Michael Stumpf

Phylodynamics for cell biologists.

T Stadler, OG Pybus, MPH Stumpf

Journal article  |  2021  |  Science

Multicellular organisms are composed of cells connected by ancestry and descent from progenitor cells. The dynamics of cell birth,..

Uncertainty in cell fate decision making: Lessons from potential landscapes of bifurcation systems

Anissa Guillemin, Elisabeth Roesch, Michael PH Stumpf

Journal article  |  2021

Cell fate decision making is known to be a complex process and is still far from being understood. The intrinsic complexity, but a..

Noise and the molecular processes underlying cell fate decision-making

Anissa Guillemin, Michael PH Stumpf

Journal article  |  2021  |  Physical Biology

Cell fate decision-making events involve the interplay of many molecular processes, ranging from signal transduction to genetic re..

Shaping the Epigenetic Landscape: Complexities and Consequences

Megan Coomer, Lucy Ham, Michael Stumpf

Journal article  |  2020

The metaphor of the Waddington epigenetic landscape has become an iconic representation of the cellular differentiation process. R..

Multi-model and network inference based on ensemble estimates: avoiding the madness of crowds

Michael PH Stumpf

Journal article  |  2020  |  Journal of the Royal Society Interface

Recent progress in theoretical systems biology, applied mathematics and computational statistics allows us to compare the performa..

Multi-model and network inference based on ensemble estimates: Avoiding the madness of crowds

MPH Stumpf

Journal article  |  2020  |  Journal of the Royal Society Interface

Recent progress in theoretical systems biology, applied mathematics and computational statistics allows us to compare the performa..

Pathway dynamics can delineate the sources of transcriptional noise in gene expression

Lucy Ham, Marcel Jackson, Michael PH Stumpf

Journal article  |  2020

Single-cell expression profiling has opened up new vistas on cellular processes. Among other important results, one stand-out obse..

Gaining confidence in inferred networks

Léo PM Diaz, Michael PH Stumpf

Journal article  |  2020

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

Repeated Decision Stumping Distils Simple Rules from Single Cell Data

Ivan Croydon Veleslavov, Michael PH Stumpf

Journal article  |  2020

Here we introduce repeated decision stumping, to distill simple models from single cell data. We develop decision trees of depth o..

GpABC: a Julia package for approximate Bayesian computation with Gaussian process emulation.

Evgeny Tankhilevich, Jonathan Ish-Horowicz, Tara Hameed, Elisabeth Roesch, Istvan Kleijn, Michael PH Stumpf, Fei He

Journal article  |  2020  |  Bioinformatics

MOTIVATION: Approximate Bayesian computation (ABC) is an important framework within which to infer the structure and parameters of..