{"id":641,"date":"2017-03-14T13:28:31","date_gmt":"2017-03-14T18:28:31","guid":{"rendered":"http:\/\/my.vanderbilt.edu\/irishlab\/?p=641"},"modified":"2018-01-19T08:55:21","modified_gmt":"2018-01-19T13:55:21","slug":"diggins-et-al-nature-methods-2017","status":"publish","type":"post","link":"https:\/\/my.vanderbilt.edu\/irishlab\/2017\/03\/diggins-et-al-nature-methods-2017\/","title":{"rendered":"Published: Diggins et al., Nature Methods 2017"},"content":{"rendered":"

Congratulations to Kirsten Diggins<\/a>\u00a0and co-authors!<\/p>\n

Diggins KE, Greenplate AR, Leelatian N, Wogsland CE, Irish JM. Characterizing cell subsets in heterogeneous tissues using marker enrichment modeling<\/a>. Nature Methods<\/strong> PMC5330853<\/a>. Pubmed<\/a>. DOI<\/a>.<\/p>\n

\u25ba This peer-reviewed methods research followed Diggins et al., Methods<\/em> 2015 and created a new algorithm for machine learning cell identity and coined the term \u201ccytotype\u201d to describe a quantified cell identity.\u00a0 Marker Enrichment Modeling (MEM) generates human- and machine-readable cytotype labels and works with a wide range of data, including fluorescence and mass cytometry, gene expression profiles, and single cell RNA-seq.\u00a0 R code for MEM<\/a> is available free for academic use. \u00a0We demonstrate the use of MEM in different types of cytometry data (fluorescence and mass cytometry) and in identifying cells in human brain tumors.<\/p>\n

\"Diggins

Diggins et al – Nature Methods 2017 MEM Fig 1<\/p><\/div>\n

This work was covered by Vanderbilt and a lay summary is available here:<\/p>\n

https:\/\/news.vanderbilt.edu\/2017\/03\/02\/new-way-to-define-cell-identity\/<\/p>\n

Marker Enrichment Modeling (MEM) code is available for academic and non-profit use and can be licensed for commercial use through VUeInnovations: \u00a0https:\/\/mem.vueinnovations.com\/<\/a><\/p>\n

Update: we have published a detailed MEM protocol, scripts, and updated code<\/a> (Diggins et al., Current Protocols in Cytometry<\/em> 2018).<\/p>\n

Diggins KE, Gandelman JS, Roe CE, Irish JM. Generating Quantitative Cell Identity Labels with Marker Enrichment Modeling (MEM).\u00a0Current Protocols in Cytometry<\/em>\u00a0<\/strong>2017. NIHMS912131. PMC in progress. \u00a0Pubmed<\/a>. \u00a0DOI<\/a>.<\/p>\n","protected":false},"excerpt":{"rendered":"

Congratulations to Kirsten Diggins\u00a0and co-authors! Diggins KE, Greenplate AR, Leelatian N, Wogsland CE, Irish JM. Characterizing cell subsets in heterogeneous tissues using marker enrichment modeling. Nature Methods PMC5330853. Pubmed. DOI. \u25ba This peer-reviewed methods research followed Diggins et al., Methods … Continue reading →<\/span><\/a><\/p>\n","protected":false},"author":565,"featured_media":570,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_monsterinsights_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0,"footnotes":"","_links_to":"","_links_to_target":""},"categories":[7,1,6],"tags":[13,11,10,12,9],"class_list":["post-641","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-irish-lab","category-news","category-publications","tag-cytotype","tag-machine-learning","tag-marker-enrichment-modeling","tag-mass-cytometry","tag-mem"],"_links":{"self":[{"href":"https:\/\/my.vanderbilt.edu\/irishlab\/wp-json\/wp\/v2\/posts\/641","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/my.vanderbilt.edu\/irishlab\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/my.vanderbilt.edu\/irishlab\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/my.vanderbilt.edu\/irishlab\/wp-json\/wp\/v2\/users\/565"}],"replies":[{"embeddable":true,"href":"https:\/\/my.vanderbilt.edu\/irishlab\/wp-json\/wp\/v2\/comments?post=641"}],"version-history":[{"count":10,"href":"https:\/\/my.vanderbilt.edu\/irishlab\/wp-json\/wp\/v2\/posts\/641\/revisions"}],"predecessor-version":[{"id":1348,"href":"https:\/\/my.vanderbilt.edu\/irishlab\/wp-json\/wp\/v2\/posts\/641\/revisions\/1348"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/my.vanderbilt.edu\/irishlab\/wp-json\/wp\/v2\/media\/570"}],"wp:attachment":[{"href":"https:\/\/my.vanderbilt.edu\/irishlab\/wp-json\/wp\/v2\/media?parent=641"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/my.vanderbilt.edu\/irishlab\/wp-json\/wp\/v2\/categories?post=641"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/my.vanderbilt.edu\/irishlab\/wp-json\/wp\/v2\/tags?post=641"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}