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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

US Booster Eligibility Decision

The US CDC director recommends that people at high risk of developing COVID-19 due to their jobs also be eligible for COVID-19 boosters, in addition to those 65 years old and older or with underlying medical conditions.

Arizona Bill Before Judge

The Arizona Daily Star reports that a judge is weighing whether a new Arizona law restricting abortion due to genetic conditions is a ban or a restriction.

Additional Genes

Wales is rolling out new genetic testing service for cancer patients, according to BBC News.

Science Papers Examine State of Human Genomic Research, Single-Cell Protein Quantification

In Science this week: a number of editorials and policy reports discuss advances in human genomic research, and more.