Statistical Model Selection Methods Applied to Biological Networks. - Michael P. H. Stumpf; Piers J. Ingram; Ian Nouvel; Carsten Wiuf (Trans. Comp. Sys. Biology, 2005)

Multi-model inference of network properties from incomplete data. - Michael P. H. Stumpf; Thomas Thorne (J. Integr. Bioinform., 2006)

Generating confidence intervals on biological networks. - Thomas Thorne; Michael P. H. Stumpf (BMC Bioinform., 2007)

SNPSTR: a database of compound microsatellite-SNP markers. - Ino Agrafioti; Michael P. H. Stumpf (Nucleic Acids Res., 2007)

Using Likelihood-Free Inference to Compare Evolutionary Dynamics of the Protein Networks of H. pylori and P. falciparum. - Oliver Ratmann; Ole Jørgensen 002; Trevor Hinkley; Michael P. H. Stumpf; Sylvia Richardson; Carsten Wiuf (PLoS Comput. Biol., 2007)

Nonidentifiability of the Source of Intrinsic Noise in Gene Expression from Single-Burst Data. - Piers J. Ingram; Michael P. H. Stumpf; Jaroslav Stark (PLoS Comput. Biol., 2008)

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)

Simulation-based model selection for dynamical systems in systems and population biology. - Tina Toni; Michael P. H. Stumpf (Bioinform., 2010)

Trees on networks: resolving statistical patterns of phylogenetic similarities among interacting proteins. - William P. Kelly; Michael P. H. Stumpf (BMC Bioinform., 2010)

Statistical inference of the time-varying structure of gene-regulation networks. - Sophie Lèbre; Jennifer Becq; Frédéric Devaux; Michael P. H. Stumpf; Gaëlle Lelandais (BMC Syst. Biol., 2010)

GPU accelerated biochemical network simulation. - Yanxiang Zhou; Juliane Liepe; Xia Sheng; Michael P. H. Stumpf; Chris P. Barnes (Bioinform., 2011)

From qualitative data to quantitative models: analysis of the phage shock protein stress response in Escherichia coli. - Tina Toni; Goran N. Jovanovic; Maxime Huvet; Martin Buck; Michael P. H. Stumpf (BMC Syst. Biol., 2011)

Which species is it? Species-driven gene name disambiguation using random walks over a mixture of adjacency matrices. - Nathan Harmston; Wendy Filsell; Michael P. H. Stumpf (Bioinform., 2012)

StochSens - matlab package for sensitivity analysis of stochastic chemical systems. - Michal Komorowski; Justina Zurauskiene; Michael P. H. Stumpf (Bioinform., 2012)

Inference of temporally varying Bayesian Networks. - Thomas Thorne; Michael P. H. Stumpf (Bioinform., 2012)

Considerate approaches to constructing summary statistics for ABC model selection. - Chris P. Barnes; Sarah Filippi; Michael P. H. Stumpf; Thomas Thorne (Stat. Comput., 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)

Maximizing the Information Content of Experiments in Systems Biology. - Juliane Liepe; Sarah Filippi; Michal Komorowski; Michael P. H. Stumpf (PLoS Comput. Biol., 2013)

On Industrial Strength Bio-design Automation. - Wolf-Ekkehard Matzke; Chris P. Barnes; Eyck Jentzsch; Thorsten Mascher; Michael P. H. Stumpf (ICTERI, 2014)

StochDecomp - Matlab package for noise decomposition in stochastic biochemical systems. - Tomasz Jetka; Agata Charzynska; Anna Gambin; Michael P. H. Stumpf; Michal Komorowski (Bioinform., 2014)

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)

Great cities look small. - Aaron Sim; Sophia N. Yaliraki; Mauricio Barahona; Michael P. H. Stumpf (CoRR, 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)

PEITH(Θ): perfecting experiments with information theory in Python with GPU support. - Leander Dony; Jonas Mackerodt; Scott Ward; Sarah Filippi; Michael P. H. Stumpf; Juliane Liepe (Bioinform., 2018)

Transition state characteristics during cell differentiation. - Rowan D. Brackston; Eszter Lakatos; Michael P. H. Stumpf (PLoS Comput. Biol., 2018)

Parametric and non-parametric gradient matching for network inference: a comparison. - Leander Dony; Fei He 002; Michael P. H. Stumpf (BMC Bioinform., 2019)

GpABC: a Julia package for approximate Bayesian computation with Gaussian process emulation. - Evgeny Tankhilevich; Jonathan Ish-Horowicz; Tara Hameed; Elisabeth Roesch; Istvan T. Kleijn; Michael P. H. Stumpf; Fei He 002 (Bioinform., 2020)

HyperGraphs.jl: representing higher-order relationships in Julia. - Léo P. M. Diaz; Michael P. H. Stumpf (Bioinform., 2022)

Hypergraphs for multiscale cycles in structured data. - Agnese Barbensi; Hee Rhang Yoon; Christian Degnbol Madsen; Deborah O. Ajayi; Michael P. H. Stumpf; Heather A. Harrington (CoRR, 2022)

Bayesian and Algebraic Strategies to Design in Synthetic Biology. - Robyn P. Araujo; Sean T. Vittadello; Michael P. H. Stumpf (Proc. IEEE, 2022)

BondGraphs.jl: composable energy-based modelling in systems biology. - Joshua Forrest; Vijay Rajagopal; Michael P. H. Stumpf; Michael Pan (Bioinform., 2023)

Repeated Decision Stumping Distils Simple Rules from Single-Cell Data. - Ivan A. Croydon-veleslavov; Michael P. H. Stumpf (J. Comput. Biol., 2024)

Learning non-equilibrium diffusions with Schrödinger bridges: from exactly solvable to simulation-free. - Stephen Y. Zhang; Michael P. H. Stumpf (CoRR, 2025)

Topological optimal transport for geometric cycle matching. - Stephen Y. Zhang; Michael P. H. Stumpf; Tom Needham; Agnese Barbensi (J. Appl. Comput. Topol., 2025)