{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,13]],"date-time":"2026-11-13T13:13:23Z","timestamp":1794575603061,"version":"4.9.1"},"reference-count":53,"publisher":"Elsevier BV","issue":"7","license":[{"start":{"date-parts":[[2026,1,1]],"date-time":"2026-01-01T00:00:00Z","timestamp":1767225600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,1,1]],"date-time":"2026-01-01T00:00:00Z","timestamp":1767225600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2026,3,20]],"date-time":"2026-03-20T00:00:00Z","timestamp":1773964800000},"content-version":"vor","delay-in-days":78,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009560","name":"American Gastroenterological Association","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100009560","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000062","name":"National Institute of Diabetes and Digestive and Kidney Diseases","doi-asserted-by":"publisher","award":["R01AI089 714-022"],"award-info":[{"award-number":["R01AI089 714-022"]}],"id":[{"id":"10.13039\/100000062","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000062","name":"National Institute of Diabetes and Digestive and Kidney Diseases","doi-asserted-by":"publisher","award":["P30DK084567"],"award-info":[{"award-number":["P30DK084567"]}],"id":[{"id":"10.13039\/100000062","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000062","name":"National Institute of Diabetes and Digestive and Kidney Diseases","doi-asserted-by":"publisher","award":["DK127998"],"award-info":[{"award-number":["DK127998"]}],"id":[{"id":"10.13039\/100000062","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000062","name":"National Institute of Diabetes and Digestive and Kidney Diseases","doi-asserted-by":"publisher","award":["DK 127157"],"award-info":[{"award-number":["DK 127157"]}],"id":[{"id":"10.13039\/100000062","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000062","name":"National Institute of Diabetes and Digestive and Kidney Diseases","doi-asserted-by":"publisher","award":["T32DK007198"],"award-info":[{"award-number":["T32DK007198"]}],"id":[{"id":"10.13039\/100000062","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000062","name":"National Institute of Diabetes and Digestive and Kidney Diseases","doi-asserted-by":"publisher","award":["DK 134321"],"award-info":[{"award-number":["DK 134321"]}],"id":[{"id":"10.13039\/100000062","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006083","name":"American Gastroenterological Association Research Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100006083","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["clinicalkey.com","clinicalkey.com.au","clinicalkey.es","clinicalkey.fr","clinicalkey.jp","cmghjournal.org","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Cellular and Molecular Gastroenterology and Hepatology"],"published-print":{"date-parts":[[2026]]},"DOI":"10.1016\/j.jcmgh.2026.101774","type":"journal-article","created":{"date-parts":[[2026,3,27]],"date-time":"2026-03-27T08:32:41Z","timestamp":1774600361000},"page":"101774","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":13,"title":["Intestinal Stem Cells From Patients With Inflammatory Bowel Disease Retain an Epigenetic Memory of Inflammation"],"prefix":"10.1016","volume":"20","author":[{"given":"Feda H.","family":"Hamdan","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mona","family":"Farhadipour","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Isaiah","family":"Perez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kimberlee","family":"Kossick","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hannah","family":"Smith","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adam","family":"Edwinson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jose M.","family":"de Hoyos-Vega","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michelle","family":"Gonzalez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Chiang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emily","family":"Klatt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kristy","family":"Rumer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mauricio Perez","family":"Pachon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mary","family":"Sagstetter","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jessica","family":"Friton","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Erin","family":"Kammer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alana","family":"English","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lucas C.S.","family":"Chini","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jarl F.","family":"Carnahan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Noah A.","family":"Baca","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jessie","family":"Hohenstein","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rohini","family":"Mopuri","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aditya","family":"Bhagwate","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laura E.","family":"Raffals","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rondell","family":"Graham","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhifu","family":"Sun","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Madhusudan","family":"Grover","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander","family":"Revzin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Kattah","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"William A.","family":"Faubion","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9254-8097","authenticated-orcid":false,"given":"Brooke R.","family":"Druliner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.jcmgh.2026.101774_bib1","doi-asserted-by":"crossref","first-page":"514","DOI":"10.1172\/JCI30587","article-title":"The fundamental basis of inflammatory bowel disease","volume":"117","author":"Strober","year":"2007","journal-title":"J Clin Invest"},{"key":"10.1016\/j.jcmgh.2026.101774_bib2","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1038\/s41572-020-0205-x","article-title":"Ulcerative colitis","volume":"6","author":"Kobayashi","year":"2020","journal-title":"Nat Rev Dis Primers"},{"key":"10.1016\/j.jcmgh.2026.101774_bib3","doi-asserted-by":"crossref","first-page":"9010","DOI":"10.1038\/s41598-021-88489-w","article-title":"Ulcerative colitis immune cell landscapes and differentially expressed gene signatures determine novel regulators and predict clinical response to biologic therapy","volume":"11","author":"Penrose","year":"2021","journal-title":"Sci Rep"},{"key":"10.1016\/j.jcmgh.2026.101774_bib4","doi-asserted-by":"crossref","first-page":"3433","DOI":"10.1016\/j.cgh.2023.01.005","article-title":"Net remission rates with biologic and small molecule treatment in ulcerative colitis: a reappraisal of the clinical trial data","volume":"21","author":"Kayal","year":"2023","journal-title":"Clin Gastroenterol Hepatol"},{"key":"10.1016\/j.jcmgh.2026.101774_bib5","doi-asserted-by":"crossref","first-page":"1345","DOI":"10.1038\/s41395-018-0162-0","article-title":"Vedolizumab for ulcerative colitis: treatment outcomes from the VICTORY Consortium","volume":"113","author":"Narula","year":"2018","journal-title":"Am J Gastroenterol"},{"key":"10.1016\/j.jcmgh.2026.101774_bib6","doi-asserted-by":"crossref","first-page":"969","DOI":"10.1093\/ecco-jcc\/jjaa232","article-title":"Outcome of ulcerative colitis 20 years after diagnosis in a prospective population-based inception cohort from South-Eastern Norway, the IBSEN study","volume":"15","author":"Monstad","year":"2021","journal-title":"J Crohns Colitis"},{"key":"10.1016\/j.jcmgh.2026.101774_bib7","doi-asserted-by":"crossref","first-page":"147","DOI":"10.2147\/CEG.S375969","article-title":"Emerging therapies for ulcerative colitis: updates from recent clinical trials","volume":"16","author":"AlAmeel","year":"2023","journal-title":"Clin Exp Gastroenterol"},{"key":"10.1016\/j.jcmgh.2026.101774_bib8","doi-asserted-by":"crossref","first-page":"1953","DOI":"10.1053\/j.gastro.2021.08.053","article-title":"Molecular characterization of limited ulcerative colitis reveals novel biology and predictors of disease extension","volume":"161","author":"Argmann","year":"2021","journal-title":"Gastroenterology"},{"issue":"Suppl 3","key":"10.1016\/j.jcmgh.2026.101774_bib9","doi-asserted-by":"crossref","first-page":"s1","DOI":"10.1136\/gutjnl-2019-318484","article-title":"British Society of Gastroenterology consensus guidelines on the management of inflammatory bowel disease in adults","volume":"68","author":"Lamb","year":"2019","journal-title":"Gut"},{"key":"10.1016\/j.jcmgh.2026.101774_bib10","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1007\/s40265-016-0676-y","article-title":"Mucosal healing in ulcerative colitis: a comprehensive review","volume":"77","author":"Boal Carvalho","year":"2017","journal-title":"Drugs"},{"key":"10.1016\/j.jcmgh.2026.101774_bib11","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1186\/s12950-020-00246-4","article-title":"Ulcerative colitis: understanding its cellular pathology could provide insights into novel therapies","volume":"17","author":"Kaur","year":"2020","journal-title":"J Inflamm (Lond)"},{"key":"10.1016\/j.jcmgh.2026.101774_bib12","doi-asserted-by":"crossref","first-page":"1033","DOI":"10.1038\/s41556-020-0567-z","article-title":"Cellular and molecular architecture of the intestinal stem cell niche","volume":"22","author":"McCarthy","year":"2020","journal-title":"Nat Cell Biol"},{"key":"10.1016\/j.jcmgh.2026.101774_bib13","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1038\/nature17039","article-title":"Reparative inflammation takes charge of tissue regeneration","volume":"529","author":"Karin","year":"2016","journal-title":"Nature"},{"key":"10.1016\/j.jcmgh.2026.101774_bib14","doi-asserted-by":"crossref","first-page":"1464","DOI":"10.1136\/gutjnl-2024-332043","article-title":"Patient-derived organoid biobank identifies epigenetic dysregulation of intestinal epithelial MHC-I as a novel mechanism in severe Crohn\u2019s disease","volume":"73","author":"Dennison","year":"2024","journal-title":"Gut"},{"key":"10.1016\/j.jcmgh.2026.101774_bib15","doi-asserted-by":"crossref","first-page":"1447","DOI":"10.1016\/j.stem.2024.08.006","article-title":"Inflammation-induced epigenetic imprinting regulates intestinal stem cells","volume":"31","author":"Zhao","year":"2024","journal-title":"Cell Stem Cell"},{"key":"10.1016\/j.jcmgh.2026.101774_bib16","doi-asserted-by":"crossref","first-page":"162","DOI":"10.1016\/j.cell.2017.12.013","article-title":"Western diet triggers NLRP3-dependent innate immune reprogramming","volume":"172","author":"Christ","year":"2018","journal-title":"Cell"},{"key":"10.1016\/j.jcmgh.2026.101774_bib17","doi-asserted-by":"crossref","DOI":"10.1126\/science.aaf1098","article-title":"Trained immunity: a program of innate immune memory in health and disease","volume":"352","author":"Netea","year":"2016","journal-title":"Science"},{"key":"10.1016\/j.jcmgh.2026.101774_bib18","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1016\/j.cell.2017.11.034","article-title":"Modulation of myelopoiesis progenitors is an integral component of trained immunity","volume":"172","author":"Mitroulis","year":"2018","journal-title":"Cell"},{"key":"10.1016\/j.jcmgh.2026.101774_bib19","doi-asserted-by":"crossref","first-page":"332","DOI":"10.1038\/s41586-018-0023-4","article-title":"Innate immune memory in the brain shapes neurological disease hallmarks","volume":"556","author":"Wendeln","year":"2018","journal-title":"Nature"},{"key":"10.1016\/j.jcmgh.2026.101774_bib20","doi-asserted-by":"crossref","first-page":"1634","DOI":"10.1016\/j.cell.2018.09.042","article-title":"Induction of autonomous memory alveolar macrophages requires T cell help and is critical to trained immunity","volume":"175","author":"Yao","year":"2018","journal-title":"Cell"},{"key":"10.1016\/j.jcmgh.2026.101774_bib21","doi-asserted-by":"crossref","first-page":"475","DOI":"10.1038\/nature24271","article-title":"Inflammatory memory sensitizes skin epithelial stem cells to tissue damage","volume":"550","author":"Naik","year":"2017","journal-title":"Nature"},{"key":"10.1016\/j.jcmgh.2026.101774_bib22","doi-asserted-by":"crossref","first-page":"1758","DOI":"10.1016\/j.stem.2021.07.001","article-title":"Establishment, maintenance, and recall of inflammatory memory","volume":"28","author":"Larsen","year":"2021","journal-title":"Cell Stem Cell"},{"key":"10.1016\/j.jcmgh.2026.101774_bib23","doi-asserted-by":"crossref","first-page":"2959","DOI":"10.1016\/j.devcel.2023.11.008","article-title":"A reversible epigenetic memory of inflammatory injury controls lineage plasticity and tumor initiation in the mouse pancreas","volume":"58","author":"Falvo","year":"2023","journal-title":"Dev Cell"},{"key":"10.1016\/j.jcmgh.2026.101774_bib24","doi-asserted-by":"crossref","DOI":"10.1126\/science.abj0486","article-title":"Epithelial memory of inflammation limits tissue damage while promoting pancreatic tumorigenesis","volume":"373","author":"Del Poggetto","year":"2021","journal-title":"Science"},{"key":"10.1016\/j.jcmgh.2026.101774_bib25","doi-asserted-by":"crossref","DOI":"10.1126\/science.abf3002","article-title":"Prenatal maternal infection promotes tissue-specific immunity and inflammation in offspring","volume":"373","author":"Lim","year":"2021","journal-title":"Science"},{"key":"10.1016\/j.jcmgh.2026.101774_bib26","doi-asserted-by":"crossref","first-page":"1762","DOI":"10.1053\/j.gastro.2011.07.050","article-title":"Long-term expansion of epithelial organoids from human colon, adenoma, adenocarcinoma, and Barrett\u2019s epithelium","volume":"141","author":"Sato","year":"2011","journal-title":"Gastroenterology"},{"key":"10.1016\/j.jcmgh.2026.101774_bib27","doi-asserted-by":"crossref","DOI":"10.3791\/52483-v","article-title":"Establishment of human epithelial enteroids and colonoids from whole tissue and biopsy","author":"Mahe","year":"2015","journal-title":"J Vis Exp"},{"key":"10.1016\/j.jcmgh.2026.101774_bib28","doi-asserted-by":"crossref","first-page":"262","DOI":"10.1038\/nature07935","article-title":"Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche","volume":"459","author":"Sato","year":"2009","journal-title":"Nature"},{"key":"10.1016\/j.jcmgh.2026.101774_bib29","doi-asserted-by":"crossref","first-page":"3759","DOI":"10.1074\/jbc.R114.635995","article-title":"Human enteroids\/colonoids and intestinal organoids functionally recapitulate normal intestinal physiology and pathophysiology","volume":"291","author":"Zachos","year":"2016","journal-title":"J Biol Chem"},{"key":"10.1016\/j.jcmgh.2026.101774_bib30","doi-asserted-by":"crossref","first-page":"631","DOI":"10.1053\/j.gastro.2024.01.007","article-title":"The FOXP3+ pro-inflammatory T cell: a potential therapeutic target in Crohn\u2019s disease","volume":"166","author":"Kosinsky","year":"2024","journal-title":"Gastroenterology"},{"key":"10.1016\/j.jcmgh.2026.101774_bib31","doi-asserted-by":"crossref","first-page":"585","DOI":"10.1053\/j.gastro.2017.10.007","article-title":"DNA methylation and transcription patterns in intestinal epithelial cells from pediatric patients with inflammatory bowel diseases differentiate disease subtypes and associate with outcome","volume":"154","author":"Howell","year":"2018","journal-title":"Gastroenterology"},{"key":"10.1016\/j.jcmgh.2026.101774_bib32","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1136\/gutjnl-2017-314817","article-title":"DNA methylation defines regional identity of human intestinal epithelial organoids and undergoes dynamic changes during development","volume":"68","author":"Kraiczy","year":"2019","journal-title":"Gut"},{"key":"10.1016\/j.jcmgh.2026.101774_bib33","doi-asserted-by":"crossref","first-page":"1295","DOI":"10.1016\/j.jcmgh.2022.08.008","article-title":"Culture-associated DNA methylation changes impact on cellular function of human intestinal organoids","volume":"14","author":"Edgar","year":"2022","journal-title":"Cell Mol Gastroenterol Hepatol"},{"key":"10.1016\/j.jcmgh.2026.101774_bib34","doi-asserted-by":"crossref","first-page":"1970","DOI":"10.3389\/fimmu.2019.01970","article-title":"Human intestinal enteroids model MHC-II in the gut epithelium","volume":"10","author":"Wosen","year":"2019","journal-title":"Front Immunol"},{"key":"10.1016\/j.jcmgh.2026.101774_bib35","doi-asserted-by":"crossref","first-page":"1564","DOI":"10.1053\/j.gastro.2020.05.064","article-title":"Ex vivo mimicking of inflammation in organoids derived from patients with ulcerative colitis","volume":"159","author":"Arnauts","year":"2020","journal-title":"Gastroenterology"},{"key":"10.1016\/j.jcmgh.2026.101774_bib36","doi-asserted-by":"crossref","first-page":"485","DOI":"10.1093\/ecco-jcc\/jjaa185","article-title":"Intestinal receptor of SARS-CoV-2 in inflamed IBD tissue seems downregulated by HNF4A in ileum and upregulated by interferon regulating factors in colon","volume":"15","author":"Verstockt","year":"2021","journal-title":"J Crohns Colitis"},{"key":"10.1016\/j.jcmgh.2026.101774_bib37","doi-asserted-by":"crossref","first-page":"4456","DOI":"10.1038\/s41598-024-55076-8","article-title":"Prolonged culturing of colonic epithelial organoids derived from healthy individuals and ulcerative colitis patients results in the decrease of LINE-1 methylation level","volume":"14","author":"Inciuraite","year":"2024","journal-title":"Sci Rep"},{"key":"10.1016\/j.jcmgh.2026.101774_bib38","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1093\/jrr\/rrt123","article-title":"A novel in vitro survival assay of small intestinal stem cells after exposure to ionizing radiation","volume":"55","author":"Yamauchi","year":"2014","journal-title":"J Radiat Res"},{"key":"10.1016\/j.jcmgh.2026.101774_bib39","doi-asserted-by":"crossref","first-page":"3117","DOI":"10.3748\/wjg.v22.i11.3117","article-title":"Tight junctions in inflammatory bowel diseases and inflammatory bowel disease associated colorectal cancer","volume":"22","author":"Landy","year":"2016","journal-title":"World J Gastroenterol"},{"key":"10.1016\/j.jcmgh.2026.101774_bib40","doi-asserted-by":"crossref","first-page":"L647","DOI":"10.1152\/ajplung.1992.262.6.L647","article-title":"Structure, function, and regulation of cellular tight junctions","volume":"262","author":"Schneeberger","year":"1992","journal-title":"Am J Physiol Lung Cell Mol Physiol"},{"key":"10.1016\/j.jcmgh.2026.101774_bib41","doi-asserted-by":"crossref","first-page":"1924","DOI":"10.1053\/j.gastro.2021.08.047","article-title":"The tight junction protein ZO-1 is dispensable for barrier function but critical for effective mucosal repair","volume":"161","author":"Kuo","year":"2021","journal-title":"Gastroenterology"},{"key":"10.1016\/j.jcmgh.2026.101774_bib42","doi-asserted-by":"crossref","first-page":"W175","DOI":"10.1093\/nar\/gkac199","article-title":"ChIP-Atlas 2021 update: a data-mining suite for exploring epigenomic landscapes by fully integrating ChIP-seq, ATAC-seq and Bisulfite-seq data","volume":"50","author":"Zou","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"10.1016\/j.jcmgh.2026.101774_bib43","doi-asserted-by":"crossref","first-page":"576","DOI":"10.1016\/j.molcel.2010.05.004","article-title":"Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities","volume":"38","author":"Heinz","year":"2010","journal-title":"Mol Cell"},{"key":"10.1016\/j.jcmgh.2026.101774_bib44","doi-asserted-by":"crossref","first-page":"4267","DOI":"10.1038\/s41467-020-18035-1","article-title":"ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation","volume":"11","author":"Bentsen","year":"2020","journal-title":"Nat Commun"},{"key":"10.1016\/j.jcmgh.2026.101774_bib45","doi-asserted-by":"crossref","first-page":"D658","DOI":"10.1093\/nar\/gkw983","article-title":"Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse","volume":"45","author":"Mei","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"10.1016\/j.jcmgh.2026.101774_bib46","doi-asserted-by":"crossref","first-page":"D729","DOI":"10.1093\/nar\/gky1094","article-title":"Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis","volume":"47","author":"Zheng","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"10.1016\/j.jcmgh.2026.101774_bib47","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1038\/nbt.1630","article-title":"GREAT improves functional interpretation of cis-regulatory regions","volume":"28","author":"McLean","year":"2010","journal-title":"Nat Biotechnol"},{"key":"10.1016\/j.jcmgh.2026.101774_bib48","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1003731","article-title":"iRegulon: from a gene list to a gene regulatory network using large motif and track collections","volume":"10","author":"Janky","year":"2014","journal-title":"PLoS Comput Biol"},{"key":"10.1016\/j.jcmgh.2026.101774_bib49","doi-asserted-by":"crossref","first-page":"609","DOI":"10.1038\/s41435-019-0057-0","article-title":"The many faces of tumor necrosis factor signaling in the intestinal epithelium","volume":"20","author":"Delgado","year":"2019","journal-title":"Genes Immun"},{"key":"10.1016\/j.jcmgh.2026.101774_bib50","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1186\/1471-2105-7-191","article-title":"STEM: a tool for the analysis of short time series gene expression data","volume":"7","author":"Ernst","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"10.1016\/j.jcmgh.2026.101774_bib51","doi-asserted-by":"crossref","first-page":"649","DOI":"10.1093\/ecco-jcc\/jjx008","article-title":"Third European evidence-based consensus on diagnosis and management of ulcerative colitis. Part 1: definitions, diagnosis, extra-intestinal manifestations, pregnancy, cancer surveillance, surgery, and ileo-anal pouch disorders","volume":"11","author":"Magro","year":"2017","journal-title":"J Crohns Colitis"},{"key":"10.1016\/j.jcmgh.2026.101774_bib52","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1002\/0471142727.mb2129s109","article-title":"ATAC-seq: a method for assaying chromatin accessibility genome-wide","volume":"109","author":"Buenrostro","year":"2015","journal-title":"Curr Protoc Mol Biol"},{"key":"10.1016\/j.jcmgh.2026.101774_bib53","doi-asserted-by":"crossref","first-page":"959","DOI":"10.1038\/nmeth.4396","article-title":"An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues","volume":"14","author":"Corces","year":"2017","journal-title":"Nat Methods"}],"container-title":["Cellular and Molecular Gastroenterology and Hepatology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2352345X26000524?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2352345X26000524?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,6,15]],"date-time":"2026-06-15T07:16:10Z","timestamp":1781507770000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2352345X26000524"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026]]},"references-count":53,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2026]]}},"alternative-id":["S2352345X26000524"],"URL":"https:\/\/doi.org\/10.1016\/j.jcmgh.2026.101774","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2025.05.24.655923","asserted-by":"object"}]},"ISSN":["2352-345X"],"issn-type":[{"value":"2352-345X","type":"print"}],"subject":[],"published":{"date-parts":[[2026]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Intestinal Stem Cells From Patients With Inflammatory Bowel Disease Retain an Epigenetic Memory of Inflammation","name":"articletitle","label":"Article Title"},{"value":"Cellular and Molecular Gastroenterology and Hepatology","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.jcmgh.2026.101774","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2026 The Authors. Published by Elsevier Inc. on behalf of American Gastroenterological Association Institute.","name":"copyright","label":"Copyright"}],"article-number":"101774"}}