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This Week in Nucleic Acids Research: Sep 18, 2013

German researchers present a computational strategy for pulling together data from multiple omics sources when doing biological assessments of gene sets. The team outlined the rationale behind its "Multi-level Ontology Analysis" algorithm, nicknamed MONA, in the study, demonstrating that the model-based method could accurately deal with multiple levels of information — both synthetic data and data generated for three studies using various molecular profiling types. Based on their findings, the study's authors say MONA "performed significantly better than conventional analyses of individual levels and yields best results even for sophisticated models including [messenger RNA] fine-tuning by microRNAs."

A team from Japan, China, and France describes its methylation-specific fluorescence in situ hybridization, or MeFISH, method for visualizing methylation status at specific sequences in another Nucleic Acids Research study. The researchers used fluorescence-labeled probes that interact differently with 5'-methylated cytosine than with the unmodified form of the base. Using the MeFISH method, which centers on so-called "inter-strand complex formation with osmium and bipyridine-containing nucleic acids," the group demonstrated that it could detect methylated satellite repeat sequences in mouse cell nuclei or chromosomes.

Finally, French researchers outline a quality-control strategy for dealing with data generated by chromatin immunoprecipitation-sequencing, or ChIP-seq, or other enrichment-based sequencing methods. The group's bioinformatics-based approach, called NGS-QCi Generator, taps raw sequencing datasets to uncover local and global quality control indicators, optimal depths, antibody and dataset comparability, and the like. For instance, the investigators applied NGS-QCi Generator to more than 5,600 publicly available datasets generated by ChIP-seq, RNA-sequencing, global run-on sequencing, and so on, developing a database to house the resulting quality control-related profiles.

The Scan

Hormone-Based Gene Therapy to Sterilize Domestic Cat

A new paper in Nature Communication suggests that gene therapy could be a safer alternative to spaying domestic cats.

Active Lifestyle Linked to Type 2 Diabetes Prevention in People at High Genetic Risk

A study in the British Journal of Sports Medicine shows that an active lifestyle goes a long way in type 2 diabetes prevention.

Beneficial, Harmful Effects of Introgression Between Wild and Domesticated European Grapes

A paper in PNAS shows that European wild grapevines were an important resource for improving the flavor of cultivated wine grapes.

Genetic Ancestry of South America's Indigenous Mapuche Traced

Researchers in Current Biology analyzed genome-wide data from more than five dozen Mapuche individuals to better understand their genetic history.