Related papers: A unified formal framework for developmental andev…
The dynamics of gene regulatory networks is governed by the interaction between deterministic biochemical reactions and molecular noise. To understand how gene regulatory networks process information during cell state transitions, we study…
Precise temporal coordination of gene expression is crucial for many developmental processes. One central question in developmental biology is how such coordinated expression patterns are robustly controlled. During embryonic development of…
The prevalence of neutral mutations implies that biological systems typically have many more genotypes than phenotypes. But can the way that genotypes are distributed over phenotypes determine evolutionary outcomes? Answering such questions…
Cell growth and gene expression, essential elements of all living systems, have long been the focus of biophysical interrogation. Advances in single-cell methods have invigorated theoretical studies into these processes. However, until…
Genetic regulatory networks with adaptive responses are widely studied in biology. Usually, models consisting only of a few nodes have been considered. They present one input receptor for activation and one output node where the adaptive…
The well-known issue of reconstructing regulatory networks from gene expression measurements has been somewhat disrupted by the emergence and rapid development of single-cell data. Indeed, the traditional way of seeing a gene regulatory…
We introduce simple models of genetic regulatory networks and we proceed to the mathematical analysis of their dynamics. The models are discrete time dynamical systems generated by piecewise affine contracting mappings whose variables…
A biologically motivated individual-based framework for evolution in network-structured populations is developed that can accommodate eco-evolutionary dynamics. This framework is used to construct a network birth and death model. The…
1) Micro-evolutionary predictions are complicated by ecological feedbacks like density dependence, while ecological predictions can be complicated by evolutionary change. A widely used approach in micro-evolution, quantitative genetics,…
The biological processes of cellular decision making and differentiation involve a plethora of signalling pathways and gene regulatory circuits. These networks, in their turn, exhibit a multitude of motifs playing crucial parts in…
Tumorigenic transformation of human epithelial cells in vitro has been described experimentally as the potential result of a process known as spontaneous immortalization. In this process a generic series of cell state transitions occur in…
Boolean networks have been widely used to explore aspects of gene regulation, traditionally with a single network. A modified form of the model to explore the effects of increasing the number of gene states has also recently been…
The complexity of gene regulatory networks in multicellular organisms makes interpretable low-dimensional models highly desirable. An attractive geometric picture, attributed to Waddington, visualizes the differentiation of a cell into…
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…
One of the characteristic features of genetic networks is their inherent robustness, that is, their ability to retain functionality in spite of the introduction of random errors. In this paper, we seek to better understand how robustness is…
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…
Identity, response to external stimuli, and spatial architecture of a living system are central topics of molecular biology. Presently, they are largely seen as a result of the interplay between a gene repertoire and the regulatory…
We study genetic networks that produce many species of non-coding RNA molecules that are present at a moderate density, as typically exists in the cell. The associations of the many species of these RNA are modeled physically, taking into…
The relationship between genotype and phenotype plays a crucial role in determining the function and robustness of biological systems. Here the evolution progresses through the change in genotype, whereas the selection is based on the…
Network science provides an indispensable theoretical framework for studying the structure and function of real complex systems. Different network models are often used for finding the rules that govern their evolution, whereby the correct…