{"id":1100,"date":"2022-05-04T16:20:00","date_gmt":"2022-05-04T14:20:00","guid":{"rendered":"https:\/\/makit.edu.umontpellier.fr\/?p=1100"},"modified":"2024-02-28T10:27:08","modified_gmt":"2024-02-28T09:27:08","slug":"anton-nekrutenkos-event-microbial-evolutionary-genomics-and-data-analysis-17-18-may-2022","status":"publish","type":"post","link":"https:\/\/makit.edu.umontpellier.fr\/fr\/2022\/05\/04\/anton-nekrutenkos-event-microbial-evolutionary-genomics-and-data-analysis-17-18-may-2022\/","title":{"rendered":"Microbial evolutionary genomics and data analysis"},"content":{"rendered":"<h5 class=\"wp-block-heading\"><strong><u>Tuesday 17 May: Mini-symposium on microbial evolutionary genomics<\/u><\/strong><\/h5>\n\n\n\n<p class=\"wp-block-paragraph\">Due to proliferation of new data generation technologies, microbial biology has become a data driven science.&nbsp;<strong>Yet there is still a limited \u201cmixing\u201d between researchers studying biological questions and their computational colleagues.<\/strong>&nbsp;The goal of this mini-symposium is to bring together representatives of the two sides (\u201cwet\u201d and \u201cdry\u201d) and discover the ways in which they can be more aware of each other\u2019s challenges and priorities. The unique combination of speakers will cover the following areas:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Analysis of microbial communities<\/li>\n\n\n\n<li>Experimental evolution<\/li>\n\n\n\n<li>Phylogenetic reconstruction<\/li>\n\n\n\n<li>Analysis of recombination<\/li>\n\n\n\n<li>Analysis of selection<\/li>\n\n\n\n<li>Data logistics and analysis automation<\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\"><strong><em>Programme and speakers<\/em><\/strong><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>09:00 \u2013 09:10<\/strong>Welcome and introduction<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>09:10 \u2013 09:45<\/strong><em>\u2018Dynamics and evolution of microbial<\/em>communities\u2019<strong>\u2013<\/strong><a href=\"https:\/\/www.sheffield.ac.uk\/biosciences\/people\/academic-staff\/ellie-harrison\"><strong>Ellie Harrison<\/strong><\/a>, University of Sheffield, UK<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>09:45 \u2013 10:05<\/strong>&nbsp;<em>\u2018Analysis of microbial communities\u2019<\/em>\u2013<a href=\"http:\/\/pagesperso.univ-brest.fr\/~maignien\/contact.html\"><strong>Lois Maignien<\/strong><\/a>University of Western Brittany, France<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>10:05 \u2013 11:00<\/strong><em>\u2018Global analytical environment for me\u2019<\/em>\u2013<a href=\"https:\/\/training.galaxyproject.org\/hall-of-fame\/shiltemann\/\"><strong>Saskia Hiltemann<\/strong><\/a>, Erasmus MC, The Netherlands<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong><em>10:25 \u2013 10:30 Coffee break<\/em><\/strong><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>11:00\u2013 11:20<\/strong><em>\u2018Evolutionary dynamics of antiobiotic resistance\u2019<\/em>\u2013<a href=\"https:\/\/www.cefe.cnrs.fr\/fr\/recherche\/ee\/gee\/800-c\/2721-stephanie-bedhomme\"><strong>St\u00e9phanie Bedhomme<\/strong><\/a>, CNRS\/ Centre for Functional and Evolutionary Ecology (CEFE), France<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>11:20 \u2013 11:40<\/strong><em>\u2018Codon bias and antibiotic resistance\u2019<\/em>\u2013<a href=\"https:\/\/www.ugent.be\/bw\/foodscience\/en\/research\/faculty\/matijn-callens.htm\"><strong>Martijn Callens<\/strong><\/a>, Ghent University, Belgium<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>11:40 \u2013 12:00<\/strong><em>\u2018Experimental evolution\u2019<\/em><strong>\u2013<\/strong><a href=\"https:\/\/www.cefe.cnrs.fr\/fr\/recherche\/ee\/gee\/803-doc\/4043-michael-finnegan\"><strong>Mike Finnegan<\/strong><\/a>, CNRS\/Centre for Functional and Evolutionary Ecology (CEFE), France<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>12:00 \u2013 12:20<\/strong><em>\u2018Coevolutionary dynamics between phages and CRISPR immunity\u2019<\/em>\u2013<a href=\"https:\/\/evolepid.cefe.cnrs.fr\/people.php?name=gandon\"><strong>Sylvain Gandon<\/strong><\/a>, CNRS\/ Centre for Functional and Evolutionary Ecology (CEFE), France<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong><em>12:20\u2013 14:00 Lunch break<\/em><\/strong><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>14:00 \u2013 14:20<\/strong><em>\u2018Molecular evolution and selection analysis\u2019<\/em>\u2013<a href=\"https:\/\/igem.temple.edu\/people\/person\/e266d9a5b7f043109baecc3c340491f6\"><strong>Sergei Kosakovsky Pond<\/strong><\/a>, Temple University, USA<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>14:20 \u2013 14:40<\/strong><em>\u2018Synthetic biology\u2019<\/em>\u2013<a href=\"http:\/\/www.cbs.cnrs.fr\/index.php\/fr\/personnel?PERS=Guillaume%20Cambray\"><strong>Guillaume Cambray<\/strong><\/a>, CNRS\/Centre for Structural Biology (CBS), France<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>14:40 \u2013 15:00<\/strong><em>\u2018Large scale analysis of pandemic data\u2019<\/em>\u2013<a href=\"https:\/\/github.com\/wm75\"><strong>Wolfgang Maier<\/strong><\/a>, University of Freiburg, Germany<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>15:00 \u2013 15:20<\/strong><em>\u2018Data analytics and representation\u2019<\/em>\u2013<a href=\"https:\/\/engineering.ucsc.edu\/people\/max\"><strong>Maximilan Haeussler<\/strong><\/a>, UC Santa Cruz, USA<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>15:20 \u2013 15:40<\/strong><em>\u2018Data analysis frameworks for microbial genomics\u2019<\/em>\u2013<strong>Anton Nekrutenko<\/strong>, Pennsylvania State University, USA &amp; MAK\u2019IT Fellow (JRU CEFE)<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>15:40 \u2013 15:50<\/strong>Closing remarks<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong><em>15:50 -16:30 Coffee break<\/em><\/strong><\/p>\n\n\n\n<h5 class=\"wp-block-heading\"><strong><u>Wednesday 18 May: Workshop on microbial data analysis<\/u><\/strong><\/h5>\n\n\n\n<p class=\"wp-block-paragraph\">The workshop will focus on the application of sequencing data (Illumina, Oxford Nanopore, PacBio) to analysis of&nbsp;<a href=\"https:\/\/training.galaxyproject.org\/training-material\/topics\/metagenomics\/\" target=\"_blank\" rel=\"noreferrer noopener\">microbial communities<\/a>,&nbsp;<a href=\"https:\/\/training.galaxyproject.org\/training-material\/search?query=assembly\" target=\"_blank\" rel=\"noreferrer noopener\">genome assembly<\/a>,&nbsp;<a href=\"https:\/\/training.galaxyproject.org\/training-material\/topics\/variant-analysis\/tutorials\/sars-cov-2-variant-discovery\/tutorial.html\" target=\"_blank\" rel=\"noreferrer noopener\">analysis of variation<\/a>, and&nbsp;<a href=\"https:\/\/stevenweaver.github.io\/hyphy-site\/tutorials\/current-release-tutorial\/\" target=\"_blank\" rel=\"noreferrer noopener\">identification of sites under selection<\/a>.<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">9:00 \u2013 12:00 \u2013 Part 1<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><em>12:00 \u2013 13:30 \u2013 Lunch break<\/em><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">13:30 \u2013 16:00 \u2013 Part 2<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Presenters:<\/strong><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li><a href=\"https:\/\/training.galaxyproject.org\/hall-of-fame\/shiltemann\/\"><strong>Saskia Hiltemann<\/strong><\/a>&nbsp;\u2013 Erasmus MC, The Netherlands<\/li>\n\n\n\n<li><a href=\"https:\/\/training.galaxyproject.org\/hall-of-fame\/hexylena\/\"><strong>Helena Rasche<\/strong><\/a>&nbsp;\u2013 Erasmus MC &amp; Avans Hogeschool, The Netherlands<\/li>\n\n\n\n<li><a href=\"https:\/\/muse.edu.umontpellier.fr\/en\/anton-nekrutenko\/\"><strong>Anton Nekrutenko<\/strong><\/a>&nbsp;\u2013 Pennsylvania State University, USA &amp; MAK\u2019IT Fellow (JRU CEFE)<\/li>\n\n\n\n<li><a href=\"https:\/\/github.com\/wm75\"><strong>Wolfgang Maier<\/strong><\/a>&nbsp;\u2013 University of Freiburg, Germany<\/li>\n<\/ul>","protected":false},"excerpt":{"rendered":"<p>Tuesday 17 May: Mini-symposium on microbial evolutionary genomics Due to proliferation of new data generation technologies, microbial biology has become a data driven science.&nbsp;Yet there is still a limited \u201cmixing\u201d between researchers studying biological questions and their computational colleagues.&nbsp;The goal of this mini-symposium is to bring together representatives of the two sides (\u201cwet\u201d and \u201cdry\u201d)&hellip;<\/p>","protected":false},"author":1087,"featured_media":1015,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"_relevanssi_hide_post":"","_relevanssi_hide_content":"","_relevanssi_pin_for_all":"","_relevanssi_pin_keywords":"","_relevanssi_unpin_keywords":"","_relevanssi_related_keywords":"","_relevanssi_related_include_ids":"","_relevanssi_related_exclude_ids":"","_relevanssi_related_no_append":"","_relevanssi_related_not_related":"","_relevanssi_related_posts":"","_relevanssi_noindex_reason":"","footnotes":""},"categories":[29229,29407],"tags":[],"class_list":["post-1100","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-actualites-en","category-seminar"],"acf":[],"_links":{"self":[{"href":"https:\/\/makit.edu.umontpellier.fr\/fr\/wp-json\/wp\/v2\/posts\/1100","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/makit.edu.umontpellier.fr\/fr\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/makit.edu.umontpellier.fr\/fr\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/makit.edu.umontpellier.fr\/fr\/wp-json\/wp\/v2\/users\/1087"}],"replies":[{"embeddable":true,"href":"https:\/\/makit.edu.umontpellier.fr\/fr\/wp-json\/wp\/v2\/comments?post=1100"}],"version-history":[{"count":0,"href":"https:\/\/makit.edu.umontpellier.fr\/fr\/wp-json\/wp\/v2\/posts\/1100\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/makit.edu.umontpellier.fr\/fr\/wp-json\/wp\/v2\/media\/1015"}],"wp:attachment":[{"href":"https:\/\/makit.edu.umontpellier.fr\/fr\/wp-json\/wp\/v2\/media?parent=1100"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/makit.edu.umontpellier.fr\/fr\/wp-json\/wp\/v2\/categories?post=1100"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/makit.edu.umontpellier.fr\/fr\/wp-json\/wp\/v2\/tags?post=1100"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}