Related papers: Novel Generic Models for Differentiating Stem Cell…
Genes are connected in complex networks of interactions where often the product of one gene is a transcription factor that alters the expression of another. Many of these networks are based on a few fundamental motifs leading to switches…
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…
Decisions in the cell that lead to its ultimate fate are important for cellular functions such as proliferation, growth, differentiation, development and death. Understanding this decision process is imperative for advancements in the…
Cellular differentiation is governed by gene regulatory networks, the high-dimensional stochastic biochemical systems that determine the transcriptional landscape and mediate cellular responses to signals and perturbations. Although…
Cells often exhibit different and stable phenotypes from the same DNA sequence. Robustness and plasticity of such cellular states are controlled by diverse transcriptional and epigenetic mechanisms, among them the modification of…
We study a system of dynamical units, each of which shows excitable or oscillatory behavior, depending on the choice of parameters. When we couple these units with repressive bonds, we can control the duration of collective oscillations for…
Gene regulatory networks (GRNs) define the regulatory relationships among molecules such as transcription factors, chromatin remodelers, and target genes. GRNs play a critical role in diverse biological processes, including development,…
Segregation of different cell types is a crucial process for the pattern formation in tissues, in particular during embryogenesis. Since the involved cell interactions are complex and difficult to measure individually in experiments,…
The cell cycle is a tightly controlled process, yet its underlying genetic network shows marked differences across species. Which of the associated structural features follow solely from the ability to impose the appropriate gene expression…
Modelling gene regulatory networks not only requires a thorough understanding of the biological system depicted but also the ability to accurately represent this system from a mathematical perspective. Throughout this chapter, we aim to…
Cellular behavior is governed by gene regulatory processes that are intrinsically dynamic and nonlinear, and are subject to non-negligible amounts of random fluctuations. Such conditions are ubiquitous in physical systems, where they have…
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…
Development combines three basic processes asymmetric --- cell division, signaling and gene regulation --- in a multitude of ways to create an overwhelming diversity of multicellular life-forms. Here, we attempt to chart this diversity…
All stem cell fate transitions, including the metabolic reprogramming of stem cells and the somatic reprogramming of fibroblasts into pluripotent stem cells, can be understood from a unified theoretical model of cell fates. Each cell fate…
We investigate the predictive power of recurrent neural networks for oscillatory systems not only on the attractor, but in its vicinity as well. For this we consider systems perturbed by an external force. This allows us to not merely…
This work gives a mathematical foundation for bifurcation from a stable equilibrium in the genome. We construct idealized dynamics associated with the genome. For this dynamics we investigate the two main bifurcations from a stable…
We introduce a minimal model description for the dynamics of transcriptional regulatory networks. It is studied within a mean-field approximation, i.e., by deterministic ode's representing the reaction kinetics, and by stochastic…
Cell fate decisions emerge as a consequence of a complex set of gene regulatory networks. Models of these networks are known to have more parameters than data can determine. Recent work, inspired by Waddington's metaphor of a landscape, has…
Systems with the coexistence of different stable attractors are widely exploited in systems biology in order to suitably model the differentiating processes arising in living cells. In order to describe genetic regulatory networks several…
A blood cell lineage consists of several consecutive developmental stages from the pluri- or multipotent stem cell to a state of terminal differentiation. Despite their importance for human biology, the regulatory pathways and gene networks…