{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,16]],"date-time":"2026-01-16T10:05:55Z","timestamp":1768557955932,"version":"3.49.0"},"reference-count":55,"publisher":"Springer Science and Business Media LLC","issue":"5","license":[{"start":{"date-parts":[[2022,5,6]],"date-time":"2022-05-06T00:00:00Z","timestamp":1651795200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2022,5,6]],"date-time":"2022-05-06T00:00:00Z","timestamp":1651795200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100007601","name":"Horizon 2020","doi-asserted-by":"publisher","award":["826494"],"award-info":[{"award-number":["826494"]}],"id":[{"id":"10.13039\/501100007601","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100010198","name":"Ministerio de Econom\u00c3\u00ada, Industria y Competitividad, Gobierno de Espa\u00c3\u00b1a","doi-asserted-by":"publisher","award":["RTI2018-094494-B-C21"],"award-info":[{"award-number":["RTI2018-094494-B-C21"]}],"id":[{"id":"10.13039\/501100010198","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100010198","name":"Ministerio de Econom\u00c3\u00ada, Industria y Competitividad, Gobierno de Espa\u00c3\u00b1a","doi-asserted-by":"publisher","award":["RTI2018-094494-B-C21"],"award-info":[{"award-number":["RTI2018-094494-B-C21"]}],"id":[{"id":"10.13039\/501100010198","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000781","name":"European Research Council","doi-asserted-by":"publisher","award":["101018587"],"award-info":[{"award-number":["101018587"]}],"id":[{"id":"10.13039\/501100000781","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100007041","name":"Universidad de Zaragoza","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100007041","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Engineering with Computers"],"published-print":{"date-parts":[[2022,10]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>The correct function of many organs depends on proper lumen morphogenesis, which requires the orchestration of both biological and mechanical aspects. However, how these factors coordinate is not yet fully understood. Here, we focus on the development of a mechanistic model for computationally simulating lumen morphogenesis. In particular, we consider the hydrostatic pressure generated by the cells\u2019 fluid secretion as the driving force and the density of the extracellular matrix as regulators of the process. For this purpose, we develop a 3D agent-based-model for lumen morphogenesis that includes cells\u2019 fluid secretion and the density of the extracellular matrix. Moreover, this computer-based model considers the variation in the biological behavior of cells in response to the mechanical forces that they sense. Then, we study the formation of the lumen under different-mechanical scenarios and conclude that an increase in the matrix density reduces the lumen volume and hinders lumen morphogenesis. Finally, we show that the model successfully predicts normal lumen morphogenesis when the matrix density is physiological and aberrant multilumen formation when the matrix density is excessive.<\/jats:p>","DOI":"10.1007\/s00366-022-01654-1","type":"journal-article","created":{"date-parts":[[2022,5,6]],"date-time":"2022-05-06T22:07:02Z","timestamp":1651874822000},"page":"4135-4149","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":14,"title":["A 3D multi-agent-based model for lumen morphogenesis: the role of the biophysical properties of the extracellular matrix"],"prefix":"10.1007","volume":"38","author":[{"given":"Daniel","family":"Camacho-G\u00f3mez","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9864-7683","authenticated-orcid":false,"given":"Jos\u00e9 Manuel","family":"Garc\u00eda-Aznar","sequence":"additional","affiliation":[]},{"given":"Mar\u00eda Jos\u00e9","family":"G\u00f3mez-Benito","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2022,5,6]]},"reference":[{"issue":"10","key":"1654_CR1","doi-asserted-by":"publisher","first-page":"1218","DOI":"10.1101\/gad.1415606","volume":"20","author":"F Hezel Aram","year":"2006","unstructured":"Hezel Aram F, Kimmelman Alec C, Stanger Ben Z, Bardeesy N, DePinho RA (2006) Genetics and biology of pancreatic ductal adenocarcinoma. Genes Dev 20(10):1218\u20131249. https:\/\/doi.org\/10.1101\/gad.1415606","journal-title":"Genes Dev"},{"issue":"5","key":"1654_CR2","doi-asserted-by":"publisher","first-page":"1607","DOI":"10.1007\/s10237-020-01294-8","volume":"19","author":"K B\u00e4umler","year":"2020","unstructured":"B\u00e4umler K, Vedula V, Sailer AM, Seo J, Chiu P, Mistelbauer G, Chan FP, Fischbein MP, Marsden AL, Fleischmann D (2020) Fluid-structure interaction simulations of patient-specific aortic dissection. Biomech Model Mechanobiol 19(5):1607\u20131628. https:\/\/doi.org\/10.1007\/s10237-020-01294-8","journal-title":"Biomech Model Mechanobiol"},{"issue":"2","key":"1654_CR3","doi-asserted-by":"publisher","first-page":"102","DOI":"10.4161\/cc.1.2.108","volume":"1","author":"MV Blagosklonny","year":"2002","unstructured":"Blagosklonny MV, Pardee AB (2002) The restriction point of the cell cycle. Cell Cycle 1(2):102\u2013109. https:\/\/doi.org\/10.4161\/cc.1.2.108","journal-title":"Cell Cycle"},{"issue":"92","key":"1654_CR4","doi-asserted-by":"publisher","first-page":"20131049","DOI":"10.1098\/rsif.2013.1049","volume":"11","author":"SEM Boas","year":"2014","unstructured":"Boas SEM, Merks RMH (2014) Synergy of cell-cell repulsion and vacuolation in a computational model of lumen formation. J R Soc Interface 11(92):20131049. https:\/\/doi.org\/10.1098\/rsif.2013.1049","journal-title":"J R Soc Interface"},{"issue":"11","key":"1654_CR5","doi-asserted-by":"publisher","first-page":"1035","DOI":"10.1038\/ncb2106","volume":"12","author":"DM Bryant","year":"2010","unstructured":"Bryant DM, Datta A, Rodriguez-Fraticelli AE, Per\u00e4nen J, Martin-Belmonte F, Mostov KE (2010) A molecular network for de novo generation of the apical surface and lumen. Nat Cell Biol 12(11):1035\u20131045. https:\/\/doi.org\/10.1038\/ncb2106","journal-title":"Nat Cell Biol"},{"key":"1654_CR6","doi-asserted-by":"publisher","first-page":"145","DOI":"10.1016\/j.jtbi.2015.07.021","volume":"383","author":"A Caiazzo","year":"2015","unstructured":"Caiazzo A, Ramis-Conde I (2015) Multiscale modelling of palisade formation in gliobastoma multiforme. J Theor Biol 383:145\u2013156. https:\/\/doi.org\/10.1016\/j.jtbi.2015.07.021","journal-title":"J Theor Biol"},{"issue":"2","key":"1654_CR7","doi-asserted-by":"publisher","first-page":"359","DOI":"10.1083\/jcb.201305044","volume":"203","author":"B Cerruti","year":"2013","unstructured":"Cerruti B, Puliafito A, Shewan AM, Wei Yu, Combes AN, Little MH, Chianale F, Primo L, Serini G, Mostov KE et al (2013) Polarity, cell division, and out-of-equilibrium dynamics control the growth of epithelial structures. J Cell Biol 203(2):359\u2013372. https:\/\/doi.org\/10.1083\/jcb.201305044","journal-title":"J Cell Biol"},{"issue":"1","key":"1654_CR8","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/s10237-014-0581-9","volume":"14","author":"S Checa","year":"2015","unstructured":"Checa S, Rausch MK, Petersen A, Kuhl E, Duda GN (2015) The emergence of extracellular matrix mechanics and cell traction forces as important regulators of cellular self-organization. Biomech Model Mechanobiol 14(1):1\u201313. https:\/\/doi.org\/10.1007\/s10237-014-0581-9","journal-title":"Biomech Model Mechanobiol"},{"issue":"7","key":"1654_CR9","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.2002842","volume":"16","author":"SB Dahl-Jensen","year":"2018","unstructured":"Dahl-Jensen SB, Yennek S, Flasse L, Larsen HL, Sever D, Karremore G, Novak I, Sneppen K, Grapin-Botton A (2018) Deconstructing the principles of ductal network formation in the pancreas. PLoS Biol 16(7):e2002842. https:\/\/doi.org\/10.1371\/journal.pbio.2002842","journal-title":"PLoS Biol"},{"issue":"21","key":"1654_CR10","doi-asserted-by":"publisher","first-page":"E4751","DOI":"10.1073\/pnas.1722154115","volume":"115","author":"S Dasgupta","year":"2018","unstructured":"Dasgupta S, Gupta K, Zhang Y, Viasnoff V, Prost J (2018) Physics of lumen growth. Proc Natl Acad Sci 115(21):E4751\u2013E4757. https:\/\/doi.org\/10.1073\/pnas.1722154115","journal-title":"Proc Natl Acad Sci"},{"issue":"3","key":"1654_CR11","doi-asserted-by":"publisher","first-page":"R126","DOI":"10.1016\/j.cub.2010.12.003","volume":"21","author":"A Datta","year":"2011","unstructured":"Datta A, Bryant DM, Mostov KE (2011) Molecular regulation of lumen morphogenesis. Curr Biol 21(3):R126\u2013R136. https:\/\/doi.org\/10.1016\/j.cub.2010.12.003","journal-title":"Curr Biol"},{"issue":"9","key":"1654_CR12","doi-asserted-by":"publisher","first-page":"675","DOI":"10.1038\/nrc1695","volume":"5","author":"J Debnath","year":"2005","unstructured":"Debnath J, Brugge JS (2005) Modelling glandular epithelial cancers in three-dimensional cultures. Nat Rev Cancer 5(9):675\u2013688. https:\/\/doi.org\/10.1038\/nrc1695","journal-title":"Nat Rev Cancer"},{"issue":"3","key":"1654_CR13","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1088\/1478-3975\/2\/3\/001","volume":"2","author":"D Drasdo","year":"2005","unstructured":"Drasdo D, H\u00f6hme S (2005) A single-cell-based model of tumor growth in vitro: monolayers and spheroids. Phys Biol 2(3):133\u2013147. https:\/\/doi.org\/10.1088\/1478-3975\/2\/3\/001","journal-title":"Phys Biol"},{"issue":"39","key":"1654_CR14","doi-asserted-by":"publisher","first-page":"19264","DOI":"10.1073\/pnas.1908481116","volume":"116","author":"C Duclut","year":"2019","unstructured":"Duclut C, Sarkar N, Prost J, J\u00fclicher F (2019) Fluid pumping and active flexoelectricity can promote lumen nucleation in cell assemblies. Proc Natl Acad Sci 116(39):19264\u201319273. https:\/\/doi.org\/10.1073\/pnas.1908481116","journal-title":"Proc Natl Acad Sci"},{"issue":"1","key":"1654_CR15","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1145\/174462.156635","volume":"13","author":"H Edelsbrunner","year":"1994","unstructured":"Edelsbrunner H, M\u00fccke EP (1994) Three-dimensional alpha shapes. ACM Trans Graph (TOG) 13(1):43\u201372. https:\/\/doi.org\/10.1145\/174462.156635","journal-title":"ACM Trans Graph (TOG)"},{"issue":"4","key":"1654_CR16","doi-asserted-by":"publisher","first-page":"e1002030","DOI":"10.1371\/journal.pcbi.1002030","volume":"7","author":"JA Engelberg","year":"2011","unstructured":"Engelberg JA, Datta A, Mostov KE, Hunt CA (2011) Mdck cystogenesis driven by cell stabilization within computational analogues. PLoS Comput Biol 7(4):e1002030. https:\/\/doi.org\/10.1371\/journal.pcbi.1002030","journal-title":"PLoS Comput Biol"},{"issue":"1","key":"1654_CR17","doi-asserted-by":"publisher","first-page":"185","DOI":"10.1016\/S0006-3495(85)83771-1","volume":"48","author":"EA Evans","year":"1985","unstructured":"Evans EA (1985) Detailed mechanics of membrane-membrane adhesion and separation. ii. discrete kinetically trapped molecular cross-bridges. Biophys J 48(1):185\u2013192. https:\/\/doi.org\/10.1016\/S0006-3495(85)83771-1","journal-title":"Biophys J"},{"issue":"21","key":"1654_CR18","doi-asserted-by":"publisher","first-page":"3649","DOI":"10.1242\/jcs.018648","volume":"121","author":"A Ferrari","year":"2008","unstructured":"Ferrari A, Veligodskiy A, Berge U, Lucas MS, Kroschewski R (2008) Rock-mediated contractility, tight junctions and channels contribute to the conversion of a preapical patch into apical surface during isochoric lumen initiation. J Cell Sci 121(21):3649\u20133663. https:\/\/doi.org\/10.1242\/jcs.018648","journal-title":"J Cell Sci"},{"issue":"45\u201346","key":"1654_CR19","doi-asserted-by":"publisher","first-page":"3583","DOI":"10.1016\/j.cma.2008.09.013","volume":"198","author":"CA Figueroa","year":"2009","unstructured":"Figueroa CA, Baek S, Taylor CA, Humphrey JD (2009) A computational framework for fluid\u2013solid-growth modeling in cardiovascular simulations. Comput Methods Appl Mech Eng 198(45\u201346):3583\u20133602. https:\/\/doi.org\/10.1016\/j.cma.2008.09.013","journal-title":"Comput Methods Appl Mech Eng"},{"issue":"1","key":"1654_CR20","doi-asserted-by":"publisher","first-page":"62","DOI":"10.1529\/biophysj.104.041459","volume":"88","author":"J Galle","year":"2005","unstructured":"Galle J, Loeffler M, Drasdo D (2005) Modeling the effect of deregulated proliferation and apoptosis on the growth dynamics of epithelial cell populations in vitro. Biophys J 88(1):62\u201375. https:\/\/doi.org\/10.1529\/biophysj.104.041459","journal-title":"Biophys J"},{"issue":"2","key":"1654_CR21","doi-asserted-by":"publisher","first-page":"e1005991","DOI":"10.1371\/journal.pcbi.1005991","volume":"14","author":"A Ghaffarizadeh","year":"2018","unstructured":"Ghaffarizadeh A, Heiland R, Friedman SH, Mumenthaler SM, Macklin P (2018) Physicell: an open source physics-based cell simulator for 3-d multicellular systems. PLoS Comput Biol 14(2):e1005991. https:\/\/doi.org\/10.1371\/journal.pcbi.1005991","journal-title":"PLoS Comput Biol"},{"issue":"20","key":"1654_CR22","doi-asserted-by":"publisher","first-page":"1809","DOI":"10.1016\/j.cub.2010.09.032","volume":"20","author":"Y Hao","year":"2010","unstructured":"Hao Y, Quansheng D, Chen X, Zheng Z, Balsbaugh JL, Maitra S, Shabanowitz J, Hunt DF, Macara IG (2010) Par3 controls epithelial spindle orientation by apkc-mediated phosphorylation of apical pins. Curr Biol 20(20):1809\u20131818. https:\/\/doi.org\/10.1016\/j.cub.2010.09.032","journal-title":"Curr Biol"},{"key":"1654_CR23","doi-asserted-by":"publisher","first-page":"515","DOI":"10.1016\/j.cma.2017.04.031","volume":"322","author":"T Heck","year":"2017","unstructured":"Heck T, Smeets B, Vanmaercke S, Bhattacharya P, Odenthal T, Ramon H, Van Oosterwyck H, Van Liedekerke P (2017) Modeling extracellular matrix viscoelasticity using smoothed particle hydrodynamics with improved boundary treatment. Comput Methods Appl Mech Eng 322:515\u2013540. https:\/\/doi.org\/10.1016\/j.cma.2017.04.031","journal-title":"Comput Methods Appl Mech Eng"},{"issue":"6","key":"1654_CR24","doi-asserted-by":"publisher","first-page":"1024","DOI":"10.1091\/mbc.e11-08-0721","volume":"23","author":"H Chi-Kuo","year":"2012","unstructured":"Chi-Kuo H, Coughlin M, Mitchison TJ (2012) Midbody assembly and its regulation during cytokinesis. Mol Biol Cell 23(6):1024\u20131034. https:\/\/doi.org\/10.1091\/mbc.e11-08-0721","journal-title":"Mol Biol Cell"},{"issue":"11","key":"1654_CR25","doi-asserted-by":"publisher","first-page":"3179","DOI":"10.1091\/mbc.9.11.3179","volume":"9","author":"S Huang","year":"1998","unstructured":"Huang S, Chen CS, Ingber DE (1998) Control of cyclin d1, p27kip1, and cell cycle progression in human capillary endothelial cells by cell shape and cytoskeletal tension. Mol Biol Cell 9(11):3179\u20133193. https:\/\/doi.org\/10.1091\/mbc.9.11.3179","journal-title":"Mol Biol Cell"},{"issue":"4","key":"1654_CR26","doi-asserted-by":"publisher","first-page":"625","DOI":"10.1083\/jcb.200807121","volume":"183","author":"AB Jaffe","year":"2008","unstructured":"Jaffe AB, Kaji N, Durgan J, Hall A (2008) Cdc42 controls spindle orientation to position the apical surface during epithelial morphogenesis. J Cell Biol 183(4):625\u2013633. https:\/\/doi.org\/10.1083\/jcb.200807121","journal-title":"J Cell Biol"},{"issue":"7438","key":"1654_CR27","doi-asserted-by":"publisher","first-page":"480","DOI":"10.1038\/nature11897","volume":"494","author":"R Kafri","year":"2013","unstructured":"Kafri R, Levy J, Ginzberg MB, Seungeun O, Lahav G, Kirschner MW (2013) Dynamics extracted from fixed cells reveal feedback linking cell growth to cell cycle. Nature 494(7438):480\u2013483. https:\/\/doi.org\/10.1038\/nature11897","journal-title":"Nature"},{"issue":"18","key":"1654_CR28","doi-asserted-by":"publisher","first-page":"1511","DOI":"10.1016\/j.cub.2009.07.069","volume":"19","author":"EA Klein","year":"2009","unstructured":"Klein EA, Yin L, Kothapalli D, Castagnino P, Byfield FJ, Tina X, Levental I, Hawthorne E, Janmey PA, Assoian RK (2009) Cell-cycle control by physiological matrix elasticity and in vivo tissue stiffening. Curr Biol 19(18):1511\u20131518. https:\/\/doi.org\/10.1016\/j.cub.2009.07.069","journal-title":"Curr Biol"},{"issue":"7730","key":"1654_CR29","doi-asserted-by":"publisher","first-page":"203","DOI":"10.1038\/s41586-018-0671-4","volume":"563","author":"E Latorre","year":"2018","unstructured":"Latorre E, Kale S, Casares L, G\u00f3mez-Gonz\u00e1lez M, Uroz M, Valon L, Nair RV, Garreta E, Montserrat N, Del Campo A et al (2018) Active superelasticity in three-dimensional epithelia of controlled shape. Nature 563(7730):203\u2013208. https:\/\/doi.org\/10.1038\/s41586-018-0671-4","journal-title":"Nature"},{"issue":"1","key":"1654_CR30","doi-asserted-by":"publisher","first-page":"73","DOI":"10.1007\/s00366-008-0107-0","volume":"25","author":"A Liu","year":"2009","unstructured":"Liu A, Wang RK, Thornburg KL, Rugonyi S (2009) Dynamic variation of hemodynamic shear stress on the walls of developing chick hearts: computational models of the heart outflow tract. Eng Comput 25(1):73\u201386. https:\/\/doi.org\/10.1007\/s00366-008-0107-0","journal-title":"Eng Comput"},{"issue":"2","key":"1654_CR31","doi-asserted-by":"publisher","first-page":"383","DOI":"10.1016\/j.cell.2006.11.051","volume":"128","author":"F Martin-Belmonte","year":"2007","unstructured":"Martin-Belmonte F, Gassama A, Datta A, Wei Yu, Rescher U, Gerke V, Mostov K (2007) Pten-mediated apical segregation of phosphoinositides controls epithelial morphogenesis through cdc42. Cell 128(2):383\u2013397. https:\/\/doi.org\/10.1016\/j.cell.2006.11.051","journal-title":"Cell"},{"issue":"32","key":"1654_CR32","doi-asserted-by":"publisher","first-page":"13124","DOI":"10.1073\/pnas.1100506108","volume":"108","author":"M Mir","year":"2011","unstructured":"Mir M, Wang Z, Shen Z, Bednarz M, Bashir R, Golding I, Prasanth SG, Popescu G (2011) Optical measurement of cycle-dependent cell growth. Proc Natl Acad Sci 108(32):13124\u201313129. https:\/\/doi.org\/10.1073\/pnas.1100506108","journal-title":"Proc Natl Acad Sci"},{"key":"1654_CR33","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1016\/j.gde.2015.01.010","volume":"32","author":"A Navis","year":"2015","unstructured":"Navis A, Bagnat M (2015) Developing pressures: fluid forces driving morphogenesis. Curr Opin Genet Dev 32:24\u201330. https:\/\/doi.org\/10.1016\/j.gde.2015.01.010","journal-title":"Curr Opin Genet Dev"},{"issue":"1","key":"1654_CR34","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.jtbi.2008.05.004","volume":"254","author":"E Palsson","year":"2008","unstructured":"Palsson E (2008) A 3-d model used to explore how cell adhesion and stiffness affect cell sorting and movement in multicellular systems. J Theor Biol 254(1):1\u201313. https:\/\/doi.org\/10.1016\/j.jtbi.2008.05.004","journal-title":"J Theor Biol"},{"issue":"3","key":"1654_CR35","doi-asserted-by":"publisher","first-page":"241","DOI":"10.1016\/j.ccr.2005.08.010","volume":"8","author":"MJ Paszek","year":"2005","unstructured":"Paszek MJ, Zahir N, Johnson KR, Lakins JN, Rozenberg GI, Gefen A, Reinhart-King CA, Margulies SS, Dembo M, Boettiger D et al (2005) Tensional homeostasis and the malignant phenotype. Cancer Cell 8(3):241\u2013254. https:\/\/doi.org\/10.1016\/j.ccr.2005.08.010","journal-title":"Cancer Cell"},{"issue":"49","key":"1654_CR36","doi-asserted-by":"publisher","first-page":"4326","DOI":"10.1038\/onc.2009.299","volume":"28","author":"PP Provenzano","year":"2009","unstructured":"Provenzano PP, Inman DR, Eliceiri KW, Keely PJ (2009) Matrix density-induced mechanoregulation of breast cell phenotype, signaling and gene expression through a fak-erk linkage. Oncogene 28(49):4326\u20134343. https:\/\/doi.org\/10.1038\/onc.2009.299","journal-title":"Oncogene"},{"issue":"4","key":"1654_CR37","doi-asserted-by":"publisher","first-page":"661","DOI":"10.1083\/jcb.201002097","volume":"189","author":"Y Qin","year":"2010","unstructured":"Qin Y, Meisen WH, Hao Y, Macara IG (2010) Tuba, a cdc42 gef, is required for polarized spindle orientation during epithelial cyst formation. J Cell Biol 189(4):661\u2013669. https:\/\/doi.org\/10.1083\/jcb.201002097","journal-title":"J Cell Biol"},{"issue":"1","key":"1654_CR38","doi-asserted-by":"publisher","first-page":"155","DOI":"10.1529\/biophysj.107.114678","volume":"95","author":"I Ramis-Conde","year":"2008","unstructured":"Ramis-Conde I, Drasdo D, Anderson ARA, Chaplain MAJ (2008) Modeling the influence of the e-cadherin-$$\\beta$$-catenin pathway in cancer cell invasion: a multiscale approach. Biophys J 95(1):155\u2013165. https:\/\/doi.org\/10.1529\/biophysj.107.114678","journal-title":"Biophys J"},{"issue":"3","key":"1654_CR39","doi-asserted-by":"publisher","first-page":"677","DOI":"10.1007\/s11538-007-9274-1","volume":"70","author":"KA Rejniak","year":"2008","unstructured":"Rejniak KA, Anderson ARA (2008) A computational study of the development of epithelial acini: I. sufficient conditions for the formation of a hollow structure. Bull Math Biol 70(3):677\u2013712. https:\/\/doi.org\/10.1007\/s11538-007-9274-1","journal-title":"Bull Math Biol"},{"issue":"5","key":"1654_CR40","doi-asserted-by":"publisher","first-page":"1450","DOI":"10.1007\/s11538-008-9308-3","volume":"70","author":"KA Rejniak","year":"2008","unstructured":"Rejniak KA, Anderson ARA (2008) A computational study of the development of epithelial acini: Ii. necessary conditions for structure and lumen stability. Bull Math Biol 70(5):1450. https:\/\/doi.org\/10.1007\/s11538-008-9308-3","journal-title":"Bull Math Biol"},{"issue":"4","key":"1654_CR41","doi-asserted-by":"publisher","first-page":"725","DOI":"10.1083\/jcb.201002047","volume":"189","author":"AE Rodriguez-Fraticelli","year":"2010","unstructured":"Rodriguez-Fraticelli AE, Vergarajauregui S, Eastburn DJ, Datta A, Alonso MA, Mostov K, Mart\u00edn-Belmonte F (2010) The cdc42 gef intersectin 2 controls mitotic spindle orientation to form the lumen during epithelial morphogenesis. J Cell Biol 189(4):725\u2013738. https:\/\/doi.org\/10.1083\/jcb.201002047","journal-title":"J Cell Biol"},{"key":"1654_CR42","doi-asserted-by":"publisher","first-page":"331","DOI":"10.1016\/j.actbio.2017.11.037","volume":"67","author":"A Rubiano","year":"2018","unstructured":"Rubiano A, Delitto D, Han S, Gerber M, Galitz C, Trevino J, Thomas RM, Hughes SJ, Simmons CS (2018) Viscoelastic properties of human pancreatic tumors and in vitro constructs to mimic mechanical properties. Acta Biomater 67:331\u2013340. https:\/\/doi.org\/10.1016\/j.actbio.2017.11.037","journal-title":"Acta Biomater"},{"issue":"6","key":"1654_CR43","doi-asserted-by":"publisher","first-page":"461","DOI":"10.1177\/030098589803500601","volume":"35","author":"KA Schafer","year":"1998","unstructured":"Schafer KA (1998) The cell cycle: a review. Vet Pathol 35(6):461\u2013478. https:\/\/doi.org\/10.1177\/030098589803500601","journal-title":"Vet Pathol"},{"key":"1654_CR44","doi-asserted-by":"publisher","first-page":"34","DOI":"10.3389\/fams.2021.680029","volume":"7","author":"S Suveges","year":"2021","unstructured":"Suveges S, Chamseddine I, Rejniak KA, Eftimie R, Trucu D (2021) Collective cell migration in a fibrous environment: a hybrid multi-scale modelling approach. Front Appl Math Stat 7:34. https:\/\/doi.org\/10.3389\/fams.2021.680029","journal-title":"Front Appl Math Stat"},{"issue":"4","key":"1654_CR45","doi-asserted-by":"publisher","first-page":"344","DOI":"10.1002\/bdrc.20106","volume":"81","author":"BC Thorne","year":"2007","unstructured":"Thorne BC, Bailey AM, DeSimone DW, Peirce SM (2007) Agent-based modeling of multicell morphogenic processes during development. Birth Defects Res C Embryo Today 81(4):344\u2013353. https:\/\/doi.org\/10.1002\/bdrc.20106","journal-title":"Birth Defects Res C Embryo Today"},{"issue":"5937","key":"1654_CR46","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1126\/science.1174294","volume":"325","author":"A Tzur","year":"2009","unstructured":"Tzur A, Kafri R, LeBleu VS, Lahav G, Kirschner MW (2009) Cell growth and size homeostasis in proliferating animal cells. Science 325(5937):167\u2013171. https:\/\/doi.org\/10.1126\/science.1174294","journal-title":"Science"},{"issue":"4","key":"1654_CR47","doi-asserted-by":"publisher","first-page":"e0195820","DOI":"10.1371\/journal.pone.0195820","volume":"13","author":"C Valero","year":"2018","unstructured":"Valero C, Amaveda H, Mora M, Garc\u00eda-Aznar JM (2018) Combined experimental and computational characterization of crosslinked collagen-based hydrogels. PLoS One 13(4):e0195820. https:\/\/doi.org\/10.1371\/journal.pone.0195820","journal-title":"PLoS One"},{"issue":"4","key":"1654_CR48","doi-asserted-by":"publisher","first-page":"401","DOI":"10.1007\/s40571-015-0082-3","volume":"2","author":"P Van Liedekerke","year":"2015","unstructured":"Van Liedekerke P, Palm MM, Jagiella N, Dirk Drasdo (2015) Simulating tissue mechanics with agent-based models: concepts, perspectives and some novel results. Comput Part Mech 2(4):401\u2013444. https:\/\/doi.org\/10.1007\/s40571-015-0082-3","journal-title":"Comput Part Mech"},{"issue":"1","key":"1654_CR49","doi-asserted-by":"publisher","first-page":"189","DOI":"10.1007\/s10237-019-01204-7","volume":"19","author":"P Van Liedekerke","year":"2020","unstructured":"Van Liedekerke P, Neitsch J, Johann T, Warmt E, Gonz\u00e0lez-Valverde I, Hoehme S, Grosser S, Kaes J, Drasdo D (2020) A quantitative high-resolution computational mechanics cell model for growing and regenerating tissues. Biomech Model Mechanobiol 19(1):189\u2013220. https:\/\/doi.org\/10.1007\/s10237-019-01204-7","journal-title":"Biomech Model Mechanobiol"},{"key":"1654_CR50","unstructured":"van Liedekerke Paul, Gannoun Lila, Loriot Axelle, Lemaigre Fr\u00e9d\u00e9ric, Drasdo Dirk (2021) Influence of cell mechanics in embryonic bile duct lumen formation: insight from quantitative modeling"},{"issue":"146","key":"1654_CR51","doi-asserted-by":"publisher","first-page":"20180415","DOI":"10.1098\/rsif.2018.0415","volume":"15","author":"G Vilanova","year":"2018","unstructured":"Vilanova G, Bur\u00e9s M, Colominas I, Gomez H (2018) Computational modelling suggests complex interactions between interstitial flow and tumour angiogenesis. J R Soc Interface 15(146):20180415. https:\/\/doi.org\/10.1098\/rsif.2018.0415","journal-title":"J R Soc Interface"},{"issue":"22","key":"1654_CR52","doi-asserted-by":"publisher","first-page":"4838","DOI":"10.1091\/mbc.e09-03-0203","volume":"20","author":"MP Wescott","year":"2009","unstructured":"Wescott MP, Rovira M, Reichert M, Von Burstin J, Means A, Leach SD, Rustgi AK (2009) Pancreatic ductal morphogenesis and the pdx1 homeodomain transcription factor. Mol Biol Cell 20(22):4838\u20134844. https:\/\/doi.org\/10.1091\/mbc.e09-03-0203","journal-title":"Mol Biol Cell"},{"issue":"3","key":"1654_CR53","doi-asserted-by":"publisher","first-page":"583","DOI":"10.1083\/jcb.200305010","volume":"163","author":"MA Wozniak","year":"2003","unstructured":"Wozniak MA, Desai R, Solski PA, Der CJ, Keely PJ (2003) Rock-generated contractility regulates breast epithelial cell differentiation in response to the physical properties of a three-dimensional collagen matrix. J Cell Biol 163(3):583\u2013595. https:\/\/doi.org\/10.1083\/jcb.200305010","journal-title":"J Cell Biol"},{"issue":"10","key":"1654_CR54","doi-asserted-by":"publisher","first-page":"e46889","DOI":"10.1371\/journal.pone.0046889","volume":"7","author":"Y-T Yeh","year":"2012","unstructured":"Yeh Y-T, Hur SS, Chang J, Wang K-C, Chiu J-J, Li Y-S, Chien S (2012) Matrix stiffness regulates endothelial cell proliferation through septin 9. PLoS One 7(10):e46889. https:\/\/doi.org\/10.1371\/journal.pone.0046889","journal-title":"PLoS One"},{"issue":"2","key":"1654_CR55","doi-asserted-by":"publisher","first-page":"275","DOI":"10.1083\/jcb.200910021","volume":"189","author":"Z Zheng","year":"2010","unstructured":"Zheng Z, Zhu H, Wan Q, Liu J, Xiao Z, Siderovski DP, Quansheng D (2010) Lgn regulates mitotic spindle orientation during epithelial morphogenesis. J Cell Biol 189(2):275\u2013288. https:\/\/doi.org\/10.1083\/jcb.200910021","journal-title":"J Cell Biol"}],"container-title":["Engineering with Computers"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00366-022-01654-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s00366-022-01654-1\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00366-022-01654-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,11,12]],"date-time":"2022-11-12T12:09:04Z","timestamp":1668254944000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s00366-022-01654-1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,5,6]]},"references-count":55,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2022,10]]}},"alternative-id":["1654"],"URL":"https:\/\/doi.org\/10.1007\/s00366-022-01654-1","relation":{},"ISSN":["0177-0667","1435-5663"],"issn-type":[{"value":"0177-0667","type":"print"},{"value":"1435-5663","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,5,6]]},"assertion":[{"value":"5 November 2021","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"25 March 2022","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"6 May 2022","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}]}}