Computational protocol: Intelligent biology and medicine in 2015: advancing interdisciplinary education, collaboration, and data science

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Protocol publication

[…] In addition to developing novel methods for analyzing data generated from new NGS techniques or the third-generation technology, application of NGS technologies to biological and medical problems also calls for extensive bioinformatics research. Bai et al. [] has investigated the variation of gene expression in blood transcriptome profile of Chinese Holstein cows associated to the milk yield traits. Totally, 100 differentially expressed genes (DEGs) between 13 high yielders and 10 low yielders were obtained, which were shown to be significantly enriched in immune response processes. Furthermore, alternative splicing analysis demonstrated that the alternative 3’ splicing site was the major splicing pattern in high yielders, however, in low yielders was exon skipping. This study allowed us to explore associations between immune traits and production traits related to milk production. In [], Zhou et al. identified 197 exons whose BMSC splicing patterns were altered by LPS via comparing RNA-seq data from LPS-treated samples versus the control. Functional analysis of these alternatively spliced genes demonstrated significant enrichment of phosphoproteins, zinc finger proteins, and proteins undergoing acetylation. Additional bioinformatics analysis strongly suggest that LPS-induced alternatively spliced exons could have major effects on protein functions by disrupting key protein functional domains, protein-protein interactions, and post-translational modifications. The study provides greater understanding of the intracellular mechanisms that underlie the therapeutic potential of BMSCs. The evolution of exceptionally powerful transporter systems in Streptomyces has enabled their adaptation to the complex soil environment. A better understanding of transport systems will allow enhanced optimization of production processes for both pharmaceutical and industrial applications of Streptomyces. In [], Zhou et al. presented a catalog of transport systems in eleven Streptomyces species and found that each of the species possesses a rich repertoire of transport proteins, which can be divided into a wide range of transporter families. To characterize the biological and medical significance of Bacillus sp. NRRL B-14911, in particular, cardiac autoimmunity, Massilamany et al. [] sought to analyze the complete genome sequence of this bacterium. The genome was found to encode several virulence factors like adhesins, invasins, colonization factors, siderophores and transporters. The availability of complete genome sequence of this bacterium may facilitate genetic manipulations to assess gene functions associated with bacterial survival and virulence, and also to establish a disease model to study the immune pathogenesis of bacterial myocarditis. In [], Bai et al. presented an improved algorithm “Read-Split-Run” (RSR) for detecting genome-wide Ire1α-targeted genes with non-canonical spliced regions at a faster speed. They compared the RSR algorithm to the “Read-Split-Walk” (RSW) algorithm when applied to mouse embryonic fibroblast cells (MEF) and the human Encyclopedia of DNA Elements (ENCODE) RNA-seq data. The new RSR algorithm outperformed others in the defined context and showed a higher efficiency in identifying novel splice junctions genome-wide. […]

Pipeline specifications

Software tools Read-Split-Run, RSW
Application RNA-seq analysis