An Object-Oriented Approach to Local Computation in Bayes Linear Belief Networks. - Darren J. Wilkinson (COMPSTAT, 1998)

Bayes linear analysis for graphical models: The geometric approach to local computation and interpretive graphics. - Michael M. Goldstein; Darren J. Wilkinson (Stat. Comput., 2000)

Restricted Prior Inference for Complex Uncertainty Structures. - Michael M. Goldstein; Darren J. Wilkinson (Ann. Math. Artif. Intell., 2001)

Conditional simulation from highly structured Gaussian systems, with application to blocking-MCMC for the Bayesian analysis of very large linear models. - Darren J. Wilkinson; Stephen K. H. Yeung (Stat. Comput., 2002)

A sparse matrix approach to Bayesian computation in large linear models. - Darren J. Wilkinson; Stephen K. H. Yeung (Comput. Stat. Data Anal., 2004)

Modelling Lipid Metabolism to Improve Healthy Ageing. - Mark Mc Auley; Janette Jones; Darren J. Wilkinson; Thomas B. L. Kirkwood (BMC Bioinform., 2005)

CaliBayes: Integration of GRID based simulation and data resources for Bayesian calibration of biological models. - Richard J. Boys; Daniel Henderson; Thomas B. L. Kirkwood; Darren J. Wilkinson; W. Eryk Wolski (BMC Bioinform., 2005)

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)

Bayesian Sequential Inference for Stochastic Kinetic Biochemical Network Models. - Andrew Golightly; Darren J. Wilkinson (J. Comput. Biol., 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)

Bayesian sequential inference for nonlinear multivariate diffusions. - Andrew Golightly; Darren J. Wilkinson (Stat. Comput., 2006)

Bayesian methods in bioinformatics and computational systems biology. - Darren J. Wilkinson (Briefings Bioinform., 2007)

The SBML discrete stochastic models test suite. - Thomas W. Evans; Colin S. Gillespie; Darren J. Wilkinson (Bioinform., 2008)

Bayesian inference for nonlinear multivariate diffusion models observed with error. - Andrew Golightly; Darren J. Wilkinson (Comput. Stat. Data Anal., 2008)

Bayesian inference for a discretely observed stochastic kinetic model. - Richard J. Boys; Darren J. Wilkinson; Thomas B. L. Kirkwood (Stat. Comput., 2008)

Markov Chain Monte Carlo Algorithms for SDE Parameter Estimation. - Darren J. Wilkinson; Andrew Golightly (Learning and Inference in Computational Systems Biology, 2010)

CaliBayes and BASIS: integrated tools for the calibration, simulation and storage of biological simulation models. - Yuhui Chen; Conor Lawless; Colin S. Gillespie; Jake Wu; Richard J. Boys; Darren J. Wilkinson (Briefings Bioinform., 2010)

Colonyzer: automated quantification of micro-organism growth characteristics on solid agar. - Conor Lawless; Darren J. Wilkinson; Alexander Young; Stephen G. Addinall; David A. Lydall (BMC Bioinform., 2010)

The Integration of Genetic Maps Using Bayesian Inference. - Howsun Jow; Madhuchhanda Bhattacharjee; Richard J. Boys; Darren J. Wilkinson (J. Comput. Biol., 2010)

An integrated dataset for in silico drug discovery. - Simon J. Cockell; Jochen Weile; Phillip W. Lord; Claire Wipat; Dmytro Andriychenko; Matthew R. Pocock; Darren J. Wilkinson; Malcolm Young; Anil Wipat (J. Integr. Bioinform., 2010)

Customizable views on semantically integrated networks for systems biology. - Jochen Weile; Matthew R. Pocock; Simon J. Cockell; Phillip W. Lord; James M. Dewar; Eva-Maria Holstein; Darren J. Wilkinson; David A. Lydall; Jennifer Hallinan; Anil Wipat (Bioinform., 2011)

Bayesian integration of networks without gold standards. - Jochen Weile; Katherine James; Jennifer Hallinan; Simon J. Cockell; Phillip W. Lord; Anil Wipat; Darren J. Wilkinson (Bioinform., 2012)

A whole-body mathematical model of cholesterol metabolism and its age-associated dysregulation. - Mark Mc Auley; Darren J. Wilkinson; Janette Jones; Thomas B. L. Kirkwood (BMC Syst. Biol., 2012)

Moment closure based parameter inference of stochastic kinetic models. - Peter Milner; Colin S. Gillespie; Darren J. Wilkinson (Stat. Comput., 2013)

Fast Bayesian parameter estimation for stochastic logistic growth models. - Jonathan Heydari; Conor Lawless; David A. Lydall; Darren J. Wilkinson (Biosyst., 2014)

Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions. - Michael Hucka; Frank T. Bergmann; Andreas Dräger; Stefan Hoops; Sarah M. Keating; Nicolas Le Novère; Chris J. Myers; Brett G. Olivier; Sven Sahle; James C. Schaff; Lucian P. Smith; Dagmar Waltemath; et al. (J. Integr. Bioinform., 2015)

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core. - Michael Hucka; Frank T. Bergmann; Stefan Hoops; Sarah M. Keating; Sven Sahle; James C. Schaff; Lucian P. Smith; Darren J. Wilkinson (J. Integr. Bioinform., 2015)

Scalable inference for Markov processes with intractable likelihoods. - Jamie Owen; Darren J. Wilkinson; Colin S. Gillespie (Stat. Comput., 2015)

Gaussian process emulation of an individual-based model simulation of microbial communities. - Oluwole K. Oyebamiji; Darren J. Wilkinson; Pahala Gedara Jayathilake; Thomas P. Curtis; S. P. Rushton; Bowen Li 005; P. Gupta (J. Comput. Sci., 2017)

Automating the Placement of Time Series Models for IoT Healthcare Applications. - Lauren Roberts; Peter Michalák; Sarah E. Heaps; Michael Trenell; Darren J. Wilkinson; Paul Watson 001 (eScience, 2018)

A hierarchical model of non-homogeneous Poisson processes for Twitter retweets. - Clement Lee; Darren J. Wilkinson (CoRR, 2018)

A Social Network Analysis of Articles on Social Network Analysis. - Clement Lee; Darren J. Wilkinson (CoRR, 2018)

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core. - Michael Hucka; Frank T. Bergmann; Andreas Dräger; Stefan Hoops; Sarah M. Keating; Nicolas Le Novère; Chris J. Myers; Brett G. Olivier; Sven Sahle; James C. Schaff; Lucian P. Smith; Dagmar Waltemath; et al. (J. Integr. Bioinform., 2018)

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core. - Michael Hucka; Frank T. Bergmann; Andreas Dräger; Stefan Hoops; Sarah M. Keating; Nicolas Le Novère; Chris J. Myers; Brett G. Olivier; Sven Sahle; James C. Schaff; Lucian P. Smith; Dagmar Waltemath; et al. (J. Integr. Bioinform., 2018)

EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies. - Alex L. Mitchell; Maxim Scheremetjew; Hubert Denise; Simon C. Potter; Aleksandra Tarkowska; Matloob Qureshi; Gustavo A. Salazar; Sebastien Pesseat; Miguel A. Boland; Fiona M. I. Hunter; Petra ten Hoopen; Blaise T. F. Alako; et al. (Nucleic Acids Res., 2018)

Composable models for online Bayesian analysis of streaming data. - Jonathan Law; Darren J. Wilkinson (Stat. Comput., 2018)

A network epidemic model for online community commissioning data. - Clement Lee; Andrew Garbett; Darren J. Wilkinson (Stat. Comput., 2018)

A review of stochastic block models and extensions for graph clustering. - Clement Lee; Darren J. Wilkinson (Appl. Netw. Sci., 2019)

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2. - Michael Hucka; Frank T. Bergmann; Claudine Chaouiya; Andreas Dräger; Stefan Hoops; Sarah M. Keating; Matthias König 003; Nicolas Le Novère; Chris J. Myers; Brett G. Olivier; Sven Sahle; James C. Schaff; et al. (J. Integr. Bioinform., 2019)

Bayesian emulation and calibration of an individual-based model of microbial communities. - Oluwole K. Oyebamiji; Darren J. Wilkinson; Bowen Li 005; Pahala Gedara Jayathilake; Paolo Zuliani; Thomas P. Curtis (J. Comput. Sci., 2019)

Systems Biology Markup Language (SBML) Level 3 Package: Distributions, Version 1, Release 1. - Lucian P. Smith; Stuart L. Moodie; Frank T. Bergmann; Colin S. Gillespie; Sarah M. Keating; Matthias König 003; Chris J. Myers; Maciek J. Swat; Darren J. Wilkinson; Michael Hucka (J. Integr. Bioinform., 2020)

A sparse Bayesian hierarchical vector autoregressive model for microbial dynamics in a wastewater treatment plant. - Naomi E. Hannaford; Sarah E. Heaps; Tom M. W. Nye; Thomas P. Curtis; Ben Allen; Andrew Golightly; Darren J. Wilkinson (Comput. Stat. Data Anal., 2023)

MGnify: the microbiome sequence data analysis resource in 2023. - Lorna J. Richardson; Ben Allen; Germana Baldi; Martin Beracochea; Maxwell L. Bileschi; Tony Burdett; Josephine Burgin; Juan Caballero; Guy Cochrane; Lucy J. Colwell; Tom Curtis; Alejandra Escobar-Zepeda; et al. (Nucleic Acids Res., 2023)

jax-smfsb: A Python library for stochastic systems biology modelling and inference. - Darren J. Wilkinson (J. Open Source Softw., 2025)