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This Week in PLoS: Jul 25, 2011

In PLoS Computational Biology, MIT's Kristen Naegle et al. present "a new computational framework for applying clustering to biological data in order to overcome the typical dependence on specific a priori assumptions and expert knowledge concerning the technical aspects of clustering," which they called the multiple clustering analysis methodology, or MCAM. This computational approach "employs an array of diverse data transformations, distance metrics, set sizes, and clustering algorithms, in a combinatorial fashion, to create a suite of clustering sets," the authors write. Naegle and her colleagues demonstrate the utility of MCAM by applying it to multiple phosphoproteomic data sets for the ERBB network, though they say their approach is "broadly applicable … for analysis of proteomic data."

Over in PLoS Genetics, investigators at the University of Geneva Medical School discuss the "influence of rare and common genetic variants on gene expression patterns, using variants identified from sequencing data from the 1,000 Genomes Project in an African and European population sample and gene expression data from lymphoblastoid cell lines." Overall, the Switzerland-based team shows that the "integration of genomic and RNA sequencing analyses allows for the joint assessment of genome sequence and genome function."

An international team led by researchers at the University of Pittsburgh this week report their use of ChIP-chip to identify 1,175 genomic regions that can be bound in vivo by DAF-12, a nuclear receptor that has roles in development and the modulation of adult aging.

Elsewhere in PLoS Genetics, the Washington University School of Medicine's Deborah Chen and her colleagues report an "example whereby quantitative differences in the biochemical activities of orthologous ancestral proteins dictate the ability of a horizontally acquired gene product to confer species-specific traits" in bacteria. More specifically, Chen et al. report their elucidation of "how the horizontally acquired pmrD gene product activates the ancestral PmrA/PmrB two-component system in Salmonella enterica but not in the closely related bacterium Escherichia coli."

The Scan

Self-Reported Hearing Loss in Older Adults Begins Very Early in Life, Study Says

A JAMA Otolaryngology — Head & Neck Surgery study says polygenic risk scores associated with hearing loss in older adults is also associated with hearing decline in younger groups.

Genome-Wide Analysis Sheds Light on Genetics of ADHD

A genome-wide association study meta-analysis of attention-deficit hyperactivity disorder appearing in Nature Genetics links 76 genes to risk of having the disorder.

MicroRNA Cotargeting Linked to Lupus

A mouse-based study appearing in BMC Biology implicates two microRNAs with overlapping target sites in lupus.

Enzyme Involved in Lipid Metabolism Linked to Mutational Signatures

In Nature Genetics, a Wellcome Sanger Institute-led team found that APOBEC1 may contribute to the development of the SBS2 and SBS13 mutational signatures in the small intestine.