{"id":15,"date":"2020-09-24T14:42:43","date_gmt":"2020-09-24T14:42:43","guid":{"rendered":"https:\/\/www.embl.org\/groups\/sharpe\/home\/"},"modified":"2024-08-30T14:25:52","modified_gmt":"2024-08-30T14:25:52","slug":"home","status":"publish","type":"page","link":"https:\/\/www.embl.org\/groups\/sharpe\/","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=6c31c788-04a1-48b8-a532-fdc251506b57&amp;pattern=node-teaser -->\n      <div data-embl-js-conditional-edit=\"6634\">\n              <h1 class=\"vf-lede\">The Sharpe group brings together an interdisciplinary team of biologists, physicists and computer scientists to build multi-scale computer simulations of a paradigm of organogenesis \u2013 mammalian limb development.<\/p>\r\n\n            <a class=\"vf-text vf-text--body-r vf-link embl-conditional-edit\" rel=\"noopener noreferrer nofollow\" href=\"\/node\/6634\" 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=\"836d9f06\">\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=498&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=\"87698\">\n              <img decoding=\"async\" class=\"vf-profile__image\" src=\"https:\/\/content.embl.org\/\/sites\/default\/files\/styles\/medium\/public\/persons\/CP-60027035.jpg?itok=GrjElgNp\" alt=\"image of James Sharpe\" \/>\n      \n              <h3 class=\"vf-profile__title\">\n                      <a href=\"https:\/\/www.embl.org\/people\/person\/james-sharpe\" class=\"vf-profile__link\">James Sharpe<\/a>\n                  <\/h3>\n      \n              <p class=\"vf-profile__job-title\">\n          Head of EMBL Barcelona\n        <\/p>\n      \n      \n      \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\/0000-0002-1434-9743\">\n            0000-0002-1434-9743\n          <\/a>\n        <\/p>\n            <a class=\"vf-text vf-text--body-r vf-link embl-conditional-edit\" rel=\"noopener noreferrer nofollow\" href=\"\/node\/87698\/87698\" 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<h3 class=\"wp-block-heading\">Previous and current research<\/h3>\n\n\n\n<p>How do networks of genes control populations of cells to build organised tissues and organs? Organ development is a multi-scale process, in which molecular and cellular events control large-scale tissue movements, but these \u2018macroscopic\u2019 dynamics are equally important in feeding-back to regulate molecular events. A full understanding of how genes control organogenesis will thus require multi-scale computer modelling, and we have chosen vertebrate limb development as a model system to explore this problem.<\/p>\n\n\n\n<p>Such a model should be based on quantitative data about dynamic tissue shapes and spatial distributions of gene activities. Traditional high-throughput and \u2018omics\u2019 technologies do not preserve spatial information, and we have therefore been developing and pioneering various 3D mesoscopic imaging technologies to generate geometric and spatial data for the model.<\/p>\n\n\n\n<p>Our research thus falls primarily into two main areas:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>To further our understanding of <em>organogenesis as a complex system<\/em>, by bringing together a diverse range of techniques from biology, physics, imaging and computer science. Within this general theme, we focus on two aspects:\n<ol class=\"wp-block-list\">\n<li>We study a well-characterised standard model of development \u2013 the vertebrate limb\/fin (using the mouse, chick and catshark). We combine experimental data (especially 3D data sets using optical projection tomography) within computational frameworks, to explore and test mechanistic hypotheses about how limb morphogenesis works. Using this approach we are studying both the physical morphogenesis (Boehm <em>et al<\/em>. 2010, <em>PLoS Biol.<\/em> and Marcon <em>et al<\/em>. 2011, <em>PLoS Comp. Biol.<\/em>) and also the genetic patterning mechanisms (Sheth <em>et al<\/em>. 2012, <em>Science<\/em> and Uzkudun et al. 2015 <em>Molecular Systems Biology<\/em>). We have used this mix of experimental and theoretical work to find evidence supporting the idea that digit patterning is achieved by a Turing reaction-diffusion system (Raspopovic <em>et al<\/em>. 2014, <em>Science<\/em>), and more recently have shown that this particular molecular systems has been conserved all the way from fish to mammals (Onimaru <em>et al<\/em>. 2016, <em>Nature Communications<\/em>).<\/li>\n\n\n\n<li>In addition to this specific model system, we are also interested in the theoretical principles by which gene regulatory networks can create controlled spatial patterns in multicellular contexts, both in a purely theoretical context (Cotterell <em>et al.<\/em> 2010, <em>Molecular Systems Biology<\/em>, Jimenez <em>et al.<\/em> 2015, <em>PNAS<\/em>, Jimenez <em>et al.<\/em> 2017, <em>Molecular Systems Biology<\/em>), and also in its application to synthetic biology (Schaerli <em>et al<\/em>. 2014, <em>Nature Communications<\/em>), and somite patterning (Cotterell <em>et al.<\/em> 2015, <em>Cell Systems<\/em>).<\/li>\n<\/ol>\n<\/li>\n<\/ul>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Building on the success of the 3D imaging technique developed within the lab called Optical Projection Tomography (OPT \u2013 <em>Science<\/em> 296:541, 2002), the other major goal of the lab is to continue developing and improving 3D and 4D imaging technology including the development of time-lapse imaging of mouse limb development in-vitro (e.g. <em>Nature Methods<\/em> 5:609-12, 2008). Our recent projects include the development of OPTiSPIM (Maeyer <em>et al<\/em>., 2014).<\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">Future projects and goals<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li>To create a full quantitative 4D \u2018atlas\u2019 of the distributed cellular activities (proliferation, integration, etc.) which together drive the mechanical process of limb bud morphogenesis.<\/li>\n\n\n\n<li>To develop realistic dynamic simulations of the gene regulatory circuits which drive the cellular activities and correct differentiation patterns.<\/li>\n\n\n\n<li>The long-term goal of the lab is to integrate the two phenomena described above into a full multi-scale model of mammalian limb development, successful enough to predict mutant phenotypes.<\/li>\n<\/ul>\n\n\n\n<p><a rel=\"noreferrer noopener\" href=\"http:\/\/erc.europa.eu\/\" target=\"_blank\">ERC ADVANCED INVESTIGATOR<\/a><\/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 size-large\"><a href=\"https:\/\/www.embl.org\/groups\/sharpe\/wp-content\/uploads\/2020\/09\/fig01_l.jpg\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"556\" class=\"vf-figure__image\" src=\"https:\/\/www.embl.org\/groups\/sharpe\/wp-content\/uploads\/2020\/09\/fig01_l-1024x556.jpg\" alt=\"scientific poster\" class=\"wp-image-56\" srcset=\"https:\/\/www.embl.org\/groups\/sharpe\/wp-content\/uploads\/2020\/09\/fig01_l-1024x556.jpg 1024w, https:\/\/www.embl.org\/groups\/sharpe\/wp-content\/uploads\/2020\/09\/fig01_l-300x163.jpg 300w, https:\/\/www.embl.org\/groups\/sharpe\/wp-content\/uploads\/2020\/09\/fig01_l-768x417.jpg 768w, https:\/\/www.embl.org\/groups\/sharpe\/wp-content\/uploads\/2020\/09\/fig01_l.jpg 1200w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><\/a><figcaption class=\"vf-figure__caption\"><strong>Figure 1<\/strong>: The Sharpe lab constructs various 2D and 3D computer models of limb development. These have allowed us to explore and dispute the proliferation gradient hypothesis (left), create a realistic map of tissue movements in 2D (centre), and explain how Hox genes affect a Turing-type mechanism to explain the basic patterning of digits (right)<\/figcaption><\/figure>\n\n<\/div>\n<\/div>\n<\/div>\n\n\n\n<hr class=\"vf-divider\">\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\">News about Sharpe group<\/h2>\n\n\n<div class=\"vf-content-hub-html\" data-cache=\"a0e1a633\">\n  <!-- Generated by: http:\/\/content.embl.org\/api\/v1\/pattern.html?filter-all-fields=Sharpe&amp;filter-content-type=article&amp;filter-field-value%5Bfield_target_display%5D=embl&amp;limit=8&amp;pattern=vf-news-item-default&amp;sort-field-value%5Bcreated%5D=DESC -->\n      <article class=\"vf-summary vf-summary--news\" data-embl-js-conditional-edit=\"1461219\">\n\n              <span class=\"vf-summary__date\">05 Feb 2026<\/span>\n      \n                    <img decoding=\"async\" src=\"https:\/\/acxngcvroo.cloudimg.io\/v7\/https:\/\/www.embl.org\/news\/wp-content\/uploads\/2026\/02\/SharpeGroupLimbLab2-1.jpg?w=600&amp;h=400&amp;force_format=jpeg&amp;q=30\" alt=\"News image\" class=\"vf-summary__image\" \/>\n      \n              <h3 class=\"vf-summary__title\">\n                      <a href=\"https:\/\/www.embl.org\/news\/science-technology\/limblab-a-tool-to-visualise-development-in-3d\/\" class=\"vf-summary__link\">LimbLab: a tool to visualise development in 3D<\/a>\n                  <\/h3>\n      \n              <p class=\"vf-summary__text\">\n                    Researchers at EMBL Barcelona have developed an open-source tool that makes working with complicated volumetric imaging data easier.\n        <\/p>\n      \n      <a class=\"vf-text vf-text--body-r vf-link embl-conditional-edit\" rel=\"noopener noreferrer nofollow\" href=\"\/node\/1461219\" target=\"_blank\">Edit<\/a>\n\n    <\/article>\n      <article class=\"vf-summary vf-summary--news\" data-embl-js-conditional-edit=\"1133983\">\n\n              <span class=\"vf-summary__date\">04 Dec 2025<\/span>\n      \n                    <img decoding=\"async\" src=\"https:\/\/acxngcvroo.cloudimg.io\/v7\/https:\/\/www.embl.org\/news\/wp-content\/uploads\/2025\/11\/202511_LimbNet_JamesAntoni.jpg?w=600&amp;h=400&amp;force_format=jpeg&amp;q=30\" alt=\"News image\" class=\"vf-summary__image\" \/>\n      \n              <h3 class=\"vf-summary__title\">\n                      <a href=\"https:\/\/www.embl.org\/news\/?p=77585\" class=\"vf-summary__link\">From static papers to living models: turning limb development research into interactive science<\/a>\n                  <\/h3>\n      \n              <p class=\"vf-summary__text\">\n                    LimbNET is a new online platform that integrates computer modelling, experimental data, and 2D live simulations.\n        <\/p>\n      \n      <a class=\"vf-text vf-text--body-r vf-link embl-conditional-edit\" rel=\"noopener noreferrer nofollow\" href=\"\/node\/1133983\" target=\"_blank\">Edit<\/a>\n\n    <\/article>\n      <article class=\"vf-summary vf-summary--news\" data-embl-js-conditional-edit=\"949041\">\n\n              <span class=\"vf-summary__date\">31 Oct 2025<\/span>\n      \n                    <img decoding=\"async\" src=\"https:\/\/acxngcvroo.cloudimg.io\/v7\/https:\/\/www.embl.org\/news\/wp-content\/uploads\/2025\/10\/Featured_ExMTokyo_25-10-17.jpg?w=600&amp;h=400&amp;force_format=jpeg&amp;q=30\" alt=\"News image\" class=\"vf-summary__image\" \/>\n      \n              <h3 class=\"vf-summary__title\">\n                      <a href=\"https:\/\/www.embl.org\/news\/science-technology\/expanding-the-biological-world-through-microscopy\/\" class=\"vf-summary__link\">Expanding the biological world through microscopy<\/a>\n                  <\/h3>\n      \n              <p class=\"vf-summary__text\">\n                    EMBL researchers have been using a powerful technique called ultrastructure expansion microscopy to peek deeper inside living organisms and understand how they function.\n        <\/p>\n      \n      <a class=\"vf-text vf-text--body-r vf-link embl-conditional-edit\" rel=\"noopener noreferrer nofollow\" href=\"\/node\/949041\" target=\"_blank\">Edit<\/a>\n\n    <\/article>\n      <article class=\"vf-summary vf-summary--news\" data-embl-js-conditional-edit=\"865485\">\n\n              <span class=\"vf-summary__date\">14 Oct 2025<\/span>\n      \n                    <img decoding=\"async\" src=\"https:\/\/acxngcvroo.cloudimg.io\/v7\/https:\/\/www.embl.org\/news\/wp-content\/uploads\/2025\/10\/1000x600px-John-Kendrew-Award-recipient-Irma-Querques_Alumni-Awards.jpg?w=600&amp;h=400&amp;force_format=jpeg&amp;q=30\" alt=\"News image\" class=\"vf-summary__image\" \/>\n      \n              <h3 class=\"vf-summary__title\">\n                      <a href=\"https:\/\/www.embl.org\/news\/people-perspectives\/where-sleeping-beauty-is-more-than-a-fairy-tale\/\" class=\"vf-summary__link\">Where \u2018Sleeping Beauty\u2019 is more than a fairy tale<\/a>\n                  <\/h3>\n      \n              <p class=\"vf-summary__text\">\n                    Better than the original fairy tale, Kendrew awardee Irma Querques\u2019s \u2018Sleeping Beauty\u2019 story offers potential for new therapeutics.\n        <\/p>\n      \n      <a class=\"vf-text vf-text--body-r vf-link embl-conditional-edit\" rel=\"noopener noreferrer nofollow\" href=\"\/node\/865485\" target=\"_blank\">Edit<\/a>\n\n    <\/article>\n      <article class=\"vf-summary vf-summary--news\" data-embl-js-conditional-edit=\"720957\">\n\n              <span class=\"vf-summary__date\">15 Sep 2025<\/span>\n      \n                    <img decoding=\"async\" src=\"https:\/\/acxngcvroo.cloudimg.io\/v7\/https:\/\/www.embl.org\/news\/wp-content\/uploads\/2025\/09\/20250815_Sharpe-singlecell2.jpg?w=600&amp;h=400&amp;force_format=jpeg&amp;q=30\" alt=\"News image\" class=\"vf-summary__image\" \/>\n      \n              <h3 class=\"vf-summary__title\">\n                      <a href=\"https:\/\/www.embl.org\/news\/science-technology\/spotting-stealth-multiplets-for-better-single-cell-experiment-design\/\" class=\"vf-summary__link\">Spotting stealth multiplets for better single-cell experiment design<\/a>\n                  <\/h3>\n      \n              <p class=\"vf-summary__text\">\n                    Researchers at EMBL Barcelona have quantitatively evaluated the risk of undetected artefacts in single-cell RNA sequencing experiments.\n        <\/p>\n      \n      <a class=\"vf-text vf-text--body-r vf-link embl-conditional-edit\" rel=\"noopener noreferrer nofollow\" href=\"\/node\/720957\" target=\"_blank\">Edit<\/a>\n\n    <\/article>\n      <article class=\"vf-summary vf-summary--news\" data-embl-js-conditional-edit=\"626243\">\n\n              <span class=\"vf-summary__date\">28 Aug 2025<\/span>\n      \n                    <img decoding=\"async\" src=\"https:\/\/acxngcvroo.cloudimg.io\/v7\/https:\/\/www.embl.org\/news\/wp-content\/uploads\/2025\/08\/20250818_RRA_meeting.jpg?w=600&amp;h=400&amp;force_format=jpeg&amp;q=30\" alt=\"News image\" class=\"vf-summary__image\" \/>\n      \n              <h3 class=\"vf-summary__title\">\n                      <a href=\"https:\/\/www.embl.org\/news\/lab-matters\/what-counts-in-science\/\" class=\"vf-summary__link\">What counts in science?<\/a>\n                  <\/h3>\n      \n              <p class=\"vf-summary__text\">\n                    A recent pan-EMBL event provided an opportunity to reflect on responsible research assessment in scientific institutions.\n        <\/p>\n      \n      <a class=\"vf-text vf-text--body-r vf-link embl-conditional-edit\" rel=\"noopener noreferrer nofollow\" href=\"\/node\/626243\" target=\"_blank\">Edit<\/a>\n\n    <\/article>\n      <article class=\"vf-summary vf-summary--news\" data-embl-js-conditional-edit=\"197889\">\n\n              <span class=\"vf-summary__date\">19 May 2025<\/span>\n      \n                    <img decoding=\"async\" src=\"https:\/\/acxngcvroo.cloudimg.io\/v7\/https:\/\/www.embl.org\/news\/wp-content\/uploads\/2025\/05\/20250519_Sites_announcement.jpg?w=600&amp;h=400&amp;force_format=jpeg&amp;q=30\" alt=\"News image\" class=\"vf-summary__image\" \/>\n      \n              <h3 class=\"vf-summary__title\">\n                      <a href=\"https:\/\/www.embl.org\/news\/embl-announcements\/leading-embls-six-sites\/\" class=\"vf-summary__link\">Leading EMBL\u2019s six sites\u00a0<\/a>\n                  <\/h3>\n      \n              <p class=\"vf-summary__text\">\n                    As Peer Bork and Ewan Birney take up interim leadership of EMBL, the organisation announces additional changes in site leadership.\n        <\/p>\n      \n      <a class=\"vf-text vf-text--body-r vf-link embl-conditional-edit\" rel=\"noopener noreferrer nofollow\" href=\"\/node\/197889\" target=\"_blank\">Edit<\/a>\n\n    <\/article>\n      <article class=\"vf-summary vf-summary--news\" data-embl-js-conditional-edit=\"196413\">\n\n              <span class=\"vf-summary__date\">10 Mar 2025<\/span>\n      \n                    <img decoding=\"async\" src=\"https:\/\/acxngcvroo.cloudimg.io\/v7\/https:\/\/www.embl.org\/news\/wp-content\/uploads\/2025\/03\/visual-limb.jpg?w=600&amp;h=400&amp;force_format=jpeg&amp;q=30\" alt=\"News image\" class=\"vf-summary__image\" \/>\n      \n              <h3 class=\"vf-summary__title\">\n                      <a href=\"https:\/\/www.embl.org\/news\/science-technology\/how-video-games-inspired-a-new-way-to-visualise-limb-development\/\" class=\"vf-summary__link\">How video games inspired a new way to visualise limb development<\/a>\n                  <\/h3>\n      \n              <p class=\"vf-summary__text\">\n                    EMBL Barcelona researchers developed a computational method that reconstructs embryonic development.\n        <\/p>\n      \n      <a class=\"vf-text vf-text--body-r vf-link embl-conditional-edit\" rel=\"noopener noreferrer nofollow\" href=\"\/node\/196413\" target=\"_blank\">Edit<\/a>\n\n    <\/article>\n  <\/div>\n\n<\/div>\n<\/div>\n\n\n<div class=\"\"><!--[vf\/content]-->\n<div class=\"vf-content\">\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\/EMBLBarcelona?ref_src=twsrc%5Etfw\">Tweets by EMBLBarcelona<\/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","protected":false},"excerpt":{"rendered":"","protected":false},"author":1,"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.embl.org\/groups\/sharpe\/wp-json\/wp\/v2\/pages\/15","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.embl.org\/groups\/sharpe\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.embl.org\/groups\/sharpe\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.embl.org\/groups\/sharpe\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.embl.org\/groups\/sharpe\/wp-json\/wp\/v2\/comments?post=15"}],"version-history":[{"count":13,"href":"https:\/\/www.embl.org\/groups\/sharpe\/wp-json\/wp\/v2\/pages\/15\/revisions"}],"predecessor-version":[{"id":18731,"href":"https:\/\/www.embl.org\/groups\/sharpe\/wp-json\/wp\/v2\/pages\/15\/revisions\/18731"}],"wp:attachment":[{"href":"https:\/\/www.embl.org\/groups\/sharpe\/wp-json\/wp\/v2\/media?parent=15"}],"wp:term":[{"taxonomy":"embl_taxonomy","embeddable":true,"href":"https:\/\/www.embl.org\/groups\/sharpe\/wp-json\/wp\/v2\/embl_taxonomy?post=15"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}