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This Week in PLoS: Jul 16, 2012

Researchers at St. Jude Children's Research Hospital use "whole-genome transcriptional sequencing to systematically identify the sRNAs of Streptococcus pneumonia" in PLoS Pathogens this week. "Furthermore, using targeted genetic approaches and Tn-seq transposon screening, we demonstrate that many of the identified sRNAs have important global and niche-specific roles in virulence," the authors add.

Over in PLoS Computational Biology, an international team led by investigators at Vrije Universiteit Brussel reports having applied an ensemble method based on multiple similarity measures in combination with generalized boosted linear models to 16S rRNA gene profiles from the initial Human Microbiome Project cohort. This approach resulted "in a global network of 3,005 significant co-occurrence and co-exclusion relationships between 197 clades occurring throughout the human microbiome," the authors write.

Elsewhere in the same journal, the Broad Institute's David Altschuler and his colleagues present a statistical framework "to estimate genotypes jointly from sequence reads, array intensities, and imputation," they write. "Our joint framework informs the use of next-generation sequencing in genome-wide association studies and supports development of improved methods for genotype calling," Altschuler and his team add.

And in PLoS One, a trio of researchers from Duke University Medical Center discuss differentially methylated regions, or DMRs, of imprinted genes in prenatal, perinatal, and postnatal samples from a large panel of human conceptal tissues. Using pyrosequencing assays at seven DMRs, the team found methlation differences in tissues from brain, liver, and placenta.

The Scan

Not as High as Hoped

The Associated Press says initial results from a trial of CureVac's SARS-CoV-2 vaccine suggests low effectiveness in preventing COVID-19.

Finding Freshwater DNA

A new research project plans to use eDNA sampling to analyze freshwater rivers across the world, the Guardian reports.

Rise in Payments

Kaiser Health News investigates the rise of payments made by medical device companies to surgeons that could be in violation of anti-kickback laws.

Nature Papers Present Ginkgo Biloba Genome Assembly, Collection of Polygenic Indexes, More

In Nature this week: a nearly complete Ginkgo biloba genome assembly, polygenic indexes for dozens of phenotypes, and more.