New Methods from the Berkeley Phylogenomics Group

submitted by: ruchira

Here we present two new algorithms hosted within the PhyloFacts phylogenomic encyclopedias.

Metaproteomics as a key technology for characterizing the human microbiome Nathan C. VerBerkmoes, Oak Ridge National Labs

submitted by: dougramsey
The human microbiome is a complex system of many microbial communities inhabiting a diversity of environmental niches throughout the human body. With at least an order of magnitude more cells and even greater diversity of genetic potential these microbial communities continually interact with the human host cells in complex but controlled manner that lead to normal human health. Our knowledge of the structure and function of these communities and the interactions with the human host is...

The Evolution of Small Bacterial Genomesin the Ultra-Oligotrophic Ocean

submitted by: dougramsey
The size and coding capacity of a genome are its most fundamental properties. What selective pressures deter mine the expansion and contraction of genomes, and how is genome size related to adaptive strategies? Very small marine microbial genomes are providing new insights into these questions. The first reports of genome sequences from the cyanobacterium Prochlorococcus and the α-proteo bacterium SAR11 (Pelagibacter) established that these very abundant marine bacterioplankton clades have...

A Genomic Encyclopedia of Bacteria and Archaea (GEBA) and the Search for the Dark Matter of the Biological Universe

submitted by: dougramsey
There is a glaring gap in microbial genome sequence availability – the currently available genome sequences show a highly biased phylogenetic distribution compared to the extent of microbial diversity known today. This bias has resulted in major limitations in our knowledge of microbial genome complexity and our understanding of the evolution, physiology and metabolic capacity of microbes. Although there have been small efforts in sequencing genomes from across the tree of life for...