{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,22]],"date-time":"2026-10-22T09:09:01Z","timestamp":1792660141584,"version":"4.5.0"},"reference-count":99,"publisher":"Elsevier BV","issue":"9","license":[{"start":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T00:00:00Z","timestamp":1630454400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T00:00:00Z","timestamp":1630454400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2022,9,6]],"date-time":"2022-09-06T00:00:00Z","timestamp":1662422400000},"content-version":"vor","delay-in-days":370,"URL":"http:\/\/www.elsevier.com\/open-access\/userlicense\/1.0\/"},{"start":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T00:00:00Z","timestamp":1630454400000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-017"},{"start":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T00:00:00Z","timestamp":1630454400000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T00:00:00Z","timestamp":1630454400000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-012"},{"start":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T00:00:00Z","timestamp":1630454400000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T00:00:00Z","timestamp":1630454400000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-004"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01HD096755"],"award-info":[{"award-number":["R01HD096755"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U01DK103147"],"award-info":[{"award-number":["U01DK103147"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000062","name":"National Institute of Diabetes and Digestive and Kidney Diseases","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000062","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Cell Stem Cell"],"published-print":{"date-parts":[[2021,9]]},"DOI":"10.1016\/j.stem.2021.04.002","type":"journal-article","created":{"date-parts":[[2021,4,28]],"date-time":"2021-04-28T11:46:38Z","timestamp":1619610398000},"page":"1516-1532.e14","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":96,"title":["Inflation-collapse dynamics drive patterning and morphogenesis in intestinal organoids"],"prefix":"10.1016","volume":"28","author":[{"given":"Naren P.","family":"Tallapragada","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7980-982X","authenticated-orcid":false,"given":"Hailey M.","family":"Cambra","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tomas","family":"Wald","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samantha","family":"Keough Jalbert","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4110-4554","authenticated-orcid":false,"given":"Diana M.","family":"Abraham","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6254-7082","authenticated-orcid":false,"given":"Ophir D.","family":"Klein","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Allon M.","family":"Klein","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.stem.2021.04.002_bib1","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1038\/s41586-019-1154-y","article-title":"Single-cell transcriptomes of the regenerating intestine reveal a revival stem cell","volume":"569","author":"Ayyaz","year":"2019","journal-title":"Nature"},{"key":"10.1016\/j.stem.2021.04.002_bib2","doi-asserted-by":"crossref","first-page":"31673","DOI":"10.1074\/jbc.R114.612697","article-title":"Piezo proteins: regulators of mechanosensation and other cellular processes","volume":"289","author":"Bagriantsev","year":"2014","journal-title":"J.\u00a0Biol. Chem."},{"key":"10.1016\/j.stem.2021.04.002_bib3","doi-asserted-by":"crossref","first-page":"940","DOI":"10.1016\/j.celrep.2014.07.019","article-title":"Quantification of crypt and stem cell evolution in the normal and neoplastic human colon","volume":"8","author":"Baker","year":"2014","journal-title":"Cell Rep."},{"key":"10.1016\/j.stem.2021.04.002_bib4","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1038\/nrm3721","article-title":"Adult intestinal stem cells: critical drivers of epithelial homeostasis and regeneration","volume":"15","author":"Barker","year":"2014","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"10.1016\/j.stem.2021.04.002_bib5","doi-asserted-by":"crossref","first-page":"1003","DOI":"10.1038\/nature06196","article-title":"Identification of stem cells in small intestine and colon by marker gene Lgr5","volume":"449","author":"Barker","year":"2007","journal-title":"Nature"},{"key":"10.1016\/j.stem.2021.04.002_bib6","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1016\/S0092-8674(02)01015-2","article-title":"Beta-catenin and TCF mediate cell positioning in the intestinal epithelium by controlling the expression of EphB\/ephrinB","volume":"111","author":"Batlle","year":"2002","journal-title":"Cell"},{"key":"10.1016\/j.stem.2021.04.002_bib7","doi-asserted-by":"crossref","first-page":"803","DOI":"10.1136\/gut.48.6.803","article-title":"Gastrointestinal cell proliferation and crypt fission are separate but complementary means of increasing tissue mass following infusion of epidermal growth factor in rats","volume":"48","author":"Berlanga-Acosta","year":"2001","journal-title":"Gut"},{"key":"10.1016\/j.stem.2021.04.002_bib8","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1053\/j.sempedsurg.2009.07.010","article-title":"The dilated bowel: a liability and an asset","volume":"18","author":"Bianchi","year":"2009","journal-title":"Semin. Pediatr. Surg."},{"key":"10.1016\/j.stem.2021.04.002_bib9","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1002\/aja.1001600105","article-title":"The stem-cell zone of the small intestinal epithelium. I. Evidence from Paneth cells in the adult mouse","volume":"160","author":"Bjerknes","year":"1981","journal-title":"Am. J. Anat."},{"key":"10.1016\/j.stem.2021.04.002_bib10","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1002\/aja.1001600107","article-title":"The stem-cell zone of the small intestinal epithelium. III. Evidence from columnar, enteroendocrine, and mucous cells in the adult mouse","volume":"160","author":"Bjerknes","year":"1981","journal-title":"Am. J. Anat."},{"key":"10.1016\/j.stem.2021.04.002_bib11","doi-asserted-by":"crossref","first-page":"674","DOI":"10.1053\/j.gastro.2017.05.019","article-title":"In\u00a0Vivo Imaging Reveals Existence of Crypt Fission and Fusion in Adult Mouse Intestine","volume":"153","author":"Bruens","year":"2017","journal-title":"Gastroenterology"},{"key":"10.1016\/j.stem.2021.04.002_bib12","doi-asserted-by":"crossref","first-page":"3475","DOI":"10.1111\/j.1742-4658.2012.08646.x","article-title":"On the biomechanics of stem cell niche formation in the gut--modelling growing organoids","volume":"279","author":"Buske","year":"2012","journal-title":"FEBS J."},{"key":"10.1016\/j.stem.2021.04.002_bib13","doi-asserted-by":"crossref","first-page":"112","DOI":"10.1038\/s41586-019-1309-x","article-title":"Hydraulic control of mammalian embryo size and cell fate","volume":"571","author":"Chan","year":"2019","journal-title":"Nature"},{"key":"10.1016\/j.stem.2021.04.002_bib14","doi-asserted-by":"crossref","first-page":"10989","DOI":"10.1038\/s41598-018-29230-y","article-title":"Intestinal crypts recover rapidly from focal damage with coordinated motion of stem cells that is impaired by aging","volume":"8","author":"Choi","year":"2018","journal-title":"Sci. Rep."},{"key":"10.1016\/j.stem.2021.04.002_bib15","doi-asserted-by":"crossref","first-page":"274","DOI":"10.1016\/j.cell.2013.07.004","article-title":"The intestinal crypt, a prototype stem cell compartment","volume":"154","author":"Clevers","year":"2013","journal-title":"Cell"},{"key":"10.1016\/j.stem.2021.04.002_bib16","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1016\/S0022-3468(96)90750-2","article-title":"Partial intestinal obstruction induces substantial mucosal proliferation in the pig","volume":"31","author":"Collins","year":"1996","journal-title":"J.\u00a0Pediatr. Surg."},{"key":"10.1016\/j.stem.2021.04.002_bib17","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1097\/MPG.0b013e3181604d27","article-title":"Crypt fission peaks early during infancy and crypt hyperplasia broadly peaks during infancy and childhood in the small intestine of humans","volume":"47","author":"Cummins","year":"2008","journal-title":"J.\u00a0Pediatr. Gastroenterol. Nutr."},{"key":"10.1016\/j.stem.2021.04.002_bib18","doi-asserted-by":"crossref","first-page":"2080","DOI":"10.1109\/TIP.2007.901238","article-title":"Image denoising by sparse 3-D transform-domain collaborative filtering","volume":"16","author":"Dabov","year":"2007","journal-title":"IEEE Trans. Image Process."},{"key":"10.1016\/j.stem.2021.04.002_bib19","article-title":"Ultra-high throughput single-cell RNA sequencing by combinatorial fluidic indexing","author":"Datlinger","year":"2019","journal-title":"bioRxiv"},{"key":"10.1016\/j.stem.2021.04.002_bib20","doi-asserted-by":"crossref","first-page":"256","DOI":"10.1016\/S1046-2023(03)00032-X","article-title":"Morphogenesis and oncogenesis of MCF-10A mammary epithelial acini grown in three-dimensional basement membrane cultures","volume":"30","author":"Debnath","year":"2003","journal-title":"Methods"},{"key":"10.1016\/j.stem.2021.04.002_bib21","doi-asserted-by":"crossref","first-page":"G1013","DOI":"10.1152\/ajpgi.00218.2007","article-title":"Expansion of intestinal stem cells associated with long-term adaptation following ileocecal resection in mice","volume":"293","author":"Dekaney","year":"2007","journal-title":"Am. J. Physiol. Gastrointest. Liver Physiol."},{"key":"10.1016\/j.stem.2021.04.002_bib22","doi-asserted-by":"crossref","first-page":"939","DOI":"10.1038\/nm.3201","article-title":"A functional CFTR assay using primary cystic fibrosis intestinal organoids","volume":"19","author":"Dekkers","year":"2013","journal-title":"Nat. Med."},{"key":"10.1016\/j.stem.2021.04.002_bib23","doi-asserted-by":"crossref","first-page":"465","DOI":"10.1016\/j.stem.2015.04.014","article-title":"Stem cell heterogeneity and plasticity in epithelia","volume":"16","author":"Donati","year":"2015","journal-title":"Cell Stem Cell"},{"key":"10.1016\/j.stem.2021.04.002_bib24","doi-asserted-by":"crossref","first-page":"4244","DOI":"10.1103\/PhysRevLett.84.4244","article-title":"Buckling instabilities of one-layered growing tissues","volume":"84","author":"Drasdo","year":"2000","journal-title":"Phys. Rev. Lett."},{"key":"10.1016\/j.stem.2021.04.002_bib25","doi-asserted-by":"crossref","first-page":"e1002515","DOI":"10.1371\/journal.pcbi.1002515","article-title":"A two-dimensional model of the colonic crypt accounting for the role of the basement membrane and pericryptal fibroblast sheath","volume":"8","author":"Dunn","year":"2012","journal-title":"PLoS Comput. Biol."},{"key":"10.1016\/j.stem.2021.04.002_bib26","doi-asserted-by":"crossref","first-page":"546","DOI":"10.1038\/nature10999","article-title":"Crowding induces live cell extrusion to maintain homeostatic cell numbers in epithelia","volume":"484","author":"Eisenhoffer","year":"2012","journal-title":"Nature"},{"key":"10.1016\/j.stem.2021.04.002_bib27","doi-asserted-by":"crossref","first-page":"100","DOI":"10.1101\/pdb.top072884","article-title":"Practical considerations for long-term time-lapse imaging of epithelial morphogenesis in three-dimensional organotypic cultures","volume":"2013","author":"Ewald","year":"2013","journal-title":"Cold Spring Harb. Protoc."},{"key":"10.1016\/j.stem.2021.04.002_bib28","doi-asserted-by":"crossref","first-page":"1518","DOI":"10.1053\/j.gastro.2012.08.031","article-title":"Redundant sources of Wnt regulate intestinal stem cells and promote formation of Paneth cells","volume":"143","author":"Farin","year":"2012","journal-title":"Gastroenterology"},{"key":"10.1016\/j.stem.2021.04.002_bib29","doi-asserted-by":"crossref","first-page":"340","DOI":"10.1038\/nature16937","article-title":"Visualization of a short-range Wnt gradient in the intestinal stem-cell niche","volume":"530","author":"Farin","year":"2016","journal-title":"Nature"},{"key":"10.1016\/j.stem.2021.04.002_bib30","doi-asserted-by":"crossref","first-page":"734","DOI":"10.1016\/j.stem.2013.09.015","article-title":"Transplantation of expanded fetal intestinal progenitors contributes to colon regeneration after injury","volume":"13","author":"Fordham","year":"2013","journal-title":"Cell Stem Cell"},{"key":"10.1016\/j.stem.2021.04.002_bib31","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1007\/978-1-4939-6475-8_9","article-title":"Using 3D Culture of Primary Mammary Epithelial Cells to Define Molecular Entities Required for Acinus Formation: Analyzing MAP Kinase Phosphatases","volume":"1501","author":"Gajewska","year":"2017","journal-title":"Methods Mol. Biol."},{"key":"10.1016\/j.stem.2021.04.002_bib32","doi-asserted-by":"crossref","first-page":"715","DOI":"10.1038\/nature15382","article-title":"Yap-dependent reprogramming of Lgr5(+) stem cells drives intestinal regeneration and cancer","volume":"526","author":"Gregorieff","year":"2015","journal-title":"Nature"},{"key":"10.1016\/j.stem.2021.04.002_bib33","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1038\/nature24489","article-title":"A single-cell survey of the small intestinal epithelium","volume":"551","author":"Haber","year":"2017","journal-title":"Nature"},{"key":"10.1016\/j.stem.2021.04.002_bib34","doi-asserted-by":"crossref","first-page":"078104","DOI":"10.1103\/PhysRevLett.107.078104","article-title":"Instabilities of monolayered epithelia: shape and structure of villi and crypts","volume":"107","author":"Hannezo","year":"2011","journal-title":"Phys. Rev. Lett."},{"key":"10.1016\/j.stem.2021.04.002_bib35","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1002\/ar.1090020402","article-title":"Variations in the wall of the large intestine and in the number and staining properties of the goblet cells","volume":"2","author":"Harvey","year":"1908","journal-title":"Anat. Rec."},{"key":"10.1016\/j.stem.2021.04.002_bib37","doi-asserted-by":"crossref","first-page":"IE.9.1","DOI":"10.1002\/cpsc.1","article-title":"Production of 3-D Airway Organoids From Primary Human Airway Basal Cells and Their Use in High-Throughput Screening","volume":"37","author":"Hild","year":"2016","journal-title":"Curr. Protoc. Stem Cell Biol."},{"key":"10.1016\/j.stem.2021.04.002_bib38","doi-asserted-by":"crossref","first-page":"625","DOI":"10.1083\/jcb.200807121","article-title":"Cdc42 controls spindle orientation to position the apical surface during epithelial morphogenesis","volume":"183","author":"Jaffe","year":"2008","journal-title":"J.\u00a0Cell Biol."},{"key":"10.1016\/j.stem.2021.04.002_bib39","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1002\/aja.1000140204","article-title":"The effects of distention of the intestine upon the shape of villi and glands","volume":"14","author":"Johnson","year":"1913","journal-title":"Am. J. Anat."},{"key":"10.1016\/j.stem.2021.04.002_bib40","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1097\/MOG.0b013e3283260900","article-title":"Ion transport in the intestine","volume":"25","author":"Kiela","year":"2009","journal-title":"Curr. Opin. Gastroenterol."},{"key":"10.1016\/j.stem.2021.04.002_bib41","doi-asserted-by":"crossref","first-page":"1187","DOI":"10.1016\/j.cell.2015.04.044","article-title":"Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells","volume":"161","author":"Klein","year":"2015","journal-title":"Cell"},{"key":"10.1016\/j.stem.2021.04.002_bib42","series-title":"A kinetic view of statistical physics","author":"Krapivsky","year":"2010"},{"key":"10.1016\/j.stem.2021.04.002_bib43","doi-asserted-by":"crossref","first-page":"e1002491","DOI":"10.1371\/journal.pbio.1002491","article-title":"Paneth Cell-Rich Regions Separated by a Cluster of Lgr5+ Cells Initiate Crypt Fission in the Intestinal Stem Cell Niche","volume":"14","author":"Langlands","year":"2016","journal-title":"PLoS Biol."},{"key":"10.1016\/j.stem.2021.04.002_bib44","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1002\/aja.1001600202","article-title":"The life history of cells in renewing systems","volume":"160","author":"Leblond","year":"1981","journal-title":"Am. J. Anat."},{"key":"10.1016\/j.stem.2021.04.002_bib45","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1038\/nmeth1015","article-title":"Three-dimensional culture models of normal and malignant breast epithelial cells","volume":"4","author":"Lee","year":"2007","journal-title":"Nat. Methods"},{"key":"10.1016\/j.stem.2021.04.002_bib46","doi-asserted-by":"crossref","first-page":"822","DOI":"10.1126\/science.1196236","article-title":"Intestinal stem cell replacement follows a pattern of neutral drift","volume":"330","author":"Lopez-Garcia","year":"2010","journal-title":"Science"},{"key":"10.1016\/j.stem.2021.04.002_bib47","doi-asserted-by":"crossref","first-page":"1651","DOI":"10.1172\/JCI0216112","article-title":"Thiazolidinone CFTR inhibitor identified by high-throughput screening blocks cholera toxin-induced intestinal fluid secretion","volume":"110","author":"Ma","year":"2002","journal-title":"J.\u00a0Clin. Invest."},{"key":"10.1016\/j.stem.2021.04.002_bib48","doi-asserted-by":"crossref","first-page":"2697","DOI":"10.1109\/TIP.2011.2121085","article-title":"A closed-form approximation of the exact unbiased inverse of the Anscombe variance-stabilizing transformation","volume":"20","author":"M\u00e4kitalo","year":"2011","journal-title":"IEEE Trans. Image Process."},{"key":"10.1016\/j.stem.2021.04.002_bib101","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1007\/978-1-4939-3603-8_2","article-title":"Lentivirus-Based Stable Gene Delivery into Intestinal Organoids","volume":"1422","author":"Maru","year":"2016","journal-title":"Methods Mol Biol"},{"key":"10.1016\/j.stem.2021.04.002_bib49","doi-asserted-by":"crossref","first-page":"861","DOI":"10.21105\/joss.00861","article-title":"UMAP: Uniform Manifold Approximation and Projection","volume":"3","author":"McInnes","year":"2018","journal-title":"J.\u00a0Open Source Softw."},{"key":"10.1016\/j.stem.2021.04.002_bib50","doi-asserted-by":"crossref","first-page":"7970385","DOI":"10.1155\/2017\/7970385","article-title":"Intestinal Stem Cell Niche: The Extracellular Matrix and Cellular Components","volume":"2017","author":"Meran","year":"2017","journal-title":"Stem Cells Int."},{"key":"10.1016\/j.stem.2021.04.002_bib51","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1016\/j.ydbio.2016.08.010","article-title":"Gastrointestinal organoids: How they gut it out","volume":"420","author":"Merker","year":"2016","journal-title":"Dev. Biol."},{"key":"10.1016\/j.stem.2021.04.002_bib52","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1007\/s11760-012-0419-9","article-title":"A fast algorithm for computation of discrete Euclidean distance transform in three or more dimensions on vector processing architectures","volume":"9","author":"Mishchenko","year":"2015","journal-title":"Signal Image Video Process."},{"key":"10.1016\/j.stem.2021.04.002_bib53","doi-asserted-by":"crossref","first-page":"456","DOI":"10.1016\/j.stem.2017.08.020","article-title":"Generation of Mouse and Human Organoid-Forming Intestinal Progenitor Cells by Direct Lineage Reprogramming","volume":"21","author":"Miura","year":"2017","journal-title":"Cell Stem Cell"},{"key":"10.1016\/j.stem.2021.04.002_bib54","doi-asserted-by":"crossref","first-page":"2471","DOI":"10.1038\/nprot.2013.153","article-title":"In\u00a0vitro expansion and genetic modification of gastrointestinal stem cells in spheroid culture","volume":"8","author":"Miyoshi","year":"2013","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.stem.2021.04.002_bib55","doi-asserted-by":"crossref","first-page":"e39596","DOI":"10.7554\/eLife.39596","article-title":"Size control of the inner ear via hydraulic feedback","volume":"8","author":"Mosaliganti","year":"2019","journal-title":"eLife"},{"key":"10.1016\/j.stem.2021.04.002_bib56","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1007\/978-1-62703-125-7_14","article-title":"Three-dimensional cultures of mouse mammary epithelial cells","volume":"945","author":"Mroue","year":"2013","journal-title":"Methods Mol. Biol."},{"key":"10.1016\/j.stem.2021.04.002_bib57","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1016\/j.celrep.2013.09.005","article-title":"Identification of Lgr5-independent spheroid-generating progenitors of the mouse fetal intestinal epithelium","volume":"5","author":"Mustata","year":"2013","journal-title":"Cell Rep."},{"key":"10.1016\/j.stem.2021.04.002_bib58","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1016\/j.mbs.2013.09.008","article-title":"Buckling of a growing tissue and the emergence of two-dimensional patterns","volume":"246","author":"Nelson","year":"2013","journal-title":"Math. Biosci."},{"key":"10.1016\/j.stem.2021.04.002_bib59","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1038\/s41586-018-0257-1","article-title":"Parasitic helminths induce fetal-like reversion in the intestinal stem cell niche","volume":"559","author":"Nusse","year":"2018","journal-title":"Nature"},{"key":"10.1016\/j.stem.2021.04.002_bib60","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1039\/C4IB00236A","article-title":"An individual based computational model of intestinal crypt fission and its application to predicting unrestrictive growth of the intestinal epithelium","volume":"7","author":"Pin","year":"2015","journal-title":"Integr. Biol."},{"key":"10.1016\/j.stem.2021.04.002_bib61","doi-asserted-by":"crossref","first-page":"964","DOI":"10.1093\/bioinformatics\/btz625","article-title":"BBKNN: fast batch alignment of single cell transcriptomes","volume":"36","author":"Pola\u0144ski","year":"2020","journal-title":"Bioinformatics"},{"key":"10.1016\/j.stem.2021.04.002_bib62","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1016\/j.stem.2009.12.007","article-title":"Spindle orientation bias in gut epithelial stem cell compartments is lost in precancerous tissue","volume":"6","author":"Quyn","year":"2010","journal-title":"Cell Stem Cell"},{"key":"10.1016\/j.stem.2021.04.002_bib63","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1016\/B978-0-12-420138-5.00002-1","article-title":"Practical considerations of objective lenses for application in cell biology","volume":"123","author":"Ross","year":"2014","journal-title":"Methods Cell Biol."},{"key":"10.1016\/j.stem.2021.04.002_bib64","doi-asserted-by":"crossref","first-page":"4422","DOI":"10.1242\/dev.153056","article-title":"Organ size control via hydraulically gated oscillations","volume":"144","author":"Ruiz-Herrero","year":"2017","journal-title":"Development"},{"key":"10.1016\/j.stem.2021.04.002_bib65","doi-asserted-by":"crossref","first-page":"469","DOI":"10.1038\/s41567-018-0055-6","article-title":"Universality of clone dynamics during tissue development","volume":"14","author":"Rulands","year":"2018","journal-title":"Nat. Phys."},{"key":"10.1016\/j.stem.2021.04.002_bib66","first-page":"1113","article-title":"Novel fixed z-direction (FiZD) kidney primordia and an organoid culture system for time-lapse confocal imaging","volume":"144","author":"Saarela","year":"2017","journal-title":"Development"},{"key":"10.1016\/j.stem.2021.04.002_bib67","first-page":"e100300","article-title":"Long-term expanding human airway organoids for disease modeling","volume":"38","author":"Sachs","year":"2019"},{"key":"10.1016\/j.stem.2021.04.002_bib68","doi-asserted-by":"crossref","first-page":"318","DOI":"10.1038\/nature11859","article-title":"Cytosystems dynamics in self-organization of tissue architecture","volume":"493","author":"Sasai","year":"2013","journal-title":"Nature"},{"key":"10.1016\/j.stem.2021.04.002_bib69","doi-asserted-by":"crossref","first-page":"1190","DOI":"10.1126\/science.1234852","article-title":"Growing self-organizing mini-guts from a single intestinal stem cell: mechanism and applications","volume":"340","author":"Sato","year":"2013","journal-title":"Science"},{"key":"10.1016\/j.stem.2021.04.002_bib70","doi-asserted-by":"crossref","first-page":"262","DOI":"10.1038\/nature07935","article-title":"Single Lgr5 stem cells build crypt-villus structures in\u00a0vitro without a mesenchymal niche","volume":"459","author":"Sato","year":"2009","journal-title":"Nature"},{"key":"10.1016\/j.stem.2021.04.002_bib71","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.stem.2021.04.002_bib72","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1038\/nature09637","article-title":"Paneth cells constitute the niche for Lgr5 stem cells in intestinal crypts","volume":"469","author":"Sato","year":"2011","journal-title":"Nature"},{"key":"10.1016\/j.stem.2021.04.002_bib73","doi-asserted-by":"crossref","first-page":"1075","DOI":"10.1038\/nature04957","article-title":"The stem-cell niche as an entity of action","volume":"441","author":"Scadden","year":"2006","journal-title":"Nature"},{"key":"10.1016\/j.stem.2021.04.002_bib74","doi-asserted-by":"crossref","first-page":"676","DOI":"10.1038\/nmeth.2019","article-title":"Fiji: an open-source platform for biological-image analysis","volume":"9","author":"Schindelin","year":"2012","journal-title":"Nat. Methods"},{"key":"10.1016\/j.stem.2021.04.002_bib75","doi-asserted-by":"crossref","first-page":"e76871","DOI":"10.1371\/journal.pone.0076871","article-title":"Generation of BAC transgenic epithelial organoids","volume":"8","author":"Schwank","year":"2013","journal-title":"PLoS ONE"},{"key":"10.1016\/j.stem.2021.04.002_bib76","doi-asserted-by":"crossref","first-page":"4166","DOI":"10.1073\/pnas.90.9.4166","article-title":"Identification of a colon mucosa gene that is down-regulated in colon adenomas and adenocarcinomas","volume":"90","author":"Schweinfest","year":"1993","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.stem.2021.04.002_bib77","doi-asserted-by":"crossref","first-page":"37962","DOI":"10.1074\/jbc.M607527200","article-title":"slc26a3 (dra)-deficient mice display chloride-losing diarrhea, enhanced colonic proliferation, and distinct up-regulation of ion transporters in the colon","volume":"281","author":"Schweinfest","year":"2006","journal-title":"J.\u00a0Biol. Chem."},{"key":"10.1016\/j.stem.2021.04.002_bib78","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1038\/s41586-019-1146-y","article-title":"Self-organization and symmetry breaking in intestinal organoid development","volume":"569","author":"Serra","year":"2019","journal-title":"Nature"},{"key":"10.1016\/j.stem.2021.04.002_bib79","doi-asserted-by":"crossref","first-page":"948","DOI":"10.1126\/science.aax0164","article-title":"Self-organization of stem cells into embryos: A window on early mammalian development","volume":"364","author":"Shahbazi","year":"2019","journal-title":"Science"},{"key":"10.1016\/j.stem.2021.04.002_bib80","doi-asserted-by":"crossref","first-page":"751","DOI":"10.1038\/nmeth.2521","article-title":"Near-infrared fluorescent proteins for multicolor in\u00a0vivo imaging","volume":"10","author":"Shcherbakova","year":"2013","journal-title":"Nat. Methods"},{"key":"10.1016\/j.stem.2021.04.002_bib81","doi-asserted-by":"crossref","first-page":"569","DOI":"10.1016\/j.cell.2015.03.041","article-title":"Bending gradients: how the intestinal stem cell gets its home","volume":"161","author":"Shyer","year":"2015","journal-title":"Cell"},{"key":"10.1016\/j.stem.2021.04.002_bib82","doi-asserted-by":"crossref","first-page":"851","DOI":"10.1016\/j.cell.2011.05.033","article-title":"Strategies for homeostatic stem cell self-renewal in adult tissues","volume":"145","author":"Simons","year":"2011","journal-title":"Cell"},{"key":"10.1016\/j.stem.2021.04.002_bib99","doi-asserted-by":"crossref","first-page":"62","DOI":"10.1002\/embr.201337799","article-title":"Biased competition between Lgr5 intestinal stem cells driven by oncogenic mutation induces clonal expansion","volume":"15","author":"Snippert","year":"2014","journal-title":"EMBO Rep"},{"key":"10.1016\/j.stem.2021.04.002_bib83","doi-asserted-by":"crossref","first-page":"134","DOI":"10.1016\/j.cell.2010.09.016","article-title":"Intestinal crypt homeostasis results from neutral competition between symmetrically dividing Lgr5 stem cells","volume":"143","author":"Snippert","year":"2010","journal-title":"Cell"},{"key":"10.1016\/j.stem.2021.04.002_bib84","doi-asserted-by":"crossref","first-page":"380","DOI":"10.1309\/V2EPTPLJRB3FGHJL","article-title":"Serrated polyps of the large intestine: a morphologic and molecular review of an evolving concept","volume":"124","author":"Snover","year":"2005","journal-title":"Am. J. Clin. Pathol."},{"key":"10.1016\/j.stem.2021.04.002_bib85","doi-asserted-by":"crossref","first-page":"180120","DOI":"10.1098\/rsob.180120","article-title":"Tales from the crypt: intestinal niche signals in tissue renewal, plasticity and cancer","volume":"8","author":"Spit","year":"2018","journal-title":"Open Biol."},{"key":"10.1016\/j.stem.2021.04.002_bib86","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1101\/sqb.2008.73.023","article-title":"Stem cells and their niches: integrated units that maintain Drosophila tissues","volume":"73","author":"Spradling","year":"2008","journal-title":"Cold Spring Harb. Symp. Quant. Biol."},{"key":"10.1016\/j.stem.2021.04.002_bib87","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1016\/j.devcel.2018.03.024","article-title":"Morphogenesis and Compartmentalization of the Intestinal Crypt","volume":"45","author":"Sumigray","year":"2018","journal-title":"Dev. Cell"},{"key":"10.1016\/j.stem.2021.04.002_bib88","doi-asserted-by":"crossref","first-page":"e07369","DOI":"10.7554\/eLife.07369","article-title":"Chemical activation of the mechanotransduction channel Piezo1","volume":"4","author":"Syeda","year":"2015","journal-title":"eLife"},{"key":"10.1016\/j.stem.2021.04.002_bib89","doi-asserted-by":"crossref","first-page":"254","DOI":"10.1016\/j.ydbio.2017.10.013","article-title":"Linking stem cell function and growth pattern of intestinal organoids","volume":"433","author":"Thalheim","year":"2018","journal-title":"Dev. Biol."},{"key":"10.1016\/j.stem.2021.04.002_bib90","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1038\/nature10408","article-title":"A reserve stem cell population in small intestine renders Lgr5-positive cells dispensable","volume":"478","author":"Tian","year":"2011","journal-title":"Nature"},{"key":"10.1016\/j.stem.2021.04.002_bib92","first-page":"3","article-title":"Morphogenesis of the small intestine during fetal development","author":"Trier","year":"1979","journal-title":"Ciba Found. Symp."},{"key":"10.1016\/j.stem.2021.04.002_bib93","doi-asserted-by":"crossref","first-page":"768","DOI":"10.1183\/13993003.01661-2015","article-title":"\u03b22-Adrenergic receptor agonists activate CFTR in intestinal organoids and subjects with cystic fibrosis","volume":"48","author":"Vijftigschild","year":"2016","journal-title":"Eur. Respir. J."},{"key":"10.1016\/j.stem.2021.04.002_bib94","doi-asserted-by":"crossref","first-page":"1246","DOI":"10.1093\/bioinformatics\/btx792","article-title":"SPRING: a kinetic interface for visualizing high dimensional single-cell expression data","volume":"34","author":"Weinreb","year":"2018","journal-title":"Bioinformatics"},{"key":"10.1016\/j.stem.2021.04.002_bib100","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1186\/s13059-017-1382-0","article-title":"SCANPY: large-scale single-cell gene expression data analysis","volume":"19","author":"Wolf","year":"2018","journal-title":"Genome Biol"},{"key":"10.1016\/j.stem.2021.04.002_bib95","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1016\/j.cels.2018.11.005","article-title":"Scrublet: Computational identification of cell doublets in single-cell transcriptomic data","volume":"8","author":"Wolock","year":"2019","journal-title":"Cell Syst."},{"key":"10.1016\/j.stem.2021.04.002_bib96","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1016\/j.stem.2017.11.001","article-title":"YAP\/TAZ-Dependent Reprogramming of Colonic Epithelium Links ECM Remodeling to Tissue Regeneration","volume":"22","author":"Yui","year":"2018","journal-title":"Cell Stem Cell"},{"key":"10.1016\/j.stem.2021.04.002_bib97","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1038\/nprot.2016.154","article-title":"Single-cell barcoding and sequencing using droplet microfluidics","volume":"12","author":"Zilionis","year":"2017","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.stem.2021.04.002_bib98","doi-asserted-by":"crossref","first-page":"1317","DOI":"10.1016\/j.immuni.2019.03.009","article-title":"Single-Cell Transcriptomics of Human and Mouse Lung Cancers Reveals Conserved Myeloid Populations across Individuals and Species","volume":"50","author":"Zilionis","year":"2019","journal-title":"Immunity"}],"container-title":["Cell Stem Cell"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1934590921001594?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1934590921001594?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,10,30]],"date-time":"2025-10-30T13:53:24Z","timestamp":1761832404000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1934590921001594"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,9]]},"references-count":99,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2021,9]]}},"alternative-id":["S1934590921001594"],"URL":"https:\/\/doi.org\/10.1016\/j.stem.2021.04.002","relation":{},"ISSN":["1934-5909"],"issn-type":[{"value":"1934-5909","type":"print"}],"subject":[],"published":{"date-parts":[[2021,9]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Inflation-collapse dynamics drive patterning and morphogenesis in intestinal organoids","name":"articletitle","label":"Article Title"},{"value":"Cell Stem Cell","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.stem.2021.04.002","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2021 Elsevier Inc.","name":"copyright","label":"Copyright"}]}}