nodalpoint.org

Way back in Nodalpoint history (probably about a year ago), we had "paper of the month" posts. They were rarely monthly and often involved more than one paper, but I always thought that it was a nice idea. So here's a few that caught my eye this month.

In the latest issue of Bioinformatics we have:

• PseudoPipe: an automated pseudogene identification pipeline. My knowledge of how we identify pseudogenes is not what it should be; this paper and the Pseudogene.org website should help out.
• A machine learning information retrieval approach to protein fold recognition seems to do just what it says on the tin.

Bioinformatics is also examining the case for and against software patents. This week, John Quackenbush (why do I know that name? Chris?) and Steven Salzberg give us the viewpoint that I'm sure most of us here favour - It is time to end the patenting of software. Next issue we get the counter argument, such as it might be.

I tend to prefer the journals with a genomics focus to those with "1001 more uses for SVMs", so in Genome Research we get Evolutionary turnover of mammalian transcription start sites from our very own IMB, Brisbane. Assumed that functionally-equivalent regulatory sites always occur in equivalent positions with orthologous sequence? You assumed wrong.

Things that caught my eye from the BMC series were Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae, Comparative genomics of regulation of heavy metal resistance in Eubacteria and Centering, scaling, and transformations: improving the biological information content of metabolomics data. Metabolomics and modelling was big in the institute where I did my first postdoc - wish I'd paid more attention at the time.