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Exchanges between the blood compartment and the surrounding tissues require a tight regulation by the endothelial barrier. Recent reports inferred that VE-cadherin, an endothelial specific cell-cell adhesion molecule, plays a pivotal role…
Cells are able to generate phenotypic diversity both during development and in response to stressful and changing environments, aiding survival. The biologically and medically vital process of a cell assuming a functionally important fate…
Enzymes are on the front lines of evolution. All living organisms rely on highly efficient, specific enzymes for growth, sustenance, and reproduction; and many diseases are a consequence of a mutation on an enzyme that affects its catalytic…
Complex dynamical systems are often modeled as networks, with nodes representing dynamical units which interact through the network's links. Gene regulatory networks, responsible for the production of proteins inside a cell, are an example…
We demonstrate the advantages of feedforward loops using a Boolean network, which is one of the discrete dynamical models for transcriptional regulatory networks. After comparing the dynamical behaviors of network embedded feedback and…
Living tissue is able to withstand large stresses in everyday life, yet it also actively adapts to dynamic loads. This remarkable mechanical behaviour emerges from the interplay between living cells and their non-living extracellular…
In multicellular organisms, several cell states coexist. For determining each cell type, cell-cell interactions are often essential, in addition to intracellular gene expression dynamics. Based on dynamical systems theory, we propose a…
The E.coli transcription network has an essentially feedforward structure, with, however, abundant feedback at the level of self-regulations. Here, we investigate how these properties emerged during evolution. An assessment of the role of…
The dynamics of gene regulatory networks are often modeled with the assumption of cellular homogeneity. However, this assumption contradicts the plethora of experimental results in a variety of systems, which designates that cell…
Boolean networks are an important class of computational models for molecular interaction networks. Boolean canalization, a type of hierarchical clustering of the inputs of a Boolean function, has been extensively studied in the context of…
The relationship between the regulatory design and the functionality of molecular networks is a key issue in biology. Modules and motifs have been associated to various cellular processes, thereby providing anecdotal evidence for…
Boolean threshold networks have recently been proposed as useful tools to model the dynamics of genetic regulatory networks, and have been successfully applied to describe the cell cycles of \textit{S. cerevisiae} and \textit{S. pombe}.…
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…
Cell neighbor exchanges play a critical role in regulating tissue fluidity during epithelial morphogenesis and repair. In vivo, these neighbor exchanges are often hindered by the formation of transiently stable four-fold vertices, which can…
Tuning of active prestress e.g. through activity of molecular motors constitutes a powerful cellular tool to adjust cellular stiffness through nonlinear material properties. Understanding this tool is an important prerequisite for our…
Metabolic networks have two properties that are generally regarded as unrelated: One, they have metabolic reactions whose single knockout is lethal for the organism, and two, they have correlated sets of reactions forming functional…
This is the second paper of a series of two about the structural properties that influence the asymptotic dynamics of Random Boolean Networks. Here we study the functionally independent clusters in which the relevant elements, introduced…
The ability of cells to sense and respond to the mechanical properties of their environments is fundamental to a range of cellular behaviours, with substrate stiffness increasingly being found to be a key signalling factor. Although active…
Cell cell and cell matrix adhesions are fundamental in all multicellular organisms. They play a key role in cellular growth, differentiation, pattern formation and migration. Cell-cell adhesion is substantial in the immune response,…
Bacteriophages are central to microbial ecosystems for balancing bacterial populations and promoting evolution by applying strong selection pressure. Here we review some of the known aspects that modulate phage-bacteria interaction in a way…