Related papers: Dynamic landscapes and statistical limits on growt…
The spread of a particular trait in a cell population often is modelled by an appropriate system of ordinary differential equations describing how the sizes of subpopulations of the cells with the same genome change in time. On the other…
To celebrate Hans Frauenfelder's achievements, we examine energy(-like) "landscapes" for complex living systems. Energy landscapes summarize all possible dynamics of some physical systems. Energy(-like) landscapes can explain some…
Stem cell regeneration is a crucial biological process for most self-renewing tissues during the development and maintenance of tissue homeostasis. In developing the mathematical models of stem cell regeneration and tissue development, cell…
Multicellular organisms exhibit a high degree of structural organization with specific cell types always occurring in characteristic locations. The conventional framework for describing the emergence of such consistent spatial patterns is…
From the response to external stimuli to cell division and death, the dynamics of living cells is based on the expression of specific genes at specific times. The decision when to express a gene is implemented by the binding and unbinding…
Investigating the emergence of a particular cell type is a recurring theme in models of growing cellular populations. The evolution of resistance to therapy is a classic example. Common questions are: when does the cell type first occur,…
The last decade has witnessed a surge of theoretical and computational models to describe the dynamics of complex gene regulatory networks, and how these interactions can give rise to multistable and heterogeneous cell populations. As the…
Understanding cell fate selection remains a central challenge in developmental biology. We present a class of simple yet biologically-motivated mathematical models for cell differentiation that generically generate oscillations and hence…
Continuum models for the spatial dynamics of growing cell populations have been widely used to investigate the mechanisms underpinning tissue development and tumour invasion. These models consist of nonlinear partial differential equations…
We introduce a nonlinear and nonlocal model that describes the range expansion of a population resulting from growth and competition for space. This type of phenomenon underlies the expansion of colonies of immotile cells which motivated…
Developmental dynamics of multicellular organism is a process that takes place in a multi-stable system in which each attractor state represents a cell type and attractor transitions correspond to cell differentiation paths. This new…
Rapid advance of experimental techniques provides an unprecedented in-depth view into complex developmental processes. Still, little is known on how the complexity of multicellular organisms evolved by elaborating developmental programs and…
Based on a non-equilibrium mechanism for spatial pattern formation we study how position information can be controlled by locally coupled discrete dynamical networks, similar to gene regulation networks of cells in a developing…
Differentiation is a key cellular process in normal tissue development that is significantly altered in cancer. Although molecular signatures characterising pluripotency and multipotency exist, there is, as yet, no single quantitative mark…
Cells use genetic switches to shift between alternate stable gene expression states, e.g., to adapt to new environments or to follow a developmental pathway. Conceptually, these stable phenotypes can be considered as attractive states on an…
Based on a recently proposed non-equilibrium mechanism for spatial pattern formation [cond-mat/0312366] we study how morphogenesis can be controlled by locally coupled discrete dynamical networks, similar to gene regulation networks of…
This paper introduces a continuous model for Multi-cellular Developmental Design. The cells are fixed on a 2D grid and exchange "chemicals" with their neighbors during the growth process. The quantity of chemicals that a cell produces, as…
We study a class of growth algorithms for directed graphs that are candidate models for the evolution of genetic regulatory networks. The algorithms involve partial duplication of nodes and their links, together with innovation of new…
Single-cell trajectory analysis aims to reconstruct the biological developmental processes of cells as they evolve over time, leveraging temporal correlations in gene expression. During cellular development, gene expression patterns…
We consider a class of biologically-motivated stochastic processes in which a unicellular organism divides its resources (volume or damaged proteins, in particular) symmetrically or asymmetrically between its progeny. Assuming the final…