Darren J. Wilkinson

46 papers Journal 43Unranked 2

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	jax-smfsb: A Python library for stochastic systems biology modelling and inference. J. Open Source Softw. Darren J. Wilkinson
2023	J	`jnl`	A sparse Bayesian hierarchical vector autoregressive model for microbial dynamics in a wastewater treatment plant. Comput. Stat. Data Anal. Naomi E. Hannaford, Sarah E. Heaps, Tom M. W. Nye, Thomas P. Curtis, Ben Allen, Andrew Golightly, Darren J. Wilkinson
2023	J	`jnl`	MGnify: the microbiome sequence data analysis resource in 2023. Nucleic Acids Res. 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, Tatiana A. Gurbich, Varsha Kale, Anton I. Korobeynikov, Shriya Raj, Alexander B. Rogers, Ekaterina A. Sakharova, Santiago Sanchez, Darren J. Wilkinson, Robert D. Finn
2020	J	`jnl`	Systems Biology Markup Language (SBML) Level 3 Package: Distributions, Version 1, Release 1. J. Integr. Bioinform. Lucian P. Smith, Stuart L. Moodie, Frank T. Bergmann, Colin S. Gillespie, Sarah M. Keating, Matthias König, Chris J. Myers, Maciek J. Swat, Darren J. Wilkinson, Michael Hucka
2019	J	`jnl`	A Review of Stochastic Block Models and Extensions for Graph Clustering. CoRR Clement Lee, Darren J. Wilkinson
2019	J	`jnl`	A review of stochastic block models and extensions for graph clustering. Appl. Netw. Sci. Clement Lee, Darren J. Wilkinson
2019	J	`jnl`	Bayesian emulation and calibration of an individual-based model of microbial communities. J. Comput. Sci. Oluwole K. Oyebamiji, Darren J. Wilkinson, Bowen Li, Pahala Gedara Jayathilake, Paolo Zuliani, Thomas P. Curtis
2019	J	`jnl`	The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2. J. Integr. Bioinform. Michael Hucka, Frank T. Bergmann, Claudine Chaouiya, Andreas Dräger, Stefan Hoops, Sarah M. Keating, Matthias König, Nicolas Le Novère, Chris J. Myers, Brett G. Olivier, Sven Sahle, James C. Schaff, Rahuman S. Malik-Sheriff, Lucian P. Smith, Dagmar Waltemath, Darren J. Wilkinson, Fengkai Zhang
2018	J	`jnl`	A Social Network Analysis of Articles on Social Network Analysis. CoRR Clement Lee, Darren J. Wilkinson
2018	J	`jnl`	A hierarchical model of non-homogeneous Poisson processes for Twitter retweets. CoRR Clement Lee, Darren J. Wilkinson
2018	J	`jnl`	A network epidemic model for online community commissioning data. Stat. Comput. Clement Lee, Andrew Garbett, Darren J. Wilkinson
2018	—	`conf`	Automating the Placement of Time Series Models for IoT Healthcare Applications. eScience Lauren Roberts, Peter Michalák, Sarah E. Heaps, Michael Trenell, Darren J. Wilkinson, Paul Watson
2018	J	`jnl`	Composable models for online Bayesian analysis of streaming data. Stat. Comput. Jonathan Law, Darren J. Wilkinson
2018	J	`jnl`	EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies. Nucleic Acids Res. 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, Clara Amid, Darren J. Wilkinson, Thomas P. Curtis, Guy Cochrane, Robert D. Finn
2018	J	`jnl`	The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core. J. Integr. Bioinform. 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, Darren J. Wilkinson
2018	J	`jnl`	The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core. J. Integr. Bioinform. 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, Darren J. Wilkinson
2017	J	`jnl`	A Network Epidemic Model for Online Community Commissioning Data. CoRR Clement Lee, Andrew Garbett, Darren J. Wilkinson
2017	J	`jnl`	Gaussian process emulation of an individual-based model simulation of microbial communities. J. Comput. Sci. Oluwole K. Oyebamiji, Darren J. Wilkinson, Pahala Gedara Jayathilake, Thomas P. Curtis, S. P. Rushton, Bowen Li, P. Gupta
2015	J	`jnl`	Scalable inference for Markov processes with intractable likelihoods. Stat. Comput. Jamie Owen, Darren J. Wilkinson, Colin S. Gillespie
2015	J	`jnl`	Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions. J. Integr. Bioinform. 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, Darren J. Wilkinson
2015	J	`jnl`	The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core. J. Integr. Bioinform. Michael Hucka, Frank T. Bergmann, Stefan Hoops, Sarah M. Keating, Sven Sahle, James C. Schaff, Lucian P. Smith, Darren J. Wilkinson
2014	J	`jnl`	Fast Bayesian parameter estimation for stochastic logistic growth models. Biosyst. Jonathan Heydari, Conor Lawless, David A. Lydall, Darren J. Wilkinson
2013	J	`jnl`	Moment closure based parameter inference of stochastic kinetic models. Stat. Comput. Peter Milner, Colin S. Gillespie, Darren J. Wilkinson
2012	J	`jnl`	A whole-body mathematical model of cholesterol metabolism and its age-associated dysregulation. BMC Syst. Biol. Mark Mc Auley, Darren J. Wilkinson, Janette Jones, Thomas B. L. Kirkwood
2012	J	`jnl`	Bayesian integration of networks without gold standards. Bioinform. Jochen Weile, Katherine James, Jennifer Hallinan, Simon J. Cockell, Phillip W. Lord, Anil Wipat, Darren J. Wilkinson
2011	J	`jnl`	Customizable views on semantically integrated networks for systems biology. Bioinform. 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
2010	J	`jnl`	An integrated dataset for in silico drug discovery. J. Integr. Bioinform. Simon J. Cockell, Jochen Weile, Phillip W. Lord, Claire Wipat, Dmytro Andriychenko, Matthew R. Pocock, Darren J. Wilkinson, Malcolm Young, Anil Wipat
2010	J	`jnl`	CaliBayes and BASIS: integrated tools for the calibration, simulation and storage of biological simulation models. Briefings Bioinform. Yuhui Chen, Conor Lawless, Colin S. Gillespie, Jake Wu, Richard J. Boys, Darren J. Wilkinson
2010	J	`jnl`	Colonyzer: automated quantification of micro-organism growth characteristics on solid agar. BMC Bioinform. Conor Lawless, Darren J. Wilkinson, Alexander Young, Stephen G. Addinall, David A. Lydall
2010	—	`ch.`	Markov Chain Monte Carlo Algorithms for SDE Parameter Estimation. Learning and Inference in Computational Systems Biology Darren J. Wilkinson, Andrew Golightly
2010	J	`jnl`	The Integration of Genetic Maps Using Bayesian Inference. J. Comput. Biol. Howsun Jow, Madhuchhanda Bhattacharjee, Richard J. Boys, Darren J. Wilkinson
2008	J	`jnl`	Bayesian inference for a discretely observed stochastic kinetic model. Stat. Comput. Richard J. Boys, Darren J. Wilkinson, Thomas B. L. Kirkwood
2008	J	`jnl`	Bayesian inference for nonlinear multivariate diffusion models observed with error. Comput. Stat. Data Anal. Andrew Golightly, Darren J. Wilkinson
2008	J	`jnl`	The SBML discrete stochastic models test suite. Bioinform. Thomas W. Evans, Colin S. Gillespie, Darren J. Wilkinson
2007	J	`jnl`	Bayesian methods in bioinformatics and computational systems biology. Briefings Bioinform. Darren J. Wilkinson
2006	J	`jnl`	BASIS: an internet resource for network modelling. J. Integr. Bioinform. Colin S. Gillespie, Darren J. Wilkinson, Daryl P. Shanley, Carole J. Proctor, Richard J. Boys, Thomas B. L. Kirkwood
2006	J	`jnl`	Bayesian Sequential Inference for Stochastic Kinetic Biochemical Network Models. J. Comput. Biol. Andrew Golightly, Darren J. Wilkinson
2006	J	`jnl`	Bayesian sequential inference for nonlinear multivariate diffusions. Stat. Comput. Andrew Golightly, Darren J. Wilkinson
2006	J	`jnl`	Tools for the SBML Community. Bioinform. Colin S. Gillespie, Darren J. Wilkinson, Carole J. Proctor, Daryl P. Shanley, Richard J. Boys, Thomas B. L. Kirkwood
2005	J	`jnl`	CaliBayes: Integration of GRID based simulation and data resources for Bayesian calibration of biological models. BMC Bioinform. Richard J. Boys, Daniel Henderson, Thomas B. L. Kirkwood, Darren J. Wilkinson, W. Eryk Wolski
2005	J	`jnl`	Modelling Lipid Metabolism to Improve Healthy Ageing. BMC Bioinform. Mark Mc Auley, Janette Jones, Darren J. Wilkinson, Thomas B. L. Kirkwood
2004	J	`jnl`	A sparse matrix approach to Bayesian computation in large linear models. Comput. Stat. Data Anal. Darren J. Wilkinson, Stephen K. H. Yeung
2002	J	`jnl`	Conditional simulation from highly structured Gaussian systems, with application to blocking-MCMC for the Bayesian analysis of very large linear models. Stat. Comput. Darren J. Wilkinson, Stephen K. H. Yeung
2001	J	`jnl`	Restricted Prior Inference for Complex Uncertainty Structures. Ann. Math. Artif. Intell. Michael M. Goldstein, Darren J. Wilkinson
2000	J	`jnl`	Bayes linear analysis for graphical models: The geometric approach to local computation and interpretive graphics. Stat. Comput. Michael M. Goldstein, Darren J. Wilkinson
1998	—	`conf`	An Object-Oriented Approach to Local Computation in Bayes Linear Belief Networks. COMPSTAT Darren J. Wilkinson