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This Week in Nucleic Acids Research: May 14, 2014

A team from China's Harbin Institute of Technology introduces the Personal Genome Browser, or PGB, in the early, online edition of Nucleic Acids Research this week. The web-based genome browser is built on a genetic-molecular-phenotypic model, the researchers say, and aims to functionally annotate and visualize individual genomes — from SNPs and small insertions and deletions to related phenotypic associations with disease risk, drug response, or physical features. As personal genomes continue to get cranked out, "the PGB can be widely used to display, interpret, and analyze personal genomes," they write, noting that the resource is expected to "greatly benefit academic researchers and clinical physicians."

Tick-borne parasites in the Babesia genus generate host immune-dodging diversity with the help of divergent Ves1 genes, according to a comparative genomics study. An international research team led by investigators in the UK and Saudi Arabia came up with high-quality draft genome sequences for three species of Babesia that are known for infecting red blood cells: B. bigemina, B. divergens, and B. bovis. Along with transcriptomic and proteomic data, a phylogenetic analysis of the parasites provided the team with insights into the diverse variant erythrocyte surface antigen proteins that parasites present to host immune systems.

Swedish researchers describe a new web user interface known as BioMet Toolbox 2.0 for bringing together metabolic information and various forms of omic data. The online interface is designed to integrate access to software such as RAVEN, which models genome-scale metabolic models patterns, and PIANO (software designed for doing analyses of omic data). "The BioMet Toolbox 2.0 offers a selection of online software tools for biological data analysis," authors of the study say, "along with free access to a collection of [genome-scale metabolic models] for their use in phenotype simulations."

The Scan

Machine Learning Helps ID Molecular Mechanisms of Pancreatic Islet Beta Cell Subtypes in Type 2 Diabetes

The approach helps overcome limitations of previous studies that had investigated the molecular mechanisms of pancreatic islet beta cells, the authors write in their Nature Genetics paper.

Culture-Based Methods, Shotgun Sequencing Reveal Transmission of Bifidobacterium Strains From Mothers to Infants

In a Nature Communications study, culture-based approaches along with shotgun sequencing give a better picture of the microbial strains transmitted from mothers to infants.

Microbial Communities Can Help Trees Adapt to Changing Climates

Tree seedlings that were inoculated with microbes from dry, warm, or cold sites could better survive drought, heat, and cold stress, according to a study in Science.

A Combination of Genetics and Environment Causes Cleft Lip

In a study published in Nature Communications, researchers investigate what combination of genetic and environmental factors come into play to cause cleft lip/palate.