Engaging the Visitor: Relevance, Participation and Motivation in Hypermedia Design. - Jonathan Cooper (ICHIM, 1993)

On the application of partial evaluation to the optimisation of cardiac electrophysiological simulations. - Jonathan Cooper; Steve McKeever; Alan Garny (PEPM, 2006)

Experience report: a Haskell interpreter for cellML. - Jonathan Cooper; Steve McKeever (ICFP, 2007)

A model-driven approach to automatic conversion of physical units. - Jonathan Cooper; Steve McKeever (Softw. Pract. Exp., 2008)

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 J. Murray; James M. Osborne; Alex Walter; S. Jonathan Chapman; Alan Garny; et al. (Comput. Phys. Commun., 2009)

An overview of the CellML API and its implementation. - Andrew K. Miller; Justin Marsh; Adam Reeve; Alan Garny; Randall Britten; Matt D. B. Halstead; Jonathan Cooper; David P. Nickerson; Poul M. F. Nielsen (BMC Bioinform., 2010)

A Posteriori Error Analysis for the Use of Lookup Tables in Cardiac Electrophysiology Simulations. - Jonathan Cooper; Jonathan P. Whiteley; David J. Gavaghan (SIAM J. Sci. Comput., 2010)

TumorML: Concept and requirements of an in silico cancer modelling markup language. - David Johnson 006; Jonathan Cooper; Steve McKeever (EMBC, 2011)

Minimum Information About a Simulation Experiment (MIASE). - Dagmar Waltemath; Richard R. Adams; Daniel A. Beard; Frank T. Bergmann; Upinder S. Bhalla; Randall Britten; Vijayalakshmi Chelliah; Mike T. Cooling; Jonathan Cooper; Edmund J. Crampin; Alan Garny; Stefan Hoops; et al. (PLoS Comput. Biol., 2011)

Connecting Models to Data in Multiscale Multicellular Tissue Simulations. - Jonathan Cooper; James M. Osborne (ICCS, 2013)

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; Megan E. Marsh; James M. Osborne; et al. (PLoS Comput. Biol., 2013)

COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project. - Frank T. Bergmann; Richard R. Adams; Stuart L. Moodie; Jonathan Cooper; Mihai Glont; Martin Golebiewski; Michael Hucka; Camille Laibe; Andrew K. Miller; David P. Nickerson; Brett G. Olivier; Nicolas Rodriguez 001; et al. (BMC Bioinform., 2014)

COMBINE archive: One File To Share Them All. - Frank T. Bergmann; Richard Adams; Stuart L. Moodie; Jonathan Cooper; Mihai Glont; Martin Golebiewski; Michael Hucka; Camille Laibe; Andrew K. Miller; David P. Nickerson; Brett G. Olivier; Nicolas Rodriguez 001; et al. (CoRR, 2014)

Chaste: A case study of parallelisation of an open source finite-element solver with applications to computational cardiac electrophysiology simulation. - Miguel O. Bernabeu; James Southern; Nicholas Wilson; Peter E. Strazdins; Jonathan Cooper; Joe Pitt-Francis (Int. J. High Perform. Comput. Appl., 2014)

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; et al. (PLoS Comput. Biol., 2014)

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2. - Frank T. Bergmann; Jonathan Cooper; Nicolas Le Novère; David P. Nickerson; Dagmar Waltemath (J. Integr. Bioinform., 2015)

Ten Simple Rules for a Successful Cross-Disciplinary Collaboration. - Bernhard Knapp; Rémi Bardenet; Miguel O. Bernabeu; Rafel Bordas; Maria Bruna; Ben Calderhead; Jonathan Cooper; Alexander G. Fletcher; Derek Groen; Bram Kuijper; Joanna Lewis; Greg J. McInerny; et al. (PLoS Comput. Biol., 2015)

Where next for the reproducibility agenda in computational biology? - Joanna Lewis; Charles E. Breeze; Jane Charlesworth; Oliver J. Maclaren; Jonathan Cooper (BMC Syst. Biol., 2016)

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3). - Frank T. Bergmann; Jonathan Cooper; Matthias König 003; Ion I. Moraru; David P. Nickerson; Nicolas Le Novère; Brett G. Olivier; Sven Sahle; Lucian P. Smith; Dagmar Waltemath (J. Integr. Bioinform., 2018)

Fault-tolerant control for commercial aircraft with actuator faults and constraints. - Yishi Liu; Xiwang Dong; Zhang Ren; Jonathan Cooper (J. Frankl. Inst., 2019)

CellML 2.0. - Michael Clerx; Michael T. Cooling; Jonathan Cooper; Alan Garny; Keri R. Moyle; David P. Nickerson; Poul M. F. Nielsen; Hugh Sorby (J. Integr. Bioinform., 2020)

Chaste: Cancer, Heart and Soft Tissue Environment. - Fergus R. Cooper; Ruth E. Baker; Miguel O. Bernabeu; Rafel Bordas; Louise Bowler; Alfonso Bueno-Orovio; Helen M. Byrne; Valentina Carapella; Louie Cardone-Noott; Jonathan Cooper; Sara Dutta; Benjamin D. Evans; et al. (J. Open Source Softw., 2020)

"A Switch Went off in my Whole Body": Lived Experiences of Fatigue and Post-Exertional Malaise in Long Covid. - Corina Sas; Yojana Lotankar; Rosalind Adam; Katherine J. Bradbury; Jonathan Cooper; Derek L. Hill; Veronica Martinez; Daniel Powell (CHI Extended Abstracts, 2023)

CellML 2.0.1. - Michael Clerx; Michael T. Cooling; Jonathan Cooper; Alan Garny; Keri R. Moyle; David P. Nickerson; Poul M. F. Nielsen; Hugh Sorby (J. Integr. Bioinform., 2023)