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For: Okuda S, Inoue Y, Adachi T. Three-dimensional vertex model for simulating multicellular morphogenesis. Biophys Physicobiol 2015;12:13-20. [PMID: 27493850 PMCID: PMC4736843 DOI: 10.2142/biophysico.12.0_13] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 07/16/2015] [Indexed: 12/01/2022]  Open
Number Cited by Other Article(s)
1
Koyama H, Okumura H, Otani T, Ito AM, Nakamura K, Kato K, Fujimori T. Effective mechanical potential of cell-cell interaction in tissues harboring cavity and in cell sheet toward morphogenesis. Front Cell Dev Biol 2024;12:1414601. [PMID: 39105171 PMCID: PMC11298474 DOI: 10.3389/fcell.2024.1414601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 07/03/2024] [Indexed: 08/07/2024]  Open
2
Belousov R, Savino S, Moghe P, Hiiragi T, Rondoni L, Erzberger A. Poissonian Cellular Potts Models Reveal Nonequilibrium Kinetics of Cell Sorting. PHYSICAL REVIEW LETTERS 2024;132:248401. [PMID: 38949349 DOI: 10.1103/physrevlett.132.248401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 04/10/2024] [Indexed: 07/02/2024]
3
Kumar N, Rangel Ambriz J, Tsai K, Mim MS, Flores-Flores M, Chen W, Zartman JJ, Alber M. Balancing competing effects of tissue growth and cytoskeletal regulation during Drosophila wing disc development. Nat Commun 2024;15:2477. [PMID: 38509115 PMCID: PMC10954670 DOI: 10.1038/s41467-024-46698-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 03/06/2024] [Indexed: 03/22/2024]  Open
4
Sego TJ, Comlekoglu T, Peirce SM, Desimone DW, Glazier JA. General, open-source vertex modeling in biological applications using Tissue Forge. Sci Rep 2023;13:17886. [PMID: 37857673 PMCID: PMC10587242 DOI: 10.1038/s41598-023-45127-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 10/16/2023] [Indexed: 10/21/2023]  Open
5
Stillman NR, Mayor R. Generative models of morphogenesis in developmental biology. Semin Cell Dev Biol 2023;147:83-90. [PMID: 36754751 PMCID: PMC10615838 DOI: 10.1016/j.semcdb.2023.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/02/2023] [Accepted: 02/02/2023] [Indexed: 02/08/2023]
6
Sego T, Comlekoglu T, Peirce SM, Desimone D, Glazier JA. General, Open-Source Vertex Modeling in Biological Applications Using Tissue Forge. RESEARCH SQUARE 2023:rs.3.rs-2886960. [PMID: 37214822 PMCID: PMC10197754 DOI: 10.21203/rs.3.rs-2886960/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
7
Cohen R, Taiber S, Loza O, Kasirer S, Woland S, Sprinzak D. Precise alternating cellular pattern in the inner ear by coordinated hopping intercalations and delaminations. SCIENCE ADVANCES 2023;9:eadd2157. [PMID: 36812313 DOI: 10.1126/sciadv.add2157] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 12/19/2022] [Indexed: 06/18/2023]
8
Modelling of Tissue Invasion in Epithelial Monolayers. Life (Basel) 2023;13:life13020427. [PMID: 36836784 PMCID: PMC9964186 DOI: 10.3390/life13020427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/20/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023]  Open
9
Novel Ground-Up 3D Multicellular Simulators for Synthetic Biology CAD Integrating Stochastic Gillespie Simulations Benchmarked with Topologically Variable SBML Models. Genes (Basel) 2023;14:genes14010154. [PMID: 36672895 PMCID: PMC9859520 DOI: 10.3390/genes14010154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 12/29/2022] [Accepted: 12/30/2022] [Indexed: 01/09/2023]  Open
10
Thalheim T, Aust G, Galle J. Organoid Cultures In Silico: Tools or Toys? BIOENGINEERING (BASEL, SWITZERLAND) 2022;10:bioengineering10010050. [PMID: 36671623 PMCID: PMC9854934 DOI: 10.3390/bioengineering10010050] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/28/2022] [Accepted: 12/29/2022] [Indexed: 01/03/2023]
11
Fuji K, Tanida S, Sano M, Nonomura M, Riveline D, Honda H, Hiraiwa T. Computational approaches for simulating luminogenesis. Semin Cell Dev Biol 2022;131:173-185. [PMID: 35773151 DOI: 10.1016/j.semcdb.2022.05.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/24/2022] [Accepted: 05/24/2022] [Indexed: 12/14/2022]
12
Nishimura R, Kato K, Saida M, Kamei Y, Takeda M, Miyoshi H, Yamagata Y, Amano Y, Yonemura S. Appropriate tension sensitivity of α-catenin ensures rounding morphogenesis of epithelial spheroids. Cell Struct Funct 2022;47:55-73. [PMID: 35732428 PMCID: PMC10511042 DOI: 10.1247/csf.22014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/06/2022] [Indexed: 11/11/2022]  Open
13
Oriola D, Marin-Riera M, Anlaş K, Gritti N, Sanaki-Matsumiya M, Aalderink G, Ebisuya M, Sharpe J, Trivedi V. Arrested coalescence of multicellular aggregates. SOFT MATTER 2022;18:3771-3780. [PMID: 35511111 DOI: 10.1039/d2sm00063f] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
14
Fletcher AG, Osborne JM. Seven challenges in the multiscale modeling of multicellular tissues. WIREs Mech Dis 2022;14:e1527. [PMID: 35023326 DOI: 10.1002/wsbm.1527] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 11/23/2020] [Accepted: 03/25/2021] [Indexed: 11/11/2022]
15
Extracellular hyaluronate pressure shaped by cellular tethers drives tissue morphogenesis. Cell 2021;184:6313-6325.e18. [PMID: 34942099 PMCID: PMC8722442 DOI: 10.1016/j.cell.2021.11.025] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 09/29/2021] [Accepted: 11/15/2021] [Indexed: 12/24/2022]
16
Brown PJ, Green JEF, Binder BJ, Osborne JM. A rigid body framework for multicellular modeling. NATURE COMPUTATIONAL SCIENCE 2021;1:754-766. [PMID: 38217146 DOI: 10.1038/s43588-021-00154-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 10/08/2021] [Indexed: 01/15/2024]
17
Mishra N, Heisenberg CP. Dissecting Organismal Morphogenesis by Bridging Genetics and Biophysics. Annu Rev Genet 2021;55:209-233. [PMID: 34460295 DOI: 10.1146/annurev-genet-071819-103748] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
18
Yang Q, Xue SL, Chan CJ, Rempfler M, Vischi D, Maurer-Gutierrez F, Hiiragi T, Hannezo E, Liberali P. Cell fate coordinates mechano-osmotic forces in intestinal crypt formation. Nat Cell Biol 2021;23:733-744. [PMID: 34155381 PMCID: PMC7611267 DOI: 10.1038/s41556-021-00700-2] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 05/14/2021] [Indexed: 02/06/2023]
19
Scott LE, Griggs LA, Narayanan V, Conway DE, Lemmon CA, Weinberg SH. A hybrid model of intercellular tension and cell-matrix mechanical interactions in a multicellular geometry. Biomech Model Mechanobiol 2020;19:1997-2013. [PMID: 32193709 PMCID: PMC7502553 DOI: 10.1007/s10237-020-01321-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 03/13/2020] [Indexed: 12/18/2022]
20
Bui J, Conway DE, Heise RL, Weinberg SH. Mechanochemical Coupling and Junctional Forces during Collective Cell Migration. Biophys J 2019;117:170-183. [PMID: 31200935 DOI: 10.1016/j.bpj.2019.05.020] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 05/09/2019] [Accepted: 05/22/2019] [Indexed: 12/31/2022]  Open
21
Escribano J, Chen MB, Moeendarbary E, Cao X, Shenoy V, Garcia-Aznar JM, Kamm RD, Spill F. Balance of mechanical forces drives endothelial gap formation and may facilitate cancer and immune-cell extravasation. PLoS Comput Biol 2019;15:e1006395. [PMID: 31048903 PMCID: PMC6497229 DOI: 10.1371/journal.pcbi.1006395] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 12/10/2018] [Indexed: 11/29/2022]  Open
22
van Drongelen R, Vazquez-Faci T, Huijben TAPM, van der Zee M, Idema T. Mechanics of epithelial tissue formation. J Theor Biol 2018;454:182-189. [PMID: 29883740 DOI: 10.1016/j.jtbi.2018.06.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 05/31/2018] [Accepted: 06/03/2018] [Indexed: 01/06/2023]
23
Hashimoto A, Nagao A, Okuda S. Topological graph description of multicellular dynamics based on vertex model. J Theor Biol 2018;437:187-201. [PMID: 29080778 DOI: 10.1016/j.jtbi.2017.10.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 10/16/2017] [Accepted: 10/20/2017] [Indexed: 11/16/2022]
24
Zhu X, Yang H. Turing Instability-Driven Biofabrication of Branching Tissue Structures: A Dynamic Simulation and Analysis Based on the Reaction⁻Diffusion Mechanism . MICROMACHINES 2018;9:E109. [PMID: 30424043 PMCID: PMC6187743 DOI: 10.3390/mi9030109] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Revised: 02/20/2018] [Accepted: 03/01/2018] [Indexed: 12/17/2022]
25
Okuda S, Miura T, Inoue Y, Adachi T, Eiraku M. Combining Turing and 3D vertex models reproduces autonomous multicellular morphogenesis with undulation, tubulation, and branching. Sci Rep 2018;8:2386. [PMID: 29402913 PMCID: PMC5799218 DOI: 10.1038/s41598-018-20678-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 01/19/2018] [Indexed: 01/13/2023]  Open
26
Thalheim T, Quaas M, Herberg M, Braumann UD, Kerner C, Loeffler M, Aust G, Galle J. Linking stem cell function and growth pattern of intestinal organoids. Dev Biol 2017;433:254-261. [PMID: 29198564 DOI: 10.1016/j.ydbio.2017.10.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 09/28/2017] [Accepted: 10/13/2017] [Indexed: 01/01/2023]
27
Wen FL, Wang YC, Shibata T. Epithelial Folding Driven by Apical or Basal-Lateral Modulation: Geometric Features, Mechanical Inference, and Boundary Effects. Biophys J 2017. [PMID: 28636924 DOI: 10.1016/j.bpj.2017.05.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]  Open
28
Okuda S, Unoki K, Eiraku M, Tsubota KI. Contractile actin belt and mesh structures provide the opposite dependence of epithelial stiffness on the spontaneous curvature of constituent cells. Dev Growth Differ 2017;59:455-464. [PMID: 28707721 DOI: 10.1111/dgd.12373] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 05/10/2017] [Accepted: 05/14/2017] [Indexed: 12/31/2022]
29
Barton DL, Henkes S, Weijer CJ, Sknepnek R. Active Vertex Model for cell-resolution description of epithelial tissue mechanics. PLoS Comput Biol 2017;13:e1005569. [PMID: 28665934 PMCID: PMC5493290 DOI: 10.1371/journal.pcbi.1005569] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Accepted: 05/12/2017] [Indexed: 12/31/2022]  Open
30
Okuda S, Eiraku M. Role of molecular turnover in dynamic deformation of a three-dimensional cellular membrane. Biomech Model Mechanobiol 2017;16:1805-1818. [PMID: 28555369 PMCID: PMC5599494 DOI: 10.1007/s10237-017-0920-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 05/13/2017] [Indexed: 11/26/2022]
31
Nematbakhsh A, Sun W, Brodskiy PA, Amiri A, Narciso C, Xu Z, Zartman JJ, Alber M. Multi-scale computational study of the mechanical regulation of cell mitotic rounding in epithelia. PLoS Comput Biol 2017;13:e1005533. [PMID: 28531187 PMCID: PMC5460904 DOI: 10.1371/journal.pcbi.1005533] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 06/06/2017] [Accepted: 04/24/2017] [Indexed: 12/20/2022]  Open
32
Modeling cell apoptosis for simulating three-dimensional multicellular morphogenesis based on a reversible network reconnection framework. Biomech Model Mechanobiol 2015;15:805-16. [DOI: 10.1007/s10237-015-0724-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 08/25/2015] [Indexed: 12/11/2022]
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