Tools for the SBML Community. - Colin S. Gillespie; Darren J. Wilkinson; Carole J. Proctor; Daryl P. Shanley; Richard J. Boys; Thomas B. L. Kirkwood (Bioinform., 2006)

BASIS: an internet resource for network modelling. - Colin S. Gillespie; Darren J. Wilkinson; Daryl P. Shanley; Carole J. Proctor; Richard J. Boys; Thomas B. L. Kirkwood (J. Integr. Bioinform., 2006)

Computational modelling of the regulation of Insulin signalling by oxidative stress. - Graham R. Smith; Daryl P. Shanley (BMC Syst. Biol., 2013)

Dynamic Modelling of Pathways to Cellular Senescence Reveals Strategies for Targeted Interventions. - Piero Dalle Pezze; Glyn Nelson; Elsje G. Otten; Viktor I. Korolchuk; Thomas B. L. Kirkwood; Thomas von Zglinicki; Daryl P. Shanley (PLoS Comput. Biol., 2014)

Integrated Stochastic Model of DNA Damage Repair by Non-homologous End Joining and p53/p21- Mediated Early Senescence Signalling. - David W. P. Dolan; Anze Zupanic; Glyn Nelson; Philip Hall; Satomi Miwa; Thomas B. L. Kirkwood; Daryl P. Shanley (PLoS Comput. Biol., 2015)

PyCoTools: a Python toolbox for COPASI. - Ciaran M. Welsh; Nicola Fullard; Carole J. Proctor; Alvaro Martinez-Guimera; Robert J. Isfort; Charles C. Bascom; Ryan Tasseff; Stefan A. Przyborski; Daryl P. Shanley (Bioinform., 2018)

TimiRGeN: R/Bioconductor package for time series microRNA-mRNA integration and analysis. - Krutik Patel; S. Chandrasegaran; I M. Clark; Carole J. Proctor; D. A. Young; Daryl P. Shanley (Bioinform., 2021)

Modelling the spatiotemporal dynamics of senescent cells in wound healing, chronic wounds, and fibrosis. - Sharmilla Chandrasegaran; James P. Sluka; Daryl P. Shanley (PLoS Comput. Biol., 2025)