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This Week in Genome Biology: Dec 16, 2009

In Genome Biology this week, University of Tartu scientists present MEM, or Multi-Experiment Matrix, a web-based tool to search for co-expressed genes across many microarray datasets. Unique features include "automatic detection, characterization and visualization of datasets that includes the strongest co-expression patterns." MEM is available for free.

In a new methods paper, scientists search for genetic interactions in Saccharomyces cerevisae. Igor Ulitsky and Ron Shamir at Tel Aviv University and the University of California, San Francisco's Nevan Krogan have developed a novel method that combines genetic interaction and genomic data to find the approximately 40 percent missing interactions in this model organism. Their results showed almost 190,000 novel interactions.

Scientists led by Jacobs University Bremen's Albert Jeltsch have studied the effect of DNA methylation on autosomal chromosomes and its subsequent effect on phenotypic differences. Looking at methylation of CpG islands on chromosome 21 in white blood cells from healthy people, they saw "novel cases of pronounced differential methylation of alleles," and that this allele-specific methylation is likely to affect about 10 percent of all genes and contribute to allele-specific expression and monoallelic gene silencing, they say.

Scientists have found that assortative mating, or the tendency of two people who share similar ancestry to mate, still persists in Latino populations and has an effect on genomic structure. In a study using 104 "ancestry markers" led by first author Neil Risch at the University of California, San Francisco, they found that in Mexican spouse pairs from Mexico City and the San Francisco Bay Area, there were strong spouse correlations for European and Native American ancestry, but no correlation in African ancestry, they say. In the Puerto Rican pairs sampled from couples from Puerto Rico and New York City, they found spouse correlations for African ancestry and European ancestry but not Native American ancestry. "Ancestry variance is predicted to decline in each generation, but less so under assortative mating," they write. "We used the current observed variances of ancestry to infer even stronger patterns of spouse ancestry correlation in previous generations."

The Scan

CDC Calls Delta "Variant of Concern"

CNN reports the US Centers for Disease Control and Prevention now considers the Delta variant of SARS-CoV-2 to be a "variant of concern."

From FDA to Venture Capital

Former FDA Commissioner Stephen Hahn is taking a position at a venture capital firm, leading some ethicists to raise eyebrows, according to the Washington Post.

Consent Questions

Nature News writes that there are questions whether informed consent was obtained for some submissions to a database of Y-chromosome profiles.

Cell Studies on Multimodal Single-Cell Analysis, Coronaviruses in Bats, Urban Microbiomes

In Cell this week: approach to analyze multimodal single-cell genomic data, analysis of bat coronaviruses, and more.