Michael P. H. Stumpf

39 papers Misc 1Journal 38
YearRankTypeTitle / Venue / Authors
2025 J jnl
Learning non-equilibrium diffusions with Schrödinger bridges: from exactly solvable to simulation-free.
CoRR
Stephen Y. Zhang, Michael P. H. Stumpf
2025 J jnl
Topological optimal transport for geometric cycle matching.
J. Appl. Comput. Topol.
Stephen Y. Zhang, Michael P. H. Stumpf, Tom Needham, Agnese Barbensi
2024 J jnl
Repeated Decision Stumping Distils Simple Rules from Single-Cell Data.
J. Comput. Biol.
Ivan A. Croydon-veleslavov, Michael P. H. Stumpf
2024 J jnl
Topological Optimal Transport for Geometric Cycle Matching.
CoRR
Stephen Y. Zhang, Michael P. H. Stumpf, Tom Needham, Agnese Barbensi
2023 J jnl
BondGraphs.jl: composable energy-based modelling in systems biology.
Bioinform.
Joshua Forrest, Vijay Rajagopal, Michael P. H. Stumpf, Michael Pan
2022 J jnl
Bayesian and Algebraic Strategies to Design in Synthetic Biology.
Proc. IEEE
Robyn P. Araujo, Sean T. Vittadello, Michael P. H. Stumpf
2022 J jnl
HyperGraphs.jl: representing higher-order relationships in Julia.
Bioinform.
Léo P. M. Diaz, Michael P. H. Stumpf
2022 J jnl
Hypergraphs for multiscale cycles in structured data.
CoRR
Agnese Barbensi, Hee Rhang Yoon, Christian Degnbol Madsen, Deborah O. Ajayi, Michael P. H. Stumpf, Heather A. Harrington
2020 J jnl
GpABC: a Julia package for approximate Bayesian computation with Gaussian process emulation.
Bioinform.
Evgeny Tankhilevich, Jonathan Ish-Horowicz, Tara Hameed, Elisabeth Roesch, Istvan T. Kleijn, Michael P. H. Stumpf, Fei He
2019 J jnl
Parametric and non-parametric gradient matching for network inference: a comparison.
BMC Bioinform.
Leander Dony, Fei He, Michael P. H. Stumpf
2018 J jnl
PEITH(Θ): perfecting experiments with information theory in Python with GPU support.
Bioinform.
Leander Dony, Jonas Mackerodt, Scott Ward, Sarah Filippi, Michael P. H. Stumpf, Juliane Liepe
2018 J jnl
Transition state characteristics during cell differentiation.
PLoS Comput. Biol.
Rowan D. Brackston, Eszter Lakatos, Michael P. H. Stumpf
2016 J jnl
Inferring extrinsic noise from single-cell gene expression data using approximate Bayesian computation.
BMC Syst. Biol.
Oleg Lenive, Paul D. W. Kirk, Michael P. H. Stumpf
2016 J jnl
MEANS: python package for Moment Expansion Approximation, iNference and Simulation.
Bioinform.
Sisi Fan, Quentin Geissmann, Eszter Lakatos, Saulius Lukauskas, Angelique Ale, Ann C. Babtie, Paul D. W. Kirk, Michael P. H. Stumpf
2015 J jnl
Great cities look small.
CoRR
Aaron Sim, Sophia N. Yaliraki, Mauricio Barahona, Michael P. H. Stumpf
2015 J jnl
SYSBIONS: nested sampling for systems biology.
Bioinform.
Rob Johnson, Paul D. W. Kirk, Michael P. H. Stumpf
2014 J jnl
Derivative processes for modelling metabolic fluxes.
Bioinform.
Justina Zurauskiene, Paul D. W. Kirk, Thomas Thorne, John Pinney, Michael P. H. Stumpf
2014 J jnl
Model Selection in Systems Biology Depends on Experimental Design.
PLoS Comput. Biol.
Daniel Silk, Paul D. W. Kirk, Chris P. Barnes, Tina Toni, Michael P. H. Stumpf
2014 Misc conf
On Industrial Strength Bio-design Automation.
ICTERI
Wolf-Ekkehard Matzke, Chris P. Barnes, Eyck Jentzsch, Thorsten Mascher, Michael P. H. Stumpf
2014 J jnl
StochDecomp - Matlab package for noise decomposition in stochastic biochemical systems.
Bioinform.
Tomasz Jetka, Agata Charzynska, Anna Gambin, Michael P. H. Stumpf, Michal Komorowski
2013 J jnl
Balancing the Robustness and Predictive Performance of Biomarkers.
J. Comput. Biol.
Paul D. W. Kirk, Aviva Witkover, Charles R. M. Bangham, Sylvia Richardson, Alexandra M. Lewin, Michael P. H. Stumpf
2013 J jnl
Maximizing the Information Content of Experiments in Systems Biology.
PLoS Comput. Biol.
Juliane Liepe, Sarah Filippi, Michal Komorowski, Michael P. H. Stumpf
2012 J jnl
Considerate approaches to constructing summary statistics for ABC model selection.
Stat. Comput.
Chris P. Barnes, Sarah Filippi, Michael P. H. Stumpf, Thomas Thorne
2012 J jnl
Inference of temporally varying Bayesian Networks.
Bioinform.
Thomas Thorne, Michael P. H. Stumpf
2012 J jnl
StochSens - matlab package for sensitivity analysis of stochastic chemical systems.
Bioinform.
Michal Komorowski, Justina Zurauskiene, Michael P. H. Stumpf
2012 J jnl
Which species is it? Species-driven gene name disambiguation using random walks over a mixture of adjacency matrices.
Bioinform.
Nathan Harmston, Wendy Filsell, Michael P. H. Stumpf
2011 J jnl
From qualitative data to quantitative models: analysis of the phage shock protein stress response in Escherichia coli.
BMC Syst. Biol.
Tina Toni, Goran N. Jovanovic, Maxime Huvet, Martin Buck, Michael P. H. Stumpf
2011 J jnl
GPU accelerated biochemical network simulation.
Bioinform.
Yanxiang Zhou, Juliane Liepe, Xia Sheng, Michael P. H. Stumpf, Chris P. Barnes
2010 J jnl
ABC-SysBio - approximate Bayesian computation in Python with GPU support.
Bioinform.
Juliane Liepe, Chris P. Barnes, Erika Cule, Kamil Erguler, Paul D. W. Kirk, Tina Toni, Michael P. H. Stumpf
2010 J jnl
Simulation-based model selection for dynamical systems in systems and population biology.
Bioinform.
Tina Toni, Michael P. H. Stumpf
2010 J jnl
Statistical inference of the time-varying structure of gene-regulation networks.
BMC Syst. Biol.
Sophie Lèbre, Jennifer Becq, Frédéric Devaux, Michael P. H. Stumpf, Gaëlle Lelandais
2010 J jnl
Trees on networks: resolving statistical patterns of phylogenetic similarities among interacting proteins.
BMC Bioinform.
William P. Kelly, Michael P. H. Stumpf
2009 J jnl
Gaussian process regression bootstrapping: exploring the effects of uncertainty in time course data.
Bioinform.
Paul D. W. Kirk, Michael P. H. Stumpf
2008 J jnl
Nonidentifiability of the Source of Intrinsic Noise in Gene Expression from Single-Burst Data.
PLoS Comput. Biol.
Piers J. Ingram, Michael P. H. Stumpf, Jaroslav Stark
2007 J jnl
Generating confidence intervals on biological networks.
BMC Bioinform.
Thomas Thorne, Michael P. H. Stumpf
2007 J jnl
SNPSTR: a database of compound microsatellite-SNP markers.
Nucleic Acids Res.
Ino Agrafioti, Michael P. H. Stumpf
2007 J jnl
Using Likelihood-Free Inference to Compare Evolutionary Dynamics of the Protein Networks of
PLoS Comput. Biol.
Oliver Ratmann, Ole Jørgensen, Trevor Hinkley, Michael P. H. Stumpf, Sylvia Richardson, Carsten Wiuf
2006 J jnl
Multi-model inference of network properties from incomplete data.
J. Integr. Bioinform.
Michael P. H. Stumpf, Thomas Thorne
2005 J jnl
Statistical Model Selection Methods Applied to Biological Networks.
Trans. Comp. Sys. Biology
Michael P. H. Stumpf, Piers J. Ingram, Ian Nouvel, Carsten Wiuf