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Papers to Catch Up On


Bayesian Phylogenetics

Kolaczkowski B, Thornton JW. (2009). Long-Branch Attraction Bias and Inconsistency in Bayesian Phylogenetics. PLoS One. 4(12):e789.

In this paper, the authors examine two different methods for inferring phylogenetic history: the Bayesian inference and the maximum likelihood methods. They demonstrate that the Bayesian inference method, when compared to the maximum likelihood method, is biased toward topologies that group long branches together. The implications of these findings suggest that trees inferred by way of the maximum likelihood method have a better chance of being more reliable than the Bayesian inference method, which is error prone.

Bornavirus in the Human Genome

Keizo Tomonaga. (2010). Endogenous non-retroviral RNA virus elements in mammalian genomes. Nature. 463(7277):84-7.

Tomonaga and his joint Japanese-American team show in this paper that elements homologous to the nucleoprotein gene of bornavirus are present in several mammalian genomes, including humans, non-human primates, rodents, and elephants. Through this study, the team says it has provided the first evidence for endogenization of non-retroviral virus-derived elements in mammalian genomes and gives novel insights into both the generation of endogenous elements and of bornavirus as a source of genetic novelty in its host.

Patterns of Mutation

Rubin AF, Green P. (2009). Mutation patterns in cancer genomes. Proceedings of the National Academies of Science. E-print.

In this paper, Rubin and Green examine patterns of nucleotide substitution in brain, pancreatic, breast, and colorectal cancers by utilizing previously published data. In it, they demonstrate that either negative or positive selection has affected only a small number of mutations and that the increased CpG mutation frequency seen in some cancers seems to occur primarily outside of CpG islands and CpG island shores. These findings reject the idea that the increase is a result of island or shore methylation followed by deamination. This re-analysis also enabled the authors to demonstrate that the relative frequency of mutations at "dinucleotide hotspots" can help aid in the detection of likely technical artifacts in large-scale studies.

Tasmanian Devil

Murchison EP, Tovar C, Hsu A, Bender HS, et al. (2010). The Tasmanian Devil Transcriptome Reveals Schwann Cell Origins of a Clonally Transmissible Cancer. Science. 327(5961):84-7.

This paper describes a large-scale genetic analysis of a transmissible cancer known as devil facial tumor disease, a major threat to the Tasmanian devil population. Using microsatellite genotyping, mitochondrial genome analysis, and deep sequencing of the DFTD transcriptome and microRNAs, the researchers generated a diagnostic marker for the devil facial tumor disease and identified a group of genes relevant to its pathology and transmission. The paper also contains a genomic data set for the Tasmanian devil that can be applied to cancer diagnosis, as well as disease evolution and conservation.

The Scan

Study Points to Tuberculosis Protection by Gaucher Disease Mutation

A mutation linked to Gaucher disease in the Ashkenazi Jewish population appears to boost Mycobacterium tuberculosis resistance in a zebrafish model of the lysosomal storage condition, a new PNAS study finds.

SpliceVault Portal Provides Look at RNA Splicing Changes Linked to Genetic Variants

The portal, described in Nature Genetics, houses variant-related messenger RNA splicing insights drawn from RNA sequencing data in nearly 335,700 samples — a set known as the 300K-RNA resource.

Automated Sequencing Pipeline Appears to Allow Rapid SARS-CoV-2 Lineage Detection in Nevada Study

Researchers in the Journal of Molecular Diagnostics describe and assess a Clear Labs Dx automated workflow, sequencing, and bioinformatic analysis method for quickly identifying SARS-CoV-2 lineages.

UK Team Presents Genetic, Epigenetic Sequencing Method

Using enzymatic DNA preparation steps, researchers in Nature Biotechnology develop a strategy for sequencing DNA, along with 5-methylcytosine and 5-hydroxymethylcytosine, on existing sequencers.