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ORCIDMichael P. H. Stumpf
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2020 – today
- 2024
[j33]Ivan A. Croydon-veleslavov, Michael P. H. Stumpf
:
Repeated Decision Stumping Distils Simple Rules from Single-Cell Data. J. Comput. Biol. 31(1): 21-40 (2024)- [i3]Stephen Y. Zhang, Michael P. H. Stumpf, Tom Needham, Agnese Barbensi:
Topological Optimal Transport for Geometric Cycle Matching. CoRR abs/2403.19097 (2024) - 2023
- [j32]Joshua Forrest, Vijay Rajagopal, Michael P. H. Stumpf, Michael Pan:
BondGraphs.jl: composable energy-based modelling in systems biology. Bioinform. 39(10) (2023) - 2022
- [j31]Léo P. M. Diaz, Michael P. H. Stumpf:
HyperGraphs.jl: representing higher-order relationships in Julia. Bioinform. 38(14): 3660-3661 (2022) - [j30]Robyn P. Araujo, Sean T. Vittadello, Michael P. H. Stumpf:
Bayesian and Algebraic Strategies to Design in Synthetic Biology. Proc. IEEE 110(5): 675-687 (2022) - [i2]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 abs/2210.07545 (2022) - 2020
- [j29]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): 3286-3287 (2020)
2010 – 2019
- 2019
- [j28]Leander Dony, Fei He, Michael P. H. Stumpf:
Parametric and non-parametric gradient matching for network inference: a comparison. BMC Bioinform. 20(1): 52 (2019) - 2018
- [j27]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): 1249-1250 (2018) - [j26]Rowan D. Brackston, Eszter Lakatos, Michael P. H. Stumpf:
Transition state characteristics during cell differentiation. PLoS Comput. Biol. 14(9) (2018) - 2016
- [j25]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): 2863-2865 (2016) - [j24]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: 81 (2016) - 2015
- [j23]Rob Johnson, Paul D. W. Kirk, Michael P. H. Stumpf:
SYSBIONS: nested sampling for systems biology. Bioinform. 31(4): 604-605 (2015) - [i1]Aaron Sim, Sophia N. Yaliraki, Mauricio Barahona, Michael P. H. Stumpf:
Great cities look small. CoRR abs/1507.05458 (2015) - 2014
- [j22]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): 137-138 (2014) - [j21]Justina Zurauskiene, Paul D. W. Kirk, Thomas Thorne, John Pinney, Michael P. H. Stumpf:
Derivative processes for modelling metabolic fluxes. Bioinform. 30(13): 1892-1898 (2014) - [j20]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) - [c1]Wolf-Ekkehard Matzke, Chris P. Barnes, Eyck Jentzsch, Thorsten Mascher, Michael P. H. Stumpf:
On Industrial Strength Bio-design Automation. ICTERI 2014: 277-299 - 2013
- [j19]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): 979-989 (2013) - [j18]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) - 2012
- [j17]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): 254-260 (2012) - [j16]Michal Komorowski, Justina Zurauskiene, Michael P. H. Stumpf:
StochSens - matlab package for sensitivity analysis of stochastic chemical systems. Bioinform. 28(5): 731-733 (2012) - [j15]Thomas Thorne, Michael P. H. Stumpf:
Inference of temporally varying Bayesian Networks. Bioinform. 28(24): 3298-3305 (2012) - [j14]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): 1181-1197 (2012) - 2011
- [j13]Yanxiang Zhou, Juliane Liepe, Xia Sheng, Michael P. H. Stumpf, Chris P. Barnes:
GPU accelerated biochemical network simulation. Bioinform. 27(6): 874-876 (2011) - [j12]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: 69 (2011) - 2010
- [j11]Tina Toni, Michael P. H. Stumpf:
Simulation-based model selection for dynamical systems in systems and population biology. Bioinform. 26(1): 104-110 (2010) - [j10]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): 1797-1799 (2010) - [j9]William P. Kelly, Michael P. H. Stumpf:
Trees on networks: resolving statistical patterns of phylogenetic similarities among interacting proteins. BMC Bioinform. 11: 470 (2010) - [j8]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: 130 (2010)
2000 – 2009
- 2009
- [j7]Paul D. W. Kirk, Michael P. H. Stumpf:
Gaussian process regression bootstrapping: exploring the effects of uncertainty in time course data. Bioinform. 25(10): 1300-1306 (2009) - 2008
- [j6]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) - 2007
- [j5]Thomas Thorne, Michael P. H. Stumpf:
Generating confidence intervals on biological networks. BMC Bioinform. 8 (2007) - [j4]Ino Agrafioti, Michael P. H. Stumpf:
SNPSTR: a database of compound microsatellite-SNP markers. Nucleic Acids Res. 35(Database-Issue): 71-75 (2007) - [j3]Oliver Ratmann, Ole Jørgensen, Trevor Hinkley, Michael P. H. Stumpf, Sylvia Richardson, Carsten Wiuf:
Using Likelihood-Free Inference to Compare Evolutionary Dynamics of the Protein Networks of H. pylori and P. falciparum. PLoS Comput. Biol. 3(11) (2007) - 2006
- [j2]Michael P. H. Stumpf, Thomas Thorne:
Multi-model inference of network properties from incomplete data. J. Integr. Bioinform. 3(2) (2006) - 2005
- [j1]Michael P. H. Stumpf, Piers J. Ingram, Ian Nouvel, Carsten Wiuf:
Statistical Model Selection Methods Applied to Biological Networks. Trans. Comp. Sys. Biology 3: 65-77 (2005)
Coauthor Index
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