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This Week in Genome Biology : Mar 28, 2012

Researchers at the Broad Institute present "a process for transcriptome analysis of bacterial communities that accommodates both intact and fragmented starting RNA and combines efficient rRNA removal with strand-specific RNA-seq" in a Genome Biology paper published online in advance. The Broad team says its approach produces highly reproducible expression profiles that enrich up to 40-fold for non-rRNA transcripts and correlate "well with profiles representing undepleted total RNA."

Brown University's Suzanne Sindi and her colleagues present GASVPro, "an algorithm combining both paired read and read depth signals into a probabilistic model which can analyze multiple alignments of reads," in a paper published online in advance in Genome Biology this week. Sindi et al. say that their algorithm "outperforms existing methods with a 50 percent to 90 percent improvement in specificity on deletions and a 50 percent improvement on inversions."

In another paper published online in advance this week, Indiana University's Kimberley Cook and her colleagues introduce a large-scale resource development project at the school's Bloomington Drosophila Stock Center, for which they are using an FLP-mediated recombination between FRT-bearing transposon insertion approach to generate chromosomal deletions. "Drosophila melanogaster now has the most extensive genomic deletion coverage and breakpoint subdivision as well as the most comprehensive inventory of haploinsufficient genes of any multicellular organism," the authors write. "The improved selection of chromosomal deletion strains will be useful to nearly all Drosophila researchers."

The Scan

Octopus Brain Complexity Linked to MicroRNA Expansions

Investigators saw microRNA gene expansions coinciding with complex brains when they analyzed certain cephalopod transcriptomes, as they report in Science Advances.

Study Tracks Outcomes in Children Born to Zika Virus-Infected Mothers

By following pregnancy outcomes for women with RT-PCR-confirmed Zika virus infections, researchers saw in Lancet Regional Health congenital abnormalities in roughly one-third of live-born children.

Team Presents Benchmark Study of RNA Classification Tools

With more than 135 transcriptomic datasets, researchers tested two dozen coding and non-coding RNA classification tools, establishing a set of potentially misclassified transcripts, as they report in Nucleic Acids Research.

Breast Cancer Risk Related to Pathogenic BRCA1 Mutation May Be Modified by Repeats

Several variable number tandem repeats appear to impact breast cancer risk and age at diagnosis in almost 350 individuals carrying a risky Ashkenazi Jewish BRCA1 founder mutation.