Michael P. H. Stumpf

Publication Activity (10 Years)

Years Active: 2005-2024
Publications (10 Years): 13

Top Topics

Gaussian Process

Systems Biology

Gene Expression

Top Venues

PLoS Comput. Biol.

Publications

Stephen Y. Zhang, Michael P. H. Stumpf, Tom Needham, Agnese Barbensi
Topological Optimal Transport for Geometric Cycle Matching. CoRR (2024)
Joshua Forrest, Vijay Rajagopal, Michael P. H. Stumpf, Michael Pan
BondGraphs.jl: composable energy-based modelling in systems biology. Bioinform. 39 (10) (2023)
Léo P. M. Diaz, Michael P. H. Stumpf
HyperGraphs.jl: representing higher-order relationships in Julia. Bioinform. 38 (14) (2022)
Agnese Barbensi, Hee Rhang Yoon, Christian Degnbol Madsen, Deborah O. Ajayi, Michael P. H. Stumpf, Heather A. Harrington
Hypergraphs for multiscale cycles in structured data. CoRR (2022)
Robyn P. Araujo, Sean T. Vittadello, Michael P. H. Stumpf
Bayesian and Algebraic Strategies to Design in Synthetic Biology. Proc. IEEE 110 (5) (2022)
Evgeny Tankhilevich, Jonathan Ish-Horowicz, Tara Hameed, Elisabeth Roesch, Istvan T. Kleijn, Michael P. H. Stumpf, Fei He
GpABC: a Julia package for approximate Bayesian computation with Gaussian process emulation. Bioinform. 36 (10) (2020)
Leander Dony, Fei He, Michael P. H. Stumpf
Parametric and non-parametric gradient matching for network inference: a comparison. BMC Bioinform. 20 (1) (2019)
Rowan D. Brackston, Eszter Lakatos, Michael P. H. Stumpf
Transition state characteristics during cell differentiation. PLoS Comput. Biol. 14 (9) (2018)
Leander Dony, Jonas Mackerodt, Scott Ward, Sarah Filippi, Michael P. H. Stumpf, Juliane Liepe
PEITH(Θ): perfecting experiments with information theory in Python with GPU support. Bioinform. 34 (7) (2018)
Oleg Lenive, Paul D. W. Kirk, Michael P. H. Stumpf
Inferring extrinsic noise from single-cell gene expression data using approximate Bayesian computation. BMC Syst. Biol. 10 (2016)
Sisi Fan, Quentin Geissmann, Eszter Lakatos, Saulius Lukauskas, Angelique Ale, Ann C. Babtie, Paul D. W. Kirk, Michael P. H. Stumpf
MEANS: python package for Moment Expansion Approximation, iNference and Simulation. Bioinform. 32 (18) (2016)
Aaron Sim, Sophia N. Yaliraki, Mauricio Barahona, Michael P. H. Stumpf
Great cities look small. CoRR (2015)
Rob Johnson, Paul D. W. Kirk, Michael P. H. Stumpf
SYSBIONS: nested sampling for systems biology. Bioinform. 31 (4) (2015)
Tomasz Jetka, Agata Charzynska, Anna Gambin, Michael P. H. Stumpf, Michal Komorowski
StochDecomp - Matlab package for noise decomposition in stochastic biochemical systems. Bioinform. 30 (1) (2014)
Justina Zurauskiene, Paul D. W. Kirk, Thomas Thorne, John Pinney, Michael P. H. Stumpf
Derivative processes for modelling metabolic fluxes. Bioinform. 30 (13) (2014)
Daniel Silk, Paul D. W. Kirk, Chris P. Barnes, Tina Toni, Michael P. H. Stumpf
Model Selection in Systems Biology Depends on Experimental Design. PLoS Comput. Biol. 10 (6) (2014)
Wolf-Ekkehard Matzke, Chris P. Barnes, Eyck Jentzsch, Thorsten Mascher, Michael P. H. Stumpf
On Industrial Strength Bio-design Automation. ICTERI (2014)
Juliane Liepe, Sarah Filippi, Michal Komorowski, Michael P. H. Stumpf
Maximizing the Information Content of Experiments in Systems Biology. PLoS Comput. Biol. 9 (1) (2013)
Paul D. W. Kirk, Aviva Witkover, Charles R. M. Bangham, Sylvia Richardson, Alexandra M. Lewin, Michael P. H. Stumpf
Balancing the Robustness and Predictive Performance of Biomarkers. J. Comput. Biol. 20 (12) (2013)
Michal Komorowski, Justina Zurauskiene, Michael P. H. Stumpf
StochSens - matlab package for sensitivity analysis of stochastic chemical systems. Bioinform. 28 (5) (2012)
Thomas Thorne, Michael P. H. Stumpf
Inference of temporally varying Bayesian Networks. Bioinform. 28 (24) (2012)
Chris P. Barnes, Sarah Filippi, Michael P. H. Stumpf, Thomas Thorne
Considerate approaches to constructing summary statistics for ABC model selection. Stat. Comput. 22 (6) (2012)
Nathan Harmston, Wendy Filsell, Michael P. H. Stumpf
Which species is it? Species-driven gene name disambiguation using random walks over a mixture of adjacency matrices. Bioinform. 28 (2) (2012)
Yanxiang Zhou, Juliane Liepe, Xia Sheng, Michael P. H. Stumpf, Chris P. Barnes
GPU accelerated biochemical network simulation. Bioinform. 27 (6) (2011)
Tina Toni, Goran N. Jovanovic, Maxime Huvet, Martin Buck, Michael P. H. Stumpf
From qualitative data to quantitative models: analysis of the phage shock protein stress response in Escherichia coli. BMC Syst. Biol. 5 (2011)
Juliane Liepe, Chris P. Barnes, Erika Cule, Kamil Erguler, Paul D. W. Kirk, Tina Toni, Michael P. H. Stumpf
ABC-SysBio - approximate Bayesian computation in Python with GPU support. Bioinform. 26 (14) (2010)
Tina Toni, Michael P. H. Stumpf
Simulation-based model selection for dynamical systems in systems and population biology. Bioinform. 26 (1) (2010)
Sophie Lèbre, Jennifer Becq, Frédéric Devaux, Michael P. H. Stumpf, Gaëlle Lelandais
Statistical inference of the time-varying structure of gene-regulation networks. BMC Syst. Biol. 4 (2010)
William P. Kelly, Michael P. H. Stumpf
Trees on networks: resolving statistical patterns of phylogenetic similarities among interacting proteins. BMC Bioinform. 11 (2010)
Paul D. W. Kirk, Michael P. H. Stumpf
Gaussian process regression bootstrapping: exploring the effects of uncertainty in time course data. Bioinform. 25 (10) (2009)
Piers J. Ingram, Michael P. H. Stumpf, Jaroslav Stark
Nonidentifiability of the Source of Intrinsic Noise in Gene Expression from Single-Burst Data. PLoS Comput. Biol. 4 (10) (2008)
Oliver Ratmann, Ole Jørgensen, Trevor Hinkley, Michael P. H. Stumpf, Sylvia Richardson, Carsten Wiuf
. PLoS Comput. Biol. 3 (11) (2007)
Thomas Thorne, Michael P. H. Stumpf
Generating confidence intervals on biological networks. BMC Bioinform. 8 (2007)
Ino Agrafioti, Michael P. H. Stumpf
SNPSTR: a database of compound microsatellite-SNP markers. Nucleic Acids Res. 35 (Database-Issue) (2007)
Michael P. H. Stumpf, Thomas Thorne
Multi-model inference of network properties from incomplete data. J. Integr. Bioinform. 3 (2) (2006)
Michael P. H. Stumpf, Piers J. Ingram, Ian Nouvel, Carsten Wiuf
Statistical Model Selection Methods Applied to Biological Networks. Trans. Comp. Sys. Biology 3 (2005)