James Osborne

Modelling the effect of subcellular mutations on the migration of cells in the colorectal crypt

Lotte B Romijn, Axel A Almet, Chin Wee Tan, James M Osborne

Journal article  |  2020  |  BMC Bioinformatics

BACKGROUND: Many cancers arise from mutations in cells within epithelial tissues. Mutations manifesting at the subcellular level i..

Addressing Interdisciplinary Difficulties in Developmental Biology/Mathematical Collaborations: A Neural Crest Example.

Donald F Newgreen, Kerry A Landman, James M Osborne

Journal article  |  2019  |  Methods in molecular biology (Clifton, N.J.)

Mathematical modeling can allow insight into the biological processes that can be difficult to access by conventional biological m..

Stochastic clonal expansion of "superstars" enhances the reserve capacity of enteric nervous system precursor cells

Dongcheng Zhang, James M Osborne, Kwaku Dad Abu-Bonsrah, Bevan L Cheeseman, Kerry A Landman, Boaz Jurkowicz, Donald F Newgreen

Journal article  |  2018  |  Developmental Biology

Cooperation, competition and antibiotic resistance in bacterial colonies

Isabel Frost, William PJ Smith, Sara Mitri, Alvaro San Millan, Yohan Davit, James M Osborne, Joe M Pitt-Francis, R Craig MacLean, Kevin R Foster

Journal article  |  2018  |  The ISME Journal

Multi-Cellular Modelling of Cellular Mechanisms Gives Insights on the Maintenance of Epidermal Tissue Structure

Claire Miller, James Osborne, Edmund Crampin

Conference Proceedings  |  2018  |  Biophysical Journal

A Multicellular Model of Intestinal Crypt Buckling and Fission

Axel A Almet, Barry D Hughes, Kerry A Landman, Inke S Nathke, James M Osborne

Journal article  |  2018  |  Bulletin of Mathematical Biology

A mathematical model of antibody-dependent cellular cytotoxicity (ADCC)

F Hoffman, D Gavaghan, J Osborne, IP Barrett, T You, H Ghadially, R Sainson, RW Wilkinson, HM Byrne

Journal article  |  2018  |  Journal of Theoretical Biology

A Fully Discrete Open Source Framework for the Simulation of Vascular Remodelling

J Osborne, Miguel O Bernabeu

Conference Proceedings  |  2018

Interkinetic nuclear migration and basal tethering facilitates post-mitotic daughter separation in intestinal organoids

Thomas D Carroll, Alistair J Langlands, James M Osborne, Ian P Newton, Paul L Appleton, Inke Nathke

Journal article  |  2017  |  Journal of Cell Science

Enteric nervous system formation: disproportionate stochastic clonal expansion of a few initiating vagal neural crest cells

Donald Newgreen, Dongcheng Zhang, James Osborne, Bevan Cheeseman, Benjamin Binder, Kerry Landman

Conference Proceedings  |  2017  |  Mechanisms of Development

Comparing individual-based approaches to modelling the self-organization of multicellular tissues

James M Osborne, Alexander G Fletcher, Joe M Pitt-Francis, Philip K Maini, David J Gavaghan

Journal article  |  2017  |  PLOS Computational Biology

The role of the Hes1 crosstalk hub in Notch-Wnt interactions of the intestinal crypt

Sophie K Kay, Heather A Harrington, Sarah Shepherd, Keith Brennan, Trevor Dale, James M Osborne, David J Gavaghan, Helen M Byrne

Journal article  |  2017  |  PLOS Computational Biology

Cell morphology drives spatial patterning in microbial communities

William PJ Smith, Yohan Davit, James M Osborne, Wook Kim, Kevin R Foster, Joe M Pitt-Francis

Journal article  |  2017  |  Proceedings of the National Academy of Sciences

How computational models contribute to our understanding of the germ line

Kathryn Atwell, Sara-Jane Dunn, James M Osborne, Hillel Kugler, E Jane Albert Hubbard

Journal article  |  2016  |  Molecular Reproduction and Development

Comparing Individual-Based Approaches to Modelling the Self-Organization of Multicellular Tissues

James Osborne, Alexander Fletcher, Joseph Pitt-Francis, Philip Maini, David Gavaghan

Journal article  |  2016

Abstract The coordinated behaviour of populations of cells plays a central role in tissue growth and renewal. Cells react to their..

Combined changes in Wnt signaling response and contact inhibition induce altered proliferation in radiation-treated intestinal crypts

S-J Dunn, JM Osborne, PL Appleton, I Nathke

Journal article  |  2016  |  Molecular Biology of the Cell

Paneth Cell-Rich Regions Separated by a Cluster of Lgr5 Cells Initiate Crypt Fission in the Intestinal Stem Cell Niche

Alistair J Langlands, Axel A Almet, Paul L Appleton, Ian P Newton, James M Osborne, Inke S Nathke

Journal article  |  2016  |  PLOS Biology

Reversible host cell remodeling underpins deformability changes in malaria parasite sexual blood stages

Megan Dearnley, Trang Chu, Yao Zhang, Oliver Looker, Changjin Huang, Nectarios Klonis, Jeff Yeoman, Shannon Kenny, Mohit Arora, James M Osborne, Rajesh Chandramohanadas, Sulin Zhang, Matthew WA Dixon, Leann Tilley

Journal article  |  2016  |  Proceedings of the National Academy of Sciences

The influence of hydrostatic pressure on tissue engineered bone development

KHL Nessler, JR Henstock, AJ El Haj, SL Waters, JP Whiteley, JM Osborne

Journal article  |  2016  |  Journal of Theoretical Biology

Mechano-logical model of C. elegans germ line suggests feedback on the cell cycle

Kathryn Atwell, Zhao Qin, David Gavaghan, Hillel Kugler, E Jane Albert Hubbard, James M Osborne

Journal article  |  2015  |  Development

A parallel implementation of an off-lattice individual-based model of multicellular populations

Daniel G Harvey, Alexander G Fletcher, James M Osborne, Joe Pitt-Francis

Journal article  |  2015  |  Computer Physics Communications

Ten Simple Rules for a Successful Cross-Disciplinary Collaboration

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, James Osborne, Verena Paulitschke, Joe Pitt-Francis, Jelena Todoric, Christian A Yates, David Gavaghan, Charlotte M Deane

Journal article  |  2015  |  PLOS Computational Biology

Computer Simulation, Visualization, and Image Processing of Cancer Data and Processes

David Johnson, James Osborne, Zhihui Wang, Kostas Marias

Journal article  |  2015  |  Cancer Informatics

Software development practices in academia: a case study comparison

Derek Groen, Xiaohu Guo, James A Grogan, Ulf D Schiller, James M Osborne

Journal article  |  2015  |  arXiv preprint arXiv:1506.05272

Multiscale Model of Colorectal Cancer Using the Cellular Potts Framework

James M Osborne

Journal article  |  2015  |  Cancer Informatics

Evaluation of the Growth Environment of a Hydrostatic Force Bioreactor for Preconditioning of Tissue-Engineered Constructs

Yvonne Reinwald, Katherine HL Leonard, James R Henstock, Jonathan P Whiteley, James M Osborne, Sarah L Waters, Philippe Levesque, Alicia J El Haj

Journal article  |  2015  |  Tissue Engineering Part C: Methods

CoGNaC: A Chaste Plugin for the Multiscale Simulation of Gene Regulatory Networks Driving the Spatial Dynamics of Tissues and Cancer

Simone Rubinacci, Alex Graudenzi, Giulio Caravagna, Giancarlo Mauri, James Osborne, Joe Pitt-Francis, Marco Antoniotti

Journal article  |  2015  |  Cancer Informatics

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, 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

Journal article  |  2014  |  PLoS Computational Biology

The Free Energy Landscape of Dimerization of a Membrane Protein, NanC

Thomas A Dunton, Joseph E Goose, David J Gavaghan, Mark SP Sansom, James M Osborne

Journal article  |  2014  |  PLoS Computational Biology

Computational Models Reveal a Passive Mechanism for Cell Migration in the Crypt

Sara-Jane Dunn, Inke S Naethke, James M Osborne

Journal article  |  2013  |  PLoS ONE

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

RD O'Dea, JM Osborne, AJ El Haj, HM Byrne, SL Waters

Journal article  |  2013  |  Journal of Mathematical Biology

Implementing vertex dynamics models of cell populations in biology within a consistent computational framework

Alexander G Fletcher, James M Osborne, Philip K Maini, David J Gavaghan

Journal article  |  2013  |  Progress in Biophysics and Molecular Biology

Colorectal cancer through simulation and experiment

Sophie K Kershaw, Helen M Byrne, David J Gavaghan, James M Osborne

Journal article  |  2013  |  Systems Biology, IET

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

Y Davit, JM Osborne, HM Byrne, D Gavaghan, J Pitt-Francis

Journal article  |  2013  |  Physical Review E

On-lattice agent-based simulation of populations of cells within the open-source Chaste framework

Grazziela P Figueredo, Tanvi V Joshi, James M Osborne, Helen M Byrne, Markus R Owen

Journal article  |  2013  |  Interface Focus

Chaste: An Open Source C plus plus 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, Megan E Marsh, James M Osborne, Pras Pathmanathan, Joe Pitt-Francis, James Southern, Nejib Zemzemi, David J Gavaghan

Journal article  |  2013  |  PLoS Computational Biology

Hydrodynamic dispersion within porous biofilms

Y Davit, H Byrne, J Osborne, J Pitt-Francis, D Gavaghan, M Quintard

Journal article  |  2013  |  Physical Review E

Connecting models to data in multiscale multicellular tissue simulations

Jonathan Cooper, James Osborne

Conference Proceedings  |  2013  |  Procedia Computer Science

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

Mark Slaymaker, James Osborne, Andrew Simpson, David Gavaghan

Journal article  |  2012  |  Systems and Synthetic Biology

The move towards in silico experimentation has resulted in the use of computational models, in addition to traditional experimenta..

A Two-Dimensional Model of the Colonic Crypt Accounting for the Role of the Basement Membrane and Pericryptal Fibroblast Sheath

Sara-Jane Dunn, Paul L Appleton, Scott A Nelson, Inke S Naethke, David J Gavaghan, James M Osborne

Journal article  |  2012  |  PLoS Computational Biology

Modelling the role of the basement membrane beneath a growing epithelial monolayer

Sara-Jane Dunn, Alexander G Fletcher, S Jonathan Chapman, David J Gavaghan, James M Osborne

Journal article  |  2012  |  Journal of Theoretical Biology

A hybrid approach to multi-scale modelling of cancer

JM Osborne, A Walter, SK Kershaw, GR Mirams, AG Fletcher, P Pathmanathan, D Gavaghan, OE Jensen, PK Maini, HM Byrne

Journal article  |  2010  |  Philosophical Transactions of the Royal Society of London A: Mathematical, Physical and Engineering Sciences

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

JM Osborne, RD O'Dea, JP Whiteley, HM Byrne, SL Waters

Journal article  |  2010  |  Journal of biomechanical engineering

A numerical method for the multiphase viscous flow equations

James M Osborne, Jonathan P Whiteley

Journal article  |  2010  |  Computer Methods in Applied Mechanics and Engineering

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, 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

Journal article  |  2009  |  Computer Physics Communications

An integrative computational model for intestinal tissue renewal

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, et al.

Journal article  |  2009  |  Cell Proliferation

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, SJ Chapman

Journal article  |  2009  |  Physical biology

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, David J Gavaghan

Journal article  |  2008  |  Philosophical Transactions of the Royal Society of London A: Mathematical, Physical and Engineering Sciences

Modelling the effect of subcellular mutations on the migration of cells in the colorectal crypt

Lotte B Romijn, Axel A Almet, Chin Wee Tan, James Osborne

Journal article

Abstract Background: Many cancers arise from mutations in cells within epithelial tissues. Mutations manifesting at the su..

Modelling the effect of subcellular mutations on the migration of cells in the colorectal crypt

Lotte B Romijn, Axel A Almet, Chin Wee Tan, James Osborne

Journal article

Abstract Background Many cancers arise from mutations in cells in epithelial tissues. Mutations manifesting at the subcell..

Modelling the effect of subcellular mutations on the migration of cells in the colorectal crypt

Lotte B Romijn, Axel A Almet, Chin Wee Tan, James Osborne

Journal article

Abstract Background: Many cancers arise from mutations in cells within epithelial tissues. Mutations manifesting at the su..