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Breakthroughs in HIV treatment, especially combination antiretroviral therapy (ART), have massively reduced AIDS-associated mortality. However, ART administration amplifies the risk of non-AIDS defining illnesses including obesity, diabetes, and cardiovascular disease, collectively known as metabolic syndrome. Initial reports suggest that ART-associated risk of metabolic syndrome correlates with socioeconomic status, a multifaceted finding that encompasses income, race, education, and diet. Therefore, determination of causal relationships is extremely challenging due to the complex interplay between viral infection, ART, and the many environmental factors.
Pubmed ID: 29731256
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PhosphoNET is an open-access, online knowledgebase developed by Kinexus Bioinformatics Corporation to foster the study of cell signaling systems to advance biomedical research in academia and industry. PhosphoNET is the world''s largest repository of known and predicted information on human phosphorylation sites, their evolutionary conservation and the identities of protein kinases that may target these sites. Search by protein name, UniProt number, IPI number, or 15 AA P-site sequence. PhosphoNET presently holds data on over 650,000 known and putative phosphorylation sites (P-sites) in over 23,000 human proteins that have been collected from the scientific literature and other reputable websites. Over 14% of these phospho-sites have been experimentally validated. The rest have been predicted with a novel P-Site Predictor algorithm developed at Kinexus with academic partners at the University of British Columbia and Simon Fraser University. With the PhosphoNET Evolution module, this website also provides information about cognate proteins in over 20 other species that may share these human phospho-sites. This helps to define the most functionally important phospho-sites as these are expected to be highly conserved in nature. With the Kinase Predictor module, listings are provided for the top 50 human protein kinases that are likely to phosphorylate each of these phospho-sites using another proprietary kinase substrate prediction algorithm developed at Kinexus. Our kinase substrate predictions are based on deduced consensus phosphorylation site amino acid frequency scoring matrices that we have determined for each of ~500 different human protein kinases. The specificity matrices are generated directly from the primary amino acid sequences of the catalytic domains of these kinases, and when available, have proven to correlate strongly with substrate prediction matrices based on alignment of known substrates of these kinases. The higher the score, the better the prospect that a kinase will phosphorylate a given site. Over 30 million kinase-substrate phospho-site pairs are quantified in PhosphoNET. Kinexus Bioinformatics Corporation has the capability to test most of these putative interactions in vitro for our clients.
View all literature mentionsOriginal SAMTOOLS package has been split into three separate repositories including Samtools, BCFtools and HTSlib. Samtools for manipulating next generation sequencing data used for reading, writing, editing, indexing,viewing nucleotide alignments in SAM,BAM,CRAM format. BCFtools used for reading, writing BCF2,VCF, gVCF files and calling, filtering, summarising SNP and short indel sequence variants. HTSlib used for reading, writing high throughput sequencing data.
View all literature mentionsA next-generation web-based application that aims to provide an integrated solution for both visualization and analysis of deep-sequencing data, along with simple access to public datasets.
View all literature mentionsSoftware package for differential gene expression analysis based on the negative binomial distribution. Used for analyzing RNA-seq data for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates.
View all literature mentionsMus musculus with name C57BL/6J from IMSR.
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