Please also see Paul DW Kirk’s Google Scholar page.

Journal publications

Consensus clustering for Bayesian mixture models
S Coleman, PDW Kirk, C Wallace
BMC bioinformatics 23 (1), 1-21 2022

Transcriptional, epigenetic and metabolic signatures in cardiometabolic syndrome defined by extreme phenotypes
D Seyres, A Cabassi, JJ Lambourne, F Burden, S Farrow, H McKinney, …
Clinical epigenetics 14 (1), 1-24 2022

Semi-supervised nonparametric Bayesian modelling of spatial proteomics
OM Crook, KS Lilley, L Gatto, PDW Kirk
The Annals of Applied Statistics 16 (4), 2554-2576 2022

In simulated data and health records, latent class analysis was the optimum multimorbidity clustering algorithm
L Nichols, T Taverner, F Crowe, S Richardson, C Yau, S Kiddle, P Kirk, …
Journal of clinical epidemiology 2022

Inferring differential subcellular localisation in comparative spatial proteomics using BANDLE
OM Crook, CTR Davies, LM Breckels, JA Christopher, L Gatto, PDW Kirk, …
Nature communications 13 (1), 1-21 2022

Investigating the stability of multimorbidity clusters within and between clustering algorithms, in simulated and health record data
L Nichols, T Taverner, F Crowe, S Richardson, C Yau, S Kiddle, P Kirk, …
Elsevier 2022

Bayesian nonparametric mixture inconsistency for the number of components: How worried should we be in practice?
Y Chaumeny, JM Moris, AC Davison, PDW Kirk
arXiv preprint arXiv:2207.14717 2022

Topological approximate Bayesian computation for parameter inference of an angiogenesis model
T Thorne, PDW Kirk, HA Harrington
Bioinformatics 38 (9), 2529-2535 2022

Temporal sequencing in multimorbidity using population-scale linked data for 1.7 million individuals with 20-year follow-up
R Owen, J Lyons, A Akbari, B Guthrie, U Agrawal, D Alexander, …
2022

A noise-augmented directional clustering approach for identifying distinct mechanisms underlying genetic associations
AJ Grant, D Gill, PDW Kirk, S Burgess
HUMAN HEREDITY, 23-24 2022

Dose-response prediction for in-vitro drug combination datasets: a probabilistic approach
L Rønneberg, PDW Kirk, M Zucknick
2022

Noise-augmented directional clustering of genetic association data identifies distinct mechanisms underlying obesity
AJ Grant, D Gill, PDW Kirk, S Burgess
PLoS genetics 18 (1), e1009975 2022

A semi-supervised Bayesian mixture modelling approach for joint batch correction and classification
S Coleman, XC Dopico, GBK Hedestam, PDW Kirk, C Wallace
bioRxiv 2022

Bayesian profile regression for clustering analysis involving a longitudinal response and explanatory variables
A Rouanet, R Johnson, ME Strauss, S Richardson, BD Tom, SR White, …
arXiv preprint arXiv:2111.04518 2021

A Bayesian semi-parametric model for thermal proteome profiling
S Fang, PDW Kirk, M Bantscheff, KS Lilley, OM Crook
Communications biology 4 (1), 1-15 2021

Detection of quantitative trait loci from RNA-seq data with or without genotypes using BaseQTL
E Vigorito, WY Lin, C Starr, PDW Kirk, SR White, C Wallace
Nature computational science 1 (6), 421-432 2021

The RNA landscape of the human placenta in health and disease
S Gong, F Gaccioli, J Dopierala, U Sovio, E Cook, PJ Volders, L Martens, …
Nature Communications 12 (1), 1-17 2021

Tailored Bayes: a risk modelling framework under unequal misclassification costs
S Karapanagiotis, U Benedetto, S Mukherjee, PDW Kirk, PJ Newcombe
arXiv preprint arXiv:2104.01822 2021

Longitudinal proteomic profiling of dialysis patients with COVID-19 reveals markers of severity and predictors of death
J Gisby, CL Clarke, N Medjeral-Thomas, TH Malik, A Papadaki, …
Elife 10, e64827 2021

MR-Clust: clustering of genetic variants in Mendelian randomization with similar causal estimates
CN Foley, AM Mason, PDW Kirk, S Burgess
Bioinformatics 37 (4), 531-541 2021

A fast and efficient colocalization algorithm for identifying shared genetic risk factors across multiple traits
CN Foley, JR Staley, PG Breen, BB Sun, PDW Kirk, S Burgess, …
Nature communications 12 (1), 1-18 2021

Genetic feature engineering enables characterisation of shared risk factors in immune-mediated diseases
OS Burren, G Reales, L Wong, J Bowes, JC Lee, A Barton, PA Lyons, …
Genome medicine 12 (1), 1-17 2020

A semi-supervised Bayesian approach for simultaneous protein sub-cellular localisation assignment and novelty detection
OM Crook, A Geladaki, DJH Nightingale, OL Vennard, KS Lilley, L Gatto, …
PLoS computational biology 16 (11), e1008288 2020

Kernel learning approaches for summarising and combining posterior similarity matrices
A Cabassi, S Richardson, PDW Kirk
arXiv preprint arXiv:2009.12852 2020

Multiple kernel learning for integrative consensus clustering of omic datasets
A Cabassi, PDW Kirk
Bioinformatics 36 (18), 4789-4796 2020

Two-step penalised logistic regression for multi-omic data with an application to cardiometabolic syndrome
A Cabassi, D Seyres, M Frontini, PDW Kirk
arXiv preprint arXiv:2008.00235 2020

Gpseudoclust: deconvolution of shared pseudo-profiles at single-cell resolution
ME Strauss, PDW Kirk, JE Reid, L Wernisch
Bioinformatics 36 (5), 1484-1491 2020

Longitudinal proteomic profiling of high-risk patients with COVID-19 reveals markers of severity and predictors of fatal disease
J Gisby, CL Clarke, N Medjeral-Thomas, TH Malik, A Papadaki, …
2020

klic: Kernel Learning Integrative Clustering
A Cabassi, PDW Kirk, M Gönen
https://CRAN.R-project.org/package=klic 2020

coca: Cluster-of-Cluster Analysis
A Cabassi, PDW Kirk
R package version 1 (2), https://CRAN.R-project.org/package=coca 2020

Fast approximate inference for variable selection in Dirichlet process mixtures, with an application to pan-cancer proteomics
OM Crook, L Gatto, PDW Kirk
Statistical applications in genetics and molecular biology 18 (6) 2019

Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen
MP Menden, D Wang, MJ Mason, B Szalai, KC Bulusu, Y Guan, T Yu, …
Nature communications 10 (1), 1-17 2019

A Bioconductor workflow for the Bayesian analysis of spatial proteomics
OM Crook, LM Breckels, KS Lilley, PDW Kirk, L Gatto
F1000Research 8 2019

A Bayesian mixture modelling approach for spatial proteomics
OM Crook, CM Mulvey, PDW Kirk, KS Lilley, L Gatto
PLoS computational biology 14 (11), e1006516 2018

A comprehensive evaluation of nasal and bronchial cytokines and chemokines following experimental rhinovirus infection in asthma: increased interferons (IFN-γ and IFN-λ) and type 2 inflammation (IL-5 and IL-13).
Hansel TT, Tunstall T, Trujillo-Torralbo M-B, Shamji B, del-Rosario J, Dhariwal J, Kirk PDW, et al.
eBioMedicine. 2017.

Retroviruses integrate into a shared, non-palindromic motif.
Kirk PDW, Huvet M, Melamed A, Maertens GN, Bangham CRM
Nature Microbiology. 2016; 2, 16212.

Inferring extrinsic noise from single-cell gene expression data using Approximate Bayesian Computation.
Lenive O, Kirk PDW, Stumpf MPH
BMC Systems Biology. 2016; 10(1), 1–17.

Robustness of MEK-ERK Dynamics and Origins of Cell-to-Cell Variability in MAPK Signaling.
Filippi S, Barnes CP, Kirk PDW, Kudo T, Kunida K, McMahon SS, et al.
Cell Reports. 2016.

MEANS: python package for Moment Expansion Approximation, iNference and Simulation
Fan S, Geissman Q, Lakatos E, Lukauskas S, Ale A, Babtie A, Kirk PDW, Stumpf MPH
Bioinformatics. First published online May 5, 2016
Software: theosysbio GitHub page.

MDI-GPU: Accelerating integrative modelling for genomic-scale data using GP-GPU computing.
Mason S, Sayyid F, Kirk PDW, Starr C, Wild D
Statistical Applications in Genetics and Molecular Biology. 2016; 15(1), 83–86.
Software: Warwick Systems Biology software page.

A Graph Theoretical Approach to Data Fusion.
Zurauskiene J*, Kirk PDW*, Stumpf MPH
Statistical Applications in Genetics and Molecular Biology. 2016.
*Joint first authors

Systems biology (un)certainties.
Kirk PDW*, Babtie AC*, Stumpf MP*.
Science. 2015 Oct 23;350(6259):386-8.
*Corresponding authors and equal contributors

Cellular Population Dynamics Control the Robustness of the Stem Cell Niche.
MacLean AL*, Kirk PDW*, Stumpf MPH
Biol Open. 2015 Oct 9. pii: bio.013714.
*Joint first authors

Multivariate moment closure techniques for stochastic kinetic models.
Lakatos E, Ale A, Kirk PDW, Stumpf MPH
J Chem Phys. 2015 Sep 7;143(9):094107.

Conditional random matrix ensembles and the stability of dynamical systems.
Kirk P*, Rolando DMY*, MacLean AL, Stumpf MPH.
New Journal of Physics. 2015 August;17(8):083025.
*Joint first authors

Phosphorelay of non-orthodox two component systems functions through a bi-molecular mechanism in vivo: the case of ArcB.
Jovanovic G, Sheng X, Ale A, Feliu E, Harrington HA, Kirk P, Wiuf C, Buck M, Stumpf MP.
Mol Biosyst. 2015 May;11(5):1348-59. doi: 10.1039/c4mb00720d.

SYSBIONS: nested sampling for systems biology.
Johnson R*, Kirk P*, Stumpf MP.
Bioinformatics. 2015 Feb 15;31(4):604-5. doi: 10.1093/bioinformatics/btu675. Epub 2014 Oct 16.
*Joint first authors

Topological sensitivity analysis for systems biology.
Babtie AC*, Kirk P*, Stumpf MP.
Proc Natl Acad Sci U S A. 2014 Dec 30;111(52):18507-12. doi: 10.1073/pnas.1414026112. Epub 2014 Dec 15.
*Joint first authors

Model selection in systems biology depends on experimental design.
Silk D, Kirk PD, Barnes CP, Toni T, Stumpf MP.
PLoS Comput Biol. 2014 Jun 12;10(6):e1003650. doi: 10.1371/journal.pcbi.1003650. eCollection 2014 Jun.

Derivative processes for modelling metabolic fluxes.
Zurauskienė J, Kirk P, Thorne T, Pinney J, Stumpf M.
Bioinformatics. 2014 Jul 1;30(13):1892-8. doi: 10.1093/bioinformatics/btu069. Epub 2014 Feb 26.

Bayesian nonparametric approaches to reconstructing oscillatory systems and the Nyquist limit.
Zurauskienė J, Kirk P, Thorne T, Stumpf MP.
Physica A: Statistical Mechanics and its Applications. 2014 March 26. [Epub ahead of print]

A framework for parameter estimation and model selection from experimental data in systems biology using approximate Bayesian computation.
Liepe J, Kirk P, Filippi S, Toni T, Barnes CP, Stumpf MP.
Nat Protoc. 2014 Feb;9(2):439-56. doi: 10.1038/nprot.2014.025. Epub 2014 Jan 23.

Balancing the Robustness and Predictive Performance of Biomarkers.
Kirk P, Witkover A, Bangham CR, Richardson S, Lewin AM, Stumpf MP.
J Comput Biol. 2013 Dec;20(12):979-89. doi: 10.1089/cmb.2013.0018

A general moment expansion method for stochastic kinetic models.
Ale A*, Kirk P*, Stumpf MP.
The Journal of Chemical Physics. 2013; 138(17). doi:10.1063/1.4802475
*Joint first authors

Model selection in systems and synthetic biology.
Kirk P*, Thorne T*, Stumpf MP.
Current Opinion in Biotechnology. 2013, doi:10.1016/j.copbio.2013.03.012
*Joint first authors

Accelerating Bayesian hierarchical clustering of time series data with a randomised algorithm.
Darkins R, Cooke EJ, Ghahramani Z, Kirk PD, Wild DL, Savage RS.
PLOS ONE. 2013; 8(4), e59795. doi:10.1371/journal.pone.0059795

P38 and JNK have opposing effects on persistence of in vivo leukocyte migration in zebrafish.
Taylor HB, Liepe J, Barthen C, Bugeon L, Huvet M, Kirk PD, Brown SB, Lamb JR, Stumpf MP, Dallman MJ.
Immunol Cell Biol. 2013 Jan;91(1):60-9. doi: 10.1038/icb.2012.57.

Bayesian correlated clustering to integrate multiple datasets.
Kirk P, Griffin JE, Savage RS, Ghahramani Z, Wild DL.
Bioinformatics. 2012 Dec 15;28(24):3290-7. doi: 10.1093/bioinformatics/bts595.

Elucidating the in vivo phosphorylation dynamics of the ERK MAP kinase using quantitative proteomics data and Bayesian model selection.
Toni T, Ozaki Y, Kirk P, Kuroda S, Stumpf MP.
Mol Biosyst. 2012 Jul 6;8(7):1921-9. doi: 10.1039/c2mb05493k.

Bayesian hierarchical clustering for microarray time series data with replicates and outlier measurements.
Cooke EJ, Savage RS, Kirk PD, Darkins R, Wild DL.
BMC Bioinformatics. 2011 Oct 13;12:399. doi: 10.1186/1471-2105-12-399.

Plasma proteome analysis in HTLV-1-associated myelopathy/tropical spastic paraparesis.
Kirk PD*, Witkover A*, Courtney A, Lewin AM, Wait R, Stumpf MP, Richardson S, Taylor GP, Bangham CR.
Retrovirology. 2011 Oct 12;8:81. doi: 10.1186/1742-4690-8-81.
*Joint first authors

Designing attractive models via automated identification of chaotic and oscillatory dynamical regimes.
Silk D, Kirk PD, Barnes CP, Toni T, Rose A, Moon S, Dallman MJ, Stumpf MP.
Nat Commun. 2011 Oct 4;2:489. doi: 10.1038/ncomms1496.

Discussion of “Stability Selection” by Meinshausen and Buhlmann
Kirk PD, Lewin A, Stumpf MP
J. Roy. Statist. Soc., Ser. B 2010 Sept; 72(4), 456-458

ABC-SysBio–approximate Bayesian computation in Python with GPU support.
Liepe J, Barnes C, Cule E, Erguler K, Kirk P, Toni T, Stumpf MP.
Bioinformatics. 2010 Jul 15;26(14):1797-9. doi: 10.1093/bioinformatics/btq278.

Gaussian process regression bootstrapping: exploring the effects of uncertainty in time course data.
Kirk PD, Stumpf MP.
Bioinformatics. 2009 May 15;25(10):1300-6. doi: 10.1093/bioinformatics/btp139.

Parameter inference for biochemical systems that undergo a Hopf bifurcation.
Kirk PD, Toni T, Stumpf MP.
Biophys J. 2008 Jul;95(2):540-9. doi: 10.1529/biophysj.107.126086.

Book chapters

Reverse engineering under uncertainty.
Kirk P, Silk D, Stumpf MP.
In: D Gomez-Cabrero and L Geris (eds.), Uncertainty in Biology: a Computational Modeling Approach. Switzerland:Springer International Publishing, Chapter 2 (2016, in press)

Conference proceedings

Automated detection of chaotic and oscillatory regimes
Silk D, Kirk PD, Barnes C, Stumpf MP
Proceedings of the Fourth International Workshop on Machine Learning in Systems Biology. 2010, pp. 59-66.