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This Week in PLoS: Apr 27, 2009

In work published in PLoS Computational Biology this week, scientists have created a catalog of clinical phenotypic features of 174 disease genes in human mitochondria. Their calculations showed that genes sharing more similar phenotypes have a stronger tendency for functional interactions, and they predict 168 high-probability disease candidates.

Each year, the International Society for Computational Biology makes two major awards to recognize excellence in the field of bioinformatics, and this year the awards have been given to Penn State's Webb Miller and UCSD's Trey Ideker.

At his blog, The Tree of Life, Jonathan Eisen points out a recent paper which he co-authored on assembling the marine metagenome using whole genome amplification on a single cell. Using FACS and multiple displacement amplification to get genomic DNA from individual cells of two marine flavobacteria from the Gulf of Maine, they were able to get estimated genome recoveries of about 91 percent and 78 percent, respectively. Their work appears in PLoS One.

Also in PLoS One, scientists genotyped single sperm to find the genetic structures of copy number variants. Using chip-based genotyping, they were able to analyze 48 previously characterized CNVs and to resolve SNP alleles and CNV haplotypes. "The highly sensitive high-throughput experimental system with haploid sperm samples as subjects may be used to facilitate detailed large-scale CNV analysis," they write in the abstract.

Finally, an international group of scientists have begun a database for open source drug discovery in tropical diseases, reports a paper in PLoS Neglected Tropical Diseases. This kernal currently contains 143 and 297 protein targets from ten pathogen genomes that are predicted to bind a known drug or a molecule similar to a known drug, respectively, says the abstract. The kernal is accessible for free here.

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.