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This Week in PLoS: Apr 9, 2012

In PLoS Genetics this week, Yamagata University's Masao Ueki and Newcastle University's Heather Cordell discuss the theoretical properties and performance of a statistic for testing interaction between two loci, linked or unlinked, which was recently proposed by Bengbu Medical College's Xuesen Wu et al. Ueki and Cordell say that while in some cases Wu et al.'s statistics "outperform competing approaches," they contain "minor errors in the formulae … resulting in tests that have higher than nominal type 1 error." The authors go on to suggest improvements in the form of "two new 'joint effects' statistics that, provided the disease is rare, are sensitive only to genuine interaction effects," and recommend that researchers either use these adjusted statistics, or take "caution when using Wu et al.'s originally proposed statistics, on account of the inflated error rate that can result."

Elsewhere in the journal, Monash University's Nathalie Uwamahoro and her colleagues show that subunits of the Mediator complex regulate adhesion in a distinct manner in Saccharomyces cerevisiae and Candida albicans, such that Med31 and Srb9/Med13 "are repressors of the FLO genes in S. cerevisiae and are activators of the ALS genes in C. albicans."

Over in PLoS Computational Biology, researchers at Life Technologies introduce an RNA-seq mapping pipeline they've implemented within the company's LifeScope software. The team "introduced new features including filter and junction mapping, annotation-aided pairing rescue and accurate mapping quality values" and "combined this pipeline with a Suffix Array Spliced Read aligner to detect chimeric transcripts," it writes.

The Scan

Follow-Up Data Requests to Biobank Participants Ineffective, Study Finds

An effort to recontact biobank enrollees for additional information reports low participation in a new BMJ Open study.

Study Finds Widespread Transmission of Resistant Bacteria in Vietnam Hospitals

A sequencing study in The Lancet Microbe finds widespread transmission of drug-resistant Escherichia coli, Klebsiella pneumoniae, and Acinetobacter baumannii in two Vietnam ICUs.

Novel Brain Cell Organoids Show Promise for Autism Research

University of Utah researchers report in Nature Communications on their development of brain cell organoids to study SHANK3-related autism.

Study Finds Few FDA Post-Market Regulatory Actions Backed by Research, Public Assessments

A Yale University-led team examines in The BMJ safety signals from the US FDA Adverse Event Reporting System and whether they led to regulatory action.