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For: Rejniak KA. An immersed boundary framework for modelling the growth of individual cells: an application to the early tumour development. J Theor Biol 2007;247:186-204. [PMID: 17416390 DOI: 10.1016/j.jtbi.2007.02.019] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2006] [Revised: 02/22/2007] [Accepted: 02/26/2007] [Indexed: 10/23/2022]
Number Cited by Other Article(s)
1
Qiu Y, Gao T, Smith BR. Mechanical deformation and death of circulating tumor cells in the bloodstream. Cancer Metastasis Rev 2024:10.1007/s10555-024-10198-3. [PMID: 38980581 DOI: 10.1007/s10555-024-10198-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 06/28/2024] [Indexed: 07/10/2024]
2
Scianna M. Selected aspects of avascular tumor growth reproduced by a hybrid model of cell dynamics and chemical kinetics. Math Biosci 2024;370:109168. [PMID: 38408698 DOI: 10.1016/j.mbs.2024.109168] [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: 09/04/2023] [Revised: 02/10/2024] [Accepted: 02/23/2024] [Indexed: 02/28/2024]
3
Tervonen A, Korpela S, Nymark S, Hyttinen J, Ihalainen TO. The Effect of Substrate Stiffness on Elastic Force Transmission in the Epithelial Monolayers over Short Timescales. Cell Mol Bioeng 2023;16:475-495. [PMID: 38099211 PMCID: PMC10716100 DOI: 10.1007/s12195-023-00772-0] [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: 10/28/2022] [Accepted: 06/26/2023] [Indexed: 12/17/2023]  Open
4
Germano DPJ, Zanca A, Johnston ST, Flegg JA, Osborne JM. Free and Interfacial Boundaries in Individual-Based Models of Multicellular Biological systems. Bull Math Biol 2023;85:111. [PMID: 37805982 PMCID: PMC10560655 DOI: 10.1007/s11538-023-01214-8] [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: 06/05/2023] [Accepted: 09/11/2023] [Indexed: 10/10/2023]
5
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]
6
Jayasinghe MK, Lee CY, Tran TTT, Tan R, Chew SM, Yeo BZJ, Loh WX, Pirisinu M, Le MTN. The Role of in silico Research in Developing Nanoparticle-Based Therapeutics. Front Digit Health 2022;4:838590. [PMID: 35373184 PMCID: PMC8965754 DOI: 10.3389/fdgth.2022.838590] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 02/16/2022] [Indexed: 12/12/2022]  Open
7
Van Liedekerke P, Gannoun L, Loriot A, Johann T, Lemaigre FP, Drasdo D. Quantitative modeling identifies critical cell mechanics driving bile duct lumen formation. PLoS Comput Biol 2022;18:e1009653. [PMID: 35180209 PMCID: PMC8856558 DOI: 10.1371/journal.pcbi.1009653] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 11/16/2021] [Indexed: 02/07/2023]  Open
8
de los Reyes AA, Kim Y. Optimal regulation of tumour-associated neutrophils in cancer progression. ROYAL SOCIETY OPEN SCIENCE 2022;9:210705. [PMID: 35127110 PMCID: PMC8808100 DOI: 10.1098/rsos.210705] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 11/19/2021] [Indexed: 06/14/2023]
9
Mathias S, Coulier A, Hellander A. CBMOS: a GPU-enabled Python framework for the numerical study of center-based models. BMC Bioinformatics 2022;23:55. [PMID: 35100968 PMCID: PMC8805507 DOI: 10.1186/s12859-022-04575-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 01/11/2022] [Indexed: 11/24/2022]  Open
10
Rey JA, Ewing JR, Sarntinoranont M. A computational model of glioma reveals opposing, stiffness-sensitive effects of leaky vasculature and tumor growth on tissue mechanical stress and porosity. Biomech Model Mechanobiol 2021;20:1981-2000. [PMID: 34363553 DOI: 10.1007/s10237-021-01488-8] [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: 10/20/2020] [Accepted: 06/29/2021] [Indexed: 11/29/2022]
11
Balogh P, Gounley J, Roychowdhury S, Randles A. A data-driven approach to modeling cancer cell mechanics during microcirculatory transport. Sci Rep 2021;11:15232. [PMID: 34315934 PMCID: PMC8316468 DOI: 10.1038/s41598-021-94445-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 07/09/2021] [Indexed: 02/07/2023]  Open
12
Vasilaki D, Bakopoulou A, Tsouknidas A, Johnstone E, Michalakis K. Biophysical interactions between components of the tumor microenvironment promote metastasis. Biophys Rev 2021;13:339-357. [PMID: 34168685 PMCID: PMC8214652 DOI: 10.1007/s12551-021-00811-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 05/03/2021] [Indexed: 02/07/2023]  Open
13
Macnamara CK. Biomechanical modelling of cancer: Agent‐based force‐based models of solid tumours within the context of the tumour microenvironment. COMPUTATIONAL AND SYSTEMS ONCOLOGY 2021. [DOI: 10.1002/cso2.1018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]  Open
14
Puleri DF, Balogh P, Randles A. Computational models of cancer cell transport through the microcirculation. Biomech Model Mechanobiol 2021;20:1209-1230. [PMID: 33765196 DOI: 10.1007/s10237-021-01452-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 03/08/2021] [Indexed: 02/07/2023]
15
Xiao W, Zhang H, Luo K, Mao C, Fan J. Immersed boundary method for multiphase transport phenomena. REV CHEM ENG 2020. [DOI: 10.1515/revce-2019-0076] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
16
Mathias S, Coulier A, Bouchnita A, Hellander A. Impact of Force Function Formulations on the Numerical Simulation of Centre-Based Models. Bull Math Biol 2020;82:132. [PMID: 33025278 PMCID: PMC7538447 DOI: 10.1007/s11538-020-00810-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 09/21/2020] [Indexed: 12/17/2022]
17
Metzcar J, Wang Y, Heiland R, Macklin P. A Review of Cell-Based Computational Modeling in Cancer Biology. JCO Clin Cancer Inform 2020;3:1-13. [PMID: 30715927 PMCID: PMC6584763 DOI: 10.1200/cci.18.00069] [Citation(s) in RCA: 157] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]  Open
18
Van Liedekerke P, Neitsch J, Johann T, Warmt E, Gonzàlez-Valverde I, Hoehme S, Grosser S, Kaes J, Drasdo D. A quantitative high-resolution computational mechanics cell model for growing and regenerating tissues. Biomech Model Mechanobiol 2019;19:189-220. [PMID: 31749071 PMCID: PMC7005086 DOI: 10.1007/s10237-019-01204-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 07/16/2019] [Indexed: 12/19/2022]
19
Karolak A, Poonja S, Rejniak KA. Morphophenotypic classification of tumor organoids as an indicator of drug exposure and penetration potential. PLoS Comput Biol 2019;15:e1007214. [PMID: 31310602 PMCID: PMC6660094 DOI: 10.1371/journal.pcbi.1007214] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 07/26/2019] [Accepted: 06/27/2019] [Indexed: 12/21/2022]  Open
20
Karolak A, Markov DA, McCawley LJ, Rejniak KA. Towards personalized computational oncology: from spatial models of tumour spheroids, to organoids, to tissues. J R Soc Interface 2019;15:rsif.2017.0703. [PMID: 29367239 DOI: 10.1098/rsif.2017.0703] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 01/02/2018] [Indexed: 02/06/2023]  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
Chen Y, Lowengrub JS. Tumor growth and calcification in evolving microenvironmental geometries. J Theor Biol 2019;463:138-154. [PMID: 30528340 DOI: 10.1016/j.jtbi.2018.12.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 11/27/2018] [Accepted: 12/03/2018] [Indexed: 10/27/2022]
23
Engblom S, Wilson DB, Baker RE. Scalable population-level modelling of biological cells incorporating mechanics and kinetics in continuous time. ROYAL SOCIETY OPEN SCIENCE 2018;5:180379. [PMID: 30225024 PMCID: PMC6124129 DOI: 10.1098/rsos.180379] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 06/18/2018] [Indexed: 06/08/2023]
24
Siregar P, Julen N, Hufnagl P, Mutter G. A general framework dedicated to computational morphogenesis Part I - Constitutive equations. Biosystems 2018;173:298-313. [PMID: 30005999 DOI: 10.1016/j.biosystems.2018.07.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 05/30/2018] [Accepted: 07/05/2018] [Indexed: 01/14/2023]
25
Cell signaling heterogeneity is modulated by both cell-intrinsic and -extrinsic mechanisms: An integrated approach to understanding targeted therapy. PLoS Biol 2018. [PMID: 29522507 PMCID: PMC5844524 DOI: 10.1371/journal.pbio.2002930] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]  Open
26
Mosaffa P, Rodríguez-Ferran A, Muñoz JJ. Hybrid cell-centred/vertex model for multicellular systems with equilibrium-preserving remodelling. INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN BIOMEDICAL ENGINEERING 2018;34:e2928. [PMID: 28898926 DOI: 10.1002/cnm.2928] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 09/06/2017] [Accepted: 09/07/2017] [Indexed: 06/07/2023]
27
Poleszczuk J, Macklin P, Enderling H. Agent-Based Modeling of Cancer Stem Cell Driven Solid Tumor Growth. Methods Mol Biol 2018;1516:335-346. [PMID: 27044046 DOI: 10.1007/7651_2016_346] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
28
Multerer MD, Wittwer LD, Stopka A, Barac D, Lang C, Iber D. Simulation of Morphogen and Tissue Dynamics. Methods Mol Biol 2018;1863:223-250. [PMID: 30324601 DOI: 10.1007/978-1-4939-8772-6_13] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
29
Zhao J, Cao Y, DiPietro LA, Liang J. Dynamic cellular finite-element method for modelling large-scale cell migration and proliferation under the control of mechanical and biochemical cues: a study of re-epithelialization. J R Soc Interface 2017;14:rsif.2016.0959. [PMID: 28404867 DOI: 10.1098/rsif.2016.0959] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 03/15/2017] [Indexed: 01/07/2023]  Open
30
Fletcher AG, Cooper F, Baker RE. Mechanocellular models of epithelial morphogenesis. Philos Trans R Soc Lond B Biol Sci 2017;372:rstb.2015.0519. [PMID: 28348253 DOI: 10.1098/rstb.2015.0519] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/31/2016] [Indexed: 01/13/2023]  Open
31
Iwasaki WM, Innan H. Simulation framework for generating intratumor heterogeneity patterns in a cancer cell population. PLoS One 2017;12:e0184229. [PMID: 28877206 PMCID: PMC5587296 DOI: 10.1371/journal.pone.0184229] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 08/21/2017] [Indexed: 11/18/2022]  Open
32
Leroy-Lerêtre M, Dimarco G, Cazales M, Boizeau ML, Ducommun B, Lobjois V, Degond P. Are Tumor Cell Lineages Solely Shaped by Mechanical Forces? Bull Math Biol 2017;79:2356-2393. [PMID: 28852950 PMCID: PMC5597711 DOI: 10.1007/s11538-017-0333-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Accepted: 08/08/2017] [Indexed: 12/19/2022]
33
Norton KA, Wallace T, Pandey NB, Popel AS. An agent-based model of triple-negative breast cancer: the interplay between chemokine receptor CCR5 expression, cancer stem cells, and hypoxia. BMC SYSTEMS BIOLOGY 2017;11:68. [PMID: 28693495 PMCID: PMC5504656 DOI: 10.1186/s12918-017-0445-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 06/30/2017] [Indexed: 12/19/2022]
34
Feng H, Ou BC, Zhao JK, Yin S, Lu AG, Oechsle E, Thasler WE. Homogeneous pancreatic cancer spheroids mimic growth pattern of circulating tumor cell clusters and macrometastases: displaying heterogeneity and crater-like structure on inner layer. J Cancer Res Clin Oncol 2017;143:1771-1786. [PMID: 28497169 DOI: 10.1007/s00432-017-2434-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 04/21/2017] [Indexed: 12/14/2022]
35
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
36
Dynamics of cancerous tissue correlates with invasiveness. Sci Rep 2017;7:43800. [PMID: 28262796 PMCID: PMC5338316 DOI: 10.1038/srep43800] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 01/30/2017] [Indexed: 11/09/2022]  Open
37
Lee W, Lim S, Kim Y. The role of myosin II in glioma invasion: A mathematical model. PLoS One 2017;12:e0171312. [PMID: 28166231 PMCID: PMC5293275 DOI: 10.1371/journal.pone.0171312] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 01/18/2017] [Indexed: 01/09/2023]  Open
38
Osborne JM, Fletcher AG, Pitt-Francis JM, Maini PK, Gavaghan DJ. Comparing individual-based approaches to modelling the self-organization of multicellular tissues. PLoS Comput Biol 2017;13:e1005387. [PMID: 28192427 PMCID: PMC5330541 DOI: 10.1371/journal.pcbi.1005387] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Revised: 02/28/2017] [Accepted: 01/28/2017] [Indexed: 12/28/2022]  Open
39
Lou Y, Chen Y. Simulating the multicellular homeostasis with a cell-based discrete receptor dynamics model: The non-mutational origin of cancer and aging. J Theor Biol 2016;404:15-29. [PMID: 27196967 DOI: 10.1016/j.jtbi.2016.04.035] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Revised: 04/26/2016] [Accepted: 04/29/2016] [Indexed: 01/07/2023]
40
Dhulekar N, Ray S, Yuan D, Baskaran A, Oztan B, Larsen M, Yener B. Prediction of Growth Factor-Dependent Cleft Formation During Branching Morphogenesis Using A Dynamic Graph-Based Growth Model. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2016;13:350-64. [PMID: 27070978 PMCID: PMC4917296 DOI: 10.1109/tcbb.2015.2452916] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
41
Rejniak KA. Circulating Tumor Cells: When a Solid Tumor Meets a Fluid Microenvironment. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016;936:93-106. [PMID: 27739044 PMCID: PMC5113997 DOI: 10.1007/978-3-319-42023-3_5] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
42
Abeddoust M, Shamloo A. A model for cell density effect on stress fiber alignment and collective directional migration. Phys Biol 2015;12:066023. [DOI: 10.1088/1478-3975/12/6/066023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
43
Three-dimensional simulations of the cell growth and cytokinesis using the immersed boundary method. Math Biosci 2015;271:118-27. [PMID: 26620886 DOI: 10.1016/j.mbs.2015.11.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 09/12/2015] [Accepted: 11/16/2015] [Indexed: 11/22/2022]
44
Kachalo S, Naveed H, Cao Y, Zhao J, Liang J. Mechanical model of geometric cell and topological algorithm for cell dynamics from single-cell to formation of monolayered tissues with pattern. PLoS One 2015;10:e0126484. [PMID: 25974182 PMCID: PMC4431879 DOI: 10.1371/journal.pone.0126484] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 04/02/2015] [Indexed: 11/19/2022]  Open
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Simulation Frameworks for Morphogenetic Problems. COMPUTATION 2015. [DOI: 10.3390/computation3020197] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Tanaka S, Sichau D, Iber D. LBIBCell: a cell-based simulation environment for morphogenetic problems. Bioinformatics 2015;31:2340-7. [PMID: 25770313 DOI: 10.1093/bioinformatics/btv147] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 03/10/2015] [Indexed: 11/13/2022]  Open
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Powathil GG, Swat M, Chaplain MA. Systems oncology: Towards patient-specific treatment regimes informed by multiscale mathematical modelling. Semin Cancer Biol 2015;30:13-20. [DOI: 10.1016/j.semcancer.2014.02.003] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 02/06/2014] [Indexed: 10/25/2022]
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Liang J, Cao Y, Gürsoy G, Naveed H, Terebus A, Zhao J. Multiscale Modeling of Cellular Epigenetic States: Stochasticity in Molecular Networks, Chromatin Folding in Cell Nuclei, and Tissue Pattern Formation of Cells. Crit Rev Biomed Eng 2015;43:323-46. [PMID: 27480462 PMCID: PMC4976639 DOI: 10.1615/critrevbiomedeng.2016016559] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Simulating tissue morphogenesis and signaling. Methods Mol Biol 2015;1189:323-38. [PMID: 25245703 DOI: 10.1007/978-1-4939-1164-6_21] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Mkrtchyan A, Åström J, Karttunen M. A new model for cell division and migration with spontaneous topology changes. SOFT MATTER 2014;10:4332-4339. [PMID: 24793724 DOI: 10.1039/c4sm00489b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
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