{"id":8913,"date":"2026-03-05T14:07:32","date_gmt":"2026-03-05T13:07:32","guid":{"rendered":"https:\/\/ubc.uu.nl\/?p=8913"},"modified":"2026-03-05T14:34:20","modified_gmt":"2026-03-05T13:34:20","slug":"cracking-the-code-of-gene-regulation-with-ai","status":"publish","type":"post","link":"https:\/\/ubc.uu.nl\/cracking-the-code-of-gene-regulation-with-ai\/","title":{"rendered":"Cracking the Code of Gene Regulation with AI"},"content":{"rendered":"\t\t<div data-elementor-type=\"wp-post\" data-elementor-id=\"8913\" class=\"elementor elementor-8913\" data-elementor-post-type=\"post\">\n\t\t\t\t\t\t<section class=\"elementor-section elementor-top-section elementor-element elementor-element-21728e9 elementor-section-boxed elementor-section-height-default elementor-section-height-default\" data-id=\"21728e9\" data-element_type=\"section\" data-e-type=\"section\">\n\t\t\t\t\t\t<div class=\"elementor-container elementor-column-gap-default\">\n\t\t\t\t\t<div class=\"elementor-column elementor-col-50 elementor-top-column elementor-element elementor-element-20c0fbd\" data-id=\"20c0fbd\" data-element_type=\"column\" data-e-type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t<div class=\"elementor-element elementor-element-23dd8a4 elementor-widget__width-initial elementor-widget elementor-widget-text-editor\" data-id=\"23dd8a4\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>Jeroen de Ridder and&nbsp;Bas van Steensel, as part of an Oncode instute initiative, introduced the lightweight&nbsp;<a href=\"https:\/\/mailings.uu.nl\/i\/3St83XkttCE-7virh0XzpG-1-7CB2tqE\" target=\"_blank\" rel=\"noopener noreferrer\">AI model PARM<\/a>&nbsp;in&nbsp;<i>Nature<\/i>. PARM accurately predicts how regulatory DNA controls gene activity. The model enables scalable interpretation of cancer-related mutations, opening new avenues for diagnostics, patient stratification and future therapies.<\/p>\n<p>This publication marks a successful collaboration project entitled PERICODE, which brought together seven Oncode institute investigators. Read Oncode&#8217;s full press release&nbsp;<a style=\"background-color: #ffffff;\" href=\"https:\/\/www.oncodeinstitute.nl\/news\/cracking-code-behind-code-how-unique-collaboration-between-oncode-investigators-reveales-rules\" target=\"_blank\" rel=\"noopener\">here.&nbsp;<\/a><\/p>\n<p><\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t<div class=\"elementor-column elementor-col-50 elementor-top-column elementor-element elementor-element-1b649c6\" data-id=\"1b649c6\" data-element_type=\"column\" data-e-type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t<div class=\"elementor-element elementor-element-e0f4ce3 elementor-widget__width-initial elementor-widget elementor-widget-image\" data-id=\"e0f4ce3\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"image.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<a href=\"https:\/\/ubc.uu.nl\/machine-learning-for-genomics\/\">\n\t\t\t\t\t\t\t<img fetchpriority=\"high\" decoding=\"async\" width=\"548\" height=\"750\" src=\"https:\/\/ubc.uu.nl\/wp-content\/uploads\/2026\/03\/Ridder-de-J-_1280x800-e1772715404855.jpg\" class=\"attachment-large size-large wp-image-8915\" alt=\"\" srcset=\"https:\/\/ubc.uu.nl\/wp-content\/uploads\/2026\/03\/Ridder-de-J-_1280x800-e1772715404855.jpg 548w, https:\/\/ubc.uu.nl\/wp-content\/uploads\/2026\/03\/Ridder-de-J-_1280x800-e1772715404855-219x300.jpg 219w\" sizes=\"(max-width: 548px) 100vw, 548px\" \/>\t\t\t\t\t\t\t\t<\/a>\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-4b1c20d elementor-widget__width-initial elementor-widget elementor-widget-spacer\" data-id=\"4b1c20d\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"spacer.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"elementor-spacer\">\n\t\t\t<div class=\"elementor-spacer-inner\"><\/div>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-64fdec0 elementor-widget__width-initial elementor-widget elementor-widget-image\" data-id=\"64fdec0\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"image.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<a href=\"https:\/\/www.nki.nl\/research\/research-groups\/bas-van-steensel\">\n\t\t\t\t\t\t\t<img decoding=\"async\" width=\"176\" height=\"257\" src=\"https:\/\/ubc.uu.nl\/wp-content\/uploads\/2026\/03\/Bas-van-Steensel-1-e1772715237560.jpg\" class=\"attachment-large size-large wp-image-8916\" alt=\"\" \/>\t\t\t\t\t\t\t\t<\/a>\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-340a09e elementor-widget__width-initial elementor-widget elementor-widget-text-editor\" data-id=\"340a09e\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<h6><a href=\"https:\/\/www.deridderlab.nl\/\" target=\"_blank\" rel=\"noopener\">Jeroen de Ridder<\/a><\/h6>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-def6f01 elementor-widget__width-initial elementor-widget elementor-widget-spacer\" data-id=\"def6f01\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"spacer.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"elementor-spacer\">\n\t\t\t<div class=\"elementor-spacer-inner\"><\/div>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-0a545b0 elementor-widget__width-initial elementor-widget elementor-widget-text-editor\" data-id=\"0a545b0\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<h6><a href=\"https:\/\/www.uu.nl\/medewerkers\/BvanSteensel\">Bas van Steensel<\/a><\/h6>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t<section class=\"elementor-section elementor-top-section elementor-element elementor-element-dbba8ae elementor-section-boxed elementor-section-height-default elementor-section-height-default\" data-id=\"dbba8ae\" data-element_type=\"section\" data-e-type=\"section\">\n\t\t\t\t\t\t<div class=\"elementor-container elementor-column-gap-default\">\n\t\t\t\t\t<div class=\"elementor-column elementor-col-100 elementor-top-column elementor-element elementor-element-0539244\" data-id=\"0539244\" data-element_type=\"column\" data-e-type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t<div class=\"elementor-element elementor-element-a894441 elementor-widget elementor-widget-text-editor\" data-id=\"a894441\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<h4><b>Publication<\/b><\/h4><p>Barbadilla-Mart\u00ednez, L., Klaassen, N., Franceschini-Santos, V.H.\u00a0<i>et al.<\/i>\u00a0<a href=\"https:\/\/doi.org\/10.1038\/s41586-025-10093-z\" target=\"_blank\" rel=\"noopener\">Regulatory grammar in human promoters uncovered by MPRA-based deep learning<\/a>.\u00a0<i>Nature<\/i>\u00a0(2026).\u00a0<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t<\/div>\n\t\t","protected":false},"excerpt":{"rendered":"<p>Jeroen de Ridder and&nbsp;Bas van Steensel, as part of an Oncode instute initiative, introduced the lightweight&nbsp;AI model PARM&nbsp;in&nbsp;Nature. PARM accurately predicts how regulatory DNA controls gene activity. The model enables scalable interpretation of cancer-related mutations, opening new avenues for diagnostics, patient stratification and future therapies. This publication marks a successful collaboration project entitled PERICODE, which [&hellip;]<\/p>\n","protected":false},"author":94,"featured_media":8930,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"_angie_page":false,"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"page_builder":"","_jetpack_memberships_contains_paid_content":false,"footnotes":""},"categories":[64,408,397],"tags":[],"class_list":["post-8913","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-news","category-news_freestyle","category-research"],"acf":[],"jetpack_sharing_enabled":true,"jetpack_featured_media_url":"https:\/\/ubc.uu.nl\/wp-content\/uploads\/2026\/03\/basandjeroen-2.png","_links":{"self":[{"href":"https:\/\/ubc.uu.nl\/wp-json\/wp\/v2\/posts\/8913","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ubc.uu.nl\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/ubc.uu.nl\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/ubc.uu.nl\/wp-json\/wp\/v2\/users\/94"}],"replies":[{"embeddable":true,"href":"https:\/\/ubc.uu.nl\/wp-json\/wp\/v2\/comments?post=8913"}],"version-history":[{"count":10,"href":"https:\/\/ubc.uu.nl\/wp-json\/wp\/v2\/posts\/8913\/revisions"}],"predecessor-version":[{"id":8926,"href":"https:\/\/ubc.uu.nl\/wp-json\/wp\/v2\/posts\/8913\/revisions\/8926"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/ubc.uu.nl\/wp-json\/wp\/v2\/media\/8930"}],"wp:attachment":[{"href":"https:\/\/ubc.uu.nl\/wp-json\/wp\/v2\/media?parent=8913"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/ubc.uu.nl\/wp-json\/wp\/v2\/categories?post=8913"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/ubc.uu.nl\/wp-json\/wp\/v2\/tags?post=8913"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}