Michael Stumpf

Open problems in mathematical biology.

Sean T Vittadello, Michael PH Stumpf

Journal article  |  2022  |  Math Biosci

Biology is data-rich, and it is equally rich in concepts and hypotheses. Part of trying to understand biological processes and sys..

A group theoretic approach to model comparison with simplicial representations

Sean T Vittadello, Michael PH Stumpf

Journal article  |  2022  |  JOURNAL OF MATHEMATICAL BIOLOGY

The complexity of biological systems, and the increasingly large amount of associated experimental data, necessitates that we deve..

The chemical Langevin equation for biochemical systems in dynamic environments

Lucy Ham, Megan A Coomer, Michael PH Stumpf

Journal article  |  2022  |  JOURNAL OF CHEMICAL PHYSICS

Modeling and simulation of complex biochemical reaction networks form cornerstones of modern biophysics. Many of the approaches de..

More is different with a vengeance.

Michael PH Stumpf

Journal article  |  2022  |  Cell Syst

In his 1972 landmark paper "More is Different," Philip W. Anderson established "complexity" as a fundamentally important subject o..

Cohesin couples transcriptional bursting probabilities of inducible enhancers and promoters.

Irene Robles-Rebollo, Sergi Cuartero, Adria Canellas-Socias, Sarah Wells, Mohammad M Karimi, Elisabetta Mereu, Alexandra G Chivu, Holger Heyn, Chad Whilding, Dirk Dormann, Samuel Marguerat, Inmaculada Rioja, Rab K Prinjha, Michael PH Stumpf, Amanda G Fisher, Matthias Merkenschlager

Journal article  |  2022  |  Nat Commun

Innate immune responses rely on inducible gene expression programmes which, in contrast to steady-state transcription, are highly ..

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

Léo PM Diaz, Michael PH Stumpf

Journal article  |  2022  |  Bioinformatics

SUMMARY: HyperGraphs.jl is a Julia package that implements hypergraphs. These are a generalization of graphs that allow us to repr..

Gaining confidence in inferred networks

Leo PM Diaz, Michael PH Stumpf

Journal article  |  2022  |  SCIENTIFIC REPORTS

Network inference is a notoriously challenging problem. Inferred networks are associated with high uncertainty and likely riddled ..

Noise distorts the epigenetic landscape and shapes cell-fate decisions

Megan A Coomer, Lucy Ham, Michael PH Stumpf

Journal article  |  2022  |  CELL SYSTEMS

Waddington’s epigenetic landscape provides a conceptual tool and, increasingly, analytical framework for the study of cell differe..

Preface

Natalia Jura, James M Murphy

Book Chapter  |  2022  |  Methods in Enzymology

Turing pattern design principles and their robustness

Sean T Vittadello, Thomas Leyshon, David Schnoerr, Michael PH Stumpf

Journal article  |  2021  |  PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

Turing patterns have morphed from mathematical curiosities into highly desirable targets for synthetic biology. For a long time, t..