Publications by Professor Darren Wilkinson - ePrints

Browsing publications by Professor Darren Wilkinson.

Newcastle Authors	Title	Year
Dr Aleksandra Svalova Dr Peter Helm Dr Dennis Prangle Professor Mohamed Rouainia Professor Stephanie Glendinning et al.	Emulating computer experiments of transport infrastructure slope stability using Gaussian processes and Bayesian inference	2021
Dr Clement Lee Professor Darren Wilkinson	A hierarchical model of non-homogeneous Poisson processes for Twitter retweets	2020
Professor Stuart Barr Dr Stephen Johnson Dr Xiaodong Ming Dr Maria-Valasia Peppa Dr Na Dong et al.	FLOOD-PREPARED: A NOWCASTING SYSTEM for REAL-TIME IMPACT ADAPTION to SURFACE WATER FLOODING in CITIES	2020
Dr Colin Gillespie Professor Darren Wilkinson Dr Allyson Lister Dr Carole Proctor	SBML Level 3: an extensible format for the exchange and reuse of biological models	2020
Dr Colin Gillespie Professor Darren Wilkinson	Systems Biology Markup Language (SBML) Level 3 Package: Distributions, Version 1, Release 1	2020
Dr Clement Lee Professor Darren Wilkinson	A Review of Stochastic Block Models and Extensions for Graph Clustering	2019
Dr Oluwole Oyebamiji Professor Darren Wilkinson Dr Bowen Li Dr Paolo Zuliani Professor Thomas Curtis et al.	Bayesian emulation and calibration of an individual-based model of microbial communities	2019
Dr Valentina Gogulancea Dr Rebeca Gonzalez-Cabaleiro Dr Bowen Li Dr Denis Taniguchi Dr Jinju Chen et al.	Individual based model links thermodynamics, chemical speciation and environmental conditions to microbial growth	2019
Dr Oluwole Oyebamiji Professor Darren Wilkinson Dr Jayathilake Pahala Gedara Professor Stephen Rushton Dr Bowen Li et al.	A Bayesian approach to modelling the impact of hydrodynamic shear stress on biofilm deformation	2018
Dr Clement Lee Dr Andy Garbett Professor Darren Wilkinson	A network epidemic model for online community commissioning data	2018
Lauren Roberts Dr Peter Michalak Dr Sarah Heaps Professor Mike Trenell Professor Darren Wilkinson et al.	Automating the placement of time series models for IoT healthcare applications	2018
Dr Jonathan Law Professor Darren Wilkinson	Composable Models for Online Bayesian Analysis of Streaming Data	2018
Professor Darren Wilkinson Professor Thomas Curtis	EBI Metagenomics in 2017: Enriching the analysis of microbial communities, from sequence reads to assemblies	2018
Professor Darren Wilkinson	Stochastic Modelling for Systems Biology, Third Edition	2018
Dr Jayathilake Pahala Gedara Dr Prashant Gupta Dr Bowen Li Dr Curtis Madsen Dr Oluwole Oyebamiji et al.	A mechanistic individual-based model of microbial communities	2017
Dr Oluwole Oyebamiji Professor Darren Wilkinson Dr Jayathilake Pahala Gedara Professor Thomas Curtis Dr Bowen Li et al.	Gaussian process emulation of an individual-based model simulation of microbial communities	2017
Dr Eva-Maria Holstein Dr Conor Lawless Dr Andrew Banks Professor Darren Wilkinson Professor David Lydall et al.	Systematic Analysis of the DNA Damage Response Network in Telomere Defective Budding Yeast	2017
Jonathan Heydari Dr Conor Lawless Professor David Lydall Professor Darren Wilkinson	Bayesian hierarchical modelling for inferring genetic interactions in yeast	2016
Dr Oluwole Oyebamiji Professor Darren Wilkinson	Statistical emulation as a tool for analysing complex multiscale stochastic biological model outputs	2016
Dr Andrew Golightly Professor Darren Wilkinson	Bayesian inference for Markov jump processes with informative observations	2015
Jamie Owen Professor Darren Wilkinson Dr Colin Gillespie	Likelihood free inference for Markov processes: a comparison	2015
Dr Siddharth Narayanan Dr Marion Dubarry Dr Conor Lawless Dr Andrew Banks Professor Darren Wilkinson et al.	Quantitative Fitness Analysis Identifies exo1∆ and Other Suppressors or Enhancers of Telomere Defects in Schizosaccharomyces pombe	2015
Jamie Owen Professor Darren Wilkinson Dr Colin Gillespie	Scalable inference for Markov processes with intractable likelihoods	2015
Professor Darren Wilkinson	The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core	2015
Dr Howsun Jow Professor Richard Boys Professor Darren Wilkinson	Bayesian identification of protein differential expression in multi-group isobaric labelled mass spectrometry data	2014
Jonathan Heydari Dr Conor Lawless Professor David Lydall Professor Darren Wilkinson	Fast Bayesian parameter estimation for stochastic logistic growth models	2014
Professor Darren Wilkinson	Do simple models lead to generality in ecology?	2013
Peter Milner Dr Colin Gillespie Professor Darren Wilkinson	Moment closure based parameter inference of stochastic kinetic models	2013
Lizzy Andrew Dr Stephanie Merchan Dr Conor Lawless Dr Andrew Banks Professor Darren Wilkinson et al.	Pentose Phosphate Pathway Function Affects Tolerance to the G-Quadruplex Binder TMPyP4	2013
Mark McAuley Professor Darren Wilkinson Emeritus Professor Thomas Kirkwood	A whole body mathematical model of cholesterol metabolism and its age associated dysregulation	2012
Jochen Weile Dr Katherine James Dr Jennifer Hallinan Dr Simon Cockell Dr Phillip Lord et al.	Bayesian integration of networks without gold standards	2012
Dr Howsun Jow Professor Richard Boys Professor Darren Wilkinson	A comparative genomics approach to the identification of QTL candidate genes	2011
Dr Guiyuan Lei Professor Richard Boys Dr Colin Gillespie Dr Amanda Greenall Professor Darren Wilkinson et al.	Bayesian inference for sparse VAR(1) models, with application to time course microarray data	2011
Dr Andrew Golightly Professor Darren Wilkinson	Bayesian parameter inference for stochastic biochemical network models using particle Markov chain Monte Carlo	2011
Dr Allyson Lister Dr Matthew Pocock Professor Darren Wilkinson	Controlled vocabularies and semantics in systems biology	2011
Dr Allyson Lister Dr Matthew Pocock Professor Darren Wilkinson	Controlled vocabularies and semantics in systems biology	2011
Jochen Weile Dr Matthew Pocock Dr Simon Cockell Dr Phillip Lord James Dewar et al.	Customizable views on semantically integrated networks for systems biology	2011
Dr Hsin Yu Chang Dr Conor Lawless Dr Stephen Addinall Morgan Taschuk Professor Anil Wipat et al.	Genome-Wide Analysis to Identify Pathways Affecting Telomere-Initiated Senescence in Budding Yeast	2011
Dr Colin Gillespie Professor Darren Wilkinson	Moment closure approximations for stochastic kinetic models with rational rate laws	2011
Professor Darren Wilkinson	Parameter inference for stochastic kinetic models of bacterial gene regulation: A Bayesian Approach to Systems Biology	2011
Dr Stephen Addinall Dr Eva-Maria Holstein Dr Conor Lawless Dr Min Yu Dr Kaye Chapman et al.	Quantitative Fitness Analysis Shows That NMD Proteins and Many Other Protein Complexes Suppress or Enhance Distinct Telomere Cap Defects	2011
Professor Darren Wilkinson	Stochastic dynamical systems	2011
Professor Darren Wilkinson	Stochastic Modelling for Systems Biology	2011
Dr Simon Cockell Jochen Weile Dr Phillip Lord Dmytro Andriychenko Dr Matthew Pocock et al.	An integrated dataset for in silico drug discovery	2010
Dr Colin Gillespie Dr Guiyuan Lei Professor Richard Boys Dr Amanda Greenall Professor Darren Wilkinson et al.	Analysing time course microarray data using Bioconductor: a case study using yeast2 Affymetrix arrays	2010
Dr Daniel Henderson Professor Richard Boys Professor Darren Wilkinson	Bayesian Calibration of a Stochastic Kinetic Computer Model Using Multiple Data Sources	2010
Dr Yuhui Chen Dr Conor Lawless Dr Colin Gillespie Professor Jingyi Wu Professor Richard Boys et al.	CaliBayes and BASIS: integrated tools for the calibration, simulation and storage of biological simulation models	2010
Dr Conor Lawless Professor Darren Wilkinson Dr Stephen Addinall Professor David Lydall	Colonyzer: automated quantification of micro-organism growth characteristics on solid agar	2010
Dr Andrew Golightly Professor Darren Wilkinson	Discussion to "Particle Markov chain Monte Carlo Methods" by Andrieu, Doucet and Holenstein	2010
Dr Daniel Henderson Professor Richard Boys Professor Darren Wilkinson	Linking systems biology models to data: a stochastic kinetic model of p53 oscillations	2010
Professor Darren Wilkinson Dr Andrew Golightly	Markov chain Monte Carlo algorithms for SDE parameter estimation	2010
Professor Darren Wilkinson	Systems Biology Markup Language (SBML): Language specification for Level 3 Version 1 Core	2010
Dr Howsun Jow Dr Madhuchhanda Bhattacharjee Professor Richard Boys Professor Darren Wilkinson	The Integration of Genetic Maps Using Bayesian Inference	2010
Mark McAuley Professor Rose Anne Kenny Emeritus Professor Thomas Kirkwood Professor Darren Wilkinson Veronica Miller et al.	A mathematical model of aging-related and cortisol induced hippocampal dysfunction	2009
Dr Daniel Henderson Professor Richard Boys Dr Conor Lawless Professor Darren Wilkinson	Bayesian Emulation and Calibration of a Stochastic Computer Model of Mitochondrial DNA Deletions in Substantia Nigra Neurons	2009
Professor Darren Wilkinson	Stochastic modelling for quantitative description of heterogeneous biological systems	2009
Dr Amanda Greenall Dr Daniel Swan Dr Heiko Peters Professor Anil Wipat Professor Darren Wilkinson et al.	A genome wide analysis of the response to uncapped telomeres in budding yeast reveals a novel role for the NAD(+) biosynthetic gene BNA2 in chromosome end protection	2008
Dr Stephen Addinall Dawn Downey Dr Min Yu Dr Mikhajlo Zubko James Dewar et al.	A Genome-wide Suppressor and Enhancer Analysis of cdc13-1 Reveals Varied Cellular Processes Influencing Telomere Capping in Saccharomyces cerevisiae	2008
Professor Richard Boys Professor Darren Wilkinson Emeritus Professor Thomas Kirkwood	Bayesian inference for a discretely observed stochastic kinetic model	2008
Dr Andrew Golightly Professor Darren Wilkinson	Bayesian inference for nonlinear multivariate diffusion models observed with error	2008
Professor Darren Wilkinson	Systems Biology Markup Language (SBML) Level 2: Structures and facilities for model definitions	2008
Dr Colin Gillespie Professor Darren Wilkinson	The SBML discrete stochastic models test suite	2008
Professor Darren Wilkinson	Bayesian methods in bioinformatics and computational systems biology	2007
Dr Carole Proctor Professor David Lydall Professor Richard Boys Dr Colin Gillespie Dr Daryl Shanley et al.	Modelling the checkpoint response to telomere uncapping in budding yeast	2007
Dr Colin Gillespie Professor Darren Wilkinson Dr Daryl Shanley Dr Carole Proctor Professor Richard Boys et al.	BASIS: an internet resource for network modelling.	2006
Dr Andrew Golightly Professor Darren Wilkinson	Bayesian sequential inference for nonlinear multivariate diffusions	2006
Dr Andrew Golightly Professor Darren Wilkinson	Bayesian sequential inference for stochastic kinetic biochemical network models	2006
Emeritus Professor Thomas Kirkwood Professor Richard Boys Dr Colin Gillespie Dr John Proctor Dr Daryl Shanley et al.	Computer modeling in the study of aging	2006
Professor Darren Wilkinson	Stochastic Modelling for Systems Biology	2006
Dr Colin Gillespie Professor Darren Wilkinson Dr Carole Proctor Dr Daryl Shanley Professor Richard Boys et al.	Tools for the SBML community	2006
Dr Andrew Golightly Professor Darren Wilkinson	Bayesian inference for stochastic kinetic models using a diffusion approximation	2005
Emeritus Professor Thomas Kirkwood Professor Richard Boys Dr Colin Gillespie Dr John Proctor Dr Daryl Shanley et al.	Computer Modeling in the Study of Aging	2005
Dr Carole Proctor Professor Richard Boys Dr Colin Gillespie Dr Daryl Shanley Professor Darren Wilkinson et al.	Modelling the actions of chaperones and their role in ageing	2005
Professor Darren Wilkinson	Parallel Bayesian Computation	2005
Dr Colin Gillespie Dr Carole Proctor Dr Daryl Shanley Professor Darren Wilkinson Professor Richard Boys et al.	Web-services for the biology community: the BASIS project	2005
Dr Colin Gillespie Dr Carole Proctor Professor Richard Boys Dr Daryl Shanley Professor Darren Wilkinson et al.	A mathematical model of ageing in yeast	2004
Professor Darren Wilkinson Stephen Yeung	A sparse matrix approach to Bayesian computation in large linear models	2004
Professor Darren Wilkinson	Discussion to Papaspiliopoulos, O., Roberts, G. O. and Skold, M., 'Non-centered parameterisation for hierarchical models and data augmentation'	2003
Linda Garside Professor Darren Wilkinson	Dynamic lattice-Markov spatio-temporal models for environmental data	2003
Linda Garside Professor Darren Wilkinson	Dynamic lattice-Markov spatio-temporal models for environmental data	2003
Emeritus Professor Thomas Kirkwood Professor Richard Boys Dr Colin Gillespie Dr Carole Proctor Dr Daryl Shanley et al.	Towards an e-biology of ageing: Integrating theory and data	2003
Professor Darren Wilkinson Stephen Yeung	Conditional simulation from highly structured Gaussian systems, with application to blocking-MCMC for the Bayesian analysis of very large linear models	2002
Professor Darren Wilkinson	Restricted prior inference for complex uncertainty structures	2001
Professor Darren Wilkinson	Bayes linear analysis for graphical models: The geometric approach to local computation and interpretive graphics	2000
Professor Richard Boys Dr Daniel Henderson Professor Darren Wilkinson	Detecting homogeneous segments in DNA sequences by using hidden Markov models	2000
Professor Kevin Glazebrook Professor Darren Wilkinson	Index-based policies for discounted multi-armed bandits on parallel machines	2000
Professor Darren Wilkinson	Multivariate DLMs for Forecasting Financial Time series, with Application to the Management of Portfolios	2000