A handful of papers in PLoS this week highlight some interesting large-scale work. In one, published in PLoS ONE, Irish researchers used phylogenetic analysis to compare the genomes of three related Aspergillus species: A. oryzae, A. nidulans, and A. fumigatus. They found that A. oryzae has about 20 percent more genes than the other two, and that only one-third of the divergent members of the 456 paralog gene pairs that they found came from horizontal gene transfer from an as of yet unidentifiable Sordariomycete species.
Also in PLoS ONE, a team of scientists led by the Plymouth Marine Lab in the UK have used 454's GS-FLX to sequence the metatranscriptome of a microbial ecosystem. Looking at both DNA and mRNA from coastal ocean in Norway, they found large numbers of novel sequences.
Dutch scientists at Erasmus University Medical Center have developed an algorithm to globally screen for exon-skipping events, which occur frequently in cancer, according to research published in PLos ONE. In proof of concept work, they paired exon arrays with PAttern based Correlation (PAC) to identify exon-skipping mutants in both cancer cell lines and clinical cancer specimens.
And over at Yale, Mark Gerstein's lab has developed improved ChIP-seq in silico for simulating experimental data models, due to finding that genomic background and binding sites are not uniformly distributed. Their research appears in PLoS Computational Biology.