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Nguyen KC, Jameson CD, Baldwin SA, Nardini JT, Smith RC, Haugh JM, Flores KB. Quantifying collective motion patterns in mesenchymal cell populations using topological data analysis and agent-based modeling. Math Biosci 2024; 370:109158. [PMID: 38373479 DOI: 10.1016/j.mbs.2024.109158] [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: 09/06/2023] [Revised: 02/06/2024] [Accepted: 02/11/2024] [Indexed: 02/21/2024]
Abstract
Fibroblasts in a confluent monolayer are known to adopt elongated morphologies in which cells are oriented parallel to their neighbors. We collected and analyzed new microscopy movies to show that confluent fibroblasts are motile and that neighboring cells often move in anti-parallel directions in a collective motion phenomenon we refer to as "fluidization" of the cell population. We used machine learning to perform cell tracking for each movie and then leveraged topological data analysis (TDA) to show that time-varying point-clouds generated by the tracks contain significant topological information content that is driven by fluidization, i.e., the anti-parallel movement of individual neighboring cells and neighboring groups of cells over long distances. We then utilized the TDA summaries extracted from each movie to perform Bayesian parameter estimation for the D'Orsgona model, an agent-based model (ABM) known to produce a wide array of different patterns, including patterns that are qualitatively similar to fluidization. Although the D'Orsgona ABM is a phenomenological model that only describes inter-cellular attraction and repulsion, the estimated region of D'Orsogna model parameter space was consistent across all movies, suggesting that a specific level of inter-cellular repulsion force at close range may be a mechanism that helps drive fluidization patterns in confluent mesenchymal cell populations.
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Affiliation(s)
- Kyle C Nguyen
- Biomathematics Graduate Program, North Carolina State University, Raleigh, NC 27607, USA; Center for Research in Scientific Computation, North Carolina State University, Raleigh, NC 27607, USA.
| | | | - Scott A Baldwin
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - John T Nardini
- Department of Mathematics and Statistics, The College of New Jersey, Ewing, NJ 08628, USA
| | - Ralph C Smith
- Department of Mathematics, North Carolina State University, Raleigh, NC 27607, USA
| | - Jason M Haugh
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Kevin B Flores
- Center for Research in Scientific Computation, North Carolina State University, Raleigh, NC 27607, USA; Department of Mathematics, North Carolina State University, Raleigh, NC 27607, USA
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BIO-LGCA: A cellular automaton modelling class for analysing collective cell migration. PLoS Comput Biol 2021; 17:e1009066. [PMID: 34129639 PMCID: PMC8232544 DOI: 10.1371/journal.pcbi.1009066] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 06/25/2021] [Accepted: 05/11/2021] [Indexed: 11/19/2022] Open
Abstract
Collective dynamics in multicellular systems such as biological organs and tissues plays a key role in biological development, regeneration, and pathological conditions. Collective tissue dynamics—understood as population behaviour arising from the interplay of the constituting discrete cells—can be studied with on- and off-lattice agent-based models. However, classical on-lattice agent-based models, also known as cellular automata, fail to replicate key aspects of collective migration, which is a central instance of collective behaviour in multicellular systems. To overcome drawbacks of classical on-lattice models, we introduce an on-lattice, agent-based modelling class for collective cell migration, which we call biological lattice-gas cellular automaton (BIO-LGCA). The BIO-LGCA is characterised by synchronous time updates, and the explicit consideration of individual cell velocities. While rules in classical cellular automata are typically chosen ad hoc, rules for cell-cell and cell-environment interactions in the BIO-LGCA can also be derived from experimental cell migration data or biophysical laws for individual cell migration. We introduce elementary BIO-LGCA models of fundamental cell interactions, which may be combined in a modular fashion to model complex multicellular phenomena. We exemplify the mathematical mean-field analysis of specific BIO-LGCA models, which allows to explain collective behaviour. The first example predicts the formation of clusters in adhesively interacting cells. The second example is based on a novel BIO-LGCA combining adhesive interactions and alignment. For this model, our analysis clarifies the nature of the recently discovered invasion plasticity of breast cancer cells in heterogeneous environments. Pattern formation during embryonic development and pathological tissue dynamics, such as cancer invasion, emerge from individual intercellular interactions. In order to study the impact of single cell dynamics and cell-cell interactions on tissue behaviour, one needs to develop space-time-dependent on- or off-lattice agent-based models (ABMs), which consider the behaviour of individual cells. However, classical on-lattice agent-based models also known as cellular automata fail to replicate key aspects of collective migration, which is a central instance of collective behaviour in multicellular systems. Here, we present the rule- and lattice-based BIO-LGCA modelling class which allows for (i) rigorous derivation of rules from biophysical laws and/or experimental data, (ii) mathematical analysis of collective migration, and (iii) computationally efficient simulations.
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Jiang Q, Fu X, Yan S, Li R, Du W, Cao Z, Qian F, Grima R. Neural network aided approximation and parameter inference of non-Markovian models of gene expression. Nat Commun 2021; 12:2618. [PMID: 33976195 PMCID: PMC8113478 DOI: 10.1038/s41467-021-22919-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 04/07/2021] [Indexed: 02/03/2023] Open
Abstract
Non-Markovian models of stochastic biochemical kinetics often incorporate explicit time delays to effectively model large numbers of intermediate biochemical processes. Analysis and simulation of these models, as well as the inference of their parameters from data, are fraught with difficulties because the dynamics depends on the system's history. Here we use an artificial neural network to approximate the time-dependent distributions of non-Markovian models by the solutions of much simpler time-inhomogeneous Markovian models; the approximation does not increase the dimensionality of the model and simultaneously leads to inference of the kinetic parameters. The training of the neural network uses a relatively small set of noisy measurements generated by experimental data or stochastic simulations of the non-Markovian model. We show using a variety of models, where the delays stem from transcriptional processes and feedback control, that the Markovian models learnt by the neural network accurately reflect the stochastic dynamics across parameter space.
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Affiliation(s)
- Qingchao Jiang
- grid.28056.390000 0001 2163 4895Key Laboratory of Smart Manufacturing in Energy Chemical Process, Ministry of Education, East China University of Science and Technology, Shanghai, China
| | - Xiaoming Fu
- grid.28056.390000 0001 2163 4895Key Laboratory of Smart Manufacturing in Energy Chemical Process, Ministry of Education, East China University of Science and Technology, Shanghai, China ,grid.4305.20000 0004 1936 7988School of Biological Sciences, The University of Edinburgh, Edinburgh, Scotland UK
| | - Shifu Yan
- grid.28056.390000 0001 2163 4895Key Laboratory of Smart Manufacturing in Energy Chemical Process, Ministry of Education, East China University of Science and Technology, Shanghai, China
| | - Runlai Li
- grid.4280.e0000 0001 2180 6431Department of Chemistry, National University of Singapore, Singapore, Singapore
| | - Wenli Du
- grid.28056.390000 0001 2163 4895Key Laboratory of Smart Manufacturing in Energy Chemical Process, Ministry of Education, East China University of Science and Technology, Shanghai, China
| | - Zhixing Cao
- grid.28056.390000 0001 2163 4895Key Laboratory of Smart Manufacturing in Energy Chemical Process, Ministry of Education, East China University of Science and Technology, Shanghai, China ,grid.28056.390000 0001 2163 4895State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Feng Qian
- grid.28056.390000 0001 2163 4895Key Laboratory of Smart Manufacturing in Energy Chemical Process, Ministry of Education, East China University of Science and Technology, Shanghai, China
| | - Ramon Grima
- grid.4305.20000 0004 1936 7988School of Biological Sciences, The University of Edinburgh, Edinburgh, Scotland UK
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Nardini JT, Baker RE, Simpson MJ, Flores KB. Learning differential equation models from stochastic agent-based model simulations. J R Soc Interface 2021; 18:20200987. [PMID: 33726540 PMCID: PMC8086865 DOI: 10.1098/rsif.2020.0987] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 02/22/2021] [Indexed: 12/15/2022] Open
Abstract
Agent-based models provide a flexible framework that is frequently used for modelling many biological systems, including cell migration, molecular dynamics, ecology and epidemiology. Analysis of the model dynamics can be challenging due to their inherent stochasticity and heavy computational requirements. Common approaches to the analysis of agent-based models include extensive Monte Carlo simulation of the model or the derivation of coarse-grained differential equation models to predict the expected or averaged output from the agent-based model. Both of these approaches have limitations, however, as extensive computation of complex agent-based models may be infeasible, and coarse-grained differential equation models can fail to accurately describe model dynamics in certain parameter regimes. We propose that methods from the equation learning field provide a promising, novel and unifying approach for agent-based model analysis. Equation learning is a recent field of research from data science that aims to infer differential equation models directly from data. We use this tutorial to review how methods from equation learning can be used to learn differential equation models from agent-based model simulations. We demonstrate that this framework is easy to use, requires few model simulations, and accurately predicts model dynamics in parameter regions where coarse-grained differential equation models fail to do so. We highlight these advantages through several case studies involving two agent-based models that are broadly applicable to biological phenomena: a birth-death-migration model commonly used to explore cell biology experiments and a susceptible-infected-recovered model of infectious disease spread.
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Affiliation(s)
- John T. Nardini
- North Carolina State University, Mathematics, Raleigh, NC, USA
| | - Ruth E. Baker
- Mathematical Institute, University of Oxford, Oxford, UK
| | - Matthew J. Simpson
- School of Mathematical Sciences, Queensland University of Technology, Brisbane 4001, Australia
| | - Kevin B. Flores
- North Carolina State University, Mathematics, Raleigh, NC, USA
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Hywood JD, Rice G, Pageon SV, Read MN, Biro M. Detection and characterization of chemotaxis without cell tracking. J R Soc Interface 2021; 18:20200879. [PMID: 33715400 PMCID: PMC8086846 DOI: 10.1098/rsif.2020.0879] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 02/15/2021] [Indexed: 02/06/2023] Open
Abstract
Swarming has been observed in various biological systems from collective animal movements to immune cells. In the cellular context, swarming is driven by the secretion of chemotactic factors. Despite the critical role of chemotactic swarming, few methods to robustly identify and quantify this phenomenon exist. Here, we present a novel method for the analysis of time series of positional data generated from realizations of agent-based processes. We convert the positional data for each individual time point to a function measuring agent aggregation around a given area of interest, hence generating a functional time series. The functional time series, and a more easily visualized swarming metric of agent aggregation derived from these functions, provide useful information regarding the evolution of the underlying process over time. We extend our method to build upon the modelling of collective motility using drift-diffusion partial differential equations (PDEs). Using a functional linear model, we are able to use the functional time series to estimate the drift and diffusivity terms associated with the underlying PDE. By producing an accurate estimate for the drift coefficient, we can infer the strength and range of attraction or repulsion exerted on agents, as in chemotaxis. Our approach relies solely on using agent positional data. The spatial distribution of diffusing chemokines is not required, nor do individual agents need to be tracked over time. We demonstrate our approach using random walk simulations of chemotaxis and experiments investigating cytotoxic T cells interacting with tumouroids.
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Affiliation(s)
- Jack D. Hywood
- Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Gregory Rice
- Department of Statistics and Actuarial Science, University of Waterloo, Waterloo, Canada
| | - Sophie V. Pageon
- EMBL Australia, Single Molecule Science node, School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Mark N. Read
- School of Computer Science & Charles Perkins Centre, University of Sydney, Sydney, Australia
| | - Maté Biro
- EMBL Australia, Single Molecule Science node, School of Medical Sciences, University of New South Wales, Sydney, Australia
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Voss-Böhme A, Gerisch A. Multi-Scale Analysis of Contact-Dependent Interaction in Tissue Aggregation and Invasion. SYSTEMS MEDICINE 2021. [DOI: 10.1016/b978-0-12-801238-3.11449-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Tambyah TA, Murphy RJ, Buenzli PR, Simpson MJ. A free boundary mechanobiological model of epithelial tissues. Proc Math Phys Eng Sci 2020; 476:20200528. [PMID: 33362419 PMCID: PMC7735320 DOI: 10.1098/rspa.2020.0528] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/21/2020] [Indexed: 12/12/2022] Open
Abstract
In this study, we couple intracellular signalling and cell-based mechanical properties to develop a novel free boundary mechanobiological model of epithelial tissue dynamics. Mechanobiological coupling is introduced at the cell level in a discrete modelling framework, and new reaction-diffusion equations are derived to describe tissue-level outcomes. The free boundary evolves as a result of the underlying biological mechanisms included in the discrete model. To demonstrate the accuracy of the continuum model, we compare numerical solutions of the discrete and continuum models for two different signalling pathways. First, we study the Rac-Rho pathway where cell- and tissue-level mechanics are directly related to intracellular signalling. Second, we study an activator-inhibitor system which gives rise to spatial and temporal patterning related to Turing patterns. In all cases, the continuum model and free boundary condition accurately reflect the cell-level processes included in the discrete model.
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Affiliation(s)
| | | | | | - Matthew J. Simpson
- School of Mathematical Sciences, Queensland University of Technology, Brisbane, Australia
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9
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Matsiaka OM, Baker RE, Simpson MJ. Continuum descriptions of spatial spreading for heterogeneous cell populations: Theory and experiment. J Theor Biol 2019; 482:109997. [PMID: 31491498 DOI: 10.1016/j.jtbi.2019.109997] [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: 05/28/2019] [Revised: 08/16/2019] [Accepted: 09/03/2019] [Indexed: 11/19/2022]
Abstract
Variability in cell populations is frequently observed in both in vitro and in vivo settings. Intrinsic differences within populations of cells, such as differences in cell sizes or differences in rates of cell motility, can be present even within a population of cells from the same cell line. We refer to this variability as cell heterogeneity. Mathematical models of cell migration, for example, in the context of tumour growth and metastatic invasion, often account for both undirected (random) migration and directed migration that is mediated by cell-to-cell contacts and cell-to-cell adhesion. A key feature of standard models is that they often assume that the population is composed of identical cells with constant properties. This leads to relatively simple single-species homogeneous models that neglect the role of heterogeneity. In this work, we use a continuum modelling approach to explore the role of heterogeneity in spatial spreading of cell populations. We employ a three-species heterogeneous model of cell motility that explicitly incorporates different types of experimentally-motivated heterogeneity in cell sizes: (i) monotonically decreasing; (ii) uniform; (iii) non-monotonic; and (iv) monotonically increasing distributions of cell size. Comparing the density profiles generated by the three-species heterogeneous model with density profiles predicted by a more standard single-species homogeneous model reveals that when we are dealing with monotonically decreasing and uniform distributions a simple and computationally efficient single-species homogeneous model can be remarkably accurate in describing the evolution of a heterogeneous cell population. In contrast, we find that the simpler single-species homogeneous model performs relatively poorly when applied to non-monotonic and monotonically increasing distributions of cell sizes. Additional results for heterogeneity in parameters describing both undirected and directed cell migration are also considered, and we find that similar results apply.
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Affiliation(s)
- Oleksii M Matsiaka
- School of Mathematical Sciences, Queensland University of Technology (QUT) Brisbane, Queensland, Australia
| | - Ruth E Baker
- Mathematical Institute, University of Oxford, Radcliffe Observatory Quarter, Woodstock Road, Oxford, United Kingdom
| | - Matthew J Simpson
- School of Mathematical Sciences, Queensland University of Technology (QUT) Brisbane, Queensland, Australia.
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Matsiaka OM, Baker RE, Shah ET, Simpson MJ. Mechanistic and experimental models of cell migration reveal the importance of cell-to-cell pushing in cell invasion. Biomed Phys Eng Express 2019. [DOI: 10.1088/2057-1976/ab1b01] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Gavagnin E, Ford MJ, Mort RL, Rogers T, Yates CA. The invasion speed of cell migration models with realistic cell cycle time distributions. J Theor Biol 2018; 481:91-99. [PMID: 30219568 DOI: 10.1016/j.jtbi.2018.09.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 09/07/2018] [Accepted: 09/10/2018] [Indexed: 01/02/2023]
Abstract
Cell proliferation is typically incorporated into stochastic mathematical models of cell migration by assuming that cell divisions occur after an exponentially distributed waiting time. Experimental observations, however, show that this assumption is often far from the real cell cycle time distribution (CCTD). Recent studies have suggested an alternative approach to modelling cell proliferation based on a multi-stage representation of the CCTD. In this paper we investigate the connection between the CCTD and the speed of the collective invasion. We first state a result for a general CCTD, which allows the computation of the invasion speed using the Laplace transform of the CCTD. We use this to deduce the range of speeds for the general case. We then focus on the more realistic case of multi-stage models, using both a stochastic agent-based model and a set of reaction-diffusion equations for the cells' average density. By studying the corresponding travelling wave solutions, we obtain an analytical expression for the speed of invasion for a general N-stage model with identical transition rates, in which case the resulting cell cycle times are Erlang distributed. We show that, for a general N-stage model, the Erlang distribution and the exponential distribution lead to the minimum and maximum invasion speed, respectively. This result allows us to determine the range of possible invasion speeds in terms of the average proliferation time for any multi-stage model.
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Affiliation(s)
- Enrico Gavagnin
- Department of Mathematical Sciences University of Bath, Claverton Down, Bath, BA2 7AY, UK.
| | - Matthew J Ford
- Centre for Research in Reproduction and Development McGill University, Montréal, H3G 1Y6, Québec
| | - Richard L Mort
- Division of Biomedical and Life Sciences Faculty of Health and Medicine Lancaster University, Bailrigg, Lancaster LA1 4YG, UK
| | - Tim Rogers
- Department of Mathematical Sciences University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Christian A Yates
- Department of Mathematical Sciences University of Bath, Claverton Down, Bath, BA2 7AY, UK
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Haridas P, Browning AP, McGovern JA, Sean McElwain DL, Simpson MJ. Three-dimensional experiments and individual based simulations show that cell proliferation drives melanoma nest formation in human skin tissue. BMC SYSTEMS BIOLOGY 2018; 12:34. [PMID: 29587750 PMCID: PMC5872522 DOI: 10.1186/s12918-018-0559-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 03/06/2018] [Indexed: 02/07/2023]
Abstract
Background Melanoma can be diagnosed by identifying nests of cells on the skin surface. Understanding the processes that drive nest formation is important as these processes could be potential targets for new cancer drugs. Cell proliferation and cell migration are two potential mechanisms that could conceivably drive melanoma nest formation. However, it is unclear which one of these two putative mechanisms plays a dominant role in driving nest formation. Results We use a suite of three-dimensional (3D) experiments in human skin tissue and a parallel series of 3D individual-based simulations to explore whether cell migration or cell proliferation plays a dominant role in nest formation. In the experiments we measure nest formation in populations of irradiated (non-proliferative) and non-irradiated (proliferative) melanoma cells, cultured together with primary keratinocyte and fibroblast cells on a 3D experimental human skin model. Results show that nest size depends on initial cell number and is driven primarily by cell proliferation rather than cell migration. Conclusions Nest size depends on cell number, and is driven primarily by cell proliferation rather than cell migration. All experimental results are consistent with simulation data from a 3D individual based model (IBM) of cell migration and cell proliferation. Electronic supplementary material The online version of this article (10.1186/s12918-018-0559-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Parvathi Haridas
- Institute of Health and Biomedical Innovation, Queensland University of Technology (QUT), Kelvin Grove, 4059, Australia.,School of Mathematical Sciences, QUT, Brisbane, 4001, Australia
| | | | - Jacqui A McGovern
- Institute of Health and Biomedical Innovation, Queensland University of Technology (QUT), Kelvin Grove, 4059, Australia
| | - D L Sean McElwain
- Institute of Health and Biomedical Innovation, Queensland University of Technology (QUT), Kelvin Grove, 4059, Australia.,School of Mathematical Sciences, QUT, Brisbane, 4001, Australia
| | - Matthew J Simpson
- Institute of Health and Biomedical Innovation, Queensland University of Technology (QUT), Kelvin Grove, 4059, Australia. .,School of Mathematical Sciences, QUT, Brisbane, 4001, Australia.
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Discrete and Continuum Approximations for Collective Cell Migration in a Scratch Assay with Cell Size Dynamics. Bull Math Biol 2018; 80:738-757. [DOI: 10.1007/s11538-018-0398-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 01/19/2018] [Indexed: 10/18/2022]
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