James Osborne : Publications
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@article{Osborne2014TenSimple,
title = "Ten simple rules for effective computational research",
author = "Osborne, James M and Bernabeu, Miguel O and Bruna, Maria and Calderhead, Ben and Cooper, Jonathan and Dalchau, Neil and Dunn, Sara-Jane and Fletcher, Alexander G and Freeman, Robin and Groen, Derek and others",
year = "2014",
journal = "PLoS Computational Biology",
number = "3",
pages = "e1003506",
publisher = "Public Library of Science San Francisco, USA",
volume = "10",
doi = "10.1371/journal.pcbi.1003506",
}
@article{Dunton2014Free,
title = "The free energy landscape of dimerization of a membrane protein, NanC",
author = "Dunton, T., Goose, J., Gavaghan, D.J., Sansom, M., and Osborne, J.M.",
year = "2014",
journal = "PLoS Computational Biology",
doi = "10.1371/journal.pcbi.1003417",
}
@article{Dunn2013Computational,
title = "Computational models reveal a passive mechanism for cell migration in the crypt",
author = "Dunn, S.J., Näthke, I., and Osborne, J.M.",
year = "2013",
journal = "PLoS One",
doi = "10.1371/journal.pone.0080516",
}
@article{Fletcher2013Implementing,
title = "Implementing vertex dynamics models in a consistent computational framework",
author = "Fletcher, A.G., Osborne, J.M., Maini, P.K., and Gavaghan, D.J.",
year = "2013",
journal = "Progress in Biophysics and Molecular Biology",
doi = "10.1016/j.pbiomolbio.2013.09.003",
}
@article{Kershaw2013Colorectal,
title = "Colorectal cancer through simulation and experiment: a review",
author = "Kershaw, S.K., Gavaghan, D.J, Byrne, H.M., and Osborne, J.M.",
year = "2013",
journal = "IET Systems Biology",
volume = "7(3)",
doi = "10.1049/iet-syb.2012.0019",
}
@article{Cooper2013Connecting,
title = "Connecting models to data in multiscale multicellular tissue simulations",
author = "Cooper, J, Osborne, J.M.",
year = "2013",
journal = "Procedia Computer Science",
pages = "712-721",
volume = "18",
doi = "10.1016/j.procs.2013.05.235",
}
@article{Davit2013Validity,
title = "Validity of the Cauchy-Born rule applied to discrete cellular-scale models of biological tissues",
author = "Davit, Y., Osborne, J.M., Byrne, H.M., Pitt-Francis, J., and Gavaghan, D.J.",
year = "2013",
journal = "Physical Review E",
doi = "10.1103/PhysRevE.87.042724",
}
@article{Figueredo2013,
title = "On-Lattice Agent-based Simulation of Populations of Cells within the Open-Source Chaste Framework.",
author = "Figueredo, G.P., Joshi, T.V., Osborne, J.M., Helen M. Byrne, H.M., and Owen, M.R.",
year = "2013",
journal = "Interface Focus",
volume = "3(2)",
doi = "10.1098/rsfs.2012.0081",
}
@article{Davit2013Hydrodynamic,
title = "Hydrodynamic dispersion within porous biofilms",
author = "Davit, Y. and Byrne, H.M. and Osborne, J.M. and Pitt-Francis, J. and Gavaghan, D.J. and Quintard, M",
year = "2013",
journal = "Phys. Rev. E",
volume = "87 (1)",
doi = "10.1103/PhysRevE.87.012718",
}
@article{MiramsChaste2013,
title = "Chaste: an open source C++ library for computational physiology and biology",
author = "Mirams, Gary R and Arthurs, Christopher J and Bernabeu, Miguel O and Bordas, Rafel and Cooper, Jonathan and Corrias, Alberto and Davit, Yohan and Dunn, Sara-Jane and Fletcher, Alexander G and Harvey, Daniel G and others",
year = "2013",
journal = "PLoS computational biology",
number = "3",
pages = "e1002970",
publisher = "Public Library of Science San Francisco, USA",
volume = "9",
doi = "10.1371/journal.pcbi.1002970",
}
@article{o2012interplay,
title = "The interplay between tissue growth and scaffold degradation in engineered tissue constructs",
author = "O’Dea, RD and Osborne, JM and El Haj, AJ and Byrne, HM and Waters, SL",
year = "2012",
journal = "Journal of Mathematical Biology",
doi = "10.1007/s00285-012-0587-9",
}
@article{Slaymaker12,
title = "On an infrastructure to support sharing and aggregating pre- and post-publication systems biology research data",
author = "Mark Slaymaker and James Osborne and Andrew Simpson and David Gavaghan",
year = "2012",
journal = "Systems and Synthetic Biology",
number = "1--2",
pages = "35--49",
volume = "6",
doi = "10.1007/s11693-012-9095-x",
}
@article{Dunn12TwoDimensional,
title = "A two-dimensional model of the colonic crypt accounting for the role of the basement membrane and pericryptal fibroblast sheath",
author = "S.-J. Dunn, and P.L. Appleton, and S.A. Nelson, and I.S. Näthke, and D.J. Gavaghan, and J.M. Osborne",
year = "2012",
edition = "8",
journal = "Plos Computational Biology",
number = "5",
pages = "e1002515",
doi = "10.1371/journal.pcbi.1002515",
}
@article{Dunn12Modelling,
title = "Modelling the role of the basement membrane in the colonic epithelium",
author = "S.-J. Dunn, and A.G. Fletcher, and S.J. Chapman, and D.J. Gavaghan, and J.M. Osborne",
year = "2012",
journal = "J. Theor. Biol.",
number = "298",
pages = "82-91",
doi = "10.1016/j.jtbi.2011.12.013",
}
@article{OzzyLongWavelength,
title = "The Influence of Bioreactor Geometry and the Mechanical Environment on Engineered Tissues",
author = "J. M. Osborne and R. D. O'Dea and J. P. Whiteley and H. M. Byrne and S. L. Waters",
year = "2010",
journal = "Journal of Biomechanical Engineering",
month = "May",
number = "5",
pages = "051006",
volume = "132",
doi = "10.1115/1.4001160",
}
@article{f20ea8a70f839df,
title = "A hybrid approach to multi-scale modelling of cancer",
author = "Osborne, J. M. and Walter, A. and Kershaw, S. K. and Mirams, G. R. and Fletcher, A. G. and Pathmanathan, P. and Gavaghan, D. and Jensen, O. E. and Maini, P. K. and Byrne, H. M.",
year = "2010",
journal = "Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences",
month = "Nov",
number = "1930",
pages = "5013--5028",
volume = "368",
doi = "10.1098/rsta.2010.0173",
}
@article{Whiteley 2010i,
title = "A numerical method for the multiphase viscous flow equations",
author = "J.M. Osborne, and J.P. Whiteley",
year = "2010",
journal = "Computer Methods in Applied Mechanics and Engineering",
pages = "3402-3417",
volume = "199",
doi = "10.1016/j.cma.2010.07.011",
}
@article{ChasteCPC09,
title = "Chaste: a test-driven approach to software development for biological modelling",
author = "Pitt-Francis, Joe and Pathmanathan, Pras and Bernabeu, Miguel O and Bordas, Rafel and Cooper, Jonathan and Fletcher, Alexander G and Mirams, Gary R and Murray, Philip and Osborne, James M and Walter, Alex and others",
year = "2009",
journal = "Computer Physics Communications",
number = "12",
pages = "2452--2471",
publisher = "North-Holland",
volume = "180",
doi = "10.1016/j.cpc.2009.07.019",
}
@article{chaste_dtm,
title = "A computational study of discrete mechanical tissue models",
author = "P Pathmanathan and J Cooper and A Fletcher and G Mirams and P Murray and J Osborne and J Pitt-Francis and A Walter and S J Chapman",
year = "2009",
journal = "Physical Biology",
number = "3",
volume = "6",
doi = "10.1088/1478-3975/6/3/036001",
}
@article{cancerchaste1,
title = "An integrative computational model for intestinal tissue renewal",
author = "Van Leeuwen and Ingeborg MM and Mirams, GR and Walter, Alex and Fletcher, A and Murray, P and Osborne, J and Varma, S and Young, SJ and Cooper, J and Doyle, B and others",
year = "2009",
journal = "Cell proliferation",
number = "5",
pages = "617--636",
publisher = "Blackwell Publishing Ltd Oxford, UK",
volume = "42",
doi = "10.1111/j.1365-2184.2009.00627.x",
}
@article{Chaste.08:Chaste,
title = "Chaste: using agile programming techniques to develop computational biology software",
author = "Pitt-Francis, Joe and Bernabeu, Miguel O and Cooper, Jonathan and Garny, Alan and Momtahan, Lee and Osborne, James and Pathmanathan, Pras and Rodriguez, Blanca and Whiteley, Jonathan P and Gavaghan, David J",
year = "2008",
journal = "Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences",
number = "1878",
pages = "3111--3136",
publisher = "The Royal Society London",
volume = "366",
doi = "10.1098/rsta.2008.0096",
}