分子网络
Topological network motifs represent functional relationships within and between regulatory and protein-protein interaction networks. Enriched motifs often aggregate into self-contained units forming functional modules. Theoretical models…
Proteins with multiple binding sites play important roles in cell signaling systems by nucleating protein complexes in which, for example, enzymes and substrates are co-localized. Proteins that specialize in this function are called by a…
Highlighting similarities and differences between networks is an informative task in investigating many biological processes. Typical examples are detecting differences between an inferred network and the corresponding gold standard, or…
The common techniques to study protein-protein proximity in vivo are not well-adapted to the capabilities and the expertise of a standard proteomics laboratory, typically based on the use of mass spectrometry. With the aim of closing this…
The ubiquity of modules in biological networks may result from an evolutionary benefit of a modular organization. For instance, modularity may increase the rate of adaptive evolution, because modules can be easily combined into new…
Network analysis became a powerful tool in recent years. Heat shock is a well-characterized model of cellular dynamics. S. cerevisiae is an appropriate model organism, since both its protein-protein interaction network (interactome) and…
We describe how noise propagates through a network by calculating the variance of the outputs. Using stochastic calculus and dynamical systems theory, we study the network topologies that accentuate or alleviate the effect of random…
Discrete models have a long tradition in engineering, including finite state machines, Boolean networks, Petri nets, and agent-based models. Of particular importance is the question of how the model structure constrains its dynamics. This…
We define a subclass of Chemical Reaction Networks called Post-Translational Modification systems. Important biological examples of such systems include MAPK cascades and two-component systems which are well-studied experimentally as well…
Networks coming from protein-protein interactions, transcriptional regulation, signaling, or metabolism may appear to have "unusual" properties. To quantify this, it is appropriate to randomize the network and test the hypothesis that the…
The analysis of non-equilibrium steady states of biochemical reaction networks relies on finding the configurations of fluxes and chemical potentials satisfying stoichiometric (mass balance) and thermodynamic (energy balance) constraints.…
Motivation: Protein interactions are fundamental building blocks of biochemical reaction systems underlying cellular functions. The complexity and functionality of such systems emerge not from the protein interactions themselves but from…
Graph theory is increasingly commonly utilised in genetics, proteomics and neuroimaging. In such fields, the data of interest generally constitute weighted graphs. Analysis of such weighted graphs often require the integration of…
Coexpression of genes or, more generally, similarity in the expression profiles poses an unsurmountable obstacle to inferring the gene regulatory network (GRN) based solely on data from DNA microarray time series. Clustering of genes with…
Computer experiments are performed to investigate why protein contact networks (networks induced by spatial contacts between amino acid residues of a protein) do not have shorter average shortest path lengths in spite of their importance to…
Human micro RNAs (miRNAs) target about 90% of the coding genes and form a complex regulatory network. We study the community structure of the miRNA co-target network considering miRNAs as the nodes which are connected by weighted links. The…
Numerous transcription factors self-assemble into different order oligomeric species in a way that is actively regulated by the cell. Until now, no general functional role has been identified for this widespread process. Here we capture the…
Can we objectively distinguish chemical systems that are able to process meaningful information from those that are not suitable for information processing? Here, we present a formal method to assess the semantic capacity of a chemical…
The question of the onset of the homochirality on prebiotic Earth still remains a fundamental question in the quest for the origin of life. Recent works in this field introduce the concept of recycling, rather than the traditional open-flow…
The response of complex networks to perturbations is of utmost importance in areas as diverse as ecosystem management, emergency response, and cell reprogramming. A fundamental property of networks is that the perturbation of one node can…