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This Week in Genome Biology : Feb 2, 2012

In a letter published online in advance in Genome Biology this week, members of the International Crocodilian Genomes Working Group announce their intention to sequence and assemble the American alligator, saltwater crocodile, and Indian gharial genomes. "We anticipate data collection and initial analyses to be complete by June 2012, and we plan to submit the genome paper within one year of finalizing these initial analyses," the team writes.

A team led by investigators at the University of Chicago this week report their use of a "Bayesian hierarchical model to estimate the enrichment of eQTLs [expression quantitative trait loci] in a wide variety of regulatory annotations" derived from 1,000 Genomes Project data. "We find that [approximately] 40 percent of eQTLs occur in open chromatin, and that they are particularly enriched in transcription factor binding sites, suggesting that many directly impact protein-DNA interactions," the authors write.

Elsewhere in Genome Biology, researchers at MIT present "MetaMerge, an algorithm for semi-automatically reconciling a pair of existing metabolic network reconstructions into a single metabolic network model." A team led by investigators at the Lawrence Berkeley National Laboratory describe "an integrated cross-species ontology consisting of over 6,500 classes representing a variety of anatomical entities, organized according to traditional anatomical classification criteria," dubbed Uberon. And researchers at Colorado State University present SpliceGrapher, "a method for predicting splice graphs that enhances curated gene models using evidence from RNA-Seq and EST alignments."

The Scan

Tens of Millions Saved

The Associated Press writes that vaccines against COVID-19 saved an estimated 20 million lives in their first year.

Supersized Bacterium

NPR reports that researchers have found and characterized a bacterium that is visible to the naked eye.

Also Subvariants

Moderna says its bivalent SARS-CoV-2 vaccine leads to a strong immune response against Omicron subvariants, the Wall Street Journal reports.

Science Papers Present Gene-Edited Mouse Models of Liver Cancer, Hürthle Cell Carcinoma Analysis

In Science this week: a collection of mouse models of primary liver cancer, and more.