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- M Xia, Qijing Shen, PK Maini, EA Gaffney, Alex Mogilner, A
new local time-decoupled squared Wasserstein-2 method for
training stochastic neural networks to reconstruct uncertain
parameters in dynamical systems, Neural Networks, In Press
- AL Krause, V Klika, E Villar-Sepulveda, AR
Champneys, EA Gaffney, Pattern Localisation in the
Swift-Hohenberg Equation via Slowly Varying Spatial
Heterogeneity, SIAM Journal on Applied Dynamical Systems, In
Press.
- LV Brown, M McConnell, R Rosler, L Peiser, BJ Schmidt, AV
Ratushny, EA Gaffney, MC Coles, Applying population
mechanistic modelling to find determinants of chimeric
antigen receptor T-cells dynamics in month-one lymphoma
patients,
Immunotherapy Advances 5(1), (2025)
- J Ayensa-Jimenez, M Perez-Aliacar, M Doweidar, E Gaffney,
M Doblare, An overview from physically-based to data-driven
approaches of the modelling and simulation of glioblastoma
progression in microfluidic devices, Archives of
Computational Methods in Engineering, https://doi.org/10.1007/s11831-025-10291-y
(2025).
- L Heirene, H Byrne, A Sepp, EA Gaffney and J Yates,
Understanding antibody–target antigen interactions and the
avidity effect using mathematical modelling, .J. R.
Soc. Interface 22: 20240710, https://doi.org/10.1098/rsif.2024.0710
(2025)
- JR Crawshaw, EA Gaffney, M Gertz, PK Maini, and A Caruso,
Modelling the Ocular Pharmacokinetics and Pharmacodynamics
of Ranibizumab for Improved Understanding and Data
Collection Strategies in Ocular Diseases, Investigative
Ophthalmology & Visual Science, 66:20 (2025).
- P Lamirande, EA Gaffney, M Gertz, PK Maini, JR Crawshaw
and A Caruso. A first passage model of intravitreal drug
delivery and residence time - influence of ocular geometry,
individual variability, and injection location, Investigative
Ophthalmology & Visual Science, 65:21 (2024).
- C Moreau, BJ Walker, RN Poon, D Soto, DI Goldman, E.
Gaffney, and KY Wan. Minimal design of a synthetic cilium, Physical
Review Research 6 (4), L042061 (2024).
- V Klika, E Gaffney, PK. Maini, On the speed of propagation
in Turing patterns for reaction-diffusion systems, Physica
D, 467, 134268, 2024.
- JP Whiteley, CP Brown, EA Gaffney, Sensitivity of
cartilage mechanical behaviour to spatial variations in
material properties, Journal of the Mechanical Behavior of
Biomedical Materials 156, 106575, (2024).
- AL Krause, EA Gaffney, TJ Jewell, V Klika, BJ Walker,
Turing instabilities are not enough to ensure pattern
formation, Bulletin of Mathematical Biology, 86:21
(2024).
- A Diez, AL Krause, PK Maini, EA Gaffney, S Seirin-Lee,
Turing pattern formation in reaction-cross-diffusion systems
with a bilayer geometry, Bulletin of Mathematical Biology 86, 13
(2024).
- MP Dalwadi, C Moreau, EA Gaffney, K Ishimoto, BJ Walker,
Generalised Jeffery's equations for rapidly spinning
particles. Part 1. Spheroids, Journal of Fluid Mechanics, 979:A1 (2024)
- MP Dalwadi, C Moreau, EA Gaffney, K Ishimoto, BJ Walker,
Generalised Jeffery's equations for rapidly spinning
particles. Part 2. Helicoidal objects with chirality, Journal of Fluid Mechanics, 979:A2 (2024).
- TJ Jewell, AL Krause, PK Maini, EA Gaffney, Patterning of
nonlocal transport models in biology: the impact of spatial
dimension, Mathematical Biosciences, 366:109093
(2023)
- J Ayensa-Jimenez, MH Doweidar, EA Gaffney, M Doblare, A
mathematical modelling study of chemotactic dynamics in cell
cultures: the impact of spatio-temporal heterogeneity, Bulletin of Mathematical Biology, 85:98
(2023).
- M Dvoriashyna, A Foss, E Gaffney, R Repetto, Mathematical
modelling of ocular epithelial transport: a review, Modeling and Artificial Intelligence in
Ophthalmology, 5:1-17 (2023).
- K Ishimoto, EA Gaffney, DJ Smith, Squirmer hydrodynamics
near a periodic surface topography, Frontiers in cell and developmental
biology 11, 1123446, 2023
- BJ Walker, K Ishimoto, EA Gaffney, Hydrodynamic
slender-body theory for local rotation at zero Reynolds
number, Physical Review Fluids 8 (3), 034101
(2023)
- JD Glover, ZR Sudderick, BBJ Shih, C Batho-Samblas, L
Charlton, ..., EA Gaffney, ...., D Headon. The developmental
basis of fingerprint pattern formation and variation, Cell 186 (5), 940-956. (2023)
- BJ Walker, K Ishimoto, EA Gaffney, Systematic
parameterizations of minimal models of microswimming, Physical Review Fluids 8 (3), 034102, 2023
- AL Krause, EA Gaffney, BJ Walker, Concentration-Dependent
Domain Evolution in Reaction-Diffusion Systems, Bulletin of Mathematical Biology 14,
(2023)
- V Klika, EA Gaffney, Upscaling the Poisson-Nernst-Planck
equations for ion transport in weakly heterogeneous charged
porous media, Applied Mathematics Letters, 137, 108482,
(2023).
- DB de Souza, HA Araujo, GC Duarte-Filho, EA Gaffney, FAN
Santos, and EP Raposo, Fock-space approach to stochastic
susceptible-infected-recovered models, Phys. Rev. E (2022) 106:014136
- LV Brown, MC Coles, M McConnell, AV Ratushny, EA Gaffney,
Analysis of cellular kinetic models suggest that
physiologically based model parameters may be inherently,
practically unidentifiable, Journal of Pharmacokinetics and
Pharmacodynamics (2022) 49:539-556
- A Sargood, EA Gaffney, AL Krause, Fixed and Distributed
Gene Expression Time Delays in Reaction-Diffusion Systems, Bull. Math Bio (2022) 84:98, 29 pages.
- L Brown, J Wagg, R Darley, A van Hateren, T Elliott, E
Gaffney, M Coles, De-risking clinical trial failure through
mechanistic simulation, Immunotherapy Advances, (2022) 2:1-15.
- M Dvoriashyna, AJE Foss, EA Gaffney, R Repetto, A
mathematical model of aqueous humor production and
composition, Investigative Ophthalmology and Visual
Science, (2022) 63:1-11.
- BJ Walker, K Ishimoto, C Moreau, EA Gaffney, MP Dalwadi,
Emergent rheotaxis of shape-changing swimmers in Poiseuille
flow, J. Fluid Mechanics (2022), doi.org/10.1017/jfm.2022.474
- EA Gaffney, MP Dalwadi, C Moreau, K Ishimoto, BJ Walker,
Canonical orbits for rapidly deforming planar microswimmers
in shear flow, Physical Review Fluids (2022) 7, L022101
- JE Jansen, D Aschenbrenner, HH Uhlig, MC Coles, EA
Gaffney, A method for the inference of cytokine interaction
networks, PLoS computational biology (2022) 18,
e1010112
- BJ Walker, K Ishimoto, EA Gaffney, C Moreau, The control
of particles in the Stokes limit, Journal of Fluid Mechanics
(2022), doi.org/10.1017/jfm.2022.253
- JP Whiteley, CP Brown, EA Gaffney, Modelling articular
cartilage: the relative motion of two adjacent
poroviscoelastic layers, Mathematical Medicine and Biology:
A Journal of the IMA, (2022), doi: 10.1093/imammb/dqac005
- BJ Walker, K Ishimoto, EA Gaffney, C Moreau, MP Dalwadi,
The effects of rapid yawing on simple swimmer models and
planar Jeffery's orbits, Physical Review Fluids, (2022) 7, 023101.
- AL Krause, EA Gaffney, PK Maini, V Klika, Modern
perspectives on near-equilibrium analysis of Turing systems,
Phil. Trans. R. Soc. A (2021) 379:20200268
- AL Krause, EA Gaffney, PK Maini, V Klika, Introduction to
recent progress and open frontiers in Turing's theory of
morphogenesis, Phil. Trans. R. Soc. A (2021) 379:20200280
- AE Kmieciak, LV Brown, MC Coles, J Wagg, A Phipps, EA
Gaffney, Predicted limited redistribution of T cells to
secondary lymphoid tissue correlates with increased risk of
haematological malignancies in asplenic patients, Scientific Reports (2021) 11:16394.
- C Moreau, K Ishimoto, EA Gaffney, BJ Walker, Control and
controllability of microswimmers by a shearing flow, Royal Society Open Science (2021),
8:211141
- EA Gaffney, K Ishimoto, BJ Walker, Modelling Motility: The
Mathematics of Spermatozoa, Frontiers in Cell and Developmental
Biology, (2021) 9:710825
- AL Krause, V Klika, PK Maini, D Headon, EA Gaffney,
Isolating Patterns in Open Reaction-Diffusion Systems, Bull. Math. Bio. (2021),
83:doi10.1007/s11538-021-00913-4
- V Tokarova, AS Perumal, M Nayak, H Shum, O Kaspar, K
Rajendran, M Mohammadi, C Tremblay, EA Gaffney, S Martel, DV
Nicolau, Patterns of bacterial motility in
microfluidics-confining environments, PNAS (2021), 118:2013925118
- TE Woolley, AL Krause, EA Gaffney, Bespoke Turing Systems,
Bull. Math. Bio. (2021)
83:doi10.1007/s11538-021-00870-y
- BJ Walker, K Ishimoto, EA Gaffney, Regularised non-uniform
segments and efficient no-slip elastohydrodynamics, Journal of Fluid Mechanics (2021), 915,
doi:10.1017/jfm.2021.139.
- LV Brown, EA Gaffney, A Ager, J Wagg, MC Coles,
Quantifying the limits of CAR T-cell delivery in mice and
men, Journal of The Royal Society Interface
(2021) 18:0201013 doi:10.1098/rsif.2020.1013
- D Aschenbrenner, M Quaranta, S Banerjee, N Ilott, J
Jansen, BA Steere, Y Chen, S Ho, K Cox, Oxford IBD Cohort
Investigators, CV Arancibia-Carcamo, M Coles, E Gaffney, S
Travis, LA Denson, S Kugathasan, J Schmitz, F Powrie, S
Sansom, HH Uhlig, Deconvolution of monocyte responses in
inflammatory bowel disease reveals an IL-1 cytokine network
that regulates IL-23, Gut (2021), 70:1023-1036.
- BJ Walker, K Ishimoto, EA Gaffney, Efficient simulation of
filament elastohydrodynamics in three dimensions, Physical Review Fluids (2020), 5:123103,
doi:10.1103/PhysRevFluids.5.123103
- GC Duarte, FAN Santos, EA Gaffney, Fock-space methods for
diffusion: Capturing volume exclusion via Fermionic
statistics, Physical Review E (2020), 102:052101,
doi:10.1103/PhysRevE.102.052101
- AL Krause, V Klika, J Halatek, PK Grant, TE Woolley, N
Dalchau, EA Gaffney, Turing Patterning in Stratified
Domains, Bull. Math. Bio. (2020), 82,
doi:10.1007/s11538-020-00809-9.
- K Ishimoto, EA Gaffney, BJ Walker. Regularized
representation of bacterial hydrodynamics. Physical Review Fluids (2020),
doi:10.1103/PhysRevFluids.5.093101
- S Seirin-Lee, EA Gaffney, A Dawes, CDC-42 interactions
with Par proteins are critical for proper patterning in
polarization, Cells (2020), DOI: 10.3390/cells9092036.
- SN Calver, EA Gaffney, EJ Walsh, WM Durham, JM Oliver, On
the thin-film asymptotics of surface-tension-driven
microfluidics, Journal of Fluid Mechanics (2020), 901,
10.1017/jfm.2020.532.
- BJ Walker, K Ishimoto, EA Gaffney, A regularised
slender-body theory of non-uniform filaments, Journal of Fluid Mechanics (2020),
899:10.1017/jfm.2020.434
- A Osojnik, EA Gaffney, M Davies, JWT Yates, HM Byrne,
Identifying and characterising the impact of excitability in
a mathematical model of tumour-immune interactions, Journal of Theoretical Biology (2020),
501:110250
- MF Adamer, HH Harrington, EA Gaffney, TE Woolley, Coloured
Noise from Stochastic Inflows in Reaction-Diffusion Systems,
Bull. Math. Bio. (2020), 82,
10.1007/s11538-020-00719-w
- BJ Walker, S Phuyal, K Ishimoto, CK Tung, EA Gaffney,
Computer-assisted beat-pattern analysis and the flagellar
waveforms of bovine spermatozoa, Royal Society Open Science (2020) 7:200769
- AL Krause, V Klika, TE Woolley, EA Gaffney, From One
Pattern into Another: Analysis of Turing Patterns in
Heterogeneous Domains via WKBJ, J. Roy Soc. Interface (2020) 20190621.
- M Dvoriashyna, AJE Foss, EA Gaffney, R Repetto, Fluid and
Solute Transport across the Retinal Pigment Epithelium: a
Theoretical Model, J. Roy Soc. Interface (2020) 20190735
- S Egginton, RWP Kissane, AA Al-Shammari, and EA Gaffney,
Quantifying fiber type-specific local capillary supply, J. Applied Physiology, (2020) 128:458-459.
- JP Whiteley, EA Gaffney, Modelling the Inclusion of
Swelling Pressure in a Tissue Level Poroviscoelastic Model
of Cartilage Deformation, Mathematical Medicine And Biology:
A Journal Of The IMA, (2020) https://doi.org/10.1093/imammb/dqaa001
- BJ Walker, K Ishimoto, H Gadelha, EA Gaffney, Filament
mechanics in half-space via regularised Stokeslet segments,
Journal of Fluid Mechanics (2019),
879:803-833.
- JE Jansen, EA Gaffney, J Wagg, MC Coles, Combining
Mathematical Models With Experimentation to Drive Novel
Mechanistic Insights Into Macrophage Function, Frontiers In Immunology (2019)
10.3389/fimmu.2019.01283
- BJ Walker, K Ishimoto, EA Gaffney, Pairwise hydrodynamic
interactions of synchronized spermatozoa, Physical Review
Fluids, (2019) 093101.
- BJ Walker, RJ Wheeler, K Ishimoto, EA Gaffney, Boundary
behaviours of Leishmania mexicana: A hydrodynamic simulation
study, Journal of Theoretical Biology (2019)
462:311-320.
- H Gadelha, EA Gaffney, Flagellar ultrastructure suppresses
buckling instabilities and enables mammalian sperm
navigation in high-viscosity media, J Roy Soc interface (2019),
https://doi.org/10.1098/rsif.2018.0668
- WKW Ho, L Freem, D Zhao, KJ Painter, TE Woolley, EA
Gaffney, MJ McGrew, A Tzika, MC Milinkovitch, P Schneider, A
Drusko, F Matthaus, JD Glover, KL Wells, JA Johansson, MG
Davey, HM Sang, M Clinton, DJ Headon, Feather arrays are
patterned by interacting signalling and cell density waves,
PLOS Biology (2019), 17, DOI:
10.1371/journal.pbio.3000132.
- V Klika and JP Whiteley and CP Brown and EA Gaffney, The
combined impact of tissue heterogeneity and fixed charge for
models of cartilage: the one-dimensional biphasic swelling
model revisited, Biomechanics and Modeling in
Mechanobiology, (2019) doi: 10.1007/s10237-019-01123-7.
- Abdullah A Al-Shammari, Roger WP Kissane, Simon Holbek,
Abigail Louise Mackey, Thomas R Andersen, Eamonn A Gaffney,
Michael Kjaer, Stuart Egginton, Integrated method for
quantitative morphometry and oxygen transport modeling in
striated muscle, J Appl Physiol (2019) 126(3):544-557
- BJ Walker, RJ Wheeler, K Ishimoto, EA Gaffney, Response of
monoflagellate pullers to a shearing flow: A simulation
study of microswimmer guidance, Physical Review E (2018) 063111
- Kenta Ishimoto, Eamonn A Gaffney, Hydrodynamic Clustering
of Human Sperm in Viscoelastic Fluids, Scientific reports (2018), 15600.
- M Dvoriashyna, AJE Foss, EA Gaffney, OE Jensen, OE, R
Repetto, Osmotic and Electroosmotic Fluid Transport across
the Retinal Pigment Epithelium: a Mathematical Model, Journal of Theoretical Biology (2018)
456:233-248.
- LV Brown, EA Gaffney, J Wagg, MC Coles, Applications of
Mechanistic Modelling to Clinical and Experimental
Immunology: An emerging technology to accelerate
immunotherapeutic discovery and development, Clinical and Experimental Immunology,
(2018) 193:284-292.
- V. Klika, M Kozak, EA Gaffney, Domain Size Driven
Instability: Self-Organisation in Systems with Advection, SIAM Journal on Applied Mathematics
(2018), 78(5), 2298-2322.
- K Ishimoto, EA Gaffney, An elastohydrodynamical simulation
study of fillament and spermatozoan swimming driven by
internal couples, IMA J. Appl. Math (2018), 83:655-679.
- LA Hutton-Smith, EA Gaffney, HM Byrne, A Caruso, PK Maini,
and NA Mazer, Theoretical Insights Into the Retinal Dynamics
of VEGF in Patients Treated with Ranibizumab, Based on an
Ocular Pharmacokinetic/Pharmacodynamic Model, Molecular Pharmaceutics, (2018),
15:2770-2784.
- DL Humphries, JA Grogan, EA Gaffney, The mechanics of
phantom Mikado networks, Journal of Physics Communications (2018)
2, UNSP 055015
- AL Krause, V Kilika, TE Woolley, EA Gaffney, Heterogeneity
induces spatiotemporal oscillations in reaction-diffusion
systems, Physical Review E (2018), 97, 052206
- C Willshire, AJ Bron, EA. Gaffney, EI Pearce, Basal Tear
Osmolarity as a metric to estimate body hydration and dry
eye severity, Progress in Retinal and Eye Research
(2018) 64:56-64.
- K Ishimoto, H Gadelha, EA Gaffney, DJ Smith, JC Kirkman
Brown, Human sperm swimming in a high viscosity mucus
analogue, J. Theoretical Biology, (2018) 446:1-10.
- L Brown, EA Gaffney, J. Wagg, M Coles, An In Silico Model
of Cytotoxic T-Lymphocyte Activation in the Lymph Node
Following Short Peptide Vaccination, J. Royal Society Interface (2018) 15
20180041; DOI: 10.1098/rsif.2018.0041
- TE Woolley, J Belmonte-Beitia, G F Calvo, JW Hopewell, EA
Gaffney, B Jones, Changes in the retreatment radiation
tolerance of the spinal cord with time after the initial
treatment, International Journal of Radiation
Biology, (2018) 94:515-531
- PA Roberts, EA Gaffney, JP Whiteley, PJ Luthert, AJE Foss,
HM Byrne, Predictive Mathematical Models for the Spread and
Treatment of Hyperoxia-induced Photoreceptor Degeneration in
Retinitis, Investigative Ophthalmology & Visual
Science, (2018) 59:1238-1249
- K Ishimoto, EA Gaffney, Boundary element methods for
particles and microswimmers in a linear viscoelastic fluid,
Journal of Fluid Mechanics (2017)
831:228-251.
- V Klika, EA Gaffney, History dependence and the continuum
approximation breakdown: the impact of domain growth on
Turing's instability, Proc Roy Soc A (2017) 20160744.
- LA Hutton-Smith, EA Gaffney, HM Byrne, PK Maini, K Gadkar,
NA Mazer, Ocular Pharmacokinetics of Therapeutic Antibodies
Given by Intravitreal Injection: Estimation of Retinal
Permeabilities Using a 3-Compartment Semi-Mechanistic Model,
Mol. Pharm (2017), 14:2690-2698.
- TE Woolley, EA Gaffney, A. Goriely, Random blebbing
motion: A simple model linking cell structural properties to
migration characteristics Phys Rev E (2017) 96, 012409
- PA Roberts, EA Gaffney, PJ Luthert, AJE Foss, HM Byrne,
Mathematical models of retinitis pigmentosa: The oxygen
toxicity hypothesis, J. Theoretical Biology, (2017) 425:53-71.
- M.A. Gilbert, S.M. White, J.M. Bullock, E.A. Gaffney,
Speeding Up The Simulation of Population Spread Models, Methods in Ecology and Evolution, (2017)
8:501-510.
- K Ishimoto, H Gadelha, EA Gaffney, DJ Smith, JC Kirkman
Brown, Coarse-Graining the Fluid Flow around a Human Sperm,
Physical Review Letters (2017) 118:124501
- Reply to Baveye and Darnault: Useful models are simple and
extendable, KZ Coyte, H Tabuteau, EA Gaffney, KR Foster, WM
Durham, PNAS, (2017) 114:E2804-E2805.
- Y. Chen, M. Chen , EA Gaffney, CP Brown, Effect of
crosslinking in cartilage-like collagen microstructures, Journal of the Mechanical Behavior of
Biomedical Materials, (2017) 66:138-143.
- DL Humphries, JA Grogan, EA Gaffney, Mechanical Cell-Cell
Communication in Fibrous Networks: The Importance of Network
Geometry, Bulletin of Mathematical Biology (2017)
79:498-524.
- Microbial competition in porous environments can select
against rapid biofilm growth, KZ Coyte, H Tabuteau, EA
Gaffney, KR Foster, WM Durham, PNAS, (2017) 114:E110-E170.
- F. Yi, EA Gaffney, S Seirin Lee, The Bifurcation Analysis
of Turing Pattern Formation Induced by Delay and Diffusion
in The Schnakenberg System, Journal Discrete and Continuous Dynamical
System B, (2017) 247:647-668.
- K Ishimoto, EA Gaffney, Mechanical tuning of mammalian
sperm behaviour by hyperactivation, rheology and substrate
adhesion: a numerical exploration, J. Royal Society Interface (2016),
13:20160633.
- LG Hutchinson, H-J Mueller, EA Gaffney, PK Maini, J Wagg,
A Phipps, C Boetsch, HM Byrne, B Ribba, Modeling
Longitudinal Preclinical Tumor Size Data to Identify
Transient Dynamics in Tumor Response to Antiangiogenic
Drugs, CPT Pharmacometrics Syst. Pharmacol (2016), doi:10.1002/psp4.12142
- LA Hutton-Smith, EA Gaffney, HM Byrne, PK Maini, D Schwab,
NA Mazer, A mechanistic model of the intravitreal
pharmacokinetics of large molecules and the pharmacodynamic
suppression of ocular vascular endothelial growth factor
levels by ranibizumab in patients with neovascular
age-related macular degeneration, Molecular pharmaceutics (2016) 13:2941-50.
- LG Hutchinson, EA Gaffney, PK Maini, J Wagg, A Phipps, HM
Byrne, Vascular phenotype identification and anti-angiogenic
treatment recommendation: A pseudo-multiscale mathematical
model of angiogenesis, Journal of Theoretical Biology (2016)
398:162-180.
- PA Roberts, EA Gaffney, PJ Luthert, AJE Foss, HM Byrne,
Retinal Oxygen Distribution and the Role of Neuroglobin, Journal of Mathematical Biology, (2016)
73:1-38.
- V Klika, EA Gaffney*, YC Chen, CP Brown, An overview of
multiphase cartilage mechanical modelling and its role in
understanding function and pathology, Journal of The Mechanical Behavior Of
Biomedical Materials (2016) 62: 139-157 [*Equal first
authors].
- PA Roberts, EA Gaffney, PJ Luthert, AJE Foss, HM Byrne,
Mathematical And Computational Models Of The Retina In
Health, Development And Disease, Progress in Retinal And Eye Research
(2016) 53:48-69.
- K Ishimoto, J Cosson, EA Gaffney, A Simulation Study of
Sperm Motility Hydrodynamics Near Fish Eggs and Spheres, Journal of Theoretical Biology, 389:
187-197 (2016).
- FAN Santos, H Gadelha, EA Gaffney, Fock space, symbolic
algebra and analytical solutions for small stochastic
systems, Physical Review E, (2015) 062714.
- H Shum, EA Gaffney, Hydrodynamic analysis of flagellated
bacteria swimming in corners of rectangular channels Physical Review E 92: 063016 (2015).
- TE Woolley, EA Gaffney, A. Goriely, Membrane shrinkage and
cortex remodelling are predicted to work in harmony to
retract blebs, Royal Society Open Science, (2015).DOI:
10.1098/rsos.150184, 15 pages.
- Duffy B, Thiyagalingam J, Walton S, Smith DJ, Trefethen A,
Kirkman-Brown JC, Gaffney EA, Chen M. Glyph-Based Video
Visualization for Semen Analysis. IEEE Trans Vis Comput Graph. (2015) 21:
980-993
- D Hauton, J Winter, AA Al-Shammari, EA Gaffney, RD Evans,
S Egginton, Maternal hypoxia decreases capillary supply and
increases metabolic inefficiency leading to divergence in
myocardial oxygen supply and demand, PLOS One (2015), DOI:
10.1371/journal.pone.0127424
- H Shum, EA Gaffney, Hydrodynamic analysis of flagellated
bacteria swimming near one and between two no-slip plane
boundaries, Physical Review E (2015) 91:033012
- K. Ishimoto, EA Gaffney, Fluid flow and sperm guidance: a
simulation study of hydrodynamic sperm rheotaxis, Journal of the Royal Society
Interface(2015), 12:20150172.
- D Hauton, J Winter, AA Al-Shammari, EA Gaffney, RD Evans,
S Egginton, Changes to both cardiac metabolism and
performance accompany acute reductions in functional
capillary supply, Biochimica et Biophysica Acta
(BBA)-General Subjects, (2015) 1850:681-690.
- K Korvasov, EA Gaffney, PK Maini, MA Ferreira, V Klika,
Investigating the Turing conditions for diffusion-driven
instability in the presence of a binding immobile substrate,
Journal of Theoretical Biology, (2015)
367:286-195.
- EA Gaffney, S Seirin Lee*, The Sensitivity of Turing
Self-Organisation to Biological Feedback Delays: 2D Models
of Fish Pigmentation, Mathematical Medicine and Biology, (2015)
32:56-78. [*Equal First Authors]
- MA Gilbert, EA Gaffney, JM Bullock, SM White, Spreading
speeds for plant populations in landscapes with low
environmental variations, Journal of Theoretical Biology (2014),
363:436-452
- EH Ooi, DJ Smith, H Gadelha, EA Gaffney, J. Kirkman-Brown
The mechanics of hyperactivation in adhered human sperm, Royal Society Open Science 2014, doi
10.1098/rsos.140230
- JB McGillen, CJ Kelly, A Martinez-Gonzalez, NK Martin, EA
Gaffney, PK Maini, Victor M Perez-Garcia, Glucose-lactate
metabolic cooperation in cancer: Insights from a spatial
mathematical model and implications for targeted therapy, Journal of Theoretical Biology (2014)
361:190-203
- K Ishimoto, EA Gaffney, A study of spermatozoan swimming
stability near a surface. Journal of Theoretical Biology (2014) 360
187-199.
- TE Woolley, PK Maini and EA Gaffney, Is pigment cell
pattern formation in zebrafish a game of cops and robbers? Pigment Cell & Melanoma Research
(2014) 27:686-687.
- K Ishimoto, EA Gaffney, Swimming efficiency of spherical
squirmers: Beyond the Lighthill theory. Phys Rev E (2014), 90 012704
- TE Woolley, EA Gaffney, SL Waters, JM Oliver, RE Baker, A
Goriely, Three mechanical models for blebbing and
multi-blebbing, IMA Journal of Applied Mathematics (2014)
79:636-660.
- AA Al-Shammari, EA Gaffney, S Egginton, Modelling
capillary oxygen supply capacity in mixed muscles: Capillary
domains revisited, Journal of Theoretical Biology, (2014)
356:47-61
- DC Markham, MJ Simpson, PK Maini, EA Gaffney, RE Baker,
Comparing methods for modelling spreading cell fronts Journal of Theoretical Biology (2014)
353:95-103.
- S Manzano, EA Gaffney, M Doblare, AH Doweidar, Cartilage
Dysfunction in ALS Patients as Side Effect of Motion Loss:
3D Mechano-Electrochemical Computational Model, Biomed Research International 179070
(2014)
- JB McGillen, EA Gaffney, NK Martin, PK Maini, A general
reaction-diffusion model of acidity in cancer invasion, J. Math. Biol. (2014), 68:1199-1224
- MA Gilbert, SM White, JM Bullock, EA Gaffney, Spreading
speeds for stage structured plant populations in fragmented
landscapes, Journal of Theoretical Biology (2014),
349:135-49.
- TE Woolley, EA Gaffney, JM Oliver, RE Baker, SL Waters, A
Goriely, Cellular blebs: pressure-driven, axisymmetric,
membrane protrusions, Biomechanics and Modeling in
Mechanobiology (2014), 13:463-476
- K Ishimoto, EA Gaffney, Squirmer dynamics near a boundary.
Phys Rev E 88, 062702 (2013).
- DC Markham, MJ Simpson, PK Maini, EA Gaffney, RE Baker,
Incorporating spatial correlations into multispecies
mean-field models, Phys. Rev E88, 052713 (2013).
- H. Gadelha, E. A. Gaffney, and A. Goriely, The counterbend
phenomenon in flagellar axonemes and cross-linked filament
bundles, PNAS 2013 110 (30) 12180-12185.
- S. Seirin Lee, RE Baker, EA Gaffney, SM White, Modelling
Aedes aegypti mosquito control via transgenic and sterile
insect techniques: Endemics and emerging outbreaks, J. Theor. Biol. (2013), 331 p78-90.
- VS Zubkov, CJW Breward, EA Gaffney, Meniscal Fluid
Dynamics near Marx's Line, Bull. Math. Bio., (2013) 75, p1524-1543.
- J Belmonte-Beitia, TE Woolley, JG Scott, PK Maini, EA
Gaffney, Modelling biological invasions: Individual to
population scales at interfaces, J. Theoretical Biology, (2013) 334:1-12.
- MP Curtis, EA Gaffney, The Three Sphere Swimmer in a
Nonlinear Viscoelastic Medium, Phys Rev E 87, 043006 (2013)
- S. Seirin Lee, RE Baker, EA Gaffney, SM White, Optimal
barrier zones for stopping the invasion of Aedes aegypti
mosquitoes via transgenic or sterile insect techniques, Theor. Ecol. (2013), 6, p427-442.
- MP Curtis, JC Kirkman-Brown, TJ Connolly, EA Gaffney,
Modelling a tethered mammalian sperm cell undergoing
hyperactivation, Journal of Theoretical Biology (2012) 309,
p1-10
- EA Gaffney, NAM Monk, RE Baker, S Seirin Lee, Reply to
Correspondence: No Oscillations in Real Activator-Inhibitor
Systems in Accomplishing Pattern Formation. Bull Math Biol. (2012) 74:2268-2271.
- H Shum, EA Gaffney, The effects of flagellar hook
compliance on motility of monotrichous bacteria: a modeling
study, Physics of Fluids (2012) Volume: 24 Issue:
6 Pages: 061901 (19 pp.)
- VS Zubkov, CJW Breward, EA Gaffney, Coupling fluid and
solute dynamics within the ocular surface tear film: a
modelling study of black line osmolarity, Bull. Math. Bio (2012) 74, p2062-93
- NK Martin, IF Robey, EA Gaffney, RJ Gillies, RA Gatenby,
PK Maini, Predicting the Safety and Efficacy of Buffer
Therapy to Raise Tumour pHe: An Integrative Modelling Study,
British J. of Cancer (2012), 7, 1280-1287.
- AA Al-Shammari, EA Gaffney, S Egginton, Re-evaluating the
Use of Voronoi Tessellations in the Assessment of Oxygen
Supply from Capillaries in Muscle. Bull. Math. Bio (2012) 74, p2204-31
- MJ Tindall, EA Gaffney, PK Maini, JP Armitage, Theoretical
insights into bacterial chemotaxis WIREs Syst Biol Med (2012) 4, p247-259.
- H Colin-Harper, TE Woolley, L Dyson, A Patel, P Potter, RE
Baker, EA Gaffney, PK Maini, PR Dash, K Patel, Age Related
changes in speed and mechanism of adult stem cell migration,
Stem Cells (2012), 30, p1182-1195.
- PK Maini, TE Woolley, RE Baker, EA Gaffney and S Seirin
Lee, Turing's model for biological pattern formation and the
robustness problem, Interface Focus (2012), 2, p487-496
- J. McGillen, NK Martin, IF Robey, EA Gaffney, PK Maini,
Applications of mathematical analysis to tumour acidity
modelling, U. Kyoto RIMS Kokyuroku Bessatsu, May
2012, 31-60.
- PDMH Verhaegen, J van Marle, A Kuehne, HJ Schouten, EA
Gaffney, PK Maini, E Middelkoop, PPM van Zuijlen, Collagen
bundle morphometry in skin and scar tissue: a novel distance
mapping method provides superior measurements compared to
Fourier analysis, Journal of Microscopy, (2012) 245 p82-89.
- TE Woolley, RE Baker, EA Gaffney, PK Maini, S Seirin-Lee,
Effects of intrinsic stochasticity on delayed
reaction-diffusion patterning systems, Phys. Rev. E (2012) 85 051914
- V Klika, RE Baker, D Headon, EA Gaffney, The influence of
receptor-mediated interactions on reaction-diffusion
mechanisms of cellular self-organisation, Bulletin of Mathematical Biology (2012) p
935-957.
- TE Woolley, RE Baker, EA Gaffney, PK Maini, Stochastic
reaction and diffusion on growing domains: Understanding the
breakdown of robust pattern formation, Phys. Rev. E 84, (2011) 046216 [16 pages]
- TE Woolley, RE Baker, EA Gaffney, PK Maini, Influence of
stochastic domain growth on pattern nucleation for diffusive
systems with internal noise, Phys. Rev. E 84, 041905 (2011) [13 pages]
- EAJ Boston, EA Gaffney, The influence of toxicity
constraints in models of chemotherapeutic protocol
escalation Math Med Biol (2011) 28 p357-384.
- C. Venkataraman, T. Sekimura, EA Gaffney, PK Maini,
A.Madzvamuse, Modeling parr-mark pattern formation during
the early development of Amago trout Phys. Rev. E 84, 041923 (2011) [13 pages]
- S Seirin Lee, EA Gaffney, RE Baker, The dynamics of Turing
patterns for morphogen-regulated growing domains with
cellular response delays, Bulletin of Mathematical Biology, (2011),
73 p2527-2551
- TE Woolley, RE Baker, EA Gaffney, PK. Maini, Power spectra
methods for a stochastic description of diffusion on
deterministically growing domains Phys. Rev. E (2011) 84, 021915 [15 pages]
- DJ Smith, EA Gaffney, H Shum, H Gadelha, JC Kirkman-Brown,
Comment on the Article by J. Elgeti, U. B. Kaupp, and G.
Gompper: Hydrodynamics of Sperm Cells Near Surfaces, Biophysical J. (2011) 100(9) p2318-2320
- AJ Bron, N Yokoi, EA Gaffney, JM Tiffany, A solute
gradient in the tear meniscus. I. A hypothesis to explain
Marx's line. The Ocular Surface (2011) 9 p70-91.
- AJ Bron, N Yokoi, EA Gaffney, JM Tiffany, A solute
gradient in the tear meniscus. II Implications for lid
margin disease, including meibomian gland dysfunction. The Ocular Surface (2011) 9 p92-97.
- J Schofield, EA Gaffney, RA Gatenby, PK Maini, Tumour
angiogenesis: The gap between theory and experiments, J. Theoretical Biology, (2011) 274,
p97-102.
- NK Martin, EA Gaffney, RA Gatenby, RJ Gillies, IF Robey,
PK. Maini, A Mathematical Model of Tumour and Blood pHe
Regulation: The HCO3 /CO2 Buffering System, Math Biosci (2011) 230 p1-11.
- EA Gaffney, H Gadelha, DJ Smith, JR Blake, JC
Kirkman-Brown, Mammalian Sperm Motility: Observation and
Theory. Annual Reviews of Fluid Mechanics, (2011),
43, p501-528.
- NK Martin, EA Gaffney, RA Gatenby, PK Maini,
Tumour-Stromal Interactions in Acid-Mediated Invasion: A
Mathematical Model, Journal Of Theoretical Biology, (2010),
267, p461-470.
- NK Martin, EA Gaffney, RA Gatenby, PK Maini, Leaky Vessels
As A Potential Source Of Stromal Acidification In Tumours, Journal Of Theoretical Biology (2010), 267
p454-460.
- S Egginton, EA Gaffney, Tissue capillary supply - it's
quality not quantity that counts!, Experimental Physiology (2010), 95,
p971-979.
- S Seirin Lee, EA Gaffney, Aberrant Behaviours of Reaction
Diffusion Self-organisation Models on Growing Domains in the
Presence of Gene Expression Time Delays, Bulletin of Mathematical Biology (2010),
72, p2161-2179.
- H Gadelha, EA Gaffney, DJ Smith, JC Kirkman-Brown,
Nonlinear instability in flagellar dynamics: a novel
modulation mechanism in sperm migration?, J. Royal Society Interface (2010) 7
p1689-1697.
- S Seirin Lee, EA Gaffney, NAM Monk, The Influence of Gene
Expression Time Delays on Gierer-Meinhardt Pattern Formation
Systems, Bulletin of Mathematical Biology (2010),
72, p2139-2160.
- H Shum, EA Gaffney, DJ Smith, Modelling bacterial
behaviour close to a no-slip plane boundary: the influence
of bacterial geometry, Proc Roy Soc A (2010) 466 p1725-1748.
- P Moreo, EA Gaffney, JM Garcia-Anzar, M Doblare, On the
modelling of biological patterns with mechanochemical
models: insights from analysis and computation, Bulletin of Mathematical Biology (2010),
72, p400-431.
- A Madzvamuse, EA Gaffney, PK Maini, Stability analysis of
reaction-diffusion systems with time-dependent coefficients
on growing domains, Journal Of Mathematical Biology (2010),
61, p133-164
- EA Gaffney, JM Tiffany, N Yokoi, AJ Bron, A Mass and
Solute Balance Model for Tear Volume and Osmolarity in The
Normal And The Dry Eye, Progress in Retinal And Eye Research
(2010), 29, p59-78.
- DJ Smith, EA Gaffney, JR Blake, Mathematical modelling of
cilia-driven transport of biological fluids, Proceedings of the Royal Society A (2009),
465, p2417-2439.
- AJ Bron, N Yokoi, EA Gaffney, JM Tiffany, Predicted
Phenotypes of Dry Eye - Proposed Consequences of its Natural
History, The Ocular Surface (2009) 7, p78-92.
- DJ Smith, EA Gaffney, H Gadelha, N Kapur, JC
Kirkman-Brown, Bend propagation in the flagella of migrating
human sperm, and its modulation by viscosity, Cell Motility & The Cytoskeleton
(2009), 66, 220-236.
- DJ Smith, EA Gaffney, JR Blake, JC Kirkman-Brown, Human
sperm accumulation near surfaces: a simulation study, J. Fluid Mechanics (2009), 621, p289-320.
- HC Monro, EA Gaffney, Modelling chemotherapy resistance in
palliation and failed cure, J. Theoretical Biology (2009), 257,
p292-302.
- DJ Smith, EA Gaffney, JR Blake, Modelling mucociliary
clearance, Respiratory Physiology & Neurobiology
(2008) 163, p178-188.
- RE Baker, EA Gaffney, PK Maini, Partial differential
equations for self-organization in cellular and
developmental biology, Nonlinearity (2008), 21, R251-290.
- DJ Smith, JR Blake, EA Gaffney, Fluid mechanics of nodal
flow due to embryonic primary cilia, Journal of The Royal Society Interface
(2008) 5, p567-573
- EA Gaffney, JK Heath, MZ Kwiatkowska, A Mass Action Model
of a Fibroblast Growth Factor Signaling Pathway and Its
Simplification, Bulletin of Mathematical Biology (2008)
68, p99-130.
- DJ Smith, EA Gaffney, JR Blake, Discrete cilia modelling
with singularity distributions, Bulletin of Mathematical Biology (2007)
69, p1477-1510.
- DJ Smith, EA Gaffney, JR. Blake, A model of tracer
transport in airway surface liquid, Bulletin of Mathematical Biology (2007)
69, p817-836.
- DJ Smith, EA Gaffney and JR Blake, A visco-elastic
traction layer model of muco-ciliary transport, Bulletin Mathematical Biology, (2007) 69,
p289-327.
- EA Gaffney, NAM Monk, Gene Expression Time Delays and
Turing Pattern Formation Systems, Bulletin Mathematical Biology (2006),
p99-130.
- EA Gaffney, The Mathematical Modelling of Adjuvant
Chemotherapy Scheduling: Incorporating the Effects of
Protocol Rest Phases and Pharmacokinetics. Bulletin of Mathematical Biology (2005)
67, p563-611.
- EA Gaffney, The Application Of Matematical Modelling To
Aspects Of Adjuvant Chemotherapy Scheduling, Journal of Mathematical Biology (2004) 48,
p375-422.
- EA Gaffney, K. Pugh, PK Maini, F. Arnold, Investigating A
Simple Model Of Wound Healing Angiogenesis, J. of Mathematical Biology (2002) 45
p337-374.
- E. Crampin, EA Gaffney, P.K. Maini, Mode Doubling And
Tripling In Reation-Diffusion Patterns On Growing Domains: A
Piecewise Linear Model, J. of Mathematical Biology (2002) 44
p107-128.
- EA. Gaffney, On Conditions For The Stability Of A Two
Component Mixed Quasimonotone Reaction Diffusion Equation, J. of Mathematical Analysis and
Applications (2001) 256, p513-524.
- EA Gaffney, PK Maini, JA Sherratt, S.Tuft, The
Mathematical Modelling Of Cell Kinetics In Corneal
Epithelial Wound Healing And Comparison With Experiment, Journal of Theoretical Biology (1999) 197,
p15-40.
- EA Gaffney, PK Maini, C. McCaig, M. Zhao, J. Forrester,
Modelling corneal epithelial wound closure in the presence
of physiological electric fields via a moving boundary
formalism, IMA Journal of Mathematics Applied in
Medicine and Biology (1999) 16, p369-393.
- E. Crampin, EA Gaffney, PK Maini, Reaction and Diffusion
on Growing Domains: Scenarios for Robust Pattern Formation,
Bulletin Mathematical Biology (1999) 61,
p1093-1120.
- EA Gaffney, PK Maini, JA Sherratt, PD Dale, Wound healing
in the corneal epithelium: biological mechanisms and
mathematical models, Journal of Theoretical Medicine (1997),
1:13-23.
- EA Gaffney, Massive hard thermal loops in curved
space-time, Nuclear Physics B (1996) 476: 275-309.
- EA Gaffney, Quark hard thermal loops in curved spacetime,
Nuclear Physics B (1996) 459:311-334.
- J Frenkel, EA Gaffney, JC Taylor, High-temperature field
theory in curved spacetime, Nuclear Physics B (1995) 439: 131-143.
- E Gaffney, Hard Thermal Loops, Weak Gravitational Fields
and The Quark Gluon Energy Momentum Tensor, Nuclear Physics B (1995) 442: 268-298.
Book Chapters/Proceedings
- Dvoriashyna, M., Foss, A.J.E., Gaffney, E.A and
Repetto, R. 2022. Mathematical models of water transport
across ocular epithelial layers in ‘Modelling of Mass
Transport Processes in Biological Media’ edited by Sid
Becker, Andrey Kuznetsov, Filippo de Monte, Giuseppe
Pontrelli and Dan Zhao. Publisher: Elsevier. ISBN:
978044315653
- K Ishimoto, EA Gaffney, Modelling Spermatozoan Swimming:
Its Capabilities and Limitations for Contributing to The
Understanding of Sperm Guidance, Flagellar mechanics and
sperm guidance, Ch.9, Flagellar mechanics and sperm
guidance, Ed. J. Cosson, Bentham Science Publishers, (2015).
- PK Maini, TE.Woolley, EA Gaffney, RE Baker, Turing's
Theory of Developmental Pattern Formation, The Once and
Future Turing, Ch 9, p137-149, edited by S.B. Cooper &
A. Hodges, Cambridge University Press 2015
- AA Al-Shammari, EA Gaffney, S Egginton, Modelling Oxygen
Capillary Supply to Striated Muscle Tissues, in Springer
Proceedings in Mathematics & Statistics 87, Advances in
Applied Mathematics, 2014
- Shum H, Gaffney EA. Ch.2 in: MJ Kim, E Steager, A Agung
Julius eds. Mathematical models for individual swimming
bacteria in Microbiorobotics: biologically inspired
microscale robotic systems. Elsevier, 2012. ISBN:
9781455778911
- M Kwiatkowska, G Norman, D Parker, O Tymchyshyn, JK
Heath, EA Gaffney, Simulation And Verification For
Computational Modelling Of Signalling Pathways, Proceedings
of the 2006 Winter Simulation Conference, L. F. Perrone, F.
P. Wieland, J. Liu, B. G. Lawson, D. M. Nicol, and R. M.
Fujimoto, eds, (2006)
- JR Blake, EA Gaffney, Modelling aspects of tracer
transport in muco-ciliary flows, In Cilia, Mucus and
Mucociliary Interactions, 26, M Salathe (Editor), New York,
Marcel Dekker, 291-302. (2001).
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