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This Week in PLoS: Jul 23, 2012

In a paper published in PLoS One, investigators at the University of Vienna and Medical University Vienna, along with their colleagues at the Austrian Academy of Sciences, this week present BiSS — Bisulfite Sequencing Scorer — "a new method applying Smith-Waterman alignment to map bisulfite-converted reads to a reference genome." Beyond predicting the methylation status of each cytosine, "BiSS also provides an estimate of the methylation degree at each genomic site," the Austrian team writes. "Thus, BiSS explores BS-seq data more extensively and provides more information for downstream analysis."

A team led by investigators at Vanderbilt University School of Medicine reports in PLoS Computational Biology on their systematic investigation of microRNA and transcription factor-mediated regulatory networks in glioblastoma. "First, we compiled GBM-related miRNAs, GBM-related genes, and known human TFs," the researchers write. Next, they identified 1,128 three-node feed-forward loops and 805 four-node feed-forward loops with statistical significance. And then, "by merging these FFLs [feed-forward loops] together, we constructed a comprehensive GBM-specific miRNA-TF mediated regulatory network," the researchers write. From there, they "extracted a composite GBM-specific regulatory network," and later show that "the GBM-specific regulatory network is promising for identification of critical miRNA components."

Over in PLoS Genetics, a large international team led by investigators at the University of Edinburgh in Scotland presents evidence that "multiple, rare, recessive variants influence human height," and outlines the framework for a methodology that is "generally applicable to heritable quantitative traits, paving the way for an investigation into inbreeding effects, and therefore genetic architecture, on a range of QT [quantitative traits] of biomedical importance," it writes.

Elsewhere in the journal, scientists in Switzerland and Portugal "review current evidence about archaic admixture and lack of strong selective sweeps in humans," and stress the importance of modeling differential admixture "in various populations to correctly reconstruct past demography," they write.

The Scan

UCLA Team Reports Cost-Effective Liquid Biopsy Approach for Cancer Detection

The researchers report in Nature Communications that their liquid biopsy approach has high specificity in detecting all- and early-stage cancers.

Machine Learning Improves Diagnostic Accuracy of Breast Cancer MRI, Study Shows

Combining machine learning with radiologists' interpretations further increased the diagnostic accuracy of MRIs for breast cancer, a Science Translational Medicine paper finds.

Genome Damage in Neurons Triggers Alzheimer's-Linked Inflammation

Neurons harboring increased DNA double-strand breaks activate microglia to lead to neuroinflammation like that seen in Alzheimer's disease, a new Science Advances study finds.

Long COVID-19 Susceptibility Clues Contained in Blood Plasma Proteome

A longitudinal study in eBioMedicine found weeks-long blood plasma proteome shifts after SARS-CoV-2 infection, along with proteomic signatures that appeared to coincide with long Covid risk.