Gaussian process regression bootstrapping: exploring the effects of uncertainty in time course data. - Paul D. W. Kirk; Michael P. H. Stumpf (Bioinform., 2009)

ABC-SysBio - approximate Bayesian computation in Python with GPU support. - Juliane Liepe; Chris P. Barnes; Erika Cule; Kamil Erguler; Paul D. W. Kirk; Tina Toni; Michael P. H. Stumpf (Bioinform., 2010)

Bayesian hierarchical clustering for microarray time series data with replicates and outlier measurements. - Emma J. Cooke; Richard S. Savage; Paul D. W. Kirk; Robert Darkins; David L. Wild (BMC Bioinform., 2011)

Bayesian correlated clustering to integrate multiple datasets. - Paul D. W. Kirk; Jim E. Griffin; Richard S. Savage; Zoubin Ghahramani; David L. Wild (Bioinform., 2012)

Balancing the Robustness and Predictive Performance of Biomarkers. - Paul D. W. Kirk; Aviva Witkover; Charles R. M. Bangham; Sylvia Richardson; Alexandra M. Lewin; Michael P. H. Stumpf (J. Comput. Biol., 2013)

Derivative processes for modelling metabolic fluxes. - Justina Zurauskiene; Paul D. W. Kirk; Thomas Thorne; John Pinney; Michael P. H. Stumpf (Bioinform., 2014)

Model Selection in Systems Biology Depends on Experimental Design. - Daniel Silk; Paul D. W. Kirk; Chris P. Barnes; Tina Toni; Michael P. H. Stumpf (PLoS Comput. Biol., 2014)

SYSBIONS: nested sampling for systems biology. - Rob Johnson; Paul D. W. Kirk; Michael P. H. Stumpf (Bioinform., 2015)

MEANS: python package for Moment Expansion Approximation, iNference and Simulation. - Sisi Fan; Quentin Geissmann; Eszter Lakatos; Saulius Lukauskas; Angelique Ale; Ann C. Babtie; Paul D. W. Kirk; Michael P. H. Stumpf (Bioinform., 2016)

Inferring extrinsic noise from single-cell gene expression data using approximate Bayesian computation. - Oleg Lenive; Paul D. W. Kirk; Michael P. H. Stumpf (BMC Syst. Biol., 2016)

A Bayesian mixture modelling approach for spatial proteomics. - Oliver M. Crook; Claire M. Mulvey; Paul D. W. Kirk; Kathryn S. Lilley; Laurent Gatto (PLoS Comput. Biol., 2018)

Multiple kernel learning for integrative consensus clustering of genomic datasets. - Alessandra Cabassi; Paul D. W. Kirk (CoRR, 2019)

A Bioconductor workflow for the Bayesian analysis of spatial proteomics. - Oliver M. Crook; Lisa M. Breckels; Kathryn S. Lilley; Paul D. W. Kirk; Laurent Gatto (F1000Research, 2019)

Multiple kernel learning for integrative consensus clustering of omic datasets. - Alessandra Cabassi; Paul D. W. Kirk (Bioinform., 2020)

GPseudoClust: deconvolution of shared pseudo-profiles at single-cell resolution. - Magdalena E. Strauß; Paul D. W. Kirk; John E. Reid; Lorenz Wernisch (Bioinform., 2020)

A semi-supervised Bayesian approach for simultaneous protein sub-cellular localisation assignment and novelty detection. - Oliver M. Crook; Aikaterini Geladaki; Daniel J. H. Nightingale; Owen L. Vennard; Kathryn S. Lilley; Laurent Gatto; Paul D. W. Kirk (PLoS Comput. Biol., 2020)

MR-Clust: clustering of genetic variants in Mendelian randomization with similar causal estimates. - Christopher N. Foley; Amy M. Mason; Paul D. W. Kirk; Stephen Burgess (Bioinform., 2021)

Detection of quantitative trait loci from RNA-seq data with or without genotypes using BaseQTL. - Elena Vigorito; Wei-Yu Lin; Colin Starr; Paul D. W. Kirk; Simon R. White; Chris Wallace 002 (Nat. Comput. Sci., 2021)

Topological approximate Bayesian computation for parameter inference of an angiogenesis model. - Thomas Thorne; Paul D. W. Kirk; Heather A. Harrington (Bioinform., 2022)

Consensus clustering for Bayesian mixture models. - Stephen Coleman; Paul D. W. Kirk; Chris Wallace 002 (BMC Bioinform., 2022)

Dose-response prediction for in-vitro drug combination datasets: a probabilistic approach. - Leiv Rønneberg; Paul D. W. Kirk; Manuela Zucknick (BMC Bioinform., 2023)

VICatMix: variational Bayesian clustering and variable selection for discrete biomedical data. - Paul D. W. Kirk; Jackie Rao (CoRR, 2024)

Permutation invariant multi-output Gaussian Processes for drug combination prediction in cancer. - Leiv Rønneberg; Vidhi Lalchand; Paul D. W. Kirk (CoRR, 2024)

Bayesian clustering with uncertain data. - Kath Nicholls; Paul D. W. Kirk; Chris Wallace 002 (PLoS Comput. Biol., 2024)

Federated Variational Inference for Bayesian Mixture Models. - Jackie Rao; Francesca Crowe; Tom Marshall; Sylvia Richardson; Paul D. W. Kirk (CoRR, 2025)

Outcome-guided spike-and-slab Lasso Biclustering: A Novel Approach for Enhancing Biclustering Techniques for Gene Expression Analysis. - Luis Vargas Mieles; Paul D. W. Kirk; Chris Wallace 002 (Stat. Comput., 2025)