Michael P. H. Stumpf

According to our database, Michael P. H. Stumpf authored at least 36 papers between 2005 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2024

Topological Optimal Transport for Geometric Cycle Matching.

Stephen Y. Zhang, Michael P. H. Stumpf, Tom Needham, Agnese Barbensi

CoRR, 2024

2023

BondGraphs.jl: composable energy-based modelling in systems biology.

Joshua Forrest, Vijay Rajagopal, Michael P. H. Stumpf, Michael Pan

Bioinform., October, 2023

2022

Bayesian and Algebraic Strategies to Design in Synthetic Biology.

Robyn P. Araujo, Sean T. Vittadello, Michael P. H. Stumpf

Proc. IEEE, 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

HyperGraphs.jl: representing higher-order relationships in Julia.

Léo P. M. Diaz, Michael P. H. Stumpf

Bioinform., 2022

2020

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

Bioinform., 2020

2019

Parametric and non-parametric gradient matching for network inference: a comparison.

Leander Dony, Fei He, Michael P. H. Stumpf

BMC Bioinform., December, 2019

2018

Transition state characteristics during cell differentiation.

Rowan D. Brackston, Eszter Lakatos, Michael P. H. Stumpf

PLoS Comput. Biol., 2018

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

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

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

2015

Great cities look small.

Aaron Sim, Sophia N. Yaliraki, Mauricio Barahona, Michael P. H. Stumpf

CoRR, 2015

SYSBIONS: nested sampling for systems biology.

Rob Johnson, Paul D. W. Kirk, Michael P. H. Stumpf

Bioinform., 2015

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

Derivative processes for modelling metabolic fluxes.

Justina Zurauskiene, Paul D. W. Kirk, Thomas Thorne, John Pinney, Michael P. H. Stumpf

Bioinform., 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

On Industrial Strength Bio-design Automation.

Wolf-Ekkehard Matzke, Chris P. Barnes, Eyck Jentzsch, Thorsten Mascher, Michael P. H. Stumpf

Proceedings of the Information and Communication Technologies in Education, Research, and Industrial Applications, 2014

2013

Maximizing the Information Content of Experiments in Systems Biology.

Juliane Liepe, Sarah Filippi, Michal Komorowski, Michael P. H. Stumpf

PLoS Comput. Biol., 2013

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

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

Inference of temporally varying Bayesian Networks.

Thomas Thorne, 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

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

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

GPU accelerated biochemical network simulation.

Yanxiang Zhou, Juliane Liepe, Xia Sheng, Michael P. H. Stumpf, Chris P. Barnes

Bioinform., 2011

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

Trees on networks: resolving statistical patterns of phylogenetic similarities among interacting proteins.

William P. Kelly, Michael P. H. Stumpf

BMC Bioinform., 2010

Simulation-based model selection for dynamical systems in systems and population biology.

Tina Toni, Michael P. H. Stumpf

Bioinform., 2010

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

2009

Gaussian process regression bootstrapping: exploring the effects of uncertainty in time course data.

Paul D. W. Kirk, Michael P. H. Stumpf

Bioinform., 2009

2008

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

2007

Using Likelihood-Free Inference to Compare Evolutionary Dynamics of the Protein Networks of <i>H. pylori</i> and <i>P. falciparum</i>.

Oliver Ratmann, Ole Jørgensen, Trevor Hinkley, Michael P. H. Stumpf, Sylvia Richardson, Carsten Wiuf

PLoS Comput. Biol., 2007

SNPSTR: a database of compound microsatellite-SNP markers.

Ino Agrafioti, Michael P. H. Stumpf

Nucleic Acids Res., 2007

Generating confidence intervals on biological networks.

Thomas Thorne, Michael P. H. Stumpf

BMC Bioinform., 2007

2006

Multi-model inference of network properties from incomplete data.

Michael P. H. Stumpf, Thomas Thorne

J. Integr. Bioinform., 2006

2005

Statistical Model Selection Methods Applied to Biological Networks.

Michael P. H. Stumpf, Piers J. Ingram, Ian Nouvel, Carsten Wiuf

Trans. Comp. Sys. Biology, 2005