{"id":584,"date":"2017-11-04T14:40:47","date_gmt":"2017-11-04T19:40:47","guid":{"rendered":"http:\/\/blogs.discovery.wisc.edu\/sysbiojournalclub\/?p=584"},"modified":"2017-11-04T14:40:47","modified_gmt":"2017-11-04T19:40:47","slug":"reconstruction-of-developmental-landscapes-by-optimal-transport-analysis-of-single-cell-gene-expression-sheds-light-on-cellular-reprogramming","status":"publish","type":"post","link":"https:\/\/blogs.discovery.wisc.edu\/sysbiojournalclub\/2017\/11\/04\/reconstruction-of-developmental-landscapes-by-optimal-transport-analysis-of-single-cell-gene-expression-sheds-light-on-cellular-reprogramming\/","title":{"rendered":"Reconstruction of developmental landscapes by optimal-transport analysis of single-cell gene expression sheds light on cellular reprogramming."},"content":{"rendered":"<p>Our next meeting will be at 11:00 on\u00a0Nov\u00a07th, in room 4160 of the Discovery building. Our Selected paper is <a href=\"https:\/\/www.biorxiv.org\/content\/early\/2017\/09\/27\/191056\">Reconstruction of developmental landscapes by optimal-transport analysis of single-cell gene expression sheds light on cellular reprogramming.<\/a><br \/>\nThe abstract is as follows.<\/p>\n<blockquote><p>Understanding the molecular programs that guide cellular differentiation during development is a major goal of modern biology. Here, we introduce an approach, WADDINGTON-OT, based on the mathematics of optimal transport, for inferring developmental landscapes, probabilistic cellular fates and dynamic trajectories from large-scale single-cell RNA-seq (scRNA-seq) data collected along a time course. We demonstrate the power of WADDINGTON-OT by applying the approach to study 65,781 scRNA-seq profiles collected at 10 time points over 16 days during reprogramming of fibroblasts to iPSCs. We construct a high-resolution map of reprogramming that rediscovers known features; uncovers new alternative cell fates including neural- and placental-like cells; predicts the origin and fate of any cell class; highlights senescent-like cells that may support reprogramming through paracrine signaling; and implicates regulatory models in particular trajectories. Of these findings, we highlight Obox6, which we experimentally show enhances reprogramming efficiency. Our approach provides a general framework for investigating cellular differentiation.<\/p><\/blockquote>\n<p>We welcome all who can join us for this discussion. Feel free to begin that discussion in the comments section below.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Our next meeting will be at 11:00 on\u00a0Nov\u00a07th, in room 4160 of the Discovery building. Our Selected paper is Reconstruction of developmental landscapes by optimal-transport analysis of single-cell gene expression sheds light on cellular reprogramming. The abstract is as follows. Understanding the molecular programs that guide cellular differentiation during development is a major goal of [&hellip;]<\/p>\n","protected":false},"author":197,"featured_media":0,"comment_status":"open","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":[],"categories":[103,133],"tags":[],"_links":{"self":[{"href":"https:\/\/blogs.discovery.wisc.edu\/sysbiojournalclub\/wp-json\/wp\/v2\/posts\/584"}],"collection":[{"href":"https:\/\/blogs.discovery.wisc.edu\/sysbiojournalclub\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/blogs.discovery.wisc.edu\/sysbiojournalclub\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/blogs.discovery.wisc.edu\/sysbiojournalclub\/wp-json\/wp\/v2\/users\/197"}],"replies":[{"embeddable":true,"href":"https:\/\/blogs.discovery.wisc.edu\/sysbiojournalclub\/wp-json\/wp\/v2\/comments?post=584"}],"version-history":[{"count":1,"href":"https:\/\/blogs.discovery.wisc.edu\/sysbiojournalclub\/wp-json\/wp\/v2\/posts\/584\/revisions"}],"predecessor-version":[{"id":585,"href":"https:\/\/blogs.discovery.wisc.edu\/sysbiojournalclub\/wp-json\/wp\/v2\/posts\/584\/revisions\/585"}],"wp:attachment":[{"href":"https:\/\/blogs.discovery.wisc.edu\/sysbiojournalclub\/wp-json\/wp\/v2\/media?parent=584"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/blogs.discovery.wisc.edu\/sysbiojournalclub\/wp-json\/wp\/v2\/categories?post=584"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/blogs.discovery.wisc.edu\/sysbiojournalclub\/wp-json\/wp\/v2\/tags?post=584"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}