{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T21:19:57Z","timestamp":1790198397544,"version":"4.1.0"},"reference-count":162,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2026,5,22]],"date-time":"2026-05-22T00:00:00Z","timestamp":1779408000000},"content-version":"vor","delay-in-days":21,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100007028","name":"Helmsley Charitable Trust","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007028","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007028","name":"Leona M and Harry B Helmsley Charitable Trust","doi-asserted-by":"crossref","award":["G118500"],"award-info":[{"award-number":["G118500"]}],"id":[{"id":"10.13039\/100007028","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,5,8]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Inflammatory bowel diseases (IBD) remain a therapeutic challenge due to their heterogeneous nature and the absence of clinically actionable biomarkers to guide precision treatment. While multi-omics studies have advanced our understanding of the disease, meaningful translation into practice has been hindered by lack of validation and a need to move from association to a more generalizable signal. Epigenetics, particularly DNA methylation, offers a promising lens to capture disease-relevant regulatory states that reflect both genetic predisposition and environmental influences. However, the path to clinical adoption has been limited by persistent computational hurdles. Here we synthesize the current landscape of IBD biomarker discovery and highlight the conceptual advantages of epigenetic signatures. We outline the main obstacles that have limited clinical translation to date, including data heterogeneity, batch effects, and the challenge of distinguishing functional \u201cdriver\u201d from non-functional \u201cpassenger\u201d epigenetic changes. We then discuss how recent advances in computational methodology\u2014spanning data harmonization, integrative modeling, and interpretable machine learning\u2014can help bridge the gap between complex datasets and reliable, deployable biomarkers. Finally, we propose a forward-looking roadmap for study design and validation aimed at moving the field toward routine clinical implementation, thereby realizing the full potential of epigenetics in IBD.<\/jats:p>","DOI":"10.1093\/ecco-jcc\/jjag022","type":"journal-article","created":{"date-parts":[[2026,2,11]],"date-time":"2026-02-11T12:44:05Z","timestamp":1770813845000},"source":"Crossref","is-referenced-by-count":1,"title":["Epigenetic biomarkers in inflammatory bowel diseases\u2014computational challenges and opportunities"],"prefix":"10.1093","volume":"20","author":[{"given":"Seokjun","family":"Lee","sequence":"first","affiliation":[{"name":"Cambridge Stem Cell Institute, University of Cambridge , Cambridge,","place":["United Kingdom"]},{"name":"Milner Therapeutics Institute, University of Cambridge , Cambridge,","place":["United Kingdom"]},{"name":"Department of Applied Mathematics and Theoretical Physics, Cambridge Centre for AI in Medicine, University of Cambridge , Cambridge,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jaesub","family":"Park","sequence":"additional","affiliation":[{"name":"Cambridge Stem Cell Institute, University of Cambridge , Cambridge,","place":["United Kingdom"]},{"name":"Milner Therapeutics Institute, University of Cambridge , Cambridge,","place":["United Kingdom"]},{"name":"Department of Applied Mathematics and Theoretical Physics, Cambridge Centre for AI in Medicine, University of Cambridge , Cambridge,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hyun Chang","family":"Lee","sequence":"additional","affiliation":[{"name":"Cambridge Stem Cell Institute, University of Cambridge , Cambridge,","place":["United Kingdom"]},{"name":"Milner Therapeutics Institute, University of Cambridge , Cambridge,","place":["United Kingdom"]},{"name":"Department of Applied Mathematics and Theoretical Physics, Cambridge Centre for AI in Medicine, University of Cambridge , Cambridge,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xingze","family":"Xu","sequence":"additional","affiliation":[{"name":"Cambridge Stem Cell Institute, University of Cambridge , Cambridge,","place":["United Kingdom"]},{"name":"Milner Therapeutics Institute, University of Cambridge , Cambridge,","place":["United Kingdom"]},{"name":"Department of Applied Mathematics and Theoretical Physics, Cambridge Centre for AI in Medicine, University of Cambridge , Cambridge,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ellie","family":"Slater","sequence":"additional","affiliation":[{"name":"Cambridge Stem Cell Institute, University of Cambridge , Cambridge,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marco","family":"Gasparetto","sequence":"additional","affiliation":[{"name":"Department of Paediatrics Gastroenterology, Norfolk and Norwich University Hospitals, Jenny Lind Children\u2019s Hospital , Norwich, Norfolk,","place":["United Kingdom"]},{"name":"Norwich Medical School, Faculty of Medicine and Health Science, University of East Anglia , Norwich, Norfolk,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Namshik","family":"Han","sequence":"additional","affiliation":[{"name":"Cambridge Stem Cell Institute, University of Cambridge , Cambridge,","place":["United Kingdom"]},{"name":"Milner Therapeutics Institute, University of Cambridge , Cambridge,","place":["United Kingdom"]},{"name":"Department of Applied Mathematics and Theoretical Physics, Cambridge Centre for AI in Medicine, University of Cambridge , Cambridge,","place":["United Kingdom"]},{"name":"Department of Quantum Information, Institute for Convergence Research and Education in Advanced Technology and Engineering, Yonsei University, Seoul,","place":["Republic of Korea"]},{"name":"Department of Nano Biomedical Engineering (NanoBME), Advanced Science Institute, Yonsei University, Seoul,","place":["Republic of Korea"]},{"name":"Center for Nanomedicine, Institute for Basic Science (IBS), Seoul,","place":["Republic of Korea"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthias","family":"Zilbauer","sequence":"additional","affiliation":[{"name":"Cambridge Stem Cell Institute, University of Cambridge , Cambridge,","place":["United Kingdom"]},{"name":"Department of Paediatrics, University of Cambridge , Cambridge,","place":["United Kingdom"]},{"name":"Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals (CUH), Addenbrooke\u2019s , Cambridge,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,5,19]]},"reference":[{"key":"2026052207460323500_jjag022-B1","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1038\/ajg.2014.357","article-title":"Treatment of IBD: where we are and where we are going","volume":"110","author":"Bernstein","year":"2015","journal-title":"Am J Gastroenterol"},{"key":"2026052207460323500_jjag022-B2","doi-asserted-by":"crossref","first-page":"1049","DOI":"10.1080\/17474124.2019.1685872","article-title":"Inflammatory bowel disease: long-term therapeutic challenges","volume":"13","author":"Ashton","year":"2019","journal-title":"Expert Rev Gastroenterol Hepatol"},{"key":"2026052207460323500_jjag022-B3","doi-asserted-by":"crossref","first-page":"S31","DOI":"10.1093\/ibd\/izz078","article-title":"Challenges in IBD research: precision medicine","volume":"25","author":"Denson","year":"2019","journal-title":"Inflamm Bowel 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