Molecular Networks
MicroRNAs can affect the protein translation using nine mechanistically different mechanisms, including repression of initiation and degradation of the transcript. There is a hot debate in the current literature about which mechanism and in…
Topological analysis of large scale protein-protein interaction networks (PINs) is important for understanding the organisational and functional principles of individual proteins. The number of interactions that a protein has in a PIN has…
Building circuits and studying their behavior in cells is a major goal of systems and synthetic biology. Synthetic biology enables the precise control of cellular states for systems studies, the discovery of novel parts, control strategies,…
The Red cell-Hb-CSF functions as a sensor adapting response to Hb heterotropic equilibriums. At the lungs O2 and Mg2+, each one increasing affinity for the other stabilize the relax (R) form [(O2)4Hb(Mg)2].(H2O)R. At tissue level, the…
Cellular functions are based on the complex interplay of proteins, therefore the structure and dynamics of these protein-protein interaction (PPI) networks are the key to the functional understanding of cells. In the last years, large-scale…
Network analysis provides a powerful framework for the interpretation of genome-wide data. While static network approaches have proved fruitful, there is increasing interest in the insights gained from the analysis of cellular networks…
Stochasticity plays important roles in molecular networks when molecular concentrations are in the range of $0.1 \mu$M to $10 n$M (about 100 to 10 copies in a cell). The chemical master equation provides a fundamental framework for studying…
A recurring motif in gene regulatory networks is transcription factors (TFs) that regulate each other, and then bind to overlapping sites on DNA, where they interact and synergistically control transcription of a target gene. Here, we…
Many of the chemical reactions that take place within a living cell are irreversible. Due to evolutionary pressures, the number of allowable reactions within these systems are highly constrained and thus the resulting metabolic networks…
Protein-protein interaction networks are useful for studying human diseases and to look for possible health care through a holistic approach. Networks are playing an increasing and important role in the understanding of physiological…
We present a novel formulation for biochemical reaction networks in the context of signal transduction. The model consists of input-output transfer functions, which are derived from differential equations, using stable equilibria. We select…
The complex interactions involved in regulation of a cell's function are captured by its interaction graph. More often than not, detailed knowledge about enhancing or suppressive regulatory influences and cooperative effects is lacking and…
We investigate numerically and analytically the formation of the frozen core in critical random Boolean networks with biased functions. We demonstrate that a previously used efficient algorithm for obtaining the frozen core, which starts…
Randomness is an unavoidable feature of the intracellular environment due to chemical reactants being present in low copy number. That phenomenon, predicted by Delbr\"uck long ago \cite{delbruck40}, has been detected in both prokaryotic…
We present schema redescription as a methodology to characterize canalization in automata networks used to model biochemical regulation and signalling. In our formulation, canalization becomes synonymous with redundancy present in the logic…
Gene networks exhibiting oscillatory dynamics are widespread in biology. The minimal regulatory designs giving rise to oscillations have been implemented synthetically and studied by mathematical modeling. However, most of the available…
Modeling stochasticity in gene regulatory networks is an important and complex problem in molecular systems biology. To elucidate intrinsic noise, several modeling strategies such as the Gillespie algorithm have been used successfully. This…
Understanding design principles of molecular interaction networks is an important goal of molecular systems biology. Some insights have been gained into features of their network topology through the discovery of graph theoretic patterns…
The TNF initiated processes are simulated using our integrative computational model with new quantitative proteomics data obtained on HeLa cell line. In spite of fact, that the model development is based on limited experimental information,…
Systems Biology has emerged in the last years as a new holistic approach based on the global understanding of cells instead of only being focused on their individual parts (genes or proteins), to better understand the complexity of human…