Viruses and Bioinformatics from Virology.uvic.ca
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Viruses and Bioinformatics from Virology.uvic.ca
Virus and bioinformatics articles with some microbiology and immunology thrown in for good measure
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Molluscum Contagiosum Virus Transcriptome in Abortively Infected Cultured Cells and a Human Skin Lesion

IMPORTANCE The inability to propagate molluscum contagiosum virus, which causes benign skin lesions in young children and more extensive infections in immunosuppressed adults, has constrained our understanding of the biology of this human-specific virus. In the present study, we characterized the RNAs synthesized in abortively infected cultured cells and a human skin lesion by next-generation sequencing. These studies provided an initial transcription map of the MOCV genome, suggested temporal regulation of gene expression, and indicated that the in vitro replication block occurs prior to intermediate and late gene expression. RNA-seq and reporter assays, as described here, may help to further evaluate MOCV gene expression and define conditions that could enable MOCV replication in vitro.
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BMC Bioinformatics | CaPSID: A bioinformatics platform for computational pathogen sequence identification in human genomes and transcriptomes

It is now well established that nearly 20% of human cancers are caused by infectious agents, and the list of human oncogenic pathogens will grow in the future for a variety of cancer types. Whole tumor transcriptome and genome sequencing by next-generation sequencing technologies presents an unparalleled opportunity for pathogen detection and discovery in human tissues but requires development of new genome-wide bioinformatics tools.

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BMC Genomics | Abstract | HTRIdb: an open-access database for experimentally verified human transcriptional regulation interactions

The HTRIdb is implemented as a relational database PostgreSQL that is connected to a web interface via the JBOSS AS that dynamically generates user-friendly HTML front-end queries using the Apache Tomcat web server. For the network visualization of interactions, HTRIdb uses the web version of the popular Cytoscape visualization tool (Cytoscape Web). The TF-TG interactions data currently present in HTRIdb have been collected from original research articles.

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