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Sci."},{"issue":"4","key":"10.1016\/j.jconrel.2026.115160_bb0920","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0214876","article-title":"Structural dynamics of tight junctions modulate the properties of the epithelial barrier","volume":"14","author":"Tervonen","year":"2019","journal-title":"PLoS One"},{"key":"10.1016\/j.jconrel.2026.115160_bb0925","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1186\/1742-4682-8-33","article-title":"Agent-based dynamic knowledge representation of Pseudomonas aeruginosa virulence activation in the stressed gut: towards characterizing host-pathogen interactions in gut-derived sepsis","volume":"8","author":"Seal","year":"2011","journal-title":"Theor. Biol. Med. Model."},{"issue":"4","key":"10.1016\/j.jconrel.2026.115160_bb0930","doi-asserted-by":"crossref","first-page":"1225","DOI":"10.1016\/j.jtbi.2010.03.027","article-title":"Model of colonic inflammation: immune modulatory mechanisms in inflammatory bowel disease","volume":"264","author":"Wendelsdorf","year":"2010","journal-title":"J. Theor. Biol."},{"issue":"9","key":"10.1016\/j.jconrel.2026.115160_bb0935","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0136139","article-title":"Sensitivity analysis of an ENteric Immunity SImulator (ENISI)-based model of immune responses to helicobacter pylori infection","volume":"10","author":"Alam","year":"2015","journal-title":"PLoS One"},{"issue":"215","key":"10.1016\/j.jconrel.2026.115160_bb0940","doi-asserted-by":"crossref","DOI":"10.1098\/rsif.2023.0756","article-title":"A mechanistic modelling approach of the host\u2013microbiota interactions to investigate beneficial symbiotic resilience in the human gut","volume":"21","author":"Haghebaert","year":"2024","journal-title":"J. R. Soc. 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Nano Macro."},{"key":"10.1016\/j.jconrel.2026.115160_bb0960","doi-asserted-by":"crossref","first-page":"126","DOI":"10.1016\/j.jiec.2021.06.021","article-title":"A Gut-Brain Axis-on-a-Chip for studying transport across epithelial and endothelial barriers","volume":"101","author":"Kim","year":"2021","journal-title":"J. Ind. Eng. Chem."},{"issue":"2","key":"10.1016\/j.jconrel.2026.115160_bb0965","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1038\/s41419-018-0304-8","article-title":"Modeling radiation injury-induced cell death and countermeasure drug responses in a human Gut-on-a-Chip","volume":"9","author":"Jalili-Firoozinezhad","year":"2018","journal-title":"Cell Death Dis."},{"issue":"1","key":"10.1016\/j.jconrel.2026.115160_bb0970","doi-asserted-by":"crossref","first-page":"21475","DOI":"10.1038\/s41598-020-78359-2","article-title":"Development of a human primary gut-on-a-chip to model inflammatory processes","volume":"10","author":"Beaurivage","year":"2020","journal-title":"Sci. Rep."},{"issue":"1","key":"10.1016\/j.jconrel.2026.115160_bb0975","doi-asserted-by":"crossref","first-page":"144","DOI":"10.1038\/s41378-023-00615-y","article-title":"Modeling gut neuro-epithelial connections in a novel microfluidic device","volume":"9","author":"de Hoyos-Vega","year":"2023","journal-title":"Microsyst. Nanoeng."},{"issue":"5","key":"10.1016\/j.jconrel.2026.115160_bb0980","doi-asserted-by":"crossref","DOI":"10.1063\/5.0168953","article-title":"Development of a dual-flow tissue perfusion device for modeling the gastrointestinal tract\u2013brain axis","volume":"17","author":"Baldwin","year":"2023","journal-title":"Biomicrofluidics"},{"key":"10.1016\/j.jconrel.2026.115160_bb0985","article-title":"Chitosan oligosaccharides regulate the occurrence and development of enteritis in a human gut-on-a-chip","volume":"10","author":"Jing","year":"2022","journal-title":"Front. Cell Dev. Biol. [Internet]"},{"issue":"1","key":"10.1016\/j.jconrel.2026.115160_bb0990","doi-asserted-by":"crossref","first-page":"E7","DOI":"10.1073\/pnas.1522193112","article-title":"Contributions of microbiome and mechanical deformation to intestinal bacterial overgrowth and inflammation in a human gut-on-a-chip","volume":"113","author":"Kim","year":"2016","journal-title":"Proc. Natl. Acad. 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Sci."},{"key":"10.1016\/j.jconrel.2026.115160_bb1005","doi-asserted-by":"crossref","DOI":"10.1016\/j.biomaterials.2019.119396","article-title":"A three-dimensional immunocompetent intestine-on-chip model as in vitro platform for functional and microbial interaction studies","volume":"220","author":"Maurer","year":"2019","journal-title":"Biomaterials"},{"key":"10.1016\/j.jconrel.2026.115160_bb1010","series-title":"Application of a Bioengineered Intestinal Epithelium for Drug Permeability and Metabolism Studies","author":"Gill","year":"2025"},{"issue":"1","key":"10.1016\/j.jconrel.2026.115160_bb1015","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1007\/s10544-016-0143-2","article-title":"Microfluidic Gut-liver chip for reproducing the first pass metabolism","volume":"19","author":"Choe","year":"2017","journal-title":"Biomed. 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Nanoeng."},{"issue":"2","key":"10.1016\/j.jconrel.2026.115160_bb1030","doi-asserted-by":"crossref","DOI":"10.20517\/mrr.2023.79","article-title":"A host-microbial metabolite interaction gut-on-a-chip model of the adult human intestine demonstrates beneficial effects upon inulin treatment of gut microbiome","volume":"3","author":"Donkers","year":"2024","journal-title":"Microbiome Res. Rep."},{"key":"10.1016\/j.jconrel.2026.115160_bb1035","doi-asserted-by":"crossref","DOI":"10.1016\/j.phrs.2023.106853","article-title":"The application of organ-on-chip models for the prediction of human pharmacokinetic profiles during drug development","volume":"195","author":"Keuper-Navis","year":"2023","journal-title":"Pharmacol. Res."},{"issue":"1","key":"10.1016\/j.jconrel.2026.115160_bb1040","doi-asserted-by":"crossref","first-page":"2805","DOI":"10.1038\/s41467-021-23072-5","article-title":"Characterization of an engineered live bacterial therapeutic for the treatment of phenylketonuria in a human gut-on-a-chip","volume":"12","author":"Nelson","year":"2021","journal-title":"Nat. Commun."},{"key":"10.1016\/j.jconrel.2026.115160_bb1045","doi-asserted-by":"crossref","first-page":"857","DOI":"10.1038\/nbt.4222","volume":"36","year":"2018","journal-title":"Nat. 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