics and Bacteriophages: A Current Assessment of the State of the Art in Relation to Bioinformatic Challenges

The current bioinformatic approaches for metavirome analyses and the inherent challenges facing the field are examined, as illustrated by the ongoing efforts in the exploration of freshwater phage populations.

The Origin of Land Plants: A Phylogenomic Perspective

The conjugating green algae (Zygnematales) are now suggested to be the extant sister group to land plants, providing the novel understanding for character evolution and early multicellular innovations in land plants.

TRUFA: A User-Friendly Web Server for de novo RNA-seq Analysis Using Cluster Computing

TRUFA (TRanscriptome User-Friendly Analysis) is an open informatics platform offering a web-based interface that generates the outputs commonly used in de novo RNA-seq analysis and comparative transcriptomics and performs particularly better when analyzing the green tea dataset.

In Silico Gene Regulatory Network of the Maurer’s Cleft Pathway in Plasmodium falciparum

The genetic regulatory network of genes identified to belong to the Maurer's clefts using regularized graphical Gaussian model is predicted and analyzed to provide more details about functional interactions and the regulation of the genes in the MCs’ pathway of P. falciparum.

Human Dispersal Out of Africa: A Lasting Debate

This review of the ongoing debates regarding how and when the authors' ancestors left Africa, how many waves of dispersal there were and what geographical routes were taken reports the validity of each, using current genetic literature coupled with some of the key archeological findings.

The Experimental Proteome of Leishmania infantum Promastigote and Its Usefulness for Improving Gene Annotations

This work performed a proteomic analysis from axenic cultured promastigotes and carried out a detailed comparison with other Leishmania experimental proteomes published to date, identifying 2352 proteins based on a search of mass spectrometry data against a database built from the six-frame translated genome sequence of L. infantum.

Bioinformatic Characterization of Mosquito Viromes within the Eastern United States and Puerto Rico: Discovery of Novel Viruses

This study sought to determine whether samples of mosquitoes collected from different sites could be differentiated using metagenomic analysis of the RNA viral fraction, and detected a number of viruses that have been previously undiscovered.

Genome Sequence and Analysis of Peptoclostridium difficile Strain ZJCDC-S82

A draft assembly and detailed sequence analysis of the C. difficile genome associated with a strain from mainland China is reported, which will facilitate the understanding of genomic diversity and evolution of C.difficile strains in this region.

Molecular Evolution of the Yersinia Major Outer Membrane Protein C (OmpC)

The predicted antigenic determinants of OmpC were located in rapidly evolving regions, which may indicate the evolutionary mechanisms of Yersinia adaptation to the host immune system.



Phylogenetic classification of proteins encoded in complete genomes

For those interested in genome-wide or more restricted comparisons of proteins across species, the Clusters of Orthologous Groups (COGs) website provides the kind of information many of us want.

Vive la différence: biogenesis and evolution of microRNAs in plants and animals

This work reveals how differences in biogenesis, function and evolution contribute to characteristic features of microRNA evolution in the two kingdoms.

Inferring the Dynamics of Diversification: A Coalescent Approach

A novel approach to infer diversification dynamics shows that biodiversity is still expanding but at a slower rate than in the past.

Antiviral RNA interference in animals: piecing together the evidence

Two recent reports provide new, compelling evidence for a functional role for antiviral RNAi in mammals.

Genes on the production line

Demande de developpement d'equipements aupres des compagnies japonaises pour un sequencage rapide de l'ADN

Hypothesis for heritable, anti-viral immunity in crustaceans and insects

Hypothesis for heritable, anti-viral immunity in crustaceans and insects and its role in immunity to infectious disease is proposed.

On Graphical and Numerical Representation of Protein Sequences

A new approach using a 3-D Cartesian coordinate system to represent protein sequences has been derived and a comparison of sequences belonging to nine different proteins is made.