- Johnston A, Baker RE, Simpson MJ (2025) Efficient inference for differential equation models without numerical solvers.
- Li Y, Simpson MJ, Wang C (2025) Lattice-based stochastic models motivate non-linear diffusion descriptions of memory-based dispersal.
- Warne DJ, Crossman K, Heron GEM, Sharp JA, Jin W, Wu P, Simpson MJ, Mengersen K, Ortiz J-C (2025) Mathematical modelling and uncertainty quantification for analysis of biphasic coral reef recovery patterns.
- Simpson MJ, Baker RE (2025) Parameter identifiability, parameter estimation and model prediction for differential equation models.
- Mills E, Clark GF, Simpson MJ, Baird M, Adams MP (2025) A generalised sigmoid growth model with energy dependence: application to quantify the tipping point for Antarctic shallow seabed algae.
Publications
- Plank MJ, Simpson MJ, Baker RE (2025) Random walk models in the life sciences: including births, deaths and local interactions. Journal of the Royal Society Interface. 22, 20240422.
- Buenzli PR, Kuba S, Murphy RJ, Simpson MJ (2025) Mechanical cell interactions on curved interfaces. Bulletin of Mathematical Biology. 87, 29.
- Liu Y, Warne DJ, Simpson MJ (2024) Likelihood-based inference, identifiability and prediction using count data from lattice-based random walk models. Physical Review E. 110, 044405.
- Plank MJ, Simpson MJ (2024) Structured methods for parameter inference and uncertainty quantification for mechanistic models in the life sciences. Royal Society Open Science. 11, 240733.
- Simpson MJ, RC Laubenbacher, RE Baker (2024) Make the most of your society journal. Bulletin of Mathematical Biology. 86, 120.
- Simpson MJ, McCue SW (2024) Fisher-KPP-type models of biological invasion: Open source computational tools, key concepts and analysis. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 480, 20240186.
- Simpson MJ, Rahman N, Tam AKY (2024) Front stability of infinitely steep travelling waves in population biology. Journal of Physics A: Mathematical and Theoretical. 57, 315601.
- Simpson MJ, Maclaren OJ (2024) Making predictions using poorly identified mathematical models. Bulletin of Mathematical Biology. 86, 82.
- Simpson MJ, Murphy KM, McCue SW, Buenzli PR (2024) Discrete and continuous mathematical models of sharp-fronted collective cell migration and invasion. Royal Society Open Science. 11, 240126.
- Murphy RJ, Maclaren OJ, Simpson MJ (2024) Implementing measurement error models with mechanistic mathematical models in a likelihood-based framework for estimation and prediction in the life sciences. Journal of the Royal Society Interface. 21, 20230402.
- Simpson MJ, Murphy RJ, Maclaren OJ (2024) Modelling count data with partial differential equation models in biology. Journal of Theoretical Biology. 580, 111732.
- VandenHeuvel DJ, Buenzli PR, Simpson MJ (2024) Pushing coarse-grained models beyond the continuum limit using equation learning. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 480, 20230619.
- Hegarty-Cremer SGD, Borggaard XG, Andreasen CM, van der Eerden BCJ, Simpson MJ, Andersen TL, Buenzli PR (2024) How osteons form: A quantitative hypothesis-testing analysis of cortical pore filling and wall asymmetry. Bone. 180, 116998.
- Murphy RJ, Gunasingh G, Haass NK, Simpson MJ (2024) Formation and growth of co-culture tumour spheroids: new mathematical models and experiments. Bulletin of Mathematical Biology. 86, 8.
- Warne DJ, Maclaren OJ, Carr EJ, Simpson MJ, Drovandi C (2024) Generalised likelihood profiles for models with intractable likelihoods. Statistics and Computing. 34: 50.
- Johnston ST, Simpson MJ (2023) Exact sharp-fronted solutions for nonlinear diffusion on evolving domains. Journal of Physics A: Mathematical and Theoretical. 56: 48LT01.
- Simpson MJ, Maclaren OJ (2023) A profile likelihood-based workflow for identifiability analysis, estimation, and prediction with mechanistic mathematical models. PLOS Computational Biology. 19: e1011515.
- Simpson MJ, Rahman N, MCCue SW, Tam AKY (2023) Survival, extinction, and interface stability in a two-phase moving boundary model of biological invasion. Physica D: Nonlinear Phenomena. 456: 133912.
- VandenHeuvel DJ, Devlin BL, Buenzli PR, Woodruff MA, Simpson MJ (2023) New computational tools and experiments reveal how geometry affects tissue growth in 3D printed scaffolds. Chemical Engineering Journal. 475: 145776.
- Johnston ST, Simpson MJ (2023) Exact solutions for diffusive transport on heterogeneous growing domains. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 479: 20230263.
- Filippini LP, Simpson MJ, Carr EJ (2023) Simplified models of diffusion in radially-symmetric geometries. Physica A: Statistical Mechanics and its Applications. 626: 129067.
- Browning AP, Simpson MJ (2023) Geometric analysis enables biological insight from complex non-identifiable models using simple surrogates. PLOS Computational Biology. 19: e1010844.
- Murphy RJ, Gunasingh G, Haass NK, Simpson MJ (2023) Growth and adaptation mechanisms of tumour spheroids with time-dependent oxygen availability. PLOS Computational Biology. 19: e1010833.
- Tam AKY, Simpson MJ (2023) Pattern formation and front stability for a moving boundary model of biological invasion and recession. Physica D: Nonlinear Phenomena. 444: 133593.
- Welsh ZG, Simpson MJ, Khan Md IH, Karim MA (2023) Generalized moisture diffusivity for food drying through multiscale modeling. Journal of Food Engineering. 340: 111309.
- Simpson MJ, Walker SA, Studerus EN, McCue SW, Murphy RJ, Maclaren OJ (2023) Profile likelihood-based parameter and predictive interval analysis guides model choice for ecological population dynamics. Mathematical Biosciences. 355: 108950.
- Murphy RJ, Maclaren OJ, Calabrese AR, Thomas PB, Warne DJ, Williams ED, Simpson MJ (2022) Computationally efficient framework for diagnosing, understanding and predicting biphasic population growth. Journal of the Royal Society Interface. 19: 20220560.
- Buenzli PR, Simpson MJ (2022) Curvature dependences of wave propagation in reaction-diffusion models. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 478: 20220582.
- Browning AP, Drovandi C, Turner IW, Jenner AL, Simpson MJ (2022) Efficient inference and identifiability analysis for differential equation models with random parameters. PLOS Computational Biology. 18: e1010734.
- VandenHeuvel DJ, Drovandi C, Simpson MJ (2022) Computationally efficient mechanism discovery for cell invasion with uncertainty quantification. PLOS Computational Biology. 18: e1010599.
- El-Hachem M, McCue SW, Simpson MJ (2022) Non-vanishing sharp-fronted travelling wave solutions of the Fisher-Kolmogorov model. Mathematical Medicine and Biology: A Journal of the IMA. 39: 226-250.
- Warne DJ, Prescott TP, Baker RE, Simpson MJ (2022) Multifidelity multilevel Monte Carlo to accelerate approximate Bayesian parameter inference for partially observed stochastic processes. Journal of Computational Physics. 469: 111543.
- Simpson MJ, Baker RE, Buenzli PR, Nicholson R, Maclaren OJ (2022) Reliable and efficient parameter estimation using approximate continuum limit descriptions of stochastic models. Journal of Theoretical Biology. 549: 111201.
- Tam AKY, Simpson MJ (2022) The effect of geometry on survival and extinction in a moving-boundary problem motivated by the Fisher-KPP equation. Physica D: Nonlinear Phenomena. 438: 133305.
- Li Y, Buenzli PR, Simpson MJ (2022) Interpreting how nonlinear diffusion affects the fate of bistable populations using a discrete modelling framework. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 478: 20220013.
- Browning AP, Ansari N, Drovandi C, Johnston A, Simpson MJ, Jenner AL (2022) Identifying cell-to-cell variability in internalisation using flow cytometry. Journal of the Royal Society Interface. 19: 20220019. Selected for the cover of Interface.
- Warne DJ, Baker RE, Simpson MJ (2022) Rapid Bayesian inference for expensive stochastic models. Journal of Computational and Graphical Statistics. 31: 512–528.
- McCue SW, Bradshaw-Hajek BH, Simpson MJ (2022) Exact time-dependent solutions of a Fisher-KPP-like equation obtained with nonclassical symmetry analysis. Applied Mathematics Letters. 132: 108151.
- Sharp JA, Browning AP, Burrage K, Simpson MJ (2022) Parameter estimation and uncertainty quantification using information geometry methods in the life sciences. Journal of the Royal Society Interface. 19: 20210940.
- Klowss JJ, Browning AP, Murphy RJ, Carr EJ, Plank MJ, Gunasingh G, Haass NK, Simpson MJ (2022) Stochastic mathematical model of 4D tumour spheroids with real-time fluorescent cell cycle labelling. Journal of the Royal Society Interface. 19: 20210903.
- Carr EJ, VandenHeuvel DJ, Wilson JM, Simpson MJ (2022) Mean exit time in irregularly-shaped annular and composite disc domains. Journal of Physics A: Mathematical and Theoretical. 55: 105002.
- El-Hachem M, McCue SW, Simpson MJ (2022) A continuum mathematical model for substrate-mediated tissue growth. Bulletin of Mathematical Biology. 84: 49.
- McCue SW, El-Hachem M, Simpson MJ (2022) Travelling waves, blow-up and extinction in the Fisher-Stefan model. Studies in Applied Mathematics. 148: 964-986
- Murphy RJ, Browning AP, Gunasingh G, Haass NK, Simpson MJ (2022) Designing and interpreting 4D tumour spheroid experiments. Communications Biology. 5: 91.
- Carr EJ, Oliver DJ, Simpson MJ (2022) Approximate analytical solution for transient heat and mass transfer across an irregular interface. Communications in Nonlinear Science and Numerical Simulation. 108: 106211.
- Warne DJ, Crossman KA, Jin W, Mengersen KL, Osborne K, Simpson MJ, Thompson AA, Wu P, Ortiz J-C (2022) Identification of two-phase recovery in hard corals across the Great Barrier Reef. Journal of Applied Ecology. 59: 153-164.
- Simpson MJ, Browning AP, Warne DJ, Maclaren OJ, Baker RE (2022) Parameter identifiability and model selection for sigmoid population growth models. Journal of Theoretical Biology. 535: 110998. Selected for the 2024 Lewis Wolpert Prize for best paper in the Journal of Theoretical Biology.
- Li Y, Johnston ST, Buenzli PR, van Heijster P, Simpson MJ (2022) Extinction of bistable populations is affected by the shape of their initial spatial distribution. Bulletin of Mathematical Biology. 84: 21.
- Browning AP, Sharp JA, Murphy RJ, Gunasingh G, Lawson B, Burrage K, Haass NK, Simpson MJ (2021) Mathematical and statistical data analysis for the structure of tumour spheroids. eLife. 10: e73020.
- Lanaro M, McLaughlin MP, Simpson MJ, Buenzli PR, Wong CS, Allenby MC, Woodruff MA (2021) A quantitative analysis of cell bridging kinetics on a scaffold using computer vision algorithms. Acta Biomaterialia. 136: 429-440.
- Welsh ZG, Simpson MJ, Khan Md IH, Karim MA (2021) A multiscale approach to estimate the cellular diffusivity during food drying . Biosystems Engineering. 212: 273-289
- Wilson DB, Woodhouse FG, Simpson MJ, Baker RE (2021) Crowded transport within networked representations of complex geometries. Communications Physics. 4: 232.
- Martina-Perez S, Simpson MJ, Baker RE (2021) Bayesian uncertainty quantification for data-driven equation learning. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 477: 20210426.
- El-Hachem M, McCue SW, Simpson MJ (2021) Travelling wave analysis of cellular invasion into surrounding tissues. Physica D: Nonlinear Phenomena. 428: 133026.
- Carr MJ, Simpson MJ, Drovandi C (2021) Estimating parameters of a stochastic cell invasion model with fluorescent cell cycle labelling using Approximate Bayesian Computation. Journal of the Royal Society Interface. 18: 20210362.
- Sharp JA, Burrage K, Simpson MJ (2021) Implementation and acceleration of optimal control for systems biology. Journal of the Royal Society Interface. 18: 20210241.
- Browning AP, Maclaren OJ, Buenzli PR, Lanaro M, Allenby MC, Woodruff MA, Simpson MJ (2021) Model-based data analysis of tissue growth in thin 3D printed scaffolds. Journal of Theoretical Biology. 528: 110852.
- Simpson MJ, Browning AP, Drovandi C, Carr EJ, Maclaren OJ, Baker RE (2021) Profile likelihood analysis for a stochastic model of diffusion in heterogeneous media. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 477: 20210214.
- Murphy RJ, Buenzli PR, Tambyah TA, Thompson EW, Hugo HJ, Baker RE, Simpson MJ (2021) The role of mechanical interactions in EMT. Physical Biology. 18: 046001.
- Li Y, van Heijster P, Simpson MJ, Wechselberger M (2021) Shock-fronted travelling waves in a reaction-diffusion model with nonlinear forward-backward-forward diffusion. Physica D: Nonlinear Phenomena. 423: 132916.
- Gavagnin E, Vittadello ST, Gunasingh G, Haass NK, Simpson MJ, Rogers T, Yates CA (2021) Synchronised oscillations in growing cell populations are explained by demographic noise. Biophysical Journal. 20: 1314-1322.
- Simpson MJ, VandenHeuvel DJ, Wilson JM, McCue SW, Carr EJ (2021) Mean exit time for diffusion on irregular domains. New Journal of Physics. 23: 043030.
- Jin W, Spoerri L, Haass NK, Simpson MJ (2021) Mathematical model of tumour spheroid experiments with real-time cell cycle imaging. Bulletin of Mathematical Biology. 83: 44.
- Hegarty-Cremer SGD, Simpson MJ, Anderson TL, Buenzli PR (2021) Modelling cell guidance and curvature control in evolving biological tissues. Journal of Theoretical Biology. 520: 110658.
- Nardini JT, Baker RE, Simpson MJ, Flores KB (2021) Learning differential equation models from stochastic agent based simulation models. Journal of the Royal Society Interface. 18: 202009874.
- Vittadello ST, McCue SW, Gunasingh G, Haass NK, Simpson MJ (2021) A novel mathematical model of heterogeneous cell proliferation. Journal of Mathematical Biology. 82: 34.
- El-Hachem M, McCue SW, Simpson MJ (2021) Invading and receding sharp-fronted travelling waves. Bulletin of Mathematical Biology. 83: 35.
- McCue SW, El-Hachem M, Simpson MJ (2021) Exact sharp-fronted travelling waves of the Fisher-KPP equation. Applied Mathematics Letters. 114: 106918.
- Browning AP, Sharp JA, Mapder T, Baker CM, Burrage K, Simpson MJ (2021) Persistence is an optimal hedging strategy for bacteria in volatile environments. 120: P133-142. Biophysical Journal. Selected for the cover of Biophysical Journal.
- Murphy RJ, Buenzli PR, Baker RE, Simpson MJ (2021) Travelling waves in a free boundary mechanobiological model of an epithelial tissue. Applied Mathematics Letters. 111: 106636
- Lagergren J, Nardini JT, Baker RE, Simpson MJ, Flores KB (2020) Biologically-informed neural networks guide mechanistic modeling from sparse experimental data. PLOS Computational Biology. 16: e1008462.
- Browning AP, Warne DJ, Burrage K, Baker RE, Simpson MJ (2020) Identifiability analysis for stochastic differential equations models in systems biology. Journal of the Royal Society Interface. 17: 20200652.
- Li Y, van Heijster P, Marangell R, Simpson MJ (2020) Travelling wave solutions in a negative nonlinear diffusion-reaction model. Journal of Mathematical Biology. 81: 1495-1522.
- Tambyah TA, Murphy RJ, Buenzli PR, Simpson MJ (2020) A free boundary mechanobiological model of epithelial tissues. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 476: 20200528.
- Surendran A, Plank MJ, Simpson MJ (2020) Small-scale spatial structure affects predator-prey dynamics and coexistence. Theoretical Ecology. 13: 537-550.
- Surendran A, Plank MJ, Simpson MJ (2020) Population dynamics with spatial structure and an Allee effect. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 476: 20200501.
- Murphy RJ, Buenzli PR, Baker RE, Simpson MJ (2020) Mechanical cell competition in heterogeneous epithelial tissues. Bulletin of Mathematical Biology. 82: 130.
- Fadai NT, Johnston ST, Simpson MJ (2020) Unpacking the Allee effect: determining individual-level mechanisms that drive global population dynamics. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 476: 20200350.
- Buenzli PR, Lanaro M, Wong CS, McLaughlin MP, Allenby MC, Woodruff MA, Simpson MJ (2020) Cell proliferation and migration explain pore bridging dynamics in 3D printed scaffolds of different pore size. Acta Biomaterialia. 114: 285-295.
- Plank MJ, Simpson MJ, Binny RN (2020) Small-scale spatial structure influences large-scale invasion rates. Theoretical Ecology. 13: 277-288.
- Carr EJ, Ryan JM, Simpson MJ (2020) Diffusion in heterogeneous discs and spheres: new closed-form expressions for exit times and homogenization formulae. The Journal of Chemical Physics. 153: 074115.
- Simpson MJ (2020) Critical length for the spreading-vanishing dichotomy in higher dimensions. ANZIAM Journal. 62: 3-17.
- El-Hachem M, McCue SW, Simpson MJ (2020) A sharp-front moving boundary model for malignant invasion. Physica D: Nonlinear Phenomena. 412: 132639.
- Fadai NT, Simpson MJ (2020) Population dynamics with threshold effects gives rise to a diverse family of Allee effects. Bulletin of Mathematical Biology. 82: 74.
- Johnston ST, Simpson MJ, Crampin EJ (2020) Predicting population extinction in lattice-based birth-death-movement models. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 476: 20200089.
- Browning AP, Jin W, Plank MJ, Simpson MJ (2020) Identifying density-dependent interactions in cell populations. Journal of the Royal Society Interface. 17: 20200143.
- Warne DJ, Baker RE, Simpson MJ (2020) A practical guide to pseudo-marginal methods for computational inference in systems biology. Journal of Theoretical Biology. 496: 110255.
- Sharp JA, Browning AP, Mapder T, Baker CM, Burrage K, Simpson MJ (2020) Designing combination therapies using multiple optimal controls. Journal of Theoretical Biology. 497: 110277.
- Vittadello ST, McCue SW, Gunasingh G, Haass NK, Simpson MJ (2020) Examining go-or-grow using fluorescent cell-cycle indicators and cell cycle-inhibiting drugs. Biophysical Journal. 118: 1243-1247. Selected for the cover of Biophysical Journal.
- Jin W, Lo K-Y, Sun Y-S, Ting Y-H, Simpson MJ (2020) Quantifying the role of different surface coatings in experimental models of wound healing. Chemical Engineering Science. 220: 115609. Selected for the cover of Chemical Engineering Science.
- Simpson MJ, Baker RE, Vittadello ST, Maclaren OJ (2020) Parameter identifiability analysis for spatiotemporal models of cell invasion. Journal of the Royal Society Interface. 17: 20200055.
- Fadai NT, Simpson MJ (2020) New travelling wave solutions of the Porous-Fisher model with a moving boundary. Journal of Physics A: Mathematical and Theoretical. 53: 095601.
- Fadai NT, Baker RE, Simpson MJ (2019) Accurate and efficient discretisations for stochastic models providing near agent-based spatial resolution at low computational cost. Journal of the Royal Society Interface. 16: 20190421.
- Surendran A, Plank MJ, Simpson MJ (2019) Spatial structure arising from chase-escape interactions with crowding. Scientific Reports. 9: 14988.
- Matsiaka OM, Baker RE, Simpson MJ (2019) Continuum descriptions of spatial spreading for heterogeneous cell populations: theory and experiment. Journal of Theoretical Biology. 482: 109997.
- Baker RE, Parker A, Simpson MJ (2019) A free boundary model of epithelial dynamics. Journal of Theoretical Biology. 481: 61 - 74.
- El-Hachem M, McCue SW, Jin W, Du Y, Simpson MJ (2019) Revisiting the Fisher-Kolmogorov-Petrovsky-Piskunov equation to interpret the spreading-extinction dichotomy. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 475: 20190378.
- Vittadello ST, McCue SW, Gunasingh G, Haass NK, Simpson MJ (2019) Mathematical models incorporating a multi-stage cell cycle replicate normally-hidden inherent synchronisation in cell proliferation. Journal of the Royal Society Interface. 16: 20190382.
- Browning AP, Woodhouse FG, Simpson MJ (2019) Reversible signal transmission in an active mechanical metamaterial. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 475: 20190146.
- Murphy RJ, Buenzli PR, Baker RE, Simpson MJ (2019) An individual-based mechanical model of cell movement in heterogeneous tissues and its coarse-grained approximation. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 475: 20180838. Selected for the cover of Proceedings A.
- McCue SW, Jin W, Moroney TJ, Lo K-Y, Chou S-E, Simpson MJ (2019) Hole-closing model reveals exponents for nonlinear degenerate diffusivity functions in cell biology. Physica D: Nonlinear Phenomena. 398: 130-140.
- Matsiaka OM, Baker RE, Shah ET, Simpson MJ (2019) Mechanistic and experimental models of cell migration reveal the importance of intercellular interactions in cell invasion. Biomedical Physics & Engineering Express. 5: 045009.
- Warne DJ, Baker RE, Simpson MJ (2019) Using experimental data and information criteria to guide model selection for reaction-diffusion problems in mathematical biology. Bulletin of Mathematical Biology. 81: 1760-1804.
- Sharp JA, Browning AP, Mapder T, Burrage K, Simpson MJ (2019) Optimal control of acute myeloid leukaemia. Journal of Theoretical Biology. 470: 30-42
- Warne DJ, Baker RE, Simpson MJ (2019) Simulation and inference algorithms for stochastic biochemical reaction networks: from basic concepts to state-of-the-art. Journal of the Royal Society Interface. 16: 20180943.
- Browning AP, Haridas P, Simpson MJ (2019) A Bayesian sequential learning framework to parameterise continuum models of melanoma invasion into human skin. Bulletin of Mathematical Biology. 81: 676-698. Selected for the 2021 Lee A Segel Prize for the best student paper in the Bulletin of Mathematical Biology.
- Simpson MJ (2019) Mathematical models of cell invasion track spatial position and progression through the cell cycle. SIAM News. 52: 1-2.
- Carr EJ, Simpson MJ (2019) New homogenization approaches for stochastic transport through heterogeneous media. Journal of Chemical Physics. 150: 044104.
- McInerney S, Carr EJ, Simpson MJ (2019) Parameterising continuum models of heat transfer in heterogeneous living skin using experimental data. International Journal of Heat and Mass Transfer. 128: 964-975.
- Jin W, Liang X, Brooks A, Futrega K, Liu X, Doran MR, Simpson MJ, Roberts MS, Wang H (2018) Modelling of the SDF-1/CXCR4 regulated in vivo homing of therapeutic mesenchymal stem/stromal cells in mice. PeerJ. 6: e6072
- Yang H, Villani RM, Wang H, Simpson MJ, Roberts MS, Tang M, Liang X (2018) The role of cellular reactive oxygen species in cancer chemotherapy. Journal of Experimental & Clinical Cancer Research. 37: 266.
- Surendran A, Plank MJ, Simpson MJ (2018) Spatial moment description of birth-death-movement processes incorporating the effects of crowding and obstacles. Bulletin of Mathematical Biology. 80: 2828-2855.
- Welsh Z, Simpson MJ, Khan Md IH, Karim MA (2018) Multiscale modelling of food drying: State of the art. Comprehensive Reviews in Food Science and Food Safety. 17: 1293-1308.
- Parker A, Simpson MJ, Baker RE (2018) The impact of experimental design choices on parameter inference for models of growing cell colonies. Royal Society Open Science. 5: 180384.
- Simpson MJ, Jin W, Vittadello ST, Tambyah TA, Ryan JM, Gunasingh G, Haass NK, McCue SW (2018) Stochastic models of cell invasion with fluorescent cell cycle indicators. Physica A: Statistical Mechanics and its Applications. 510: 375-386.
- Haridas P, Browning AP, McGovern JA, McElwain DLS, Simpson MJ (2018) Three-dimensional experiments and individual based simulations show that cell proliferation drives melanoma nest formation in human skin tissue. BMC Systems Biology. 12: 34.
- Matsiaka OM, Penington CJ, Baker RE, Simpson MJ (2018) Discrete and continuum approximations for collective cell migration in a scratch assay with cell size dynamics. Bulletin of Mathematical Biology. 80: 738-757.
- Warne DJ, Baker RE, Simpson MJ (2018) Multilevel rejection sampling for approximate Bayesian computation. Computational Statistics & Data Analysis. 124: 71–86.
- Jin W, McCue SW, Simpson MJ (2018) Extended logistic growth model for heterogeneous populations Journal of Theoretical Biology. 445: 51-61.
- Vittadello ST, McCue SW, Gunasingh G, Haass NK, Simpson MJ (2018) Mathematical models for cell migration with real-time cell cycle dynamics. Biophysical Journal. 114: 1241 – 1253.
- Carr EJ, Simpson MJ (2018) Rapid calculation of maximum particle lifetime for diffusion in complex geometries. Journal of Chemical Physics. 148: 094113.
- Simpson MJ (2018) Calculating groundwater response times for flow in heterogeneous porous media. Groundwater. 56: 337-342.
- Jin W, Lo K-Y, Chou S-E, McCue SW, Simpson MJ (2018) The role of initial geometry in experimental models of wound closing. Chemical Engineering Science. 179: 221-226. Selected for the cover of Chemical Engineering Science.
- Carr EJ, Simpson MJ (2018) Accurate and efficient calculation of response times for groundwater flow. Journal of Hydrology. 558: 470–481.
- Browning AP, McCue SW, Binny RN, Plank MJ, Shah ET, Simpson MJ (2018) Inferring parameters for a lattice-free model of cell migration and proliferation using experimental data. Journal of Theoretical Biology. 437: 251-260.
- Warne DJ, Baker RE, Simpson MJ (2017) Optimal quantification of contact inhibition in cell populations . Biophysical Journal (Biophysical Letter). 113: 1920-1924.
- Simpson MJ, Plank MJ (2017) Simplified calculation of diffusivity for a lattice-based random walk with a single obstacle. Results in Physics. 7: 3346-3348.
- Simpson MJ, McInerney S, Carr EJ, Cuttle L (2017) Quantifying the efficacy of first aid treatments for burn injuries using mathematical modelling and in vivo porcine experiments. Scientific Reports. 7: 10925
- Haridas P, McGovern JA, McElwain DLS, Simpson MJ (2017) Quantitative comparison of the spreading and invasion of radial growth phase and metastatic melanoma cells in a three-dimensional human skin equivalent model. PeerJ. 5: e3754.
- Jin W, Penington CJ, McCue SW, Simpson MJ (2017) A computational modelling framework to quantify the effects of passaging cell lines. PLOS ONE. 12: e0181941.
- Browning AP, McCue SW, Simpson MJ (2017) A Bayesian computational approach to explore the optimal duration of a cell proliferation assay. Bulletin of Mathematical Biology. 79: 1888-1906.
- Haridas P, Penington CJ, McGovern JA, McElwain DLS, Simpson MJ (2017) Quantifying rates of cell migration and cell proliferation in co-culture barrier assays reveals how skin and melanoma cells interact during melanoma spreading and invasion. Journal of Theoretical Biology. 423: 13-25.
- Matsiaka OM, Penington CJ, Baker RE, Simpson MJ (2017) Continuum approximations for lattice-free multi-species models of collective cell migration. Journal of Theoretical Biology. 422: 1-11.
- Jin W, Shah ET, Penington CJ, McCue SW, Maini PK, Simpson MJ (2017) Logistic proliferation of cells in scratch assays is delayed. Bulletin of Mathematical Biology. 79: 1028-1050.
- Zheng M, Liu F, Liu Q, Burrage K, Simpson MJ (2017) A novel numerical approximation of the time fractional reaction-diffusion equation with a moving boundary. Journal of Computational Physics. 338: 493-510.
- Simpson MJ, Lo K-Y, Sun Y-S (2017) Quantifying the roles of random motility and directed motility using advection-diffusion theory for a 3T3 fibroblast cell migration assay stimulated with an electric field. BMC Systems Biology. 11: 39.
- Johnston ST, Baker RE, Simpson MJ (2017) A new and accurate continuum description of moving fronts. New Journal of Physics. 19: 033010.
- Johnston ST, Baker RE, McElwain DLS, Simpson MJ (2017) Co-operation, competition and crowding: a discrete framework linking Allee kinetics, nonlinear diffusion, shocks and sharp-fronted travelling waves. Scientific Reports. 7: 42134.
- Simpson MJ (2017) Critical time scales for morphogen gradient formation: Concentration or gradient criteria. International Journal of Heat and Mass Transfer. 106: 570-572.
- Jazaei F, Simpson MJ, Clement TP (2017) Understanding time scales of diffusive fluxes and the implication for steady state and steady shape conditions. Geophysical Research Letters. 44: 174-180.
- Jin W, Penington CJ, McCue SW, Simpson MJ (2016) Stochastic simulation tools and continuum models for describing two-dimensional collective cell spreading with universal growth functions. Physical Biology. 13: 056003.
- Ellery AJ, Baker RE, Simpson MJ (2016). An analytical method for disentangling the roles of adhesion and crowding for random walk models on a crowded lattice. Fast Track Letter, Physical Biology. 13: 05LT02.
- Taylor PR, Baker RE, Simpson MJ, Yates CA (2016) Coupling volume-excluding compartment-based models of diffusion at different scales: Voronoi and pseudo-compartment approaches. Journal of the Royal Society Interface. 13: 2016336.
- Penington CJ, Baker RE, Simpson MJ (2016) Exits in order: how crowding affects particle lifetimes. The Journal of Chemical Physics. 144: 244107.
- Andrews CJ, Cuttle L, Simpson MJ (2016) Quantifying the role of burn temperature, burn duration and skin thickness in an in vivo animal skin model of heat conduction. International Journal of Heat and Mass Transfer. 101: 542-549.
- Ellery AJ, Baker RE, Simpson MJ (2016) Distinguishing between short-time non-Fickian diffusion, and long-time Fickian diffusion for a random walk on a crowded lattice. Communication, The Journal of Chemical Physics. 144: 171104.
- Johnston ST, Baker RE, Simpson MJ (2016) Filling the gaps: A robust description of adhesive birth-death-movement processes. Physical Review E. 93: 042413.
- Johnston ST, Ross JV, Binder BJ, McElwain DLS, Haridas P, Simpson MJ (2016) Quantifying the effect of experimental design choices for in vitro scratch assays. Journal of Theoretical Biology. 400: 19-31.
- Haridas P, McGovern JA, Kashyap AS, McElwain DLS, Simpson MJ (2016) Standard melanoma-associated markers do not identify the MM127 metastatic melanoma cell line. Scientific Reports. 6: 24569.
- Binny RN, Haridas P, James A, Law R, Simpson MJ, Plank MJ (2016) Spatial structure arising from neighbour-dependent bias in collective cell movement. PeerJ. 4: e1689.
- Binder BJ, Simpson MJ (2016) Cell density and cell size dynamics during in vitro tissue growth experiments: Implications for mathematical models of collective cell behaviour. Applied Mathematical Modelling. 40: 3438-3446.
- Ellery AJ, Baker RE, McCue SW, Simpson MJ (2016) Modeling transport through an environment crowded by a mixture of obstacles of different shapes and sizes. Physica A: Statistical Mechanics and its Applications. 449: 74-84.
- Jin W, Shah ET, Penington CJ, McCue SW, Chopin LK, Simpson MJ (2016) Reproducibility of scratch assays is affected by the initial degree of confluence: experiments, modelling and model selection. Journal of Theoretical Biology. 390: 136-145.
- Jazaei F, Simpson MJ, Clement TP (2016) Spatial analysis of aquifer response times for radial flow processes: Nondimensional analysis and laboratory-scale tests. Journal of Hydrology. 532: 1-8.
- Irons C, Plank MJ, Simpson MJ (2016) Lattice-free models of directed cell motility. Physica A: Statistical Mechanics and its Applications. 442: 110-121.
- Ellery AJ, Baker RE, Simpson MJ (2015) Calculating the Fickian diffusivity for a lattice-based random walk with agents and obstacles of different shapes and sizes. Physical Biology. 12: 066010.
- Taylor PR, Yates CA, Simpson MJ, Baker RE (2015) Reconciling transport models across scales: the role of volume exclusion. Rapid Communication, Physical Review E. 92: 040701(R).
- Simpson MJ, Sharp JA, Morrow LC, Baker RE (2015) Exact solutions of coupled multispecies linear reaction-diffusion equations on a uniformly growing domain. PLOS ONE. 10: e0138894.
- Simpson MJ, Baker RE (2015) Exact calculations of survival probability for diffusion on growing lines, disks and spheres: the role of dimension. The Journal of Chemical Physics. 143: 094109.
- Johnston ST, Shah ET, Chopin LK, McElwain DLS, Simpson MJ (2015) Estimating cell diffusivity and cell proliferation rate by interpreting IncuCyte ZOOM assay data using the Fisher-Kolmogorov model. BMC Systems Biology. 9: 38.
- Simpson MJ, Morrow LC (2015) Analytical model of reactive transport processes with spatially variable coefficients. Royal Society Open Science. 2: 140348.
- Simpson MJ, Baker RE (2015) Spatial moment techniques for modelling biological processes. Bulletin of Mathematical Biology. 77: 581-585.
- Markham DC, Simpson MJ, Baker RE (2015) Choosing an appropriate modelling framework for analysing multispecies co-culture experiments. Bulletin of Mathematical Biology. 77: 713-734.
- Simpson MJ, Sharp JA, Baker RE (2015) Survival probability for a diffusive process on a growing domain. Physical Review E. 91: 042701.
- Vo BN, Drovandi CC, Pettitt AN, Simpson MJ (2015) Quantifying uncertainty in parameter estimates for stochastic models of collective cell spreading using approximate Bayesian computation. Mathematical Biosciences. 263: 133-142.
- Simpson MJ (2015) Exact solutions of linear reaction-diffusion processes on a uniformly growing domain: Criteria for successful colonization. PLOS ONE. 10: e0117949.
- Johnston ST, Simpson MJ, Baker RE (2015) Modelling the movement of interacting cell populations: A moment dynamics approach. Journal of Theoretical Biology. 370: 81-92.
- Binder BJ, Simpson MJ (2015) Spectral analysis of pair-correlation bandwidth: Application to cell biology images. Royal Society Open Science. 2: 140494.
- Jazaei F, Simpson MJ, Clement TP (2014) An analytical framework for quantifying aquifer response time scales associated with transient boundary conditions. Journal of Hydrology. 519: 1642-1648.
- Johnston ST, Simpson MJ, McElwain DLS, Binder BJ, Ross JV (2014) Interpreting scratch assays using pair density dynamics and approximate Bayesian computation. Royal Society Open Biology. 4: 140097.
- Treloar KK, Simpson MJ, Binder BJ, McElwain DLS, Baker RE (2014) Assessing the role of spatial correlations during collective cell spreading. Scientific Reports. 4: 5713.
- Johnston ST, Simpson MJ, McElwain DLS (2014) How much information can be obtained from tracking the position of the leading edge in a scratch assay? Journal of the Royal Society Interface. 11: 20140325.
- Treloar KK, Simpson MJ, McElwain DLS, Baker RE (2014) Are in vitro estimates of cell diffusivity and cell proliferation rate sensitive to assay geomentry? Journal of Theoretical Biology. 356: 71-84.
- Young HM, Bergner AJ, Simpson MJ, McKeown SJ, Hao MM, Anderson CR, Enomoto H (2014) Colonizing while migrating: How do individual enteric neural crest cells behave? BMC Biology. 12: 23.
- Simpson MJ, Ellery AJ (2014) Exact series solutions of reactive transport models with general initial conditions. Journal of Hydrology. 513: 7-12.
- Agnew DJG, Green JEF, Brown TM, Simpson MJ, Binder BJ (2014) Distinguishing between mechanisms of cell aggregation using pair-correlation functions. Journal of Theoretical Biology. 352: 16-23.
- Markham DC, Simpson MJ, Maini PK, Gaffney EA, Baker RE (2014) Comparing methods for modelling spreading cell fronts. Journal of Theoretical Biology. 353: 95-103.
- Ellery AJ, Simpson MJ, McCue SW, Baker RE (2014) Characterizing transport through a crowded environment with different obstacle sizes. The Journal of Chemical Physics. 140: 054108.
- Simpson MJ, Haridas P, McElwain DLS (2014) Do pioneer cells exist? PLOS ONE. 9: e85488.
- Simpson MJ, Sharp JA, Baker RE (2014) Distinguishing between mean-field, moment dynamics and stochastic descriptions of birth-death-movement processes. Physica A: Statistical Mechanics and its Applications. 395: 236-246.
- Treloar KK,Simpson MJ, Haridas P, Manton KJ, Leavesley DI, McElwain DLS, Baker RE (2013). Multiple types of data are required to identify the mechanisms influencing the spatial expansion of melanoma cell colonies. BMC Systems Biology. 7: 137.
- Johnston ST, Simpson MJ, Plank MJ (2013) Lattice-free descriptions of collective motion with crowding and adhesion. Physical Review E. 88: 062720.
- Ellery AJ, Simpson MJ, McCue SW, Baker RE (2013) A simplified approach for calculating the moments of action for linear reaction-diffusion equations. Physical Review E. 88: 054102.
- Markham DC, Simpson MJ, Maini PK, Gaffney EA, Baker RE (2013) Incorporating spatial correlations into multi-species mean-field models. Physical Review E. 88: 052713.
- Simpson MJ, Jazaei F, Clement TP (2013) How long does it take for aquifer recharge or aquifer discharge processes to reach steady state? Journal of Hydrology. 501: 241-248.
- Bowden LG, Simpson MJ, Baker RE (2013) Design and interpretation of cell trajectory assays. Journal of the Royal Society Interface. 10: 20130630.
- Plank MJ, Simpson MJ (2013) Lattice-free models of cell invasion: discrete simulations and travelling waves. Bulletin of Mathematical Biology. 75: 2150-2166.
- Binder BJ, Simpson MJ (2013) Quantifying spatial structure in experimental observations and agent-based simulations using pair-correlation functions. Physical Review E. 88: 022705.
- Ellery AJ, Simpson MJ, McCue SW (2013) Comment on Local accumulation times for source, diffusion and degradation models in two and three dimensions. The Journal of Chemical Physics. 139: 017101.
- Markham DC, Simpson MJ, Baker RE (2013) Simplified method for including spatial correlations in mean-field approximations. Physical Review E. 87: 062702.
- Treloar KK, Simpson MJ (2013) Sensitivity of edge detection methods for quantifying cell migration assays. PLOS ONE. 8: e67389.
- Simpson MJ, Foy BH, McCue SW (2013) Travelling waves for a velocity-jump model of cell migration and proliferation. Mathematical Biosciences. 244: 98-106.
- Simpson MJ, Binder BJ, Haridas P, Wood BK, Treloar KK, McElwain DLS, Baker RE (2013) Experimental and modelling investigations of monolayer development with clustering. Bulletin of Mathematical Biology. 75: 871-889.
- Simpson MJ, Treloar KK, Binder BJ, Haridas P, Manton KJ, Leavesley DI, McElwain DLS, Baker RE (2013) Quantifying the roles of cell motility and cell proliferation in a circular barrier assay. Journal of the Royal Society Interface. 10: 20130007.
- Treloar KK, Simpson MJ, McCue SW (2013) Velocity-jump processes with proliferation. Journal of Physics A: Mathematical and Theoretical. 46: 015003. Highlighted by IOP Insights.
- Simpson MJ, Ellery AJ, McCue SW, Baker RE (2013) Critical timescales and time intervals for coupled linear processes. ANZIAM Journal. 54: 127-142.
- Ellery AJ, Simpson MJ, McCue SW, Baker RE (2012) Moments of action provide insight into critical times for advection-diffusion-reaction processes. Physical Review E. 86: 031136.
- Simpson MJ, Mercer GN (2012) Infectious disease modelling. ANZIAM Journal. 54: 1-2.
- Binder BJ, Ross JV, Simpson MJ (2012) A hybrid model for studying spatial aspects of infectious diseases. ANZIAM Journal. 54: 37-49.
- Johnston ST, Simpson MJ, Baker RE (2012) Mean-field descriptions of collective migration with strong adhesion. Physical Review E. 85: 051922.
- Plank MJ, Simpson MJ (2012) Models of collective cell behaviour with crowding effects: comparing lattice-based and lattice-free approaches. Journal of the Royal Society Interface. 9: 2983-2996.
- Ellery AJ, Simpson MJ, McCue SW, Baker RE (2012) Critical timescales for advection–diffusion–reaction processes. Physical Review E. 85: 041135.
- Baker RE, Simpson MJ (2012) Models of collective cell motion for cell populations with different aspect ratio: diffusion, proliferation and travelling waves. Physica A: Statistical Mechanics and its Applications. 391: 3729-3750.
- Simpson MJ, Ellery AJ (2012) An analytical solution for diffusion and nonlinear uptake of oxygen in a spherical cell. Applied Mathematical Modelling. 36: 3329-3334.
- Treloar KK, Simpson MJ, McCue SW (2011) Velocity-jump models with crowding effects. Physical Review E. 84: 061920.
- Chang SW, Clement TP, Simpson MJ, Lee K-K (2011) Does sea-level rise have an impact on saltwater intrusion? Advances in Water Resources. 34: 1283-1291.
- Simpson MJ, Baker RE (2011) Corrected mean-field models for spatially-dependent advection-diffusion-reaction phenomena. Physical Review E. 83: 051922.
- Ellery AJ, Simpson MJ (2011) An analytical method to solve a general class of nonlinear reactive transport models. Chemical Engineering Journal. 169: 313-318.
- Simpson MJ, Baker RE, McCue SW (2011) Models of collective cell spreading with variable cell aspect ratio: A motivation for degenerate diffusion models. Physical Review E. 83: 021901.
- Simpson MJ, Towne C, McElwain DLS, Upton Z (2010) Migration of breast cancer cells: Understanding the roles of volume exclusion and cell-to-cell adhesion. Physical Review E. 82: 041901.
- Baker RE, Simpson MJ (2010) Correcting mean-field approximations for birth-death-movement processes. Physical Review E. 82: 041905.
- Simpson MJ, Landman KA, Hughes BD (2010) Cell invasion with proliferation mechanisms motivated by time-lapse data. Physica A: Statistical Mechanics and its Applications. 389: 3779-3790.
- Fernando AE, Landman KA, Simpson MJ (2010) Nonlinear diffusion and exclusion processes. Physical Review E. 81: 011903.
- Simpson MJ, Landman KA, Hughes BD, Fernando AE (2010) A model for mesoscale patterns in motile populations. Physica A: Statistical Mechanics and its Applications. 389: 1412-1424.
- Simpson MJ, Hughes BD, Landman KA (2009) Diffusing populations: Ghosts or Folks? Australasian Journal of Engineering Education. 15: 59-68.
- Simpson MJ, Landman KA, Hughes BD (2009) Pathlines in exclusion processes. Physical Review E. 79: 031920.
- Simpson MJ (2009) Depth-averaging errors in reactive transport modelling. Water Resources Research. 45: W02505.
- Simpson MJ, Landman KA, Hughes BD (2009) Distinguishing between directed and undirected cell motility within an invading cell population. Bulletin of Mathematical Biology. 71: 781-799.
- Simpson MJ, Landman KA, Hughes BD (2009) Multi-species simple exclusion processes. Physica A: Statistical Mechanics and its Applications. 388: 399-406.
- Binder BJ, Landman KA, Simpson MJ, Mariani M, Newgreen DF (2008) Modeling proliferative tissue growth: a general approach and an avian case study. Physical Review E. 78: 031912.
- Landman KA, Simpson MJ, Pettet GJ (2008) Tactically-driven nonmonotone travelling waves. Physica D: Nonlinear Phenomena. 237: 678-691.
- Simpson MJ, Landman KA (2008) Theoretical analysis and physical interpretation of temporal truncation errors in operator split algorithms. Mathematics and Computers in Simulation. 77: 9-21.
- Simpson MJ (2008) Discussion of Direct and split operator approaches with ELLAM for reactive transport equations. AIChE Journal. 54: 588-588.
- Simpson MJ, Merrifield A, Landman KA, Hughes BD (2007) Simulating invasion with cellular automata: connecting cell-scale and population-scale properties. Physical Review E. 76: 021918.
- Simpson MJ, Landman KA (2007) Nonmonotone chemotactic invasion: High-resolution simulations, phase plane analysis and new benchmark problems. Journal of Computational Physics. 225: 6-12.
- Simpson MJ, Landman KA (2007) Analysis of split operator methods applied to reactive transport with Monod kinetics. Advances in Water Resources. 30: 2026-2033.
- Simpson MJ, Landman KA, Bhaganagarapu K (2007) Coalescence of interacting cell populations. Journal of Theoretical Biology. 247: 525-543.
- Landman KA, Simpson MJ, Newgreen DF (2007) Mathematical and experimental insight into the development of the enteric nervous system and Hirschsprung's Disease. Development, Growth and Differentiation. 49: 277-286.
- Simpson MJ, Zhang DC, Mariani M, Landman KA, Newgreen DF (2007) Cell proliferation drives neural crest cell invasion of the intestine. Developmental Biology. 302: 553-568. Selected for the cover of Developmental Biology.
- Simpson MJ (2007) Reply to comment on Computing residence times for flow towards a pumping well: Nomograph solution and validity of the small draw-down approximation. Hydrogeology Journal. 15: 431-432.
- Simpson MJ, Landman KA, Hughes BD, Newgreen DF (2006) Looking inside an invasion wave of cells using continuum models: Proliferation is the key. Journal of Theoretical Biology. 243: 343-360.
- Simpson MJ, Landman KA, Newgreen DF (2006) Chemotactic and diffusive migration on a non-uniformly growing domain: Numerical algorithm development and applications. Journal of Computational and Applied Mathematics. 192: 282-300.
- Simpson MJ, Landman KA (2006) Characterizing and minimizing the operator split error for Fisher's equation. Applied Mathematics Letters. 19: 604-612.
- Simpson MJ, Landman KA, Clement TP (2005) Assessment of a non-traditional operator split algorithm for simulation of reactive transport. Mathematics and Computers in Simulation. 70: 44-60.
- Simpson MJ (2005) Computing residence times for flow towards a pumping well: Nomograph solution and validity of the small draw-down approximation. Hydrogeology Journal. 13: 889-894.
- Landman KA, Simpson MJ, Slater JL, Newgreen FD (2005) Diffusive and chemotactic cellular migration: smooth and discontinuous travelling wave solutions. SIAM Journal on Applied Mathematics. 65: 1420-1442.
- Simpson MJ (2004) SEAWAT-2000: Variable-density flow processes and integrated MT3DMS transport processes. Groundwater. 42: 642-645.
- Simpson MJ, Clement TP (2004) Improving the worthiness of the Henry problem as a benchmark for density-dependent ground water flow problems. Water Resources Research. 40: W01504.
- Simpson MJ, Clement TP, Yeomans FE (2003) Analytical model for computing residence times near a pumping well. Groundwater. 41: 351-354.
- Simpson MJ, Clement TP, Gallop TA (2003) Laboratory and numerical investigation of flow and transport near a seepage-face boundary. Groundwater. 41: 690-700.
- Simpson MJ, Clement TP (2003) A theoretical analysis of the worthiness of Henry and Elder problems as benchmarks of density-dependent groundwater flow models. Advances in Water Resources. 26: 17-31.
- Simpson MJ, Clement TP (2003) Comparison of finite difference and finite element solutions to the variably saturated flow equation. Journal of Hydrology. 270: 49-64.