thumbnail — Publications — Theoretical Systems Biology Group

Gaining Confidence in Inferred Networks

Diaz, Léo P. M. and Stumpf, Michael P.H. (2022). Scientific Reports, 12(1), 2394.
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2022Leo DiazMarch 3, 2022thumbnail

Noise Distorts the Epigenetic Landscape and Shapes Cell-Fate Decisions

Coomer, Megan A. and Ham, Lucy and Stumpf, Michael P.H. (2022). Cell Systems, 13(1), 83-102.e6.
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2021Leo DiazMarch 3, 2022thumbnail

Turing Pattern Design Principles and Their Robustness

Vittadello, Sean T. and Leyshon, Thomas and Schnoerr, David and Stumpf, Michael P.H. (2021). Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 379(2213), 20200272.
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2021Leo DiazMarch 3, 2022thumbnail

The Design Principles of Discrete Turing Patterning Systems

Leyshon, Thomas and Tonello, Elisa and Schnoerr, David and Siebert, Heike and Stumpf, Michael P.H. (2021). Journal of Theoretical Biology, 531, 110901.
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2021Leo DiazMarch 3, 2022thumbnail

Bayesian and Algebraic Strategies to Design in Synthetic Biology

Araujo, Robyn P. and Vittadello, Sean T. and Stumpf, Michael P.H. (2021). Proceedings of the IEEE, 1-13.
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2021Leo DiazMarch 3, 2022thumbnail

A Group Theoretic Approach to Model Comparison With Simplicial Representations

Vittadello, Sean T. and Stumpf, Michael P.H. (2021). arXiv:2111.02170 [q-Bio.QM].
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2021Leo DiazMarch 3, 2022thumbnail

Pathway Dynamics Can Delineate the Sources of Transcriptional Noise in Gene Expression

Ham, Lucy and Jackson, Marcel and Stumpf, Michael P.H. (2021). ELife, 10, e69324.
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2021Leo DiazMarch 3, 2022thumbnail

Julia for Biologists

Roesch, Elisabeth and Greener, Joe G. and MacLean, Adam L. and Nassar, Huda and Rackauckas, Christopher and Holy, Timothy E. and Stumpf, Michael P.H. (2021). arXiv:2109.09973 [q-Bio].
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2021Leo DiazMarch 3, 2022thumbnail

Inferring Better Gene Regulation Networks from Single-Cell Data

Stumpf, Michael P.H. (2021). Current Opinion in Systems Biology, 27, 100342.
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2021Leo DiazMarch 3, 2022thumbnail

Statistical and Computational Challenges for Whole Cell Modelling

Stumpf, Michael P.H. (2021). Current Opinion in Systems Biology, 26, 58-63.
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2021Leo DiazMarch 3, 2022thumbnail

Collocation Based Training of Neural Ordinary Differential Equations

Roesch, Elisabeth and Rackauckas, Christopher and Stumpf, Michael P.H. (2021). Statistical Applications in Genetics and Molecular Biology, 20(2), 37-49.
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2021Leo DiazMarch 3, 2022thumbnail

Phylodynamics for Cell Biologists

Stadler, Tanja and Pybus, Oliver G. and Stumpf, Michael P.H. (2021). Science, 371(6526), eaah6266.
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2021Leo DiazMarch 3, 2022thumbnail

The Chemical Langevin Equation for Biochemical Systems in Dynamic Environments

Ham, Lucy and Coomer, Megan A. and Stumpf, Michael P.H. (2021). bioRxiv, 473404.
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2021Leo DiazMarch 3, 2022thumbnail

Model Comparison Via Simplicial Complexes and Persistent Homology

Vittadello, Sean T. and Stumpf, Michael P.H. (2021). Royal Society Open Science, 8(10), 211361.
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2021Leo DiazMarch 3, 2022thumbnail

Uncertainty in Cell Fate Decision Making: Lessons From Potential Landscapes of Bifurcation Systems

Guillemin, Anissa and Roesch, Elisabeth and Stumpf, Michael P.H. (2021). bioRxiv, 425143.
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2021Leo DiazMarch 3, 2022thumbnail

Noise and the Molecular Processes Underlying Cell Fate Decision-Making

Guillemin, Anissa and Stumpf, Michael P.H. (2021). Physical Biology, 18(1), 011002.
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2021Leo DiazMarch 3, 2022thumbnail

Multi-Model and Network Inference Based on Ensemble Estimates: Avoiding the Madness of Crowds

Stumpf, Michael P.H. (2020). Journal of the Royal Society Interface, 17(171).
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2020Leo DiazMarch 3, 2022thumbnail

GpABC: a Julia Package for Approximate Bayesian Computation With Gaussian Process Emulation

Tankhilevich, Evgeny and Ish-Horowicz, Jonathan and Hameed, Tara and Roesch, Elisabeth and Kleijn, Istvan and Stumpf, Michael P.H. and He, Fei (2020). Bioinformatics, 36(10), 3286-87.
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2020Leo DiazMarch 3, 2022thumbnail

Exactly Solvable Models of Stochastic Gene Expression

Ham, Lucy and Schnoerr, David and Brackston, Rowan D. and Stumpf, Michael P.H. (2020). The Journal of Chemical Physics, 152, 144106.
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2020Leo DiazMarch 3, 2022thumbnail

Extrinsic Noise and Heavy-Tailed Laws in Gene Expression

Ham, Lucy and Brackston, Rowan D. and Stumpf, Michael P.H. (2020). Physical Review Letters, 124(10), 108101.
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2020Leo DiazMarch 2, 2022thumbnail

Decision Tree Models and Cell Fate Choice

Veleslavov, Ivan Croydon and Stumpf, Michael P.H. (2020). bioRxiv, 423629.
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2020Leo DiazMarch 2, 2022thumbnail

Repeated Decision Stumping Distils Simple Rules from Single Cell Data

Veleslavov, Ivan A. and Stumpf, Michael P.H. (2020). bioRxiv, 288662.
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2020Leo DiazMarch 2, 2022thumbnail

Parameter Inference in Dynamical Systems With Co-Dimension 1 Bifurcations

Roesch, Elisabeth, and Stumpf, Michael P.H. (2019). Royal Society Open Science, 6(10), 190747.
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2019Leo DiazMarch 2, 2022thumbnail

A Comprehensive Network Atlas Reveals That Turing Patterns Are Common but Not Robust

Scholes, Natalie S. and Schnoerr, David and Isalan, Mark and Stumpf, Michael P.H. (2019). Cell Systems, 9(3), 243-257.e4.
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2019Leo DiazMarch 2, 2022thumbnail

Proteolytic Dynamics of Human 20S Thymoproteasome

Kuckelkorn, Ulrike and Stübler, Sabine and Textoris-Taube, Kathrin and Kilian, Christiane and Niewienda, Agathe and Henklein, Petra and Janek, Katharina and Stumpf, Michael P.H. and Mishto, Michele and Liepe, Juliane (2019). Journal of Biological Chemistry, 294 (19), 7740-54.
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2019Leo DiazMarch 2, 2022thumbnail

Parametric and Non-Parametric Gradient Matching for Network Inference: A Comparison

Dony, Leander and He, Fei and Stumpf, Michael PH (2019). BMC Bioinformatics, 20(1), 52.
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2019ScienceSitesSeptember 18, 2019thumbnail

Quantifying Dynamic Regulation in Metabolic Pathways with Nonparametric Flux Inference

He, Fei and Stumpf, Michael PH (2019). Biophysical Journal, 116(10), 2035-2046.
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2019ScienceSitesSeptember 18, 2019thumbnail

Closed-Form Bayesian Inference of Graphical Model Structures by Averaging Over Trees

Schwaller, Loïc and Robin, Stéphane and Stumpf, Michael (2019). Journal de la Société Française de Statistique, 160(2), 1-23.
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2019ScienceSitesSeptember 18, 2019thumbnail

An Information-Theoretic Framework for Deciphering Pleiotropic and Noisy Biochemical Signaling

Jetka, Tomasz and Nienałtowski, Karol and Filippi, Sarah and Stumpf, Michael PH and Komorowski, Michał (2018). Nature Communications, 9(1), 4591.
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2018ScienceSitesSeptember 18, 2019thumbnail

Transition State Characteristics During Cell Differentiation

Brackston, Rowan D and Lakatos, Eszter and Stumpf, Michael PH (2018). PLoS Computational Biology, 14(9), e1006405.
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2018ScienceSitesSeptember 18, 2019thumbnail

Construction of Quasipotentials for Stochastic Dynamical Systems: An Optimization Approach

Brackston, Rowan D and Wynn, Andrew and Stumpf, Michael PH (2018). Physical Review E, 98(2), 022136.
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2018ScienceSitesSeptember 18, 2019thumbnail

How to Deal With Parameters for Whole-Cell Modelling

Babtie, Ann C and Stumpf, Michael PH (2017). Journal of The Royal Society Interface, 14, 133, 20170237.
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2017ScienceSitesSeptember 17, 2019thumbnail

Learning Regulatory Models for Cell Development From Single Cell Transcriptomic Data

Babtie, Ann C and Chan, Thalia E and Stumpf, Michael PH (2017). Current Opinion in Systems Biology, 5, 72-81.
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2017ScienceSitesSeptember 17, 2019thumbnail

Model of Host-Pathogen Interaction Dynamics Links In Vivo Optical Imaging and Immune Responses

Ale, Angelique and Crepin, Valerie F and Collins, James W and Constantinou, Nicholas and Habibzay, Maryam and Babtie, Ann C and Frankel, Gad and Stumpf, Michael PH (2017). Infection and Immunity, 85, 1, e00606-16.
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2017ScienceSitesSeptember 17, 2019thumbnail

Gene Regulatory Network Inference From Single-Cell Data Using Multivariate Information Measures

Chan, Thalia E and Stumpf, Michael PH and Babtie, Ann C (2017). Cell Systems, 5(3), 251-267.
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2017ScienceSitesSeptember 17, 2019thumbnail

Stem Cell Differentiation as a Non-Markov Stochastic Process

Stumpf, Patrick S and Smith, Rosanna CG and Lenz, Michael and Schuppert, Andreas and Müller, Franz-Josef and Babtie, Ann and Chan, Thalia E and Stumpf, Michael PH and Please, Colin P and Howison, Sam D and others (2017). Cell Systems, 5(3), 268-282.
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2017ScienceSitesSeptember 17, 2019thumbnail

Control Mechanisms for Stochastic Biochemical Systems Via Computation of Reachable Sets

Lakatos, Eszter and Stumpf, Michael PH (2017). Royal Society Open Science, 4(8), 160790.
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2017ScienceSitesSeptember 17, 2019thumbnail

Single Cell Phenotyping Reveals Heterogeneity Among Hematopoietic Stem Cells Following Infection

MacLean, Adam L and Smith, Maia A and Liepe, Juliane and Sim, Aaron and Khorshed, Reema and Rashidi, Narges M and Scherf, Nico and Krinner, Axel and Roeder, Ingo and Lo Celso, Cristina and others (2017). Stem Cells, 35(11), 2292-2304.
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2017ScienceSitesSeptember 17, 2019thumbnail

Protein Degradation Rate Is the Dominant Mechanism Accounting for the Differences in Protein Abundance of Basal p53 in a Human Breast and Colorectal Cancer Cell Line

Lakatos, Eszter and Salehi-Reyhani, Ali and Barclay, Michael and Stumpf, Michael PH and Klug, David R (2017). PLoS ONE, 12(5), e0177336.
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2017ScienceSitesSeptember 17, 2019thumbnail

A Large Fraction of HLA Class I Ligands Are Proteasome-Generated Spliced Peptides

Liepe, Juliane and Marino, Fabio and Sidney, John and Jeko, Anita and Bunting, Daniel E and Sette, Alessandro and Kloetzel, Peter M and Stumpf, Michael PH and Heck, Albert JR and Mishto, Michele (2016). Science, 354(6310), 354-358}.
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2016ScienceSitesSeptember 16, 2019thumbnail

Inferring Extrinsic Noise From Single-Cell Gene Expression Data Using Approximate Bayesian Computation

Lenive, Oleg and Kirk, Paul DW and Stumpf, Michael PH (2016). BMC Systems Biology, 10(1), 81.
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2016ScienceSitesSeptember 16, 2019thumbnail

Feedback Mechanisms Control Coexistence in a Stem Cell Model of Acute Myeloid Leukaemia

Crowell, Helena L and MacLean, Adam L and Stumpf, Michael PH (2016). Journal of Theoretical Biology, 401, 43-53.
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2016ScienceSitesSeptember 16, 2019thumbnail

Robustness of MEK-ERK Dynamics and Origins of Cell-to-Cell Variability in MAPK Signaling

Filippi, Sarah and Barnes, Chris P and Kirk, Paul DW and Kudo, Takamasa and Kunida, Katsuyuki and McMahon, Siobhan S and Tsuchiya, Takaho and Wada, Takumi and Kuroda, Shinya and Stumpf, Michael PH (2016). Cell Reports, 15(11), 2524-2535.
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2016ScienceSitesSeptember 16, 2019thumbnail

Systems Analysis of the Dynamic Inflammatory Response to Tissue Damage Reveals Spatiotemporal Properties of the Wound Attractant Gradient

Weavers, Helen and Liepe, Juliane and Sim, Aaron and Wood, Will and Martin, Paul and Stumpf, Michael PH (2016). Current Biology, 26(15), 1975-1989.
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2016ScienceSitesSeptember 16, 2019thumbnail

Accurate Reconstruction of Cell and Particle Tracks From 3D Live Imaging Data

Liepe, Juliane and Sim, Aaron and Weavers, Helen and Ward, Laura and Martin, Paul and Stumpf, Michael PH (2016). Cell Systems, 3(1), 102-107.
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2016ScienceSitesSeptember 12, 2019thumbnail

Coalescent Models for Developmental Biology and the Spatio-Temporal Dynamics of Growing Tissues

Smadbeck, Patrick and Stumpf, Michael PH (2016). Journal of The Royal Society, 13(117), 20160112.
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2016ScienceSitesSeptember 12, 2019thumbnail

A Graph Theoretical Approach to Data Fusion

Žurauskienė, Justina and Kirk, Paul DW and Stumpf, Michael PH (2016). Statistical Applications in Genetics and Molecular Biology, 15(2), 107-122.
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2016ScienceSitesSeptember 12, 2019thumbnail

Multivariate Moment Closure Techniques for Stochastic Kinetic Models

Lakatos, Eszter and Ale, Angelique and Kirk, Paul DW and Stumpf, Michael PH (2015). The Journal of Chemical Physics, 143(9), 094107.
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2015ScienceSitesSeptember 12, 2019thumbnail

Phosphorelay of Non-Orthodox Two Component Systems Functions Through a Bi-Molecular Mechanism In Vivo: The Case of ArcB

Jovanovic, Goran and Sheng, Xia and Ale, Angelique and Feliu, Elisenda and Harrington, Heather A and Kirk, Paul and Wiuf, Carsten and Buck, Martin and Stumpf, Michael PH (2015). Molecular BioSystems, 11(5). 1348-1359.
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2015ScienceSitesSeptember 12, 2019thumbnail

Goldstein-Kac Telegraph Processes With Random Speeds: Path Probabilities, Likelihoods, and Reported Lévy Flights

Sim, Aaron and Liepe, Juliane and Stumpf, Michael PH (2015). Physical Review E, 91(4), 042115.
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2015ScienceSitesSeptember 12, 2019thumbnail

Conditional Random Matrix Ensembles and the Stability of Dynamical Systems

Kirk, Paul and Rolando, Delphine MY and MacLean, Adam L and Stumpf, Michael PH (2015). New Journal of Physics, 17(8), 083025.
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2015ScienceSitesSeptember 12, 2019thumbnail

Cellular Population Dynamics Control the Robustness of the Stem Cell Niche

MacLean, Adam L and Kirk, Paul DW and Stumpf, Michael PH (2015). Biology Open, 4(11), 1420-1426.
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2015ScienceSitesSeptember 12, 2019thumbnail

Information Processing by Simple Molecular Motifs and Susceptibility to Noise

Mc Mahon, Siobhan S and Lenive, Oleg and Filippi, Sarah and Stumpf, Michael PH (2015). Journal of the Royal Society Interface, 12(110), 20150597.
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2015ScienceSitesSeptember 12, 2019thumbnail

Quantitative Time-Resolved Analysis Reveals Intricate, Differential Regulation of Standard-and Immuno-Proteasomes

Liepe, Juliane and Holzhütter, Hermann-Georg and Bellavista, Elena and Kloetzel, Peter M and Stumpf, Michael PH and Mishto, Michele (2015). eLife, 4, e07545.
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2015ScienceSitesSeptember 12, 2019thumbnail

Inference of Random Walk Models to Describe Leukocyte Migration

Jones, Phoebe JM and Sim, Aaron and Taylor, Harriet B and Bugeon, Laurence and Dallman, Magaret J and Pereira, Bernard and Stumpf, Michael PH and Liepe, Juliane (2015). Physical Biology, 12(6), 066001.
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2015ScienceSitesSeptember 10, 2019thumbnail

Systems Biology (Un)Certainties

Kirk, PDW and Babtie, Ann C and Stumpf, Michael PH (2015). Science, 350(6259), 386-388.
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2015ScienceSitesSeptember 10, 2019thumbnail

Topological Sensitivity Analysis for Systems Biology

Babtie, Ann C and Kirk, Paul and Stumpf, Michael PH (2014). Proceedings of the National Academy of Sciences,111(52), 18507-18512.
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2014ScienceSitesSeptember 10, 2019thumbnail

Overlapping Genes: A Window on Gene Evolvability

Huvet, Maxime and Stumpf, Michael PH (2014). BMC Genomics, 15(1), 721.
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2014ScienceSitesSeptember 10, 2019thumbnail

A Framework for Parameter Estimation and Model Selection From Experimental Data in Systems Biology Using Approximate Bayesian Computation

Liepe, Juliane and Kirk, Paul and Filippi, Sarah and Toni, Tina and Barnes, Chris P and Stumpf, Michael PH (2014). Nature Protocols, 9(2), 439.
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2014ScienceSitesSeptember 10, 2019thumbnail

The Ecology in the Hematopoietic Stem Cell Niche Determines the Clinical Outcome in Chronic Myeloid Leukemia

MacLean, Adam L and Filippi, Sarah and Stumpf, Michael PH (2014). Proceedings of the National Academy of Sciences, 111(10), 3883-3888.
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2014ScienceSitesSeptember 10, 2019thumbnail

Bayesian Non-Parametric Approaches to Reconstructing Oscillatory Systems and the Nyquist Limit

Žurauskienė, Justina and Kirk, Paul and Thorne, Thomas and Stumpf, Michael PH (2014). Physica A: Statistical Mechanics and its Applications, 407, 33-42.
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2014ScienceSitesSeptember 10, 2019thumbnail

Nuclear to Cytoplasmic Shuttling of ERK Promotes Differentiation of Muscle Stem/Progenitor Cells

Michailovici, Inbal and Harrington, Heather A and Azogui, Hadar Hay and Yahalom-Ronen, Yfat and Plotnikov, Alexander and Ching, Saunders and Stumpf, Michael PH and Klein, Ophir D and Seger, Rony and Tzahor, Eldad (2014). Development, 141(13), 2611-2620.
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2014ScienceSitesSeptember 10, 2019thumbnail

Model Selection in Systems Biology Depends on Experimental Design

Silk, Daniel and Kirk, Paul DW and Barnes, Chris P and Toni, Tina and Stumpf, Michael PH (2014). PLoS Computational Biology (2014). 10(6), e1003650.
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2014ScienceSitesSeptember 10, 2019thumbnail

Proteasome Isoforms Exhibit Only Quantitative Differences in Cleavage and Epitope Generation

Mishto, Michele and Liepe, Juliane and Textoris-Taube, Kathrin and Keller, Christin and Henklein, Petra and Weberruß, Marion and Dahlmann, Burkhardt and Enenkel, Cordula and Voigt, Antje and Kuckelkorn, Ulrike and others (2014). European Journal of Immunology, 44(12), 3508-3521.
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2014ScienceSitesSeptember 10, 2019thumbnail

Maximizing the Information Content of Experiments in Systems Biology

Liepe, Juliane and Filippi, Sarah and Komorowski, Michał and Stumpf, Michael PH (2013). PLoS Computational Biology, 9(1), e1002888.
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2013ScienceSitesSeptember 10, 2019thumbnail

Decomposing Noise in Biochemical Signaling Systems Highlights the Role of Protein Degradation

Komorowski, Michał and Miękisz, Jacek and Stumpf, Michael PH (2013). Biophysical Journal, 104(8), 1783-1793.
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2013ScienceSitesSeptember 10, 2019thumbnail

Cellular Compartments Cause Multistability and Allow Cells to Process More Information

Harrington, Heather A and Feliu, Elisenda and Wiuf, Carsten and Stumpf, Michael PH (2013). Biophysical Journal, 104(8), 1824-1831.
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2013ScienceSitesSeptember 10, 2019thumbnail

On Optimality of Kernels for Approximate Bayesian Computation Using Sequential Monte Carlo

Filippi, Sarah and Barnes, Chris P and Cornebise, Julien and Stumpf, Michael PH (2013). Statistical applications in genetics and molecular biology, 12(1), 87-107.
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2013ScienceSitesSeptember 9, 2019thumbnail

Population Dynamics of Normal and Leukaemia Stem Cells in the Haematopoietic Stem Cell Niche Show Distinct Regimes Where Leukaemia Will Be Controlled

MacLean, Adam L and Lo Celso, Cristina and Stumpf, Michael PH (2013). Journal of The Royal Society Interface, 10(81), 20120968.
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2013ScienceSitesSeptember 9, 2019thumbnail

Model Selection in Systems and Synthetic Biology

Kirk, Paul and Thorne, Thomas and Stumpf, Michael PH (2013). Current Opinion in Biotechnology, 24(4), 767-774.
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2013ScienceSitesSeptember 9, 2019thumbnail

A General Moment Expansion Method for Stochastic Kinetic Models

Ale, Angelique and Kirk, Paul and Stumpf, Michael PH (2013). The Journal of Chemical Physics, 138(17), 174101.
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2013ScienceSitesSeptember 9, 2019thumbnail

Balancing the Robustness and Predictive Performance of Biomarkers

Kirk, Paul and Witkover, Aviva and Bangham, Charles RM and Richardson, Sylvia and Lewin, Alexandra M and Stumpf, Michael PH (2013). Journal of Computational Biology, 20(12), 979-989.
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2013ScienceSitesSeptember 9, 2019thumbnail

Optimizing Threshold-Schedules for Sequential Approximate Bayesian Computation: Applications to Molecular Systems

Silk, Daniel and Filippi, Sarah and Stumpf, Michael PH (2013). Statistical Applications in Genetics and Molecular Biology, 12(5), 603-618.
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2013ScienceSitesSeptember 9, 2019thumbnail