Alex Fletcher    About    Research    Publications    People    PhD projects    DynoCaTs

Publications

Papers

  1. CM Cammarota, NS Dawney, PM Bellomio, M Jüng, AG Fletcher, TM Finegan, DT Berglstralh (2023). The mechanical influence of densification on epithelial architecture. PLOS Comput Biol. 20:e1012001. DOI

  2. I Groves, J Holmshaw, D Furley, E Manning, K Chinnaiya, M Towers, BD Evans, M Placzek, AG Fletcher (2023). Accurate staging of chick embryonic tissues via deep learning of salient features. Development. dev.202068. DOI

  3. S Montes-Olivas, D Legge, A Lund, AG Fletcher, AC Williams, L Marucci, M Homer (2023). In-silico and in-vitro morphometric analysis of intestinal organoids. PLOS Comput Biol. 19:e1011386. DOI

  4. SE Strawbridge, E Corujo-Simon, AN Fletcher, J Nichols, AG Fletcher (2023). insideOutside: an accessible algorithm for classifying interior and exterior points, with applications in embryology. Biol Open 12:bio060055 DOI

  5. A Schmidt, T Finegan, M Häring, D Kong, AG Fletcher, Z Alam, J Grosshans, F Wolf, M Peifer (2023). Polychaetoid/ZO-1 strengthens cell junctions under tension while localizing differently than core adherens junction proteins. Mol Biol Cell 4:ar81 DOI

  6. CGM Johnson, AG Fletcher, OS Soyer (2022). ChemChaste: Simulating spatially inhomogenous biochemical reaction-diffusion systems for modelling cell-environment feedbacks. GigaScience. 11:giac051 DOI

  7. A Nestor-Bergmann, G Blanchard, N Hervieux, AG Fletcher, J Etienne, B Sanson (2022). Adhesion-regulated junction slippage controls cell intercalation dynamics in an Apposed-Cortex Adhesion Model. PLOS Comput Biol. 18:e1009812. DOI

  8. R Niehus, NM Oliveira, A Li, AG Fletcher, K Foster (2021). The evolution of strategy in bacterial warfare: quorum sensing, stress responses, and the regulation of bacteriocins and antibiotics. eLife. 10:e69756 DOI

  9. L Gonay, C Spourquet, M Baudoin, L Lepers, P Lemoine, AG Fletcher, E Hanert, CE Pierreux (2021). Modelling of epithelial growth, fission and lumen formation during embryonic thyroid development: a combination of computational and experimental approaches. Front Endocrinol. 12:516 DOI

  10. AG Fletcher, JM Osborne (2021). Seven challenges in the multiscale modelling of multicellular tissues. WIREs Mech Dis. e1527. DOI

  11. K Campbell, E Noel, AG Fletcher, N Bulgakova (2020). Contemporary morphogenesis. Philos Trans R Soc B 375:20190549. DOI

  12. I Groves, M Placzek, AG Fletcher (2020). Of mitogens and morphogens: modelling Sonic Hedgehog mechanisms in vertebrate development. Philos Trans R Soc B 375:20190660. DOI

  13. L Ruske, J Kursawe, A Tsakiridis, V Wilson, AG Fletcher, RA Blythe, LJ Schumacher (2020). Coupled differentiation and division of embryonic stem cells inferred from clonal snapshots. Phys Biol. 17:065009 DOI

  14. TE Gorochowski, S Hauert, J Kreft, L Marucci, NR Stillman, TD Tang, L Bandiera, V Bartoli, DOR Dixon, AJH Fedorec, H Fellermann, AG Fletcher, T Foster, L Giuggioli, A Matyjaszkiewicz, S McCormick, S Montes Olivas, J Naylor, A Rubio Denniss, D Ward (2020). Towards engineering biosystems with emergent collective functions. Front Bioeng Biotechnol. 8:705 DOI

  15. FR Cooper, RE Baker, MO Bernabeu, R Bordas, L Bowler, A Bueno-Orovio, HM Byrne, V Carapella, L Cardone-Noott, J Cooper, S Dutta, BD Evans, AG Fletcher, JA Grogan, W Guo, DG Harvey, M Hendrix, D Kay, J Kursawe, PK Maini, B McMillan, GR Mirams, JM Osborne, P Pathmanathan, JM Pitt-Francis, M Robinson, B Rodriguez, RJ Spiteri, and David J Gavaghan (2020). Chaste: Cancer, Heart and Soft Tissue Environment. J Open Source Softw. 5:1848 DOI

  16. D Ward, S Montes Olivas, AG Fletcher, M Homer, L Marucci (2020). Cross-talk between Hippo and Wnt signalling pathways in intestinal crypts: insights from an agent-based model. Comput Struct Biotechnol J. 18:230-240 DOI

  17. DR Grimes, AG Fletcher (2020). Close encounters of the cell kind: The impact of contact inhibition on tumor growth and cancer models. Bull Math Biol. 82: 20 DOI

  18. TM Finegan, N Hervieux, A Nestor-Bergmann, AG Fletcher, GB Blanchard, B Sanson (2019). The tricellular vertex-specific adhesion molecule Sidekick facilitates polarised cell intercalation during Drosophila axis extension. PLOS Biol. 7:e3000522 DOI

  19. JG Scott, PK Maini, ARA Anderson, AG Fletcher (2019). Inferring tumour proliferative organisation from phylogenetic tree measures in a computational model. Syst Biol. syz070 DOI

  20. RL Cooper, VJ Lloyd, N Di-Poï, AG Fletcher, PM Barrett, G Fraser (2019). Conserved gene signalling and a derived patterning mechanism underlie the development of avian footpad scales. EvoDevo. 10:19 DOI

  21. KH Fisher, D Strutt, AG Fletcher (2019). Experimental and theoretical evidence for bidirectional signalling via core planar polarity protein complexes in Drosophila. iScience. 17:49-66 DOI

  22. JG Scott, A Dhawan, A Hjelmeland, J Lathia, A Chumakova, M Hitomi, AG Fletcher, PK Maini, ARA Anderson (2019). Recasting the cancer stem cell hypothesis: unification using a continuum model of microenvironmental forces. Curr Stem Cell Rep. 5:22-30 DOI

  23. C Pin, A Parker, L Vaux, A Patterson, A Modasia, D Muraro, AG Fletcher, HM Byrne, PK Maini, AJM Watson (2018). Elevated apoptosis impairs epithelial cell turnover and shortens villi in TNF-driven intestinal inflammation. Cell Death Dis. 10:108 DOI

  24. TM Finegan, D Na, AV Skeeters, C Cammarota, TJ Nadasi, NS Dawney, AG Fletcher, PW Oakes, DT Bergstralh (2018). Tissue tension and not interphase cell shape determines cell division orientation in the Drosophila follicular epithelium. EMBO J. 38:e100072 DOI / Cover image

  25. R Cooper, A Thiery, AG Fletcher, D Delbarre, L Rasch, G Fraser (2018). An ancient Turing reaction-diffusion mechanism regulates skin denticle patterning in sharks. Sci Adv. 4:eaau5484 DOI

  26. D Muraro, A Parker, L Vaux, S Filippi, AA Almet, AG Fletcher, AJM Watson, C Pin, PK Maini, HM Byrne (2018). TNFα-driven injury delays cell migration to villi in the intestinal epithelium. J R Soc Interface. 15:20180037 DOI

  27. GB Blanchard, AG Fletcher, LJ Schumacher (2018). The devil is in the mesoscale: mechanical and behavioural heterogeneity in collective cell movement. Semin Cell Dev Biol. S1084-9521(17)30557-8 DOI

  28. J Kursawe, RE Baker, AG Fletcher (2018). Approximate Bayesian computation reveals the importance of repeated measurements for parameterising cell-based models of growing tissues. J Theor Biol. 443:66-81 DOI

  29. B Lambert, AL MacLean, AG Fletcher, AN Combes, MH Little, HM Byrne (2018). Bayesian inference of agent-based models: a tool for studying kidney branching morphogenesis. J Math Biol. 76:1673-1697 DOI

  30. F Cooper, RE Baker, AG Fletcher (2017). Numerical analysis of the immersed boundary method for cell-based simulation. SIAM J Sci Comput. 39:B943-B967. DOI

  31. KH Fisher, D Strutt, AG Fletcher (2017). Integrating planar polarity and tissue mechanics in computational models of epithelial morphogenesis. Curr Opin Syst Biol. 5:41-49. DOI

  32. OJ Maclaren, A Parker, C Pin, SR Carding, AJM Watson, AG Fletcher, HM Byrne, PK Maini (2017). A hierarchical Bayesian framework for understanding the spatiotemporal dynamics of the intestinal epithelium. PLOS Comput Biol. 13:e1005688. DOI

  33. J Kursawe, RE Baker, AG Fletcher (2017). Impact of implementation choices on quantitative predictions of cell-based computational models. J Comput Phys. 345:752-767. DOI

  34. S Godwin, D Ward, E Pedone, M Homer, AG Fletcher, L Marucci (2017). An extended model for culture-dependent heterogeneous gene expression and proliferation dynamics in mouse embryonic stem cells. npj Syst Biol Appl. 3:19. DOI

  35. A Bucksch, A Atta-Boateng, AF Azihou, D Battogtokh, A Baumgartner, BM Binder, SA Braybrook, C Chang, V Coneva, TJ DeWitt, AG Fletcher, MA Gehan, DH Diaz-Martinez, L Hong, AS Iyer-Pascuzzi, LL Klein, S Leiboff, M Li, JP Lynch, A Maizel, JN Maloof, RJC Markelz, CC Martinez, LA Miller, W Mio, W Palubicki, H Poorter, C Pradal, CA Price, E Puttonen, JB Reese, R Rellán-Álvarez, EP Spalding, EE Sparks, CN Topp, JH Williams, DH Chitwood (2017). Morphological plant modeling: Unleashing geometric and topologic potential within the plant sciences. Front Plant Sci. 8:900. DOI

  36. JM Osborne, AG Fletcher, JM Pitt-Francis, PK Maini, DJ Gavaghan (2017). Comparing individual-based approaches to modelling the self-organization of multicellular tissues. PLOS Comput Biol. 13:e1005387. DOI

  37. AG Fletcher, F Cooper, RE Baker (2017). Mechanocellular models of epithelial morphogenesis. Philos Trans R Soc B. 372. DOI

  38. A Parker, OJ Maclaren, AG Fletcher, D Muraro, P Kreuzaler, HM Byrne, PK Maini, AJM Watson, C Pin (2017). Proliferation within small intestinal crypts is the principal driving force for cell migration on villi. FASEB J. 31:636-649. DOI

  39. J Kursawe, R Bardenet, JJ Zartman, RE Baker, AG Fletcher (2016). Robust cell tracking in epithelial tissues through identification of maximum common subgraphs. J R Soc Interface. 13. DOI

  40. RJ Tetley, GB Blanchard, AG Fletcher, RJ Adams, B Sanson (2016). Unipolar distributions of junctional Myosin II identify cell stripe boundaries that drive cell intercalation throughout Drosophila axis extension. eLife 5:e12094. DOI

  41. A Dhawan, TA Graham, AG Fletcher (2016). A computational modelling approach for deriving biomarkers to predict cancer risk in premalignant disease. Cancer Prev Res. 9:283-295. DOI / Cover image

  42. JG Scott, AG Fletcher, ARA Anderson, PK Maini (2016). Spatial metrics of tumour vascular organisation predict radiation efficacy in a computational model. PLOS Comput Biol. 12:e1004712. DOI

  43. J Kursawe, PA Brodskiy, JJ Zartman, RE Baker, AG Fletcher (2015). Capabilities and limitations of tissue size control through passive mechanical forces. PLOS Comput Biol. 11:e1004679. DOI

  44. R Niehus, S Mitri, AG Fletcher, KR Foster (2015). Migration and horizontal gene transfer divide microbial genomes into multiple niches. Nat Commun. 6. DOI

  45. D Nichol, P Jeavons, AG Fletcher, RA Bonomo, PK Maini, JL Paul, RA Gatenby, ARA Anderson, JG Scott (2015). Steering evolution with sequential therapy to prevent the emergence of bacterial antibiotic resistance. PLOS Comput Biol. 11:e1004493. DOI

  46. C Narciso, Q Wu, P Brodskiy, G Garston, RE Baker, AG Fletcher, JJ Zartman (2015). Patterning of wound-induced intercellular Ca2+ flashes in a developing epithelium. Phys Biol. 12:056005. DOI

  47. AG Fletcher, PJ Murray, PK Maini (2015). Multiscale modelling of intestinal crypt organization and carcinogenesis. Math Mod Meth Appl Sci. 25:2563-2585. DOI

  48. OJ Maclaren, HM Byrne, AG Fletcher, PK Maini (2015). Models, measurement and inference in epithelial tissue dynamics. Math Biosci Eng. 12:1321-1340. DOI

  49. DG Harvey, AG Fletcher, JM Osborne, JM Pitt-Francis (2014). A parallel implementation of an off-lattice individual-based model of multicellular populations. Comput Phys Commun. 192:130-137. DOI

  50. B Knapp, R Bardenet, MO Bernabeu, R Bordas, M Bruna, B Calderhead, J Cooper, AG Fletcher, D Groen, B Kuijper, J Lewis, G McInerny, T Minssen, JM Osborne, V Paulitschke, J Pitt-Francis, J Todoric, CA Yates, DJ Gavaghan, CM Deane (2014). Ten simple rules for a successful cross-disciplinary collaboration. PLoS Comput Biol. 11:e1004214. DOI

  51. JG Scott, AG Fletcher, PK Maini, ARA Anderson, P. Gerlee (2014). A filter-flow perspective of hematogenous metastasis offers a non-genetic paradigm for personalized cancer therapy. Eur J Cancer. 50:3068-3075. DOI

  52. DR Grimes, AG Fletcher, M Partridge (2014). Oxygen consumption dynamics in steady-state tumour models. R Soc Open Sci. 1:140080. DOI / Cover image

  53. AM Baker, B Cereser, S Melton, AG Fletcher, M Rodriguez-Justo, PJ Tadrous, A Humphries, G Elia, SAC McDonald, NA Wright, BD Simons, M Jansen, TA Graham (2014). Quantification of crypt and stem cell evolution in the normal and neoplastic human colon. Cell Rep. 8:940-947. DOI

  54. G Rosser, RE Baker, JP Armitage, AG Fletcher (2014). Modelling and analysis of bacterial tracks suggest an active reorientation mechanism in Rhodobacter sphaeroides. J R Soc Interface. 11:20140320. DOI

  55. AG Fletcher, M Osterfield, RE Baker, SY Shvartsman (2014). Vertex models of epithelial morphogenesis. Biophys J. 106:2291-2304. DOI

  56. JM Osborne, MO Bernabeu, M Bruna, B Calderhead, J Cooper, N Dalchau, SJ Dunn, AG Fletcher, R Freeman, D Groen, B Knapp, GJ McInerny, GR Mirams, JM Pitt-Francis, B Sengupta, DW Wright, CA Yates, DJ avaghan, S Emmott, C Deane (2014). Ten simple rules for effective computational research. PLOS Comput Biol. 10:e1003506. DOI

  57. AG Fletcher, JM Osborne, PK Maini, DJ Gavaghan (2013). Implementing vertex dynamics models of cell populations in biology within a consistent computational framework. Prog Biophys Mol Biol. 113:299-326. DOI

  58. K Bloch, H Smith, V van Hamel Parsons, DJ Gavaghan, C Kelly, AG Fletcher, PK Maini, R Callaghan (2013). Metabolic alterations during the growth of tumour spheroids. Cell Biochem Biophys. 68:615-628. DOI

  59. G Rosser, AG Fletcher, DA Wilkinson, JA de Beyer, CA Yates, JP Armitage, PK Maini, RE Baker (2013). Novel methods for analysing bacterial tracks reveal persistence in Rhodobacter sphaeroides. PLoS Comput Biol. 9:e1003276. DOI

  60. JP Vincent, AG Fletcher, LA Baena-Lopez (2013). Mechanisms and mechanics of cell competition in epithelia. Nat Rev Mol Cell Biol. 14:1-11. DOI

  61. G Rosser, AG Fletcher, PK Maini, RE Baker (2013). The effect of sampling rate on observed statistics in a correlated random walk. J R Soc Interface. 10:20130273. DOI

  62. B Lloyd-Lewis, AG Fletcher, TC Dale, HM Byrne (2013). Towards a quantitative understanding of the Wnt/beta-catenin pathway through simulation and experiment. WIREs Syst Biol Med. 5:391-407. DOI

  63. GR Mirams, CJ Arthurs, MO Bernabeu, R Bordas, J Cooper, A Corrias, Y Davit, SJ Dunn, AG Fletcher, DG Harvey, ME Marsh, JM Osborne, P Pathmanathan, JM Pitt-Francis, J Southern, N Zemzemi, DJ Gavaghan (2013). Chaste: an open source C++ library for computational physiology and biology. PLoS Comput Biol. 9:e1002970. DOI

  64. GR Mirams, AG Fletcher, PK Maini, HM Byrne (2012). A theoretical investigation of the effect of dysregulated proliferation and adhesion on monoclonal conversion in the colonic crypt. J Theor Biol. 312:143-156. DOI

  65. R Dello Ioio, C Galinha, AG Fletcher, SP Grigg, A Molnar, V Willemsen, B Scheres, S Sabatini, D Baulcombe, PK Maini, M Tsiantis (2012). A PHABULOSA/cytokinin feedback loop controls root growth in Arabidopsis. Curr Biol. 22:1699-1704. DOI

  66. AG Fletcher, CJW Breward, SJ Chapman (2012). Mathematical modelling of monoclonal conversion in the colonic crypt. J Theor Biol. 300:118-133. DOI

  67. SJ Dunn, AG Fletcher, SJ Chapman, DJ Gavaghan, JM Osborne (2011). Modelling the role of the basement membrane beneath a growing epithelial monolayer. J Theor Biol. 298:82-91. DOI

  68. PJ Murray, A Walter, AG Fletcher, CM Edwards, MJ Tindall, PK Maini (2011). Comparing a discrete and continuum model of the intestinal crypt. Phys Biol. 8:026011. DOI

  69. JM Osborne, A Walter, SK Kershaw, GR Mirams, AG Fletcher, P Pathmanathan, DJ Gavaghan, OE Jensen, PK Maini, HM Byrne (2010). A hybrid approach to multiscale modelling of cancer. Phil Trans R Soc A. 368:5013-5028. DOI

  70. IMM van Leeuwen, GR Mirams, A Walter, AG Fletcher, PJ Murray, JM Osborne, S Varma, SJ Young, J Cooper, B Doyle, JM Pitt-Francis, L Momtahan, P Pathmanathan, JP Whiteley, SJ Chapman, DJ Gavaghan, OE Jensen, JR King, PK Maini, SL Waters, HM Byrne (2009). An integrative computational model for intestinal tissue renewal. Cell Prolif. 42:617-636. DOI

  71. P Pathmanathan, J. Cooper, AG Fletcher, GR Mirams, L. Momtahan, PJ Murray, JM Osborne, JM Pitt-Francis, SJ Chapman (2009). A computational study of discrete mechanical tissue models. Phys Biol. 6:036001. DOI

  72. JM Pitt-Francis, P Pathmanathan, MO Bernabeu, R Bordas, J Cooper, AG Fletcher, GR Mirams, P Murray, JM Osborne, A Walter, SJ Chapman, A Garny, IMM van Leeuwen, PK Maini, B Rodriguez, SL Waters, JP Whiteley, HM Byrne, DJ Gavaghan (2009). Chaste: a test-driven approach to software development for biological modelling. Comput Phys Commun. 180:2452-2471. DOI

Book chapters

  1. JG Scott, P Gerlee, D Basanta, AG Fletcher, PK Maini, ARA Anderson (2013). Mathematical modeling of the metastatic process. In Experimental Metastasis: Modelling and Analysis, 189-208, Springer Netherlands. DOI

  2. AG Fletcher, GR Mirams, PJ Murray, A Walter, JW Kang, KH Cho, PK Maini, HM Byrne (2010). Multiscale modeling of colonic crypts and early colorectal cancer. In Multiscale Cancer Modeling, 111-134, CRC Press. DOI

Preprints

  1. SE Strawbridge, AK Schrattel, P Humphreys, KA Jones, J Artus, A-K Hadjantonakis, AG Fletcher, J Nichols (2024). Donor embryonic stem cells impede host epiblast specification in 8-cell stage chimeras by crowding and FGF4 signalling. bioRxiv

  2. AN Fletcher, AG Fletcher (2024). Variance of the distance to the boundary of convex domains in R2 and R3. arXiv

  3. SH Friedman, ARA Anderson, DM Bortz, AG Fletcher, HB Frieboes, A Ghaffarizadeh, DR Grimes, A Hawkins-Daarud, S Hoehme, EF Juarez, C Kesselman, RMH Merks, SM Mumenthaler, PK Newton, K-A Norton, R Rawat, RC Rockne, D Ruderman, J Scott, SS Sindi, JL Sparks, K Swanson, DB Agus, P Macklin (2016). MultiCellDS: a standard and a community for sharing multicellular data. bioRxiv

  4. A Buttenschoen, A Elkenawi, F El Moustaid, AG Fletcher, C Grassberger, E Kim, A Marusyk, H-L McClelland, D Miroshnychenko, D Nichol, J Mullinax, C O’Farrely (2016). Harnessing the lymphocyte meta-phenotype to optimize adoptive cell therapy. bioRxiv

  5. PA Brodskiy, PM Eberts, C Narciso, J Kursawe, AG Fletcher, JJ Zartman (2016). QuickStitch for seamless stitching of confocal mosaics through high-pass filtering and recursive normalization. bioRxiv