James Osborne : Publications

Journal papers

• [1]

  Ten simple rules for effective computational research

  James M Osborne‚ Miguel O Bernabeu‚ Maria Bruna‚ Ben Calderhead‚ Jonathan Cooper‚ Neil Dalchau‚ Sara−Jane Dunn‚ Alexander G Fletcher‚ Robin Freeman‚ Derek Groen and others

  In PLoS Computational Biology. Vol. 10. No. 3. Pages e1003506. 2014.

  Details about Ten simple rules for effective computational research | BibTeX data for Ten simple rules for effective computational research | DOI (10.1371/journal.pcbi.1003506)

• [2]

  The free energy landscape of dimerization of a membrane protein‚ NanC

  Dunton T. Goose J. Gavaghan D.J. Sansom M. and J.M. Osborne

  In PLoS Computational Biology. 2014.

  Details about The free energy landscape of dimerization of a membrane protein‚ NanC | BibTeX data for The free energy landscape of dimerization of a membrane protein‚ NanC | DOI (10.1371/journal.pcbi.1003417)

• [3]

  Computational models reveal a passive mechanism for cell migration in the crypt

  Dunn S.J. Näthke I. and J.M. Osborne

  In PLoS One. 2013.

  Details about Computational models reveal a passive mechanism for cell migration in the crypt | BibTeX data for Computational models reveal a passive mechanism for cell migration in the crypt | DOI (10.1371/journal.pone.0080516)

• [4]

  Implementing vertex dynamics models in a consistent computational framework

  Fletcher A.G. Osborne J.M. Maini P.K. and D.J. Gavaghan

  In Progress in Biophysics and Molecular Biology. 2013.

  Details about Implementing vertex dynamics models in a consistent computational framework | BibTeX data for Implementing vertex dynamics models in a consistent computational framework | DOI (10.1016/j.pbiomolbio.2013.09.003)

• [5]

  Colorectal cancer through simulation and experiment: a review

  Kershaw S.K. Gavaghan D.J Byrne H.M. and J.M. Osborne

  In IET Systems Biology. Vol. 7(3). 2013.

  Details about Colorectal cancer through simulation and experiment: a review | BibTeX data for Colorectal cancer through simulation and experiment: a review | DOI (10.1049/iet-syb.2012.0019)

• [6]

  Connecting models to data in multiscale multicellular tissue simulations

  J.M. Cooper J Osborne

  In Procedia Computer Science. Vol. 18. Pages 712−721. 2013.

  Details about Connecting models to data in multiscale multicellular tissue simulations | BibTeX data for Connecting models to data in multiscale multicellular tissue simulations | DOI (10.1016/j.procs.2013.05.235)

• [7]

  Validity of the Cauchy−Born rule applied to discrete cellular−scale models of biological tissues

  Davit Y. Osborne J.M. Byrne H.M. Pitt−Francis J. and D.J. Gavaghan

  In Physical Review E. 2013.

  Details about Validity of the Cauchy−Born rule applied to discrete cellular−scale models of biological tissues | BibTeX data for Validity of the Cauchy−Born rule applied to discrete cellular−scale models of biological tissues | DOI (10.1103/PhysRevE.87.042724)

• [8]

  On−Lattice Agent−based Simulation of Populations of Cells within the Open−Source Chaste Framework.

  Figueredo G.P. Joshi T.V. Osborne J.M. Helen M. Byrne H.M. and M.R. Owen

  In Interface Focus. Vol. 3(2). 2013.

  Details about On−Lattice Agent−based Simulation of Populations of Cells within the Open−Source Chaste Framework. | BibTeX data for On−Lattice Agent−based Simulation of Populations of Cells within the Open−Source Chaste Framework. | DOI (10.1098/rsfs.2012.0081)

• [9]

  Hydrodynamic dispersion within porous biofilms

  Y. Davit‚ H.M. Byrne‚ J.M. Osborne‚ J. Pitt−Francis‚ D.J. Gavaghan and M Quintard

  In Phys. Rev. E. Vol. 87 (1). 2013.

  Details about Hydrodynamic dispersion within porous biofilms | BibTeX data for Hydrodynamic dispersion within porous biofilms | DOI (10.1103/PhysRevE.87.012718)

• [10]

  Chaste: an open source C++ library for computational physiology and biology

  Gary R Mirams‚ Christopher J Arthurs‚ Miguel O Bernabeu‚ Rafel Bordas‚ Jonathan Cooper‚ Alberto Corrias‚ Yohan Davit‚ Sara−Jane Dunn‚ Alexander G Fletcher‚ Daniel G Harvey and others

  In PLoS computational biology. Vol. 9. No. 3. Pages e1002970. 2013.

  Details about Chaste: an open source C++ library for computational physiology and biology | BibTeX data for Chaste: an open source C++ library for computational physiology and biology | DOI (10.1371/journal.pcbi.1002970)

• [11]

  The interplay between tissue growth and scaffold degradation in engineered tissue constructs

  RD O’Dea‚ JM Osborne‚ AJ El Haj‚ HM Byrne and SL Waters

  In Journal of Mathematical Biology. 2012.

  Details about The interplay between tissue growth and scaffold degradation in engineered tissue constructs | BibTeX data for The interplay between tissue growth and scaffold degradation in engineered tissue constructs | DOI (10.1007/s00285-012-0587-9)

• [12]

  On an infrastructure to support sharing and aggregating pre− and post−publication systems biology research data

  Mark Slaymaker‚ James Osborne‚ Andrew Simpson and David Gavaghan

  In Systems and Synthetic Biology. Vol. 6. No. 1–2. Pages 35–49. 2012.

  Details about On an infrastructure to support sharing and aggregating pre− and post−publication systems biology research data | BibTeX data for On an infrastructure to support sharing and aggregating pre− and post−publication systems biology research data | DOI (10.1007/s11693-012-9095-x)

• [13]

  A two−dimensional model of the colonic crypt accounting for the role of the basement membrane and pericryptal fibroblast sheath

  S.−J. Dunn‚ P.L. Appleton‚ S.A. Nelson‚ I.S. Näthke‚ D.J. Gavaghan and J.M. Osborne

  In Plos Computational Biology. No. 5. Pages e1002515. 2012.

  Details about A two−dimensional model of the colonic crypt accounting for the role of the basement membrane and pericryptal fibroblast sheath | BibTeX data for A two−dimensional model of the colonic crypt accounting for the role of the basement membrane and pericryptal fibroblast sheath | DOI (10.1371/journal.pcbi.1002515)

• [14]

  Modelling the role of the basement membrane in the colonic epithelium

  S.−J. Dunn‚ A.G. Fletcher‚ S.J. Chapman‚ D.J. Gavaghan and J.M. Osborne

  In J. Theor. Biol.. No. 298. Pages 82−91. 2012.

  Details about Modelling the role of the basement membrane in the colonic epithelium | BibTeX data for Modelling the role of the basement membrane in the colonic epithelium | DOI (10.1016/j.jtbi.2011.12.013)

• [15]

  A hybrid approach to multi−scale modelling of cancer

  J. M. Osborne‚ A. Walter‚ S. K. Kershaw‚ G. R. Mirams‚ A. G. Fletcher‚ P. Pathmanathan‚ D. Gavaghan‚ O. E. Jensen‚ P. K. Maini and H. M. Byrne

  In Philosophical Transactions of the Royal Society A: Mathematical‚ Physical and Engineering Sciences. Vol. 368. No. 1930. Pages 5013–5028. November, 2010.

  Details about A hybrid approach to multi−scale modelling of cancer | BibTeX data for A hybrid approach to multi−scale modelling of cancer | DOI (10.1098/rsta.2010.0173)

• [16]

  A numerical method for the multiphase viscous flow equations

  J.M. Osborne and J.P. Whiteley

  In Computer Methods in Applied Mechanics and Engineering. Vol. 199. Pages 3402−3417. 2010.

  Details about A numerical method for the multiphase viscous flow equations | BibTeX data for A numerical method for the multiphase viscous flow equations | DOI (10.1016/j.cma.2010.07.011)

• [17]

  The Influence of Bioreactor Geometry and the Mechanical Environment on Engineered Tissues

  J. M. Osborne‚ R. D. O'Dea‚ J. P. Whiteley‚ H. M. Byrne and S. L. Waters

  In Journal of Biomechanical Engineering. Vol. 132. No. 5. Pages 051006. May, 2010.

  Details about The Influence of Bioreactor Geometry and the Mechanical Environment on Engineered Tissues | BibTeX data for The Influence of Bioreactor Geometry and the Mechanical Environment on Engineered Tissues | DOI (10.1115/1.4001160)

• [18]

  Chaste: a test−driven approach to software development for biological modelling

  Joe Pitt−Francis‚ Pras Pathmanathan‚ Miguel O Bernabeu‚ Rafel Bordas‚ Jonathan Cooper‚ Alexander G Fletcher‚ Gary R Mirams‚ Philip Murray‚ James M Osborne‚ Alex Walter and others

  In Computer Physics Communications. Vol. 180. No. 12. Pages 2452–2471. 2009.

  Details about Chaste: a test−driven approach to software development for biological modelling | BibTeX data for Chaste: a test−driven approach to software development for biological modelling | DOI (10.1016/j.cpc.2009.07.019)

• [19]

  A computational study of discrete mechanical tissue models

  P Pathmanathan‚ J Cooper‚ A Fletcher‚ G Mirams‚ P Murray‚ J Osborne‚ J Pitt−Francis‚ A Walter and S J Chapman

  In Physical Biology. Vol. 6. No. 3. 2009.

  Details about A computational study of discrete mechanical tissue models | BibTeX data for A computational study of discrete mechanical tissue models | DOI (10.1088/1478-3975/6/3/036001)

• [20]

  An integrative computational model for intestinal tissue renewal

  Van Leeuwen‚ Ingeborg MM‚ GR Mirams‚ Alex Walter‚ A Fletcher‚ P Murray‚ J Osborne‚ S Varma‚ SJ Young‚ J Cooper‚ B Doyle and others

  In Cell proliferation. Vol. 42. No. 5. Pages 617–636. 2009.

  Details about An integrative computational model for intestinal tissue renewal | BibTeX data for An integrative computational model for intestinal tissue renewal | DOI (10.1111/j.1365-2184.2009.00627.x)

• [21]

  Chaste: using agile programming techniques to develop computational biology software

  Joe Pitt−Francis‚ Miguel O Bernabeu‚ Jonathan Cooper‚ Alan Garny‚ Lee Momtahan‚ James Osborne‚ Pras Pathmanathan‚ Blanca Rodriguez‚ Jonathan P Whiteley and David J Gavaghan

  In Philosophical Transactions of the Royal Society A: Mathematical‚ Physical and Engineering Sciences. Vol. 366. No. 1878. Pages 3111–3136. 2008.

  Details about Chaste: using agile programming techniques to develop computational biology software | BibTeX data for Chaste: using agile programming techniques to develop computational biology software | DOI (10.1098/rsta.2008.0096)