Simulation and inference algorithms for stochastic biochemical reaction networks: from basic concepts to state-of-the-art
Stochasticity is a key characteristic of intracellular processes such as gene regulation and
chemical signalling. Therefore, characterizing stochastic effects in biochemical systems is …
chemical signalling. Therefore, characterizing stochastic effects in biochemical systems is …
'The Forms of Tissues, or Cell-aggregates': D'Arcy Thompson's influence and its limits
F Graner, D Riveline - Development, 2017 - journals.biologists.com
In two chapters of his book On Growth and Form, D'Arcy Thompson used numerous
biological and physical observations to show how principles from mathematics and physics …
biological and physical observations to show how principles from mathematics and physics …
Pushing coarse-grained models beyond the continuum limit using equation learning
DJ VandenHeuvel, PR Buenzli… - Proceedings of the …, 2024 - royalsocietypublishing.org
Mathematical modelling of biological population dynamics often involves proposing high-
fidelity discrete agent-based models that capture stochasticity and individual-level …
fidelity discrete agent-based models that capture stochasticity and individual-level …
Multi-scale computational study of the mechanical regulation of cell mitotic rounding in epithelia
A Nematbakhsh, W Sun, PA Brodskiy… - PLoS computational …, 2017 - journals.plos.org
Mitotic rounding during cell division is critical for preventing daughter cells from inheriting an
abnormal number of chromosomes, a condition that occurs frequently in cancer cells. Cells …
abnormal number of chromosomes, a condition that occurs frequently in cancer cells. Cells …
Inferring parameters for a lattice-free model of cell migration and proliferation using experimental data
Collective cell spreading takes place in spatially continuous environments, yet it is often
modelled using discrete lattice-based approaches. Here, we use data from a series of cell …
modelled using discrete lattice-based approaches. Here, we use data from a series of cell …
Modeling perspectives on the intestinal crypt, a canonical system for growth, mechanics, and remodeling
The intestinal epithelium is crucial to maintaining a healthy gut. Central to this are the crypts
of Lieberkühn, which coordinate the rapid self-renewal of the epithelium to protect the small …
of Lieberkühn, which coordinate the rapid self-renewal of the epithelium to protect the small …
Collective chemotaxis through noisy multicellular gradient sensing
Collective cell migration in response to a chemical cue occurs in many biological processes
such as morphogenesis and cancer metastasis. Clusters of migratory cells in these systems …
such as morphogenesis and cancer metastasis. Clusters of migratory cells in these systems …
A hierarchical Bayesian model for understanding the spatiotemporal dynamics of the intestinal epithelium
OJ Maclaren, A Parker, C Pin, SR Carding… - PLoS Computational …, 2017 - journals.plos.org
Our work addresses two key challenges, one biological and one methodological. First, we
aim to understand how proliferation and cell migration rates in the intestinal epithelium are …
aim to understand how proliferation and cell migration rates in the intestinal epithelium are …
Sense and sensitivity: physical limits to multicellular sensing, migration, and drug response
J Varennes, A Mugler - Molecular pharmaceutics, 2016 - ACS Publications
Metastasis is a process of cell migration that can be collective and guided by chemical cues.
Viewing metastasis in this way, as a physical phenomenon, allows one to draw upon …
Viewing metastasis in this way, as a physical phenomenon, allows one to draw upon …
Intermediate adhesion maximizes migration velocity of multicellular clusters
Collections of cells exhibit coherent migration during morphogenesis, cancer metastasis,
and wound healing. In many cases, bigger clusters split, smaller subclusters collide and …
and wound healing. In many cases, bigger clusters split, smaller subclusters collide and …