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This Week in Nucleic Acids Research: Mar 16, 2016

By doing array-based analyses of microRNAs in dozens of biopsy samples, a German team has developed an atlas of miRNAs across human tissues types. As they report in Nucleic Acids Research, the researchers profiled nearly 2,000 miRNAs in 61 tissues taken from two individuals post-mortem, uncovering 143 miRNAs present across the tissues as well as 1,364 miRNAs found in at least one tissue. Using a tissue specificity index, they went on to assess the tissue-specific clustering and distribution of these miRNAs — analyses that suggest most miRNAs are found in more than one, but not all, tissues. The resulting human miRNA atlas, known as TissueAtlas, is available online.

Researchers from the Chinese Academy of Sciences present a method for marrying microbial 16S ribosomal RNA gene sequence and metagenomic sequence data. The approach, called 'ribosomal RNA gene flanking region sequencing' (RiboFR-Seq), is designed to include protein-coding gene sequences neighboring 16S genes of interest to help link them to metagenomic sequences for the same sample. The team validated and demonstrated this RiboFR-Seq strategy in a clonal strain of bacteria as well as more complicated mixtures of microbes in saliva and within marine kelp. "We believe that RiboFR-Seq, which provides an integrated view of 16S rRNA profiles and metagenomes, will help us better understand diverse microbial communities," the study's authors write.

A Mayo Clinic team introduces a freely available computational tool called NetDecoder that's designed to tease apart the composition and activity of biological networks in a context-dependent manner. Using available gene expression information and clues from existing protein interaction data, the method comes up with a context-specific interactome with the help of pairwise phenotypic comparative approaches, the investigators explain. In their own proof-of-principle experiments, they applied NetDecoder to case studies of breast cancer, dyslipidemia, and Alzheimer's disease, uncovering key 'network router' genes and disease-related pathways that are particularly active in these conditions.