Publications

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  • Alexander G Fletcher, J. Osborne. Seven challenges in the multiscale modeling of multicellular tissues. WIREs Mechanisms of Disease, 2021. doi: 10.1002/wsbm.1527.

  • L. Romijn, Axel A Almet, Chin Wee Tan, J. Osborne. Modelling the effect of subcellular mutations on the migration of cells in the colorectal crypt.. BMC bioinformatics, 21, 95 (16pp), 2020. doi: 10.1186/s12859-020-3391-3.

  • C. Miller , J. Osborne. Understanding the regulation of epidermal tissue thickness by cellular and subcellular processes using multiscale modelling. 2020.

  • TJ Sego, Josua O Aponte-Serrano, Juliano Ferrari Gianlupi, Samuel R Heaps, Kira Breithaupt, Lutz Brusch, Jessica Crawshaw, J. Osborne, Ellen M Quardokus, Richard K Plemper, James A Glazier. A modular framework for multiscale, multicellular, spatiotemporal modeling of acute primary viral infection and immune response in epithelial tissues and its application to drug therapy timing and effectiveness.. PLoS Comput Biol, 16, e1008451 (51pp), 2020. doi: 10.1371/journal.pcbi.1008451.

  • Domenic PJ Germano, J. Osborne. A mathematical model of cell fate selection on a dynamic tissue.. Journal of Theoretical Biology, 514, 110535 (9pp), 2020. doi: 10.1016/j.jtbi.2020.110535.

  • Fergus Cooper, Ruth Baker, Miguel Bernabeu, Rafel Bordas, Louise Bowler, Alfonso Bueno-Orovio, Helen Byrne, Valentina Carapella, Louie Cardone-Noott, Sara Dutta, Benjamin Evans, Alexander Fletcher, James Grogan, Wenxian Guo, Daniel Harvey, Maurice Hendrix, David Kay, Jochen Kursawe, Philip Maini, Beth McMillan, Gary Mirams, J. Osborne, Pras Pathmanathan, Joe Pitt-Francis, Martin Robinson, Blanca Rodriguez, Raymond Spiteri, David Gavaghan. Chaste: Cancer, Heart and Soft Tissue Environment. The Journal of Open Source Software, 5, 1848, 2020. doi: 10.21105/joss.01848.

  • Donald F Newgreen, K. Landman, J. Osborne. Addressing Interdisciplinary Difficulties in Developmental Biology/Mathematical Collaborations: A Neural Crest Example.. Methods in molecular biology (Clifton, N.J.), 1976, 21-36, 2019. doi: 10.1007/978-1-4939-9412-0_2.

  • I Frost, WPJ Smith, S Mitri, AS Millan, Y. Davit, J. Osborne, JM Pitt-Francis, RC MacLean, KR Foster. Cooperation, competition and antibiotic resistance in bacterial colonies. ISME Journal, 1582-1593, 2018. doi: 10.1038/s41396-018-0090-4.

  • D Zhang, J. Osborne, KD Abu-Bonsrah, B. Cheeseman, K. Landman, B Jurkowicz, DF Newgreen. Stochastic clonal expansion of “superstars” enhances the reserve capacity of enteric nervous system precursor cells. Developmental Biology, S287-S296, 2018. doi: 10.1016/j.ydbio.2018.01.020.

  • F Hoffman, D Gavaghan, J. Osborne, IP Barrett, T You, H Ghadially, R Sainson, RW Wilkinson, HM Byrne. A mathematical model of antibody-dependent cellular cytotoxicity (ADCC). Journal of Theoretical Biology, 436, 39-50, 2018. doi: 10.1016/j.jtbi.2017.09.031.

  • C. Miller , J. Osborne, E. Crampin. Multi-Cellular Modelling of Cellular Mechanisms Gives Insights on the Maintenance of Epidermal Tissue Structure. Biophysical Journal, 114, 678A-679A, 2018.

  • J. Osborne, Miguel O Bernabeu. A Fully Discrete Open Source Framework for the Simulation of Vascular Remodelling. IEEE Explore, 2018.

  • Axel A Almet, Barry D Hughes, Kerry A Landman, Inke S Näthke, Inke S Nathke, J. Osborne. A Multicellular Model of Intestinal Crypt Buckling and Fission.. Bull Math Biol, 335-359, 2017. doi: 10.1007/s11538-017-0377-z.

  • J. Osborne, Alexander G Fletcher, Joe M Pitt-Francis, Philip K Maini, David J Gavaghan. Comparing individual-based approaches to modelling the self-organization of multicellular tissues. PLoS Computational Biology, 13, e1005387 (34pp), 2017. doi: 10.1371/journal.pcbi.1005387.

  • Sophie K Kay, Heather A Harrington, Sarah Shepherd, Keith Brennan, Trevor Dale, J. Osborne, David J Gavaghan, Helen M Byrne. The role of the Hes1 crosstalk hub in Notch-Wnt interactions of the intestinal crypt. PLoS Computational Biology, 13, e1005400 (28pp), 2017. doi: 10.1371/journal.pcbi.1005400.

  • William PJ Smith, Yohan Davit, J. Osborne, Wook Kim, Kevin R Foster, Joe M Pitt-Francis. Cell morphology drives spatial patterning in microbial communities. Proceedings of the National Academy of Sciences of the United States of America, 114, E280-E286, 2017. doi: 10.1073/pnas.1613007114.

  • Thomas D Carroll, Alistair J Langlands, J. Osborne, Ian P Newton, Paul L Appleton, Inke Nathke, I Näthke. Interkinetic nuclear migration and basal tethering facilitates post-mitotic daughter separation in intestinal organoids. Journal of Cell Science, 130, 3862-3877, 2017. doi: 10.1242/jcs.211656.

  • Donald Newgreen, Dongcheng Zhang, J. Osborne, B. Cheeseman, B. Binder, K. Landman. Enteric nervous system formation: disproportionate stochastic clonal expansion of a few initiating vagal neural crest cells. Mechanisms of Development, 145, S40-S41, 2017. doi: 10.1016/j.mod.2017.04.061.

  • Megan Dearnley, Chu Trang, Yao Zhang, Oliver Looker, Changjin Huang, Nectarios Klonis, Jeff Yeoman, Mohit Arora, J. Osborne, Rajesh Chandramohanadas, Leann Tilley, Matthew Dixon. Reversible host cell remodeling underpins deformability changes in malaria parasite sexual blood stages. American Journal of Tropical Medicine and Hygiene, 95, 589 (1pp), 2016.

  • Kathryn Atwell, Sara-Jane Dunn, J. Osborne, Hillel Kugler, E Jane Albert Hubbard. How computational models contribute to our understanding of the germ line. Molecular Reproduction and Development, 83, 944-957, 2016. doi: 10.1002/mrd.22735.

  • Alistair J Langlands, Axel A Almet, Paul L Appleton, Ian P Newton, J. Osborne, Inke S Nathke, IS Näthke. Paneth Cell-Rich Regions Separated by a Cluster of Lgr5+Cells Initiate Crypt Fission in the Intestinal Stem Cell Niche. PLoS Biology, 14, e1002491 (31pp), 2016. doi: 10.1371/journal.pbio.1002491.

  • S-J Dunn, J. Osborne, PL Appleton, I Nathke, I Näthke. Combined changes in Wnt signaling response and contact inhibition induce altered proliferation in radiation-treated intestinal crypts. Molecular Biology of the Cell, 27, 1863-1874, 2016. doi: 10.1091/mbc.E15-12-0854.

  • Megan Dearnley, Trang Chu, Yao Zhang, Oliver Looker, Changjin Huang, Nectarios Klonis, Jeff Yeoman, Shannon Kenny, Mohit Arora, J. Osborne, Rajesh Chandramohanadas, Matthew WA Dixon, Leann Tilley. Reversible host cell remodeling underpins deformability changes in malaria parasite sexual blood stages. Proceedings of the National Academy of Sciences of the United States of America, 113, 4800-4805, 2016. doi: 10.1073/pnas.1520194113.

  • KHL Nessler, JR Henstock, AJ El Haj, SL Waters, JP Whiteley, J. Osborne, KHL Neßler. The influence of hydrostatic pressure on tissue engineered bone development. Journal of Theoretical Biology, 394, 149-159, 2016. doi: 10.1016/j.jtbi.2015.12.020.

  • J. Osborne, Alexander Fletcher, Joseph Pitt-Francis, Philip Maini, David Gavaghan. Comparing individual-based approaches to modelling the self-organization of multicellular tissues. 2016. doi: 10.1101/074351.

  • Bernhard Knapp, Remi Bardenet, Miguel O Bernabeu, Rafel Bordas, Maria Bruna, Ben Calderhead, Jonathan Cooper, Alexander G Fletcher, Derek Groen, Bram Kuijper, Joanna Lewis, Greg McInerny, Timo Minssen, J. Osborne, Verena Paulitschke, Joe Pitt-Francis, Jelena Todoric, Christian A Yates, David Gavaghan, Charlotte M Deane. Ten Simple Rules for a Successful Cross-Disciplinary Collaboration. PLoS Computational Biology, 11, e1004214 (7pp), 2015. doi: 10.1371/journal.pcbi.1004214.

  • Daniel G Harvey, Alexander G Fletcher, J. Osborne, Joe Pitt-Francis. A parallel implementation of an off-lattice individual-based model of multicellular populations. Computer Physics Communications, 192, 130-137, 2015. doi: 10.1016/j.cpc.2015.03.005.

  • J. Osborne. Multiscale Model of Colorectal Cancer Using the Cellular Potts Framework. Cancer Informatics, 14, 83-93, 2015. doi: 10.4137/CIN.S19332.

  • Simone Rubinacci, Alex Graudenzi, Giulio Caravagna, Giancarlo Mauri, J. Osborne, Joe Pitt-Francis, Marco Antoniotti. CoGNaC: A Chaste Plugin for the Multiscale Simulation of Gene Regulatory Networks Driving the Spatial Dynamics of Tissues and Cancer. Cancer Informatics, 14, 53-65, 2015. doi: 10.4137/CIN.S19965.

  • Kathryn Atwell, Zhao Qin, David Gavaghan, Hillel Kugler, E Jane Albert Hubbard, J. Osborne. Mechano-logical model of C. elegans germ line suggests feedback on the cell cycle. Development, 142, 3902-3911, 2015. doi: 10.1242/dev.126359.

  • Derek Groen, Xiaohu Guo, James A Grogan, Ulf D Schiller, J. Osborne. Software development practices in academia: a case study comparison. arXiv preprint arXiv:1506.05272, 2015.

  • Yvonne Reinwald, Katherine HL Leonard, James R Henstock, Jonathan P Whiteley, J. Osborne, Sarah L Waters, Philippe Levesque, Alicia J El Haj. Evaluation of the Growth Environment of a Hydrostatic Force Bioreactor for Preconditioning of Tissue-Engineered Constructs. Tissue Engineering Part C - Methods, 21, 1-14, 2015. doi: 10.1089/ten.tec.2013.0476.

  • David Johnson, J. Osborne, Z. Wang, Kostas Marias. Computer Simulation, Visualization, and Image Processing of Cancer Data and Processes. Cancer Informatics, 14, 105-108, 2015. doi: 10.4137/CIN.S37982.

  • J. Osborne, M. Bernabeu, Maria Bruna, Ben Calderhead, Jonathan Cooper, Neil Dalchau, Sara-Jane Dunn, Alexander G Fletcher, Robin Freeman, Derek Groen, Bernhard Knapp, Greg J McInerny, Gary R Mirams, Joe Pitt-Francis, Biswa Sengupta, David W Wright, Christian A Yates, David J Gavaghan, Stephen Emmott, Charlotte Deane. Ten Simple Rules for Effective Computational Research. PLoS Computational Biology, 10, e1003506 (3pp), 2014. doi: 10.1371/journal.pcbi.1003506.

  • Thomas A Dunton, Joseph E Goose, David J Gavaghan, Mark SP Sansom, J. Osborne. The Free Energy Landscape of Dimerization of a Membrane Protein, NanC. PLoS Computational Biology, 10, e1003417 (28pp), 2014. doi: 10.1371/journal.pcbi.1003417.

  • Sophie K Kershaw, Helen M Byrne, David J Gavaghan, J. Osborne. Colorectal cancer through simulation and experiment. IET Systems Biology, 7, 57-73, 2013. doi: 10.1049/iet-syb.2012.0019.

  • Y. Davit, H Byrne, J. Osborne, J Pitt-Francis, D Gavaghan, M Quintard. Hydrodynamic dispersion within porous biofilms. Physical Review E, 87, 012718 (16pp), 2013. doi: 10.1103/PhysRevE.87.012718.

  • Jonathan Cooper, J. Osborne. Connecting models to data in multiscale multicellular tissue simulations. 2013 International Conference on Computational Science, 18, 712-721, 2013. doi: 10.1016/j.procs.2013.05.235.

  • Sara-Jane Dunn, Inke S Naethke, J. Osborne, IS Näthke. Computational Models Reveal a Passive Mechanism for Cell Migration in the Crypt. PLoS One, 8, e80516 (18pp), 2013. doi: 10.1371/journal.pone.0080516.

  • Alexander G Fletcher, J. Osborne, Philip K Maini, David J Gavaghan. Implementing vertex dynamics models of cell populations in biology within a consistent computational framework. Progress in Biophysics & Molecular Biology, 113, 299-326, 2013. doi: 10.1016/j.pbiomolbio.2013.09.003.

  • J. Osborne, AJ El Haj, HM Byrne, SL Waters, RD O’Dea. The interplay between tissue growth and scaffold degradation in engineered tissue constructs. Journal of Mathematical Biology, 67, 1199-1225, 2013. doi: 10.1007/s00285-012-0587-9.

  • Grazziela P Figueredo, Tanvi V Joshi, J. Osborne, Helen M Byrne, Markus R Owen. On-lattice agent-based simulation of populations of cells within the open-source Chaste framework. Interface Focus, 3, 20120081 (11pp), 2013. doi: 10.1098/rsfs.2012.0081.

  • Y. Davit, J. Osborne, HM Byrne, D Gavaghan, J Pitt-Francis. Validity of the Cauchy-Born rule applied to discrete cellular-scale models of biological tissues. Physical Review E, 87, 042724 (13pp), 2013. doi: 10.1103/PhysRevE.87.042724.

  • Gary R Mirams, Christopher J Arthurs, M. Bernabeu, Rafel Bordas, Jonathan Cooper, Alberto Corrias, Y. Davit, Sara-Jane Dunn, Alexander G Fletcher, D. Harvey , Megan E Marsh, J. Osborne, Pras Pathmanathan, Joe Pitt-Francis, James Southern, Nejib Zemzemi, David J Gavaghan. Chaste: An Open Source C plus plus Library for Computational Physiology and Biology. PLoS Computational Biology, 9, e1002970 (8pp), 2013. doi: 10.1371/journal.pcbi.1002970.

  • M Slaymaker, J. Osborne, A. Simpson, D Gavaghan. On an infrastructure to support sharing and aggregating pre- and post-publication systems biology research data. Systems and Synthetic Biology, 6, 35-49, 2012. doi: 10.1007/s11693-012-9095-x.

  • Sara-Jane Dunn, Alexander G Fletcher, S Jonathan Chapman, David J Gavaghan, J. Osborne. Modelling the role of the basement membrane beneath a growing epithelial monolayer. Journal of Theoretical Biology, 298, 82-91, 2012. doi: 10.1016/j.jtbi.2011.12.013.

  • Sara-Jane Dunn, Paul L Appleton, Scott A Nelson, Inke S Naethke, David J Gavaghan, J. Osborne, IS Näthke. A Two-Dimensional Model of the Colonic Crypt Accounting for the Role of the Basement Membrane and Pericryptal Fibroblast Sheath. PLoS Computational Biology, 8, e1002515 (20pp), 2012. doi: 10.1371/journal.pcbi.1002515.

  • J. Osborne, A Walter, SK Kershaw, GR Mirams, AG Fletcher, P Pathmanathan, D Gavaghan, OE Jensen, PK Maini, HM Byrne. A hybrid approach to multi-scale modelling of cancer. Philosophical Transactions of the Royal Society of London Series A - Mathematical, Physical and Engineering Sciences, 368, 5013-5028, 2010. doi: 10.1098/rsta.2010.0173.

  • J. Osborne, JP Whiteley, HM Byrne, SL Waters, RD O Dea, RD O’Dea. The Influence of Bioreactor Geometry and the Mechanical Environment on Engineered Tissues. Journal of Biomechanical Engineering-Transactions Of The Asme, 132, 051006 (12pp), 2010. doi: 10.1115/1.4001160.

  • J. Osborne, Jonathan P Whiteley. A numerical method for the multiphase viscous flow equations. Computer Methods in Applied Mechanics And Engineering, 199, 3402-3417, 2010. doi: 10.1016/j.cma.2010.07.011.

  • Joe Pitt-Francis, Pras Pathmanathan, M. Bernabeu, Rafel Bordas, Jonathan Cooper, Alexander G Fletcher, Gary R Mirams, Philip Murray, J. Osborne, Alex Walter, S Jon Chapman, Alan Garny, Ingeborg MM van Leeuwen, Philip K Maini, Blanca Rodriguez, Sarah L Waters, Jonathan P Whiteley, Helen M Byrne, David J Gavaghan, B Rodríguez. Chaste: A test-driven approach to software development for biological modelling. Computer Physics Communications, 180, 2452-2471, 2009. doi: 10.1016/j.cpc.2009.07.019.

  • IMM van Leeuwen, GR Mirams, A Walter, A Fletcher, P Murray, J. Osborne, S Varma, SJ Young, J Cooper, B Doyle, J Pitt-Francis, L Momtahan, P Pathmanathan, JP Whiteley, SJ Chapman, DJ Gavaghan, OE Jensen, JR King, PK Maini, SL Waters, HM Byrne, others. An integrative computational model for intestinal tissue renewal. Cell Proliferation, 42, 617-636, 2009. doi: 10.1111/j.1365-2184.2009.00627.x.

  • P Pathmanathan, J Cooper, A Fletcher, G Mirams, P Murray, J. Osborne, J Pitt-Francis, A Walter, SJ Chapman. A computational study of discrete mechanical tissue models. Physical Biology, 6, 036001 (14pp), 2009. doi: 10.1088/1478-3975/6/3/036001.

  • Joe Pitt-Francis, M. Bernabeu, Jonathan Cooper, Alan Garny, Lee Momtahan, J. Osborne, Pras Pathmanathan, Blanca Rodriguez, Jonathan P Whiteley, David J Gavaghan. Chaste: using agile programming techniques to develop computational biology software. Philosophical Transactions of the Royal Society of London Series A - Mathematical, Physical and Engineering Sciences, 366, 3111-3136, 2008. doi: 10.1098/rsta.2008.0096.