Related papers: Modeling biological networks: from single gene sys…
Gene Regulatory Networks are networks of interactions in biological organisms responsible for determining the production levels of proteins and peptides. Proteins are workers of a cell factory, and their production defines the goal of a…
We investigate the evolution of Boolean networks subject to a selective pressure which favors robustness against noise, as a model of evolved genetic regulatory systems. By mapping the evolutionary process into a statistical ensemble and…
The evolutionary origins of structural features in reconstructed gene-regulatory networks (GRNs) remain poorly understood, especially given the random aspects of gene expression. Here, we extend a classical model of GRN evolution to allow a…
We present a model of adaptive regulatory networks consisting of a simple biologically-motivated rewiring procedure coupled to an elementary stability criterion. The resulting networks exhibit a characteristic stationary heavy-tailed degree…
A single gene, regulating its own expression via a positive feedback loop, constitutes a common motif in gene regulatory networks and signalling cascades. Recent experiments on the development of competence in the bacterial population…
Biological systems and processes are networks of complex nonlinear regulatory interactions between nucleic acids, proteins, and metabolites. A natural way in which to represent these interaction networks is through the use of a graph. In…
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…
Biological structure and function depend on complex regulatory interactions between many genes. A wealth of gene expression data is available from high-throughput genome-wide measurement technologies, but effective gene regulatory network…
We study the dynamics of gene activities in relatively small size biological networks (up to a few tens of nodes), e.g. the activities of cell-cycle proteins during the mitotic cell-cycle progression. Using the framework of deterministic…
Self-regulation of living tissue as an example of self-organization phenomena in hierarchical systems of biological, ecological, and social nature is under consideration. The characteristic feature of these systems is the absence of any…
MicroRNAs are small non-coding nucleotide sequences that regulate target protein expression at post-transcriptional levels. Biogenesis of microRNA is a highly regulated multi-step pathway. Regulation of miRNA biogenesis can be caused…
Autoinducers are small signaling molecules that mediate intercellular communication in microbial populations and trigger coordinated gene expression via "quorum sensing". Elucidating the mechanisms that control autoinducer production is,…
We present the methods and results of a two-stage modeling process that generates candidate gene-regulatory networks of the bacterium B. subtilis from experimentally obtained, yet mathematically underdetermined microchip array data. By…
A common feature of biological networks is the geometric property of self-similarity. Molecular regulatory networks through to circulatory systems, nervous systems, social systems and ecological trophic networks, show self-similar…
Recent work on synthetic rescues has shown that the targeted deletion of specific metabolic genes can often be used to rescue otherwise non-viable mutants. This raises a fundamental biophysical question: to what extent can the whole-cell…
Evolving biomolecular networks have to combine the stability against perturbations with flexibility allowing their constituents to assume new roles in the cell. Gene duplication followed by functional divergence of associated proteins is a…
Organisms are equipped with regulatory systems that display a variety of dynamical behaviours ranging from simple stable steady states, to switching and multistability, to oscillations. Earlier work has shown that oscillations in protein…
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…
Self-regulation of living tissue as an example of self-organization phenomena in active fractal systems of biological, ecological, and social nature is under consideration. The characteristic feature of these systems is the absence of any…
The innate immune system, acting as the first line of host defense, senses and adapts to foreign challenges through complex intracellular and intercellular signaling networks. Endotoxin tolerance and priming elicited by macrophages are…