{"id":23,"date":"2025-02-11T13:58:26","date_gmt":"2025-02-11T13:58:26","guid":{"rendered":"https:\/\/www.ebi.ac.uk\/research\/ewald\/?page_id=23"},"modified":"2025-02-13T16:46:21","modified_gmt":"2025-02-13T16:46:21","slug":"home","status":"publish","type":"page","link":"https:\/\/www.ebi.ac.uk\/research\/ewald\/","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=16be6546-4f98-45d8-9b9f-fcb388b35478&amp;pattern=node-teaser -->\n      <div data-embl-js-conditional-edit=\"195239\">\n              <h1 class=\"vf-lede\">Our group uses machine learning and multi-omics integration to identify and characterise chemical hazards to humans and ecosystems. We analyse omics data measured after cellular perturbations, with a particular interest in image-based cell profiling.<\/p>\r\n\n            <a class=\"vf-text vf-text--body-r vf-link embl-conditional-edit\" rel=\"noopener noreferrer nofollow\" href=\"\/node\/195239\" 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=\"672d7368\">\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=604&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=\"191071\">\n              <img decoding=\"async\" class=\"vf-profile__image\" src=\"https:\/\/content.embl.org\/\/sites\/default\/files\/styles\/medium\/public\/persons\/CP-60045225.jpg?itok=_wq2u1e8\" alt=\"image of Jessica Ewald\" \/>\n      \n              <h3 class=\"vf-profile__title\">\n                      <a href=\"https:\/\/www.ebi.ac.uk\/people\/person\/jessica-ewald\" class=\"vf-profile__link\">Jessica Ewald<\/a>\n                  <\/h3>\n      \n              <p class=\"vf-profile__job-title\">\n          Group Leader\n        <\/p>\n      \n      \n      \n              \n                  <p class=\"vf-profile__email | vf-u-last-item\">\n            jewald [at] ebi.ac.uk\n          <\/p>\n              \n      \n                                      \n            <a class=\"vf-text vf-text--body-r vf-link embl-conditional-edit\" rel=\"noopener noreferrer nofollow\" href=\"\/node\/191071\/191071\" 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-2\"><div><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<p class=\"wp-block-paragraph\"><strong>Our main website is <a href=\"https:\/\/ewaldlab.org\/\">www.ewaldlab.org\/<\/a> &#8211; please visit it for more detailed and up-to-date information. <\/strong><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Most chemicals in commercial use have never been assessed for their potential to cause harm to humans or ecosystems. Drug discovery programs routinely screen thousands to millions of compounds in computational and cellular models to understand how they perturb biological systems. Our group aims to re-purpose drug discovery technologies and data to investigate the potential toxicity of human-created compounds that are used in society and released into the environment. We develop computational approaches to:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>learn multi-omics signatures of compound-induced toxicity<\/li>\n\n\n\n<li>link perturbations at the molecular and cellular level to adverse outcomes at the organ and organism level.<\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\"><strong>Benchmarking multi-omics data for toxicity detection<\/strong><\/h2>\n\n\n\n<p class=\"wp-block-paragraph\">With the <a href=\"https:\/\/oasisconsortium.org\/\">OASIS Consortium<\/a> (8 academic institutions, 2 non-profits, 7 government agencies, and 16 pharma\/agchem companies), we are collecting multi-omic dose-response data in 5 cell lines for ~1500 compounds with pre-existing human or rat <em>in vivo<\/em> liver toxicity data. The compounds include pharmaceuticals, pesticides, and industrial compounds. The overall objective is to determine whether profiling data from cells can predict <em>in vivo<\/em> liver toxicity. Sub-objectives include understanding species-specific compound toxicity (human, rat), interpreting compound mode-of-action from omics data, and developing new methods for integrating image-based profiles with transcriptomics and proteomics data.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\"><strong>Extracting information from images of cells<\/strong><\/h2>\n\n\n\n<p class=\"wp-block-paragraph\">Cell Painting is a high-content, image-based profiling assay that captures morphological and subcellular changes in cells using multiplexed fluorescent stains to measure phenotypic responses to perturbations (Figure 1). It captures detailed mode-of-action information while being at least 1000 times cheaper than other single-cell omics methods. Even though Cell Painting data has single-cell resolution, most analyses are done at the population level. We develop new methods for investigating single-cell heterogeneity in response to chemical perturbations. This includes using deep learning to learn representations of cells that reveal subtle cell states and developing custom image analysis workflows to identify and quantify phenotypes that are relevant to toxicity, for example lipid accumulation or multi-nucleation.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\"><strong>Inferring compound mode-of-action using reference atlases<\/strong><\/h2>\n\n\n\n<p class=\"wp-block-paragraph\">There are large, public Cell Painting datasets that contain profiles for >100,000 compounds and ~20,000 genetic perturbations, which contain rich mode-of-action signals. Studies that profile environmental contaminants are often smaller, usually containing ~100-1000 compounds with unknown modes-of-action. We adapt computational methods for creating single-cell RNA-seq reference atlases for image-based profiles. The objective is to map Cell Painting data from environmental toxicity screens to large, well-annotated reference datasets so that we can infer the mode-of-action of uncharacterized compounds.<\/p>\n\n<\/div>\n<\/div>\n\n\n<div><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<figure class=\"vf-figure wp-block-image  | vf-figure--align vf-figure--align-centered  size-full\"><img loading=\"lazy\" decoding=\"async\" width=\"500\" height=\"500\" class=\"vf-figure__image\" src=\"https:\/\/www.ebi.ac.uk\/research\/ewald\/wp-content\/uploads\/2025\/02\/Fig1_PHH_hydrocortisone_LR.png\" alt=\"\" class=\"wp-image-48\" srcset=\"https:\/\/www.ebi.ac.uk\/research\/ewald\/wp-content\/uploads\/2025\/02\/Fig1_PHH_hydrocortisone_LR.png 500w, https:\/\/www.ebi.ac.uk\/research\/ewald\/wp-content\/uploads\/2025\/02\/Fig1_PHH_hydrocortisone_LR-300x300.png 300w, https:\/\/www.ebi.ac.uk\/research\/ewald\/wp-content\/uploads\/2025\/02\/Fig1_PHH_hydrocortisone_LR-150x150.png 150w\" sizes=\"auto, (max-width: 500px) 100vw, 500px\" \/><figcaption class=\"vf-figure__caption\">Primary human hepatocytes stained with the standard Cell Painting dyes that reveal the DNA, RNA, ER, mitochondria, actin, and Golgi sub-cellular compartments. Our group extracts information from these types of images and analyses them just like other omics datasets.<\/figcaption><\/figure>\n\n<\/div>\n<\/div>\n<\/div>\n\n\n\n\n\n<div >\n\n    \n    \n<\/div>\n\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\" \n             href=\"https:\/\/www.embl.org\/jobs\" \n             id=\"section-link\">\n            Latest jobs            <svg aria-hidden=\"true\" \n                 class=\"vf-section-header__icon | vf-icon vf-icon-arrow--inline-end\" \n                 width=\"24\" height=\"24\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\">\n              <path 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>\n          <\/a>\n        <\/h2>\n      <\/div>\n        <div>\n<div class=\"vf-content-hub-html\" data-cache=\"72c5d39a\">\n  <!-- Generated by: http:\/\/content.embl.org\/api\/v1\/pattern.html?filter-content-type=jobs&amp;limit=2&amp;pattern=vf-jobs-snippet&amp;sort-field-value%5Bcreated%5D=DESC -->\n      <article class=\"vf-summary vf-summary--job\" data-embl-js-conditional-edit=\"2480029\">\n            <h3 class=\"vf-summary__title\">\n        <a href=\"https:\/\/embl.wd103.myworkdayjobs.com\/EMBL\/job\/Hinxton-Cambridgeshire\/Plant-Genomics-and-Variation-Team-Leader_JR4407-1\" class=\"vf-summary__link\">Plant Genomics and Variation Team Leader<\/a>\n    <\/h3>\n                    <p class=\"vf-summary__meta\">\n\n          Technology in <a href=\"\/\/www.ebi.ac.uk\/\" class=\"vf-summary__link\">EMBL-EBI Hinxton<\/a>\n          \n        <\/p>\n                            <p class=\"vf-summary__text\">\n          Are you ready to shape the future of crop genomics, invertebrate genomics and genetic variation resources at one of the world&#039;s leading bioinformatics institutes? We are seeking an internationally minded, community-focused Team Leader with expertise in genomics, particularly crop plants and their as&#8230;\n        <\/p>\n                    <p class=\"vf-summary__date\">\n          <span class=\"date-days-remaining\" data-datetime=\"1791759600\" data-timezone=\"Europe\/Berlin\">\n            Closes on <span>12th October.<\/span>\n          <\/span>\n                      Posted 2nd September 2026\n                  <\/p>\n            <a class=\"vf-text vf-text--body-r vf-link embl-conditional-edit\" rel=\"noopener noreferrer nofollow\" href=\"\/node\/2480029\" target=\"_blank\">Edit<\/a>\n\n    <\/article>\n      <article class=\"vf-summary vf-summary--job\" data-embl-js-conditional-edit=\"2453347\">\n            <h3 class=\"vf-summary__title\">\n        <a href=\"https:\/\/embl.wd103.myworkdayjobs.com\/EMBL\/job\/Hinxton-Cambridgeshire\/Senior-Site-Reliability-Engineer_JR3587\" class=\"vf-summary__link\">Senior Site Reliability Engineer<\/a>\n    <\/h3>\n                    <p class=\"vf-summary__meta\">\n\n          Technology in <a href=\"\/\/www.ebi.ac.uk\/\" class=\"vf-summary__link\">EMBL-EBI Hinxton<\/a>\n          \n        <\/p>\n                            <p class=\"vf-summary__text\">\n          Want your engineering skills to enable real scientific breakthroughs? We\u2019re looking for a Senior Site Reliability Engineer to join our highly skilled IT Operations team at EMBL-EBI.At EMBL-EBI, our IT &amp; Technical Services department underpins groundbreaking research that improves human and planetary&#8230;\n        <\/p>\n                    <p class=\"vf-summary__date\">\n          <span class=\"date-days-remaining\" data-datetime=\"1789945200\" data-timezone=\"Europe\/Berlin\">\n            Closes on <span>21st September.<\/span>\n          <\/span>\n                      Posted 27th August 2026\n                  <\/p>\n            <a class=\"vf-text vf-text--body-r vf-link embl-conditional-edit\" rel=\"noopener noreferrer nofollow\" href=\"\/node\/2453347\" target=\"_blank\">Edit<\/a>\n\n    <\/article>\n  <\/div>\n\n<\/div>\n<\/div>\n\n\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":6,"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-23","page","type-page","status-publish","hentry"],"acf":[],"embl_taxonomy_terms":[],"_links":{"self":[{"href":"https:\/\/www.ebi.ac.uk\/research\/ewald\/wp-json\/wp\/v2\/pages\/23","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.ebi.ac.uk\/research\/ewald\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.ebi.ac.uk\/research\/ewald\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/research\/ewald\/wp-json\/wp\/v2\/users\/6"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/research\/ewald\/wp-json\/wp\/v2\/comments?post=23"}],"version-history":[{"count":3,"href":"https:\/\/www.ebi.ac.uk\/research\/ewald\/wp-json\/wp\/v2\/pages\/23\/revisions"}],"predecessor-version":[{"id":50,"href":"https:\/\/www.ebi.ac.uk\/research\/ewald\/wp-json\/wp\/v2\/pages\/23\/revisions\/50"}],"wp:attachment":[{"href":"https:\/\/www.ebi.ac.uk\/research\/ewald\/wp-json\/wp\/v2\/media?parent=23"}],"wp:term":[{"taxonomy":"embl_taxonomy","embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/research\/ewald\/wp-json\/wp\/v2\/embl_taxonomy?post=23"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}