background: rna plays key role in many aspects of biological processes and its tertiary structure is critical for its biological function. rna secondary structure represents various significant portions of rna tertiary structure. since the biological function of rna is concluded indirectly from its primary structure, it would be important to analyze the relations between the rna sequences and t...

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 discrete dynamical models, we characterize the dynamical modifications in response to structural perturbations in the network connectivities. In particular, w...

Most existing approaches for gene selection are based on evaluating the statistical relevance. However, there are remarkable discrepancies between statistical relevance and biological relevance. It is important to consider biological relevance for crucial genes identification. The task of detecting biological relevance presents two major challenges: first, how to define different types of measu...

Network motifs are statistically overrepresented sub-structures (sub-graphs) in a network, and have been recognized as 'the simple building blocks of complex networks'. Study of biological network motifs may reveal answers to many important biological questions. The main difficulty in detecting larger network motifs in biological networks lies in the facts that the number of possible sub-graphs...

In the post-genomic era, genome-wide experiments have become commonplace and methods to interrogate such datasets are becomingly increasingly important. One approach to analyzing these large datasets is to model the experimental observations using a network approach. In a process known as (re)construction, inference, identification or reverse engineering, model parameters are fit to the data yi...

Transport networks are vital components of multicellular organisms, distributing nutrients and removing waste products. Animal and plant transport systems are branching trees whose architecture is linked to universal scaling laws in these organisms. In contrast, many fungi form reticulated mycelia via the branching and fusion of thread-like hyphae that continuously adapt to the environment. Fun...

SUMMARY The increasing availability of large network datasets along with the progresses in experimental high-throughput technologies have prompted the need for tools allowing easy integration of experimental data with data derived form network computational analysis. In order to enrich experimental data with network topological parameters, we have developed the Cytoscape plug-in CentiScaPe. The...

The goal of systems biology is to define all of the elements present in a given system and to create an interaction network between these components so that the behavior of the system, as a whole and in parts, can be explained under specified conditions. The elements constituting the network that influences the development of atherosclerosis could be genes, pathways, transcript levels, proteins...