{"id":15,"date":"2021-07-14T11:31:47","date_gmt":"2021-07-14T11:31:47","guid":{"rendered":"https:\/\/www.ebi.ac.uk\/research-beta\/finn\/home\/"},"modified":"2022-01-12T10:02:16","modified_gmt":"2022-01-12T10:02:16","slug":"home","status":"publish","type":"page","link":"https:\/\/www.ebi.ac.uk\/research\/finn\/","title":{"rendered":"Home"},"content":{"rendered":"<div class=\"vf-grid vf-grid__col-3 | vf-u-margin__bottom--800\">\n      <div class=\"vf-grid__col--span-2\">\n      <div class=\"vf-content-hub-html\">\n  <!-- Generated by: http:\/\/content.embl.org\/api\/v1\/pattern.html?filter-content-type=profiles&amp;filter-uuid=f339e7ce-763a-452b-ad9a-f0b27d074427&amp;pattern=node-teaser -->\n      <div data-embl-js-conditional-edit=\"142394\">\n              <h1 class=\"vf-lede\">The Finn research group focuses on developing computational approaches for the reconstruction of genomes from metagenomes, and investigates the distribution of microbes and functions in different environments.<\/p>\r\n\n            <a class=\"vf-text vf-text--body-r vf-link embl-conditional-edit\" rel=\"noopener noreferrer nofollow\" href=\"\/node\/142394\" target=\"_blank\">Edit<\/a>\n    <\/div>\n  <\/div>\n    <\/div>\n      <div >\n\n<!-- <style>\n  .vf-content-hub-html {\n    --vf-stack-margin--custom: unset !important;\n  }\n<\/style> -->\n\n    <div class=\"vf-content-hub-html vf-stack vf-stack--600\" data-cache=\"3d87f118\">\n      <!-- Generated by: http:\/\/content.embl.org\/api\/v1\/pattern.html?filter-content-type=person&amp;filter-field-value%5Bfield_person_positions.entity.field_position_membership%5D=leader&amp;filter-field-value%5Bfield_person_positions.entity.field_position_team.entity.field_foreignid%5D=534&amp;filter-ref-entity%5Bfield_person_positions%5D%5Btitle%5D=&amp;filter-ref-entity%5Bfield_person_positions%5D%5Bfield_position_primary%5D=1&amp;hide%5Bteam%2Cmobile%2Cphones%5D=1&amp;limit=5&amp;pattern=vf-profile-inline&amp;sort-field-value%5Bchanged%5D=DESC -->\n                \n                            <article class=\"vf-profile vf-profile--very-easy vf-profile--medium vf-profile--inline\" data-embl-js-conditional-edit=\"85008\">\n              <img decoding=\"async\" class=\"vf-profile__image\" src=\"https:\/\/content.embl.org\/\/sites\/default\/files\/styles\/medium\/public\/persons\/CP-60018634.jpg?itok=gYUuaQjx\" alt=\"image of Robert Finn\" \/>\n      \n              <h3 class=\"vf-profile__title\">\n                      <a href=\"https:\/\/www.ebi.ac.uk\/people\/person\/rob-finn\" class=\"vf-profile__link\">Robert Finn<\/a>\n                  <\/h3>\n      \n              <p class=\"vf-profile__job-title\">\n          Section Head, Team Leader and Senior Scientist\n        <\/p>\n      \n      \n      \n              \n                  <p class=\"vf-profile__email | vf-u-last-item\">\n            rdf [at] ebi.ac.uk\n          <\/p>\n              \n      \n                                      \n              <p class=\"vf-profile__uuid\">\n          <span>ORCID:<\/span>\n          <a class=\"vf-profile__link vf-profile__link--secondary\" href=\"https:\/\/europepmc.org\/authors\/0000-0001-8626-2148\">\n            0000-0001-8626-2148\n          <\/a>\n        <\/p>\n            <a class=\"vf-text vf-text--body-r vf-link embl-conditional-edit\" rel=\"noopener noreferrer nofollow\" href=\"\/node\/85008\/85008\" target=\"_blank\">\n        Edit\n      <\/a>\n    <\/article>\n  <\/div>\n\n  <\/div>\n<\/div>\n\n\n\n<div class=\"vf-grid | vf-grid__col-3\"><div class=\"vf-grid__col--span-2\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<h2 class=\"wp-block-heading\">What we do<\/h2>\n\n\n\n<p>We explore the entire microbiome, including the important yet understudied viral and eukaryotic (single-cell) fractions, to elucidate the functions of microbial communities, as well as their complex interplay and dynamics.<\/p>\n\n\n\n<p>In doing this, we also consider the genomic plasticity and diversity generated by mobile genetic elements (MGE), which can create opportunistic pathogens and\/or drug resistant microbes.&nbsp;<\/p>\n\n\n\n<p>Finally, we constantly evaluate and adopt new technologies (e.g. long-read sequencing) to overcome technical and analytical challenges, such as capturing microbial diversity from complex samples, obtaining high-quality genomes from low-yield environments, and reducing the computational overheads to achieve in-field, real-time surveillance.\u00a0<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">Achievements<\/h2>\n\n\n\n<p>Our large-scale studies have identified thousands of novel species, which are now driving new developments in the <a href=\"https:\/\/www.ebi.ac.uk\/metagenomics\/\" target=\"_blank\" rel=\"noreferrer noopener\">MGnify microbiome resource<\/a>. We have:<\/p>\n\n\n\n<ul class=\"wp-block-list\"><li>Defined a new blueprint for the human gut microbiome by generating the <a rel=\"noreferrer noopener\" href=\"https:\/\/www.nature.com\/articles\/s41587-020-0603-3\" target=\"_blank\">Unified Human Gastrointestinal Genome (UHGG)<\/a> collection based on large-scale metagenomic analysis. This represents nearly 5,000 species, 70% of which have never been experimentally cultured to date.<\/li><li>Developed and used the new VIRify tool to <a rel=\"noreferrer noopener\" href=\"https:\/\/www.cell.com\/cell\/fulltext\/S0092-8674(21)00072-6\" target=\"_blank\">identify genomes of 142,000 viral species comprising the viral catalogue<\/a>, generated by mining 28,000 globally distributed human gut metagenomes.<\/li><li>Developed the new <a href=\"https:\/\/genomebiology.biomedcentral.com\/articles\/10.1186\/s13059-020-02155-4\">EukCC tool<\/a> to assess eukaryotic genome quality.<\/li><li>Produced the Skin Microbial Genome Collection (SMGC), spanning viruses, bacteria, and eukaryotes obtained from human skin.<\/li><li>Developed pipelines to enable the incorporation of long-read metagenomic sequences.<\/li><\/ul>\n\n\n\n<h2 class=\"wp-block-heading\">Future projects and goals&nbsp;<\/h2>\n\n\n\n<p>Our overarching goal is to decode the role of microbial communities in health and disease. We will exploit these new and expanding genomic resources to elucidate compositional changes and to address key knowledge gaps, including uncharacterised human microbiomes from under-represented geographical regions.&nbsp;<\/p>\n\n\n\n<p>We will study the functional repertoire encoded by these newly discovered genomes to identify those with key roles in microbial adaptation to a particular ecological niche.&nbsp;<\/p>\n\n\n\n<p>We will also focus efforts on the detection, prevalence, and impact of MGE (e.g. plasmids, phages, and transposons) to facilitate insights into their roles in community function, and exploit their functions in applied settings, for example fuelling new greener approaches to industrial biotechnology.&nbsp;<\/p>\n\n\n\n<p>Finally, we will pursue real-world applications of metagenomics techniques, such as pathogen surveillance or the study of complex symbionts.<\/p>\n\n<\/div>\n<\/div>\n\n\n<div class=\"\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<figure class=\"vf-figure wp-block-image\"><img decoding=\"async\" class=\"vf-figure__image\" src=\"https:\/\/lh4.googleusercontent.com\/SIzKQXJJ_McuN7xo-rtE7_ffL7C9uNBh5mVO2_debdIyRpYJEkM7PrkWSY9TpAytsjqErmqElFyOwTQDnnYp1eVhNamagmlHNRenzfVzJTxoI34EWkIrGv1i9TUZfsoymnzcV2TS\" alt=\"\"\/><figcaption class=\"vf-figure__caption\"><meta charset=\"utf-8\">Phylogenetic tree showing the distribution of metagenome assembled genomes of novel species (green, inner)\u00a0 we\u00a0 recovered from human gut samples. The outer ring shows the different phyla.<\/figcaption><\/figure>\n\n\n\n<figure class=\"wp-block-embed is-type-rich is-provider-twitter wp-block-embed-twitter\"><div class=\"vf-embed vf-embed--16x9\">\n<a class=\"twitter-timeline\" data-width=\"500\" data-height=\"750\" data-dnt=\"true\" href=\"https:\/\/twitter.com\/robdfinn?ref_src=twsrc%5Etfw\">Tweets by robdfinn<\/a><script async src=\"https:\/\/platform.twitter.com\/widgets.js\" charset=\"utf-8\"><\/script>\n<\/div><\/figure>\n\n<\/div>\n<\/div>\n<\/div>\n\n\n\n\n\n<div >\n\n    \n    \n<\/div>\n\n\n\n<div class=\"embl-grid embl-grid--has-centered-content | vf-u-margin__top--800\">\n    <div class=\"vf-section-header\">\n  <h2 class=\"vf-section-header__heading\">\n    <a class=\"vf-section-header__heading vf-section-header__heading--is-link\" href=\"https:\/\/www.ebi.ac.uk\/services\"\n      id=\"section-link\"> Data resources <svg aria-hidden=\"true\"\n        class=\"vf-section-header__icon | vf-icon vf-icon-arrow--inline-end\" width=\"24\" height=\"24\"\n        xmlns=\"http:\/\/www.w3.org\/2000\/svg\">\n        <path\n          d=\"M0 12c0 6.627 5.373 12 12 12s12-5.373 12-12S18.627 0 12 0C5.376.008.008 5.376 0 12zm13.707-5.209l4.5 4.5a1 1 0 010 1.414l-4.5 4.5a1 1 0 01-1.414-1.414l2.366-2.367a.25.25 0 00-.177-.424H6a1 1 0 010-2h8.482a.25.25 0 00.177-.427l-2.366-2.368a1 1 0 011.414-1.414z\"\n          fill=\"\" fill-rule=\"nonzero\"><\/path>\n      <\/svg><\/a><\/h2><\/div>\n    <div>\n      <\/div>\n  <div><\/div>\n<\/div>\n\n\n\n<p><\/p>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":5,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"footnotes":""},"embl_taxonomy":[],"class_list":["post-15","page","type-page","status-publish","hentry"],"acf":[],"embl_taxonomy_terms":[],"_links":{"self":[{"href":"https:\/\/www.ebi.ac.uk\/research\/finn\/wp-json\/wp\/v2\/pages\/15","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.ebi.ac.uk\/research\/finn\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.ebi.ac.uk\/research\/finn\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/research\/finn\/wp-json\/wp\/v2\/users\/5"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/research\/finn\/wp-json\/wp\/v2\/comments?post=15"}],"version-history":[{"count":10,"href":"https:\/\/www.ebi.ac.uk\/research\/finn\/wp-json\/wp\/v2\/pages\/15\/revisions"}],"predecessor-version":[{"id":83,"href":"https:\/\/www.ebi.ac.uk\/research\/finn\/wp-json\/wp\/v2\/pages\/15\/revisions\/83"}],"wp:attachment":[{"href":"https:\/\/www.ebi.ac.uk\/research\/finn\/wp-json\/wp\/v2\/media?parent=15"}],"wp:term":[{"taxonomy":"embl_taxonomy","embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/research\/finn\/wp-json\/wp\/v2\/embl_taxonomy?post=15"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}