Michael P. H. Stumpf
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View article: Intercellular signaling drives robust cell fate and patterning in multicellular systems
Intercellular signaling drives robust cell fate and patterning in multicellular systems Open
Cells do not act in isolation; they communicate with each other through a complex network of signals. In multicellular organisms, cell signaling buffers against fluctuations in gene expression. Its effect, however, on multistability—the ab…
View article: Towards a mathematical framework for modelling cell fate dynamics
Towards a mathematical framework for modelling cell fate dynamics Open
An adult human body is made up of some 30 to 40 trillion cells, all of which stem from a single fertilized egg cell. The process by which the right cells appear to arrive in their right numbers at the right time at the right place – develo…
View article: The topological properties of the protein universe
The topological properties of the protein universe Open
Deep learning methods have revolutionised our ability to predict protein structures, allowing us a glimpse into the entire protein universe. As a result, our understanding of how protein structure drives function is now lagging behind our …
View article: Molecular noise modulates transitions in the cell-fate differentiation landscape
Molecular noise modulates transitions in the cell-fate differentiation landscape Open
Waddington's epigenetic landscape has become one of biology's cornerstone metaphors, widely used both conceptually and computationally. Cell types are often associated with the stable stationary points or valleys of this landscape. In prev…
View article: Mapping, Modeling, and Reprogramming Cell-Fate Decision-Making Systems
Mapping, Modeling, and Reprogramming Cell-Fate Decision-Making Systems Open
Many cellular processes involve information processing and decision-making. We can probe these processes at increasing molecular detail. The analysis of heterogeneous data remains a challenge that requires new ways of thinking about cells …
View article: The two-clock problem in population dynamics
The two-clock problem in population dynamics Open
Biological time can be measured in two ways: in generations and in physical time. When generation intervals differ between individuals, these two clocks diverge, which impedes our ability to relate mathematical models to real populations. …
View article: Cell size distributions in lineages
Cell size distributions in lineages Open
Cells actively regulate their size during the cell cycle to maintain volume homeostasis across generations. While various mathematical models of cell size regulation have been proposed to explain how this is achieved, relating these models…
View article: Towards a mathematical framework for modelling cell fate dynamics
Towards a mathematical framework for modelling cell fate dynamics Open
An adult human body is made up of some 30 to 40 trillion cells, all of which stem from a single fertilized egg cell. The process by which the right cells appear to arrive in their right numbers at the right time at the right place -- devel…
View article: Mapping, modeling, and reprogramming cell-fate decision making systems
Mapping, modeling, and reprogramming cell-fate decision making systems Open
Many cellular processes involve information processing and decision making. We can probe these processes at increasing molecular detail. The analysis of heterogeneous data remains a challenge that requires new ways of thinking about cells …
View article: A three-node Turing gene circuit forms periodic spatial patterns in bacteria
A three-node Turing gene circuit forms periodic spatial patterns in bacteria Open
Turing patterns are self-organizing systems that can form spots, stripes, or labyrinths. Proposed examples in tissue organization include zebrafish pigmentation, digit spacing, and many others. The theory of Turing patterns in biology has …
View article: Cell size distributions in lineages
Cell size distributions in lineages Open
Cells actively regulate their size during the cell cycle to maintain volume homeostasis across generations. While various mathematical models of cell size regulation have been proposed to explain how this is achieved, relating these models…
View article: Geometry of the Space of Partitioned Networks: A Unified Theoretical and Computational Framework
Geometry of the Space of Partitioned Networks: A Unified Theoretical and Computational Framework Open
Interactions and relations between objects may be pairwise or higher-order in nature, and so network-valued data are ubiquitous in the real world. The "space of networks", however, has a complex structure that cannot be adequately describe…
View article: Approximate Bayesian computation for inferring Waddington landscapes from single-cell data
Approximate Bayesian computation for inferring Waddington landscapes from single-cell data Open
Single-cell technologies allow us to gain insights into cellular processes at unprecedented resolution. In stem cell and developmental biology snapshot data allow us to characterize how the transcriptional states of cells change between su…
View article: A stochastic vs deterministic perspective on the timing of cellular events
A stochastic vs deterministic perspective on the timing of cellular events Open
View article: Topological Optimal Transport for Geometric Cycle Matching
Topological Optimal Transport for Geometric Cycle Matching Open
Topological data analysis is a powerful tool for describing topological signatures in real world data. An important challenge in topological data analysis is matching significant topological signals across distinct systems. In geometry and…
View article: A Three-Node Turing Gene Circuit Forms Periodic Spatial Patterns in Bacteria
A Three-Node Turing Gene Circuit Forms Periodic Spatial Patterns in Bacteria Open
View article: The Topological Properties of the Protein Universe
The Topological Properties of the Protein Universe Open
Deep learning methods have revolutionized our ability to predict protein structures, allowing us a glimpse into the entire protein universe. As a result, our understanding of how protein structure drives function is now lagging behind our …
View article: BondGraphs.jl: composable energy-based modelling in systems biology
BondGraphs.jl: composable energy-based modelling in systems biology Open
Summary BondGraphs.jl is a Julia implementation of bond graphs. Bond graphs provide a modelling framework that describes energy flow through a physical system and by construction enforce thermodynamic constraints. The framework is widely u…
View article: Approximate Bayesian Computation for Inferring Waddington Landscapes from Single Cell Data
Approximate Bayesian Computation for Inferring Waddington Landscapes from Single Cell Data Open
Single cell technologies allow us to gain insights into cellular processes at unprecedented resolution. In stem cell and developmental biology snapshot data allows us to characterise how the transcriptional state of cells changes between s…
View article: The timing of cellular events: a stochastic vs deterministic perspective
The timing of cellular events: a stochastic vs deterministic perspective Open
Changes in cell state are driven by key molecular events whose timing can often be measured experimentally. Of particular interest is the time taken for the levels of RNA or protein molecules to reach a critical threshold defining the trig…
View article: Author Correction: Julia for biologists
Author Correction: Julia for biologists Open
View article: BondGraphs.jl: Composable energy-based modelling in systems biology
BondGraphs.jl: Composable energy-based modelling in systems biology Open
Summary BondGraphs.jl is a Julia implementation of bond graphs. Bond graphs provide a modelling framework that describes energy flow through a physical system and by construction enforce thermodynamic constraints. The framework is widely u…
View article: Frontiers of Mathematical Biology: A workshop honouring Professor Edmund Crampin
Frontiers of Mathematical Biology: A workshop honouring Professor Edmund Crampin Open
• Edmund Crampin was Professor of Systems Biology at the University of Melbourne. He passed away on 15 May 2021. • A workshop in honour of Edmund was held at the University of Melbourne in November 2022. • 11 of his colleagues gave scienti…
View article: Julia for biologists
Julia for biologists Open
View article: Hypergraph Animals
Hypergraph Animals Open
Here we introduce simple structures for the analysis of complex hypergraphs, hypergraph animals. These structures are designed to describe the local node neighbourhoods of nodes in hypergraphs. We establish their relationships to lattice a…
View article: Energy dependence of signalling dynamics and robustness in bacterial two component systems
Energy dependence of signalling dynamics and robustness in bacterial two component systems Open
One of the best known ways bacteria cells understand and respond to the environment are through Two-Component Systems (TCS). These signalling systems are highly diverse in function and can detect a range of physical stimuli including molec…
View article: Learning cell-specific networks from dynamics and geometry of single cells
Learning cell-specific networks from dynamics and geometry of single cells Open
Cell dynamics and biological function are governed by intricate networks of molecular interactions. Inferring these interactions from data is a notoriously difficult inverse problem. The majority of existing network inference methods work …
View article: Hypergraphs for multiscale cycles in structured data
Hypergraphs for multiscale cycles in structured data Open
Scientific data has been growing in both size and complexity across the modern physical, engineering, life and social sciences. Spatial structure, for example, is a hallmark of many of the most important real-world complex systems, but its…
View article: A group theoretic approach to model comparison with simplicial representations
A group theoretic approach to model comparison with simplicial representations Open
View article: Cohesin couples transcriptional bursting probabilities of inducible enhancers and promoters
Cohesin couples transcriptional bursting probabilities of inducible enhancers and promoters Open