An agent-based model for cell microenvironment simulation using FLAMEGPU2.

Dawn C. Walker

Carlos Borau Robert Chisholm Paul Richmond Dawn C. Walker An agent-based model for cell microenvironment simulation using FLAMEGPU2. 108831 2024 179 Comput. Biol. Medicine https://doi.org/10.1016/j.compbiomed.2024.108831 db/journals/cbm/cbm179.html#BorauCRW24 streams/journals/cbm

Kenneth Y. Wertheim Robert Chisholm Paul Richmond Dawn C. Walker Multicellular model of neuroblastoma proposes unconventional therapy based on multiple roles of p53. 1012648 2024 20 PLoS Comput. Biol. 12 https://doi.org/10.1371/journal.pcbi.1012648 db/journals/ploscb/ploscb20.html#WertheimCRW24 streams/journals/ploscb

Malwina Matella Keith D. Hunter Saba Balasubramanian Dawn C. Walker The Use of Virtual Tissue Constructs That Include Morphological Variability to Assess the Potential of Electrical Impedance Spectroscopy to Differentiate between Thyroid and Parathyroid Tissues during Surgery. 2198 2024 April 24 Sensors 7 https://doi.org/10.3390/s24072198 db/journals/sensors/sensors24.html#MatellaHBW24

Carlos Borau Kenneth Y. Wertheim Silvia Hervas-Raluy Diego Sainz-DeMena Dawn C. Walker Robert Chisholm Paul Richmond V. Varella Marco Viceconti Aaron Montero Elisabet Gregori-Puigjané Jordi Mestres Marek Kasztelnik José Manuel García-Aznar A multiscale orchestrated computational framework to reveal emergent phenomena in neuroblastoma. 107742 2023 November 241 Comput. Methods Programs Biomed. https://doi.org/10.1016/j.cmpb.2023.107742 db/journals/cmpb/cmpb241.html#BorauWHSWCRVVMGMKA23

Malwina Matella Dawn C. Walker Keith D. Hunter Computational Modelling of Probe Configurations for Electrical Impedance Spectroscopy-based Differentiation of Thyroid and Parathyroid Tissues. 1-6 2023 MeMeA https://doi.org/10.1109/MeMeA57477.2023.10171880 conf/memea/2023 db/conf/memea/memea2023.html#MatellaWH23

James P. Heath Keith D. Hunter Craig Murdoch Dawn C. Walker Computational Modelling for Electrical Impedance Spectroscopy-Based Diagnosis of Oral Potential Malignant Disorders (OPMD). 5913 2022 22 Sensors 15 https://doi.org/10.3390/s22155913 db/journals/sensors/sensors22.html#HeathHMW22

Tim Ingham-Dempster Ria Rosser Bernard Corfe Dawn C. Walker From cell to multi-crypt: Agent-based models of the human colon suggests novel processes of Field cancerisation. 101066 2020 41 J. Comput. Sci. https://doi.org/10.1016/j.jocs.2019.101066 db/journals/jocs/jocs41.html#Ingham-Dempster20

Tim Ingham-Dempster Bernard Corfe Dawn C. Walker A cellular based model of the colon crypt suggests novel effects for Apc phenotype in colorectal carcinogenesis. 125-131 2018 24 J. Comput. Sci. https://doi.org/10.1016/j.jocs.2017.06.013 db/journals/jocs/jocs24.html#Ingham-Dempster18

Marco Viceconti Simone Bnà Daniele Tartarini Stelios Sfakianakis James A. Grogan Dawn C. Walker Samuel Gamble Debora Testi VPH-HF: A software framework for the execution of complex subject-specific physiology modelling workflows. 101-114 2018 25 J. Comput. Sci. https://doi.org/10.1016/j.jocs.2018.02.009 https://www.wikidata.org/entity/Q130189569 db/journals/jocs/jocs25.html#VicecontiBTSGWG18

Zhen Zhang 0005 Matthew Bedder Stephen L. Smith 0002 Dawn C. Walker Saqib Shabir Jennifer Southgate Characterization and classification of adherent cells in monolayer culture using automated tracking and evolutionary algorithms. 110-121 2016 146 Biosyst. https://doi.org/10.1016/j.biosystems.2016.05.009 https://www.wikidata.org/entity/Q38766291 db/journals/biosystems/biosystems146.html#ZhangBSWSS16

Zhen Zhang 0005 Matthew Bedder Stephen L. Smith 0002 Dawn C. Walker Saqib Shabir Jennifer Southgate Automated Motion Analysis of Adherent Cells in Monolayer Culture. 185-194 2015 IPCAT https://doi.org/10.1007/978-3-319-23108-2_16 conf/ipcat/2015 db/conf/ipcat/ipcat2015.html#ZhangBSWSS15 Daniele Tartarini Kewei Duan Nicolas Gruel Debora Testi Dawn C. Walker Marco Viceconti The VPH Hypermodelling framework for cancer multiscale models in the clinical practice. 1-4 2014 IARWISOI https://doi.org/10.1109/IARWISOCI.2014.7034642 conf/iarwisoci/2014 db/conf/iarwisoci/iarwisoci2014.html#TartariniDGTWV14

Mark Burkitt Dawn C. Walker Daniela M. Romano Alireza Fazeli Constructing Complex 3D Biological Environments from Medical Imaging Using High Performance Computing. 643-654 2012 9 IEEE ACM Trans. Comput. Biol. Bioinform. 3 https://doi.org/10.1109/TCBB.2011.69 https://doi.ieeecomputersociety.org/10.1109/TCBB.2011.69 https://dl.acm.org/doi/10.1109/TCBB.2011.69 https://www.wikidata.org/entity/Q51582105 db/journals/tcbb/tcbb9.html#BurkittWRF12

Alfonso Caiazzo David Evans 0005 Jean-Luc Falcone Jan Hegewald Eric Lorenz Bernd Stahl Dinan Wang Jörg Bernsdorf Bastien Chopard Julian Gunn D. Rodney Hose Manfred Krafczyk Patricia V. Lawford Rod H. Smallwood Dawn C. Walker Alfons G. Hoekstra A Complex Automata approach for in-stent restenosis: Two-dimensional multiscale modelling and simulations. 9-17 2011 2 J. Comput. Sci. 1 https://doi.org/10.1016/j.jocs.2010.09.002 db/journals/jocs/jocs2.html#CaiazzoEFHLSWBCGHKLSWH11

Mark Burkitt Dawn C. Walker Daniela M. Romano Alireza Fazeli Modelling sperm behaviour in a 3D environment. 141-149 2011 CMSB https://doi.org/10.1145/2037509.2037531 conf/cmsb/2011 db/conf/cmsb/cmsb2011.html#BurkittWRF11

Paul Richmond Dawn C. Walker Simon Coakley Daniela M. Romano High performance cellular level agent-based simulation with FLAME for the GPU. 334-347 2010 11 Briefings Bioinform. 3 https://doi.org/10.1093/bib/bbp073 https://www.wikidata.org/entity/Q51724800 db/journals/bib/bib11.html#RichmondWCR10

Mark Burkitt Daniela M. Romano Dawn C. Walker Alireza Fazeli 3D Modelling of Complex Biological Structures: The Oviduct. 255-262 2010 TPCG https://doi.org/10.2312/LocalChapterEvents/TPCG/TPCG10/255-262 conf/tpcg/2010 db/conf/tpcg/tpcg2010.html#BurkittRWF10

Dawn C. Walker Jennifer Southgate The virtual cell - a candidate co-ordinator for 'middle-out' modelling of biological systems. 450-461 2009 10 Briefings Bioinform. 4 https://doi.org/10.1093/bib/bbp010 https://www.wikidata.org/entity/Q37416872 db/journals/bib/bib10.html#WalkerS09

Alfonso Caiazzo David Evans 0005 Jean-Luc Falcone Jan Hegewald Eric Lorenz Bernd Stahl Dinan Wang Jörg Bernsdorf Bastien Chopard Julian Gunn D. Rodney Hose Manfred Krafczyk Patricia V. Lawford Rod H. Smallwood Dawn C. Walker Alfons G. Hoekstra Towards a Complex Automata Multiscale Model of In-Stent Restenosis. 705-714 2009 ICCS (1) https://doi.org/10.1007/978-3-642-01970-8_70 conf/iccS/2009-1 db/conf/iccS/iccS2009-1.html#CaiazzoEFHLSWBCGHKLSWH09

Dawn C. Walker Nikolaos T. Georgopoulos Jennifer Southgate From pathway to population - a multiscale model of juxtacrine EGFR-MAPK signalling. 102 2008 2 BMC Syst. Biol. https://doi.org/10.1186/1752-0509-2-102 https://www.wikidata.org/entity/Q30486327 db/journals/bmcsb/bmcsb2.html#WalkerGS08

Saba Balasubramanian Matthew Bedder Jörg Bernsdorf Simone Bnà Carlos Borau Mark Burkitt Alfonso Caiazzo Robert Chisholm Bastien Chopard Simon Coakley Bernard Corfe Kewei Duan David Evans 0005 Jean-Luc Falcone Alireza Fazeli Samuel Gamble José Manuel García-Aznar Nikolaos T. Georgopoulos Elisabet Gregori-Puigjané James A. Grogan Nicolas Gruel Julian Gunn James P. Heath Jan Hegewald Silvia Hervas-Raluy Alfons G. Hoekstra D. Rodney Hose Keith D. Hunter Tim Ingham-Dempster Marek Kasztelnik Manfred Krafczyk Patricia V. Lawford Eric Lorenz Malwina Matella Jordi Mestres Aaron Montero Craig Murdoch Paul Richmond Daniela RomanoDaniela M. Romano Ria Rosser Diego Sainz-DeMena Stelios Sfakianakis Saqib Shabir Rod H. Smallwood Stephen L. Smith 0002 Jennifer Southgate Bernd Stahl Daniele Tartarini Debora Testi V. Varella Marco Viceconti Dinan Wang Kenneth Y. Wertheim Zhen Zhang 0005