Michael Stumpf

Inferring better gene regulation networks from single-cell data

Michael PH Stumpf

Journal article  |  2021  |  Current Opinion in Systems Biology

Collocation based training of neural ordinary differential equations.

Elisabeth Roesch, Christopher Rackauckas, Michael PH Stumpf

Journal article  |  2021  |  Stat Appl Genet Mol Biol

The predictive power of machine learning models often exceeds that of mechanistic modeling approaches. However, the interpretabili..

Statistical and computational challenges for whole cell modelling

MPH Stumpf

Journal article  |  2021  |  Current Opinion in Systems Biology

Mathematical modelling of whole biological cells opens up new opportunities for fundamental and applied biology. In particular in ..

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..

Gene Regulatory Network Inference

Ann C Babtie, Michael PH Stumpf, Thomas Thorne

Book Chapter  |  2021

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..

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..