Alex Fletcher    About    Research    Publications    People

Publications

Preprints

  1. TM Finegan, D Na, AV Skeeters, NS Dawney, PW Oakes, AG Fletcher, T Bergstralh (2017). Bimodal spindle orientation drives tissue regularity in a proliferating epithelium. bioRxiv

  2. JG Scott, A Dhawan, A Hjelmeland, J Lathia, M Hitomi, AG Fletcher, PK Maini, ARA Anderson (2017). Recasting the cancer stem cell hypothesis: unification using a continuum model of microenvironmental forces. bioRxiv

  3. B Lambert, AL MacLean, AG Fletcher, AN Coombes, MH Little, HM Byrne (2017). Bayesian inference of agent-based models: a tool for studying kidney branching morphogenesis. bioRxiv

  4. 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

  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

Papers

  1. F Cooper, RE Baker, AG Fletcher (2017). Numerical analysis of the immersed boundary method for cell-based simulation. SIAM J Sci Comput. In press. DOI

  2. KH Fisher, D Strutt, AG Fletcher (2017). Integrating planar polarity and tissue mechanics in computational models of epithelial morphogenesis. Curr Opin Syst Biol. In press. DOI

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

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

  16. 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

  17. 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

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

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

  20. 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

  21. 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

  22. 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

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

  24. 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

  25. 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

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

  27. 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

  28. 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

  29. 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

  30. 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

  31. 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

  32. 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

  33. 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

  34. 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

  35. 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

  36. 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

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

  38. 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

  39. 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

  40. 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

  41. 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

  42. 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

  43. JM Pitt-Francis, P Pathmanathan, MO Bernabeu, R. Bordas, J. Cooper, AG Fletcher, et al (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