Discovering meaningful gene interactions is crucial for the identification of novel regulatory processes in cells. Building accurately the related graphs remains challenging due to the large number of possible solutions from available data. Nonetheless, enforcing a priori on the graph structure, such as modularity, may reduce network indeterminacy issues. BRANE Clust (Biologically-Related A pri...

One of the main challenges of the post-genomic era is the understanding of how gene expression is controlled. Changes in gene expression lay behind diverse biological phenomena such as development, disease and the adaptation to different environmental conditions. Despite the availability of well-established methods to identify these changes, tools to discern how gene regulation is orchestrated ...

One of the pressing open problems of computational systems biology is the elucidation of the topology of genetic regulatory networks (GRNs) using high throughput genomic data, in particular microarray gene expression data. The Dialogue for Reverse Engineering Assessments and Methods (DREAM) challenge aims to evaluate the success of GRN inference algorithms on benchmarks of simulated data. In th...

The interplay of interactions between DNA, RNA and proteins leads to genetic regulatory networks (GRN) and in turn controls the gene regulation. Directly or indirectly in a cell such molecules either interact in a positive or in repressive manner therefore it is hard to obtain the accurate computational models through which the final state of a cell can be predicted with certain accuracy. This ...

The foxa regulatory gene is of central importance for endoderm specification across Bilateria, and this gene lies at an essential node of the well-characterized sea urchin endomesoderm gene regulatory network (GRN). Here we experimentally dissect the cis-regulatory system that controls the complex pattern of foxa expression in these embryos. Four separate cis-regulatory modules (CRMs) cooperate...

The emergence of the neural crest has been proposed to play a key role in early vertebrate evolution by remodeling the chordate head into a "new head" that enabled early vertebrates to shift from filter feeding to active predation. Here we show that the genome of the basal chordate, amphioxus, contains homologs of most vertebrate genes implicated in a putative neural crest gene regulatory netwo...

Gene regulatory networks (GRNs) provide insights into the mechanisms of differential gene expression at a systems level. GRNs that relate to metazoan development have been studied extensively. However, little is still known about the design principles, organization and functionality of GRNs that control physiological processes such as metabolism, homeostasis and responses to environmental cues....

While significant progress had been made in synthetic biology over the last decade, researchers still lack a reliable tool for computeraided design of gene regulatory networks (GRN), one that can reveal the full range of nonlinear dynamic behaviors in a single run. Here, we propose a network design cycle that utilizes both the qualitative simulation of GRNs modeled by a class of ODE equations a...

One can think of a Gene Regulatory Network (GRN) as a network of relations among strands of DNA (genes) and the regulatory activities associated with those genes (Dougherty and Braga-Neto, 2006). This general definition allows for many mathematical (usually dynamical) systems to be called GRNs. The goodness of each such model is evaluated using several important criteria: the level of descripti...

Gene regulatory networks (GRNs) are complex control systems that deal with the interaction of genes, which eventually control cellular processes at the protein level. The investigation of GRN provides huge information on cellular processes and gene functions and at last contributes to knowledge in genetics and in turn quality of life. By understanding the dynamics of these networks using correc...