分子网络
A bioinformatics platform is introduced aimed at identifying models of disease-specific pathways, as well as a set of network measures that can quantify changes in terms of global structure or single link disruptions.The approach integrates…
In vertebrates, olfactory sensory neurons choose only one olfactory receptor to produce out of ~2000 possibilities. The mechanism for how this singular receptor expression occurs is unknown. Here we propose a mechanism that can…
Motivation: Usefulness of analysis derived from Affymetrix microarrays depends largely upon the reliability of files describing the correspondence between probe sets, genes and transcripts. In particular, in case a gene is targeted by two…
We show that certain non-linear dynamical systems with non-linearities in the form of Hill functions, can be approximated by piecewise linear dynamical systems. The resulting piecewise systems have closed form solutions that can be used to…
This paper is a mathematical study of some aspects of the signalling pathway leading to the activation of the transcription factor NFAT (nuclear factor of activated T cells). Activation takes place by dephosphorylation at multiple sites.…
Cells are regulated by networks of controllers having many targets, and targets affected by many controllers, but these "many-to-many" combinatorial control systems are poorly understood. Here we analyze distinct cellular networks…
Cells in a developing embryo have no direct way of "measuring" their physical position. Through a variety of processes, however, the expression levels of multiple genes come to be correlated with position, and these expression levels thus…
The phenotype of any organism on earth is, in large part, the consequence of interplay between numerous gene products encoded in the genome, and such interplay between gene products affects the evolutionary fate of the genome itself through…
Negative and positive transcriptional feedback loops are present in natural and synthetic genetic oscillators. A single gene with negative transcriptional feedback needs a time delay and sufficiently strong nonlinearity in the transmission…
We report on a case of autocatalytic feedback in a template directed synthesis of a self-complementary hexa-PNA from two trimeric building blocks. The course of the reaction was monitored in the presence of increasing initial concentrations…
Interaction networks, consisting of agents linked by their interactions, are ubiquitous across many disciplines of modern science. Many methods of analysis of interaction networks have been proposed, mainly concentrating on node degree…
Variability in the tumorigenic potential among cancer cells within a tumor population is an unresolved fundamental issue in cancer biology. It is important to know whether cancer cells with higher tumorigenic potential, such as cancer stem…
Berg and Purcell [Biophys. J. 20, 193 (1977)] calculated how the accuracy of concentration sensing by single-celled organisms is limited by noise from the small number of counted molecules. Here we generalize their results to the sensing of…
We consider the problem of inferring the unknown parameters of a stochastic biochemical network model from a single measured time-course of the concentration of some of the involved species. Such measurements are available, e.g., from…
Allosteric drugs are increasingly used because they produce fewer side effects. Allosteric signal propagation does not stop at the 'end' of a protein, but may be dynamically transmitted across the cell. Here, we propose that the concept of…
We define catalytic networks as chemical reaction networks with an essentially catalytic reaction pathway: one which is on in the presence of certain catalysts and off in their absence. We show that examples of catalytic networks include…
We present a general computational theory of cancer and its developmental dynamics. The theory is based on a theory of the architecture and function of developmental control networks which guide the formation of multicellular organisms.…
Binding and unbinding of ligands to specific sites of a macromolecule are one of the most elementary molecular interactions inside the cell that embody the computational processes of biological regulations. The interaction between…
The large-scale shape and function of metabolic networks are intriguing topics of systems biology. Such networks are on one hand commonly regarded as modular (i.e. built by a number of relatively independent subsystems), but on the other…
We propose the concepts of distributed robustness and r-robustness, well adapted to functional genetics. Then we discuss the robustness of the relaxation time using a chemical reaction description of genetic and signalling networks. First,…