{"id":7974,"date":"2021-07-15T13:36:32","date_gmt":"2021-07-15T17:36:32","guid":{"rendered":"https:\/\/www.bumc.bu.edu\/compbiomed\/?p=7974"},"modified":"2021-07-15T13:36:32","modified_gmt":"2021-07-15T17:36:32","slug":"multi-resolution-characterization-of-molecular-taxonomies-in-bulk-and-single-cell-transcriptomics-data","status":"publish","type":"post","link":"https:\/\/www.bumc.bu.edu\/compbiomed\/2021\/07\/15\/multi-resolution-characterization-of-molecular-taxonomies-in-bulk-and-single-cell-transcriptomics-data\/","title":{"rendered":"Multi-resolution characterization of molecular taxonomies in bulk and single-cell transcriptomics data"},"content":{"rendered":"<p><em>(Source: Oxford Academic)<\/em><\/p>\n<p>New publication from Dr. Stefano Monti, Associate Professor of Medicine in the Section of Computational Biomedicine. See below for a brief summary and click the link to read the whole article.<\/p>\n<p><span>As high-throughput genomics assays become more efficient and cost effective, their utilization has become standard in large-scale biomedical projects. These studies are often explorative, in that relationships between samples are not explicitly defined\u00a0<\/span><em>a priori<\/em><span>, but rather emerge from data-driven discovery and annotation of molecular subtypes, thereby informing hypotheses and independent evaluation. Here, we present\u00a0<\/span><em>K2Taxonomer<\/em><span>, a novel unsupervised recursive partitioning algorithm and associated R package that utilize ensemble learning to identify robust subgroups in a \u2018taxonomy-like\u2019 structure.\u00a0<\/span><em>K2Taxonomer<\/em><span>\u00a0was devised to accommodate different data paradigms, and is suitable for the analysis of both bulk and single-cell transcriptomics, and other \u2018-omics\u2019, data. For each of these data types, we demonstrate the power of\u00a0<\/span><em>K2Taxonomer<\/em><span>\u00a0to discover known relationships in both simulated and human tissue data. We conclude with a practical application on breast cancer tumor infiltrating lymphocyte (TIL) single-cell profiles, in which we identified co-expression of translational machinery genes as a dominant transcriptional program shared by T cells subtypes, associated with better prognosis in breast cancer tissue bulk expression data.<\/span><\/p>\n<p>Click <a href=\"https:\/\/academic.oup.com\/nar\/advance-article\/doi\/10.1093\/nar\/gkab552\/6312745\">here<\/a> to read more.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>(Source: Oxford Academic) New publication from Dr. Stefano Monti, Associate Professor of Medicine in the Section of Computational Biomedicine. See below for a brief summary and click the link to read the whole article. As high-throughput genomics assays become more efficient and cost effective, their utilization has become standard in large-scale biomedical projects. These studies [&hellip;]<\/p>\n","protected":false},"author":16142,"featured_media":7975,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":[],"categories":[3],"tags":[],"_links":{"self":[{"href":"https:\/\/www.bumc.bu.edu\/compbiomed\/wp-json\/wp\/v2\/posts\/7974"}],"collection":[{"href":"https:\/\/www.bumc.bu.edu\/compbiomed\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.bumc.bu.edu\/compbiomed\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.bumc.bu.edu\/compbiomed\/wp-json\/wp\/v2\/users\/16142"}],"replies":[{"embeddable":true,"href":"https:\/\/www.bumc.bu.edu\/compbiomed\/wp-json\/wp\/v2\/comments?post=7974"}],"version-history":[{"count":1,"href":"https:\/\/www.bumc.bu.edu\/compbiomed\/wp-json\/wp\/v2\/posts\/7974\/revisions"}],"predecessor-version":[{"id":7976,"href":"https:\/\/www.bumc.bu.edu\/compbiomed\/wp-json\/wp\/v2\/posts\/7974\/revisions\/7976"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.bumc.bu.edu\/compbiomed\/wp-json\/wp\/v2\/media\/7975"}],"wp:attachment":[{"href":"https:\/\/www.bumc.bu.edu\/compbiomed\/wp-json\/wp\/v2\/media?parent=7974"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.bumc.bu.edu\/compbiomed\/wp-json\/wp\/v2\/categories?post=7974"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.bumc.bu.edu\/compbiomed\/wp-json\/wp\/v2\/tags?post=7974"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}