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This Week in Nucleic Acids Research : Jun 13, 2012

In Nucleic Acids Research Webserver Issue preprints published online in advance this week, more than two dozen groups present Web tools they've generated for genomics, proteomics, and more.

Researchers at Humboldt-Universität in Berlin present GeneView, a semantic search engine that is "built upon a comprehensively annotated version of PubMed abstracts and openly available PubMed Central full texts." The authors say this "semi-structured representation of biomedical texts enables a number of features extending classical search engines." For one, users can query entries using unique database identifiers, the Humboldt-Universität researchers say.

Investigators at Spain's Centro de Investigación Príncipe Felipe present a variant analysis tool dubbed Variant, which "reports information on the variants found that include consequence type and annotations taken from different databases and repositories," including the GWAS catalog, OMIM, and COSMIC. "Variant also produces a rich variety of annotations that include information on the regulatory — transcription factor or miRNA-binding sites, et cetera — or structural roles, or on the selective pressures on the sites affected by the variation," the authors write in Nucleic Acids Research.

And a team led by researchers at the University of Turku and Åbo Akademi University in Finland present what they call the BiForce Toolbox — a Web tool that aims "to address the demand for high-throughput analysis of pairwise epistasis in GWAS of quantitative and disease traits across all commonly used computer systems." Unlike other such tools, BiForce Toolbox "incorporates additional tests of interactions involving SNPs with significant marginal effects, potentially increasing the power of detection of epistasis," the authors write.

The Scan

Not Yet a Permanent One

NPR says the lack of a permanent Food and Drug Administration commissioner has "flummoxed" public health officials.

Unfair Targeting

Technology Review writes that a new report says the US has been unfairly targeting Chinese and Chinese-American individuals in economic espionage cases.

Limited Rapid Testing

The New York Times wonders why rapid tests for COVID-19 are not widely available in the US.

Genome Research Papers on IPAFinder, Structural Variant Expression Effects, Single-Cell RNA-Seq Markers

In Genome Research this week: IPAFinder method to detect intronic polyadenylation, influence of structural variants on gene expression, and more.