Authors: De Carli, Alice, Kapelyukh, Yury, Kursawe, Jochen, Chaplain, Mark Andrew Joseph, Wolf, C Roland, Hamis, Sara Jasmin
Superior Title: De Carli , A , Kapelyukh , Y , Kursawe , J , Chaplain , M A J , Wolf , C R & Hamis , S J 2024 , ' Simulating BRAFV600E-MEK-ERK signalling dynamics in response to vertical inhibition treatment strategies ' , npj Systems Biology and Applications , vol. 10 , 51 . https://doi.org/10.1038/s41540-024-00379-9
Subject Terms: Mathematical model, Melanoma, Drug resistance, Drug combinations
File Description: application/pdf
Relation: https://research-portal.st-andrews.ac.uk/en/researchoutput/simulating-brafv600emekerk-signalling-dynamics-in-response-to-vertical-inhibition-treatment-strategies(00255e2e-0463-4af3-8033-208310e6022d).html
Availability:
https://doi.org/10.1038/s41540-024-00379-9
https://research-portal.st-andrews.ac.uk/en/researchoutput/simulating-brafv600emekerk-signalling-dynamics-in-response-to-vertical-inhibition-treatment-strategies(00255e2e-0463-4af3-8033-208310e6022d).html
https://research-repository.st-andrews.ac.uk/bitstream/10023/29909/1/DeCarli-2024-Simulating_BRAFV600E-MEK-ERK-npjSBA-10-51-CCBY.pdf
Superior Title: Macfarlane , F R , Chaplain , M A J & Eftimie , R 2022 , ' Modelling rheumatoid arthritis : a hybrid modelling framework to describe pannus formation in a small joint ' , ImmunoInformatics , vol. 6 , 100014 . https://doi.org/10.1016/j.immuno.2022.100014
Subject Terms: Rheumatoid arthritis, Hybrid model, Stochasticity, Immune response
File Description: application/pdf
Availability:
https://doi.org/10.1016/j.immuno.2022.100014
https://risweb.st-andrews.ac.uk/portal/en/researchoutput/modelling-rheumatoid-arthritis(b30fb68f-d4cc-43ed-9a56-cc31af52b89e).html
https://research-repository.st-andrews.ac.uk/bitstream/10023/25378/1/Macfarlane_2022_Immunoinformatics_Modelling_RA_CC.pdf
Authors: Hamis, Sara J., Kapelyukh, Yury, McLaren, Aileen, Henderson, Colin J., Wolf, C. Roland, Chaplain, Mark A. J.
Superior Title: Hamis , S J , Kapelyukh , Y , McLaren , A , Henderson , C J , Wolf , C R & Chaplain , M A J 2021 , ' Quantifying ERK activity in response to inhibition of the BRAFV600E-MEK-ERK cascade using mathematical modelling ' , British Journal of Cancer , vol. 125 , pp. 1552-1560 . https://doi.org/10.1038/s41416-021-01565-w
Subject Terms: Computational science, Melanoma, Numerical simulations, /dk/atira/pure/subjectarea/asjc/2700/2730, name=Oncology, /dk/atira/pure/subjectarea/asjc/1300/1306, name=Cancer Research
File Description: application/pdf
Superior Title: Villa , C , Chaplain , M A J , Gerisch , A & Lorenzi , T 2021 , ' Mechanical models of pattern and form in biological tissues : the role of stress-strain constitutive equations ' , Bulletin of Mathematical Biology , vol. 83 , 80 . https://doi.org/10.1007/s11538-021-00912-5
Subject Terms: Pattern formation, Mechanical models, Murray-Oster theory, Biological tissues, Stress-strain constitutive equations, Linear viscoelasticity
File Description: application/pdf
Availability:
https://doi.org/10.1007/s11538-021-00912-5
https://risweb.st-andrews.ac.uk/portal/en/researchoutput/mechanical-models-of-pattern-and-form-in-biological-tissues(feb5fb3b-fffb-467b-9ef6-42d5fe885fde).html
https://research-repository.st-andrews.ac.uk/bitstream/10023/23254/1/Villa_2021_BMB_MechanicalModels_CC.pdf
Authors: Hamis, Sara Jasmin, Kapelyukh, Yury, Henderson, Colin J., Wolf, C. Roland, Chaplain, Mark Andrew Joseph
Superior Title: Hamis , S J , Kapelyukh , Y , Henderson , C J , Wolf , C R & Chaplain , M A J 2021 , ' Quantifying ERK activity in response to inhibition of the BRAFV600E-MEK-ERK cascade using mathematical modelling ' , British Journal of Cancer , vol. First Online . https://doi.org/10.1038/s41416-021-01565-w
Subject Terms: Computational science, Melanoma, Numerical simulations
File Description: application/pdf
Availability:
https://doi.org/10.1038/s41416-021-01565-w
https://risweb.st-andrews.ac.uk/portal/en/researchoutput/quantifying-erk-activity-in-response-to-inhibition-of-the-brafv600emekerk-cascade-using-mathematical-modelling(45fffd8b-e1a8-403c-984d-8c9db417f670).html
https://research-repository.st-andrews.ac.uk/bitstream/10023/24104/1/Hamis_2021_BJoC_Quantifying_ERK_activity_CC.pdf
Superior Title: Franssen , L C , Sfakianakis , N & Chaplain , M A J 2021 , ' A novel 3D atomistic-continuum cancer invasion model : in silico simulations of an in vitro organotypic invasion assay ' , Journal of Theoretical Biology , vol. 522 , 110677 . https://doi.org/10.1016/j.jtbi.2021.110677
Subject Terms: Cancer invasion, Organotypic assay, Atomistic-continuum model
File Description: application/pdf
Availability:
https://doi.org/10.1016/j.jtbi.2021.110677
https://risweb.st-andrews.ac.uk/portal/en/researchoutput/a-novel-3d-atomisticcontinuum-cancer-invasion-model(d0d6a4a6-429c-490a-9e3c-9067d6164132).html
https://research-repository.st-andrews.ac.uk/bitstream/10023/25111/1/elsarticle_template_compressed.pdf
Authors: Liu, Ruirui, Higley, Kathryn, Swat, Maciej, Chaplain, Mark Andrew Joseph, Powathil, Gibin, Glazier, James
Superior Title: Liu , R , Higley , K , Swat , M , Chaplain , M A J , Powathil , G & Glazier , J 2021 , ' Development of a coupled simulation toolkit for computational radiation biology based on Geant4 and CompuCell3D ' , Physics in Medicine and Biology , vol. 66 , no. 4 , 045026 . https://doi.org/10.1088/1361-6560/abd4f9
Subject Terms: Computational radiation biology, Geant4, CompuCell3D, RADCELL, Coupled simulation, Microbeam radiation therapy, Vascular tumour simulation
File Description: application/pdf
Availability:
https://doi.org/10.1088/1361-6560/abd4f9
https://risweb.st-andrews.ac.uk/portal/en/researchoutput/development-of-a-coupled-simulation-toolkit-for-computational-radiation-biology-based-on-geant4-and-compucell3d(ea2fe428-bc00-40b8-b845-9c503f0c7a04).html
https://research-repository.st-andrews.ac.uk/bitstream/10023/24841/1/Liu_2021_Development_of_a_coupled_PMB_AAM.pdf
Superior Title: Hamis , S , Yates , J , Chaplain , M A J & Powathil , G G 2021 , ' Targeting cellular DNA damage responses in cancer : an in vitro -calibrated agent-based model simulating monolayer and spheroid treatment responses to ATR-inhibiting drugs ' , Bulletin of Mathematical Biology , vol. 83 , no. 10 , 103 . https://doi.org/10.1007/s11538-021-00935-y
Subject Terms: DNA damage response inhibition, Agent-based model, Mathemathical oncology, AZD6738
File Description: application/pdf
Availability:
https://doi.org/10.1007/s11538-021-00935-y
https://risweb.st-andrews.ac.uk/portal/en/researchoutput/targeting-cellular-dna-damage-responses-in-cancer(c1704657-424a-4321-b841-aa4431a07cb5).html
https://research-repository.st-andrews.ac.uk/bitstream/10023/23870/1/Hamis_BoMB_Targeting_cellular_DNa_damage_CC.pdf
Authors: Xiao, Yunchen, Thomas, Len, Chaplain, Mark Andrew Joseph
Superior Title: Xiao , Y , Thomas , L & Chaplain , M A J 2021 , ' Calibrating models of cancer invasion : parameter estimation using approximate Bayesian computation and gradient matching ' , Royal Society Open Science , vol. 8 , no. 6 , 202237 . https://doi.org/10.1098/rsos.202237
Subject Terms: Tumour cells, Cancer invasion, Metastasis, Approximate Bayesian computation, Bhattacharyya distance, Gradient matching, Generalized additive models
File Description: application/pdf
Authors: Pitcher, Michael John, Dobson, Simon Andrew, Kelsey, Tom, Chaplain, Mark Andrew Joseph, Sloan, Derek James, Gillespie, Stephen Henry, Bowness, Ruth
Superior Title: Pitcher , M J , Dobson , S A , Kelsey , T , Chaplain , M A J , Sloan , D J , Gillespie , S H & Bowness , R 2020 , ' How mechanistic in silico modelling can improve our understanding of TB disease and treatment ' , International Journal of Tuberculosis and Lung Disease , vol. 24 , no. 11 , pp. 1145-1150 . https://doi.org/10.5588/ijtld.20.0107
Subject Terms: TB modelling, Disease models, Statistical modelling, Within-host mechanistic model
File Description: application/pdf
Relation: https://research-portal.st-andrews.ac.uk/en/researchoutput/how-mechanistic-in-silico-modelling-can-improve-our-understanding-of-tb-disease-and-treatment(c847b1ec-88e1-4f6a-96c3-cfabc7b7c89c).html
Availability:
https://doi.org/10.5588/ijtld.20.0107
https://research-portal.st-andrews.ac.uk/en/researchoutput/how-mechanistic-in-silico-modelling-can-improve-our-understanding-of-tb-disease-and-treatment(c847b1ec-88e1-4f6a-96c3-cfabc7b7c89c).html
https://research-repository.st-andrews.ac.uk/bitstream/10023/20951/1/Pitcher_2020_How_mechanistic_in_silico_IJTLD_1145_CCBY.pdf
Authors: Bellomo, Nicola, Bingham, Richard, Chaplain, Mark A. J., Dosi, Giovanni, Forni, Guido, Knopoff, Damian A., Lowengrub, John, Twarock, Reidun, Virgillito, Maria Enrica
Superior Title: Bellomo , N , Bingham , R , Chaplain , M A J , Dosi , G , Forni , G , Knopoff , D A , Lowengrub , J , Twarock , R & Virgillito , M E 2020 , ' A multiscale model of virus pandemic : heterogeneous interactive entities in a globally connected world ' , Mathematical Models and Methods in Applied Sciences , vol. 30 , no. 08 , pp. 1591-1651 . https://doi.org/10.1142/s0218202520500323
Subject Terms: COVID-19, Living systems, Immune competition, Complexity, Multiscale problems, Spatial patterns, Networks, Intracellular infection dynamics, Viral quasispecies, Virus structure modelling, SARS-CoV-2
File Description: application/pdf
Superior Title: Franßen , L C & Chaplain , M A J 2020 , ' A mathematical multi-organ model for bidirectional epithelial-mesenchymal transitions in the metastatic spread of cancer ' , IMA Journal of Applied Mathematics , vol. 85 , no. 5 , pp. 724-761 . https://doi.org/10.1093/imamat/hxaa022
Subject Terms: Mathematical oncology, Epithelial-mesenchymal transition, Metastatic spread, Multi-organ model, Tumour microenvironment, Individual-based model
File Description: application/pdf
Availability:
https://doi.org/10.1093/imamat/hxaa022
https://risweb.st-andrews.ac.uk/portal/en/researchoutput/a-mathematical-multiorgan-model-for-bidirectional-epithelialmesenchymal-transitions-in-the-metastatic-spread-of-cancer(a7f0f317-25fe-4d9e-989f-0b76aff9f924).html
https://research-repository.st-andrews.ac.uk/bitstream/10023/23929/1/franssen_chaplain_IMAMAT_2019_181.R1.pdf
Superior Title: Macnamara , C K , Caiazzo , A , Ramis-Conde , I & Chaplain , M A J 2020 , ' Computational modelling and simulation of cancer growth and migration within a 3D heterogeneous tissue : the effects of fibre and vascular structure ' , Journal of Computational Science , vol. 40 , 101067 . https://doi.org/10.1016/j.jocs.2019.101067
Subject Terms: Cancer modelling, Individual-based model, Cell-matrix interaction, Vasculature, Finite element method
File Description: application/pdf
Availability:
https://doi.org/10.1016/j.jocs.2019.101067
https://risweb.st-andrews.ac.uk/portal/en/researchoutput/computational-modelling-and-simulation-of-cancer-growth-and-migration-within-a-3d-heterogeneous-tissue(aacceb9e-d12c-4c01-8735-9c49a5fbc1e8).html
https://research-repository.st-andrews.ac.uk/bitstream/10023/21169/1/CKM_AC_IRC_MAJC_NOV2019.pdf
Superior Title: Chaplain , M A J , Lorenzi , T & Macfarlane , F R 2020 , ' Bridging the gap between individual-based and continuum models of growing cell populations ' , Journal of Mathematical Biology , vol. 80 , no. 1-2 , pp. 343-371 . https://doi.org/10.1007/s00285-019-01391-y
Subject Terms: Growing cell populations, Pressure-driven cell movement, Pressure-limited growth, Individual-based models, Continuum models
File Description: application/pdf
Availability:
https://doi.org/10.1007/s00285-019-01391-y
https://risweb.st-andrews.ac.uk/portal/en/researchoutput/bridging-the-gap-between-individualbased-and-continuum-models-of-growing-cell-populations(381bb8b1-279e-4a83-87b4-ddde772a1e50).html
https://research-repository.st-andrews.ac.uk/bitstream/10023/20063/1/Manuscript_Revision_nored.pdf
Superior Title: Macfarlane , F R , Chaplain , M A J & Lorenzi , T 2020 , ' A hybrid discrete-continuum approach to model Turing pattern formation ' , Mathematical Biosciences and Engineering , vol. 17 , no. 6 , pp. 7442-7479 . https://doi.org/10.3934/mbe.2020381
Subject Terms: Cell pattern formation, Turing patterns, Hybrid models, Individual-based models, Reaction-diffusion systems
File Description: application/pdf
Availability:
https://doi.org/10.3934/mbe.2020381
https://risweb.st-andrews.ac.uk/portal/en/researchoutput/a-hybrid-discretecontinuum-approach-to-model-turing-pattern-formation(656ba9a0-543c-4b9a-a675-72e96ac6186b).html
https://research-repository.st-andrews.ac.uk/bitstream/10023/20961/1/Macfarlane_2020_A_hybrid_discrete_MBE_7442_CCBY.pdf
Superior Title: Villa , C , Chaplain , M A J & Lorenzi , T 2020 , ' Evolutionary dynamics in vascularised tumours under chemotherapy : mathematical modelling, asymptotic analysis and numerical simulations ' , Vietnam Journal of Mathematics , vol. First Online . https://doi.org/10.1007/s10013-020-00445-9
Subject Terms: Vascularised tumours, Evolutionary dynamics, Intra-tumour heterogeneity, Resistance to chemotherapy, Mathematical oncology, Non-local partial differential equations
File Description: application/pdf
Availability:
https://doi.org/10.1007/s10013-020-00445-9
https://risweb.st-andrews.ac.uk/portal/en/researchoutput/evolutionary-dynamics-in-vascularised-tumours-under-chemotherapy(72279180-451c-442a-9b0e-7de674c2b9b8).html
https://research-repository.st-andrews.ac.uk/bitstream/10023/20767/1/Villa_2020_VJM_Evolutionary_CC.pdf
Superior Title: Sfakianakis , N , Madzvamuse , A & Chaplain , M A J 2020 , ' A hybrid multiscale model for cancer invasion of the extracellular matrix ' , Multiscale Modeling and Simulation: A SIAM Interdisciplinary Journal , vol. 18 , no. 2 , pp. 824–850 . https://doi.org/10.1137/18M1189026
Subject Terms: Cancer invasion, Multiscale modelling, Hybrid continuum-discrete, Coupled partial and stochastic partial differential equations
File Description: application/pdf
Availability:
https://doi.org/10.1137/18M1189026
https://risweb.st-andrews.ac.uk/portal/en/researchoutput/a-hybrid-multiscale-model-for-cancer-invasion-of-the-extracellular-matrix(835e0e06-5b9e-445d-8ade-37870a4076cb).html
https://research-repository.st-andrews.ac.uk/bitstream/10023/19387/1/sfakianakis_etal_siammms2020.pdf
Superior Title: Preedy , K , Chaplain , M A J , Leybourne , D , Marion , G & Karley , A 2020 , ' Learning-induced switching costs in a parasitoid can maintain diversity of host aphid phenotypes although biocontrol is destabilized under abiotic stress ' , Journal of Animal Ecology , vol. Early View . https://doi.org/10.1111/1365-2656.13189
Subject Terms: Climate change, Drought, Hamiltonella defensa, Mathematical model, Parasitoid, Symbiont
File Description: application/pdf
Availability:
https://doi.org/10.1111/1365-2656.13189
https://risweb.st-andrews.ac.uk/portal/en/researchoutput/learninginduced-switching-costs-in-a-parasitoid-can-maintain-diversity-of-host-aphid-phenotypes-although-biocontrol-is-destabilized-under-abiotic-stress(50a8aa8a-45de-423c-8f0e-877227a0ed00).html
https://research-repository.st-andrews.ac.uk/bitstream/10023/21736/1/JAE_2019_00275.R1_revision2_finaldraft.pdf
Authors: Stace, Rebecca E. A., Stiehl, Thomas, Chaplain, Mark A. J., Marciniak-Czochra, Anna, Lorenzi, Tommaso
Superior Title: Stace , R E A , Stiehl , T , Chaplain , M A J , Marciniak-Czochra , A & Lorenzi , T 2020 , ' Discrete and continuum phenotype-structured models for the evolution of cancer cell populations under chemotherapy ' , Mathematical Modelling of Natural Phenomena , vol. 15 , 14 . https://doi.org/10.1051/mmnp/2019027
Subject Terms: Cancer cell populations, Chemotherapy, Epigenetic drugs, Individual-based models, Nonlocal parabolic equations
File Description: application/pdf
Availability:
https://doi.org/10.1051/mmnp/2019027
https://risweb.st-andrews.ac.uk/portal/en/researchoutput/discrete-and-continuum-phenotypestructured-models-for-the-evolution-of-cancer-cell-populations-under-chemotherapy(5966d364-10fb-4ce2-8d89-794934d97897).html
https://research-repository.st-andrews.ac.uk/bitstream/10023/19709/1/Staceetal_final.pdf
Superior Title: Macfarlane , F R , Chaplain , M A J & Eftimie , R 2020 , ' Quantitative Predictive Modelling Approaches to Understanding Rheumatoid Arthritis : A Brief Review ' , Cells , vol. 9 , no. 1 , 74 . https://doi.org/10.3390/cells9010074
Subject Terms: rheumatoid arthritis, mathematical models, deterministic models, ODEs, PDEs, probabilistic models, /dk/atira/pure/subjectarea/asjc/2700/2700, name=General Medicine
File Description: application/pdf