分子网络
Predicting protein interactions is one of the more interesting challenges of the post-genomic era. Many algorithms address this problem as a binary classification problem: given two proteins represented as two vectors of features, predict…
Background: A classical problem in metabolic design is to maximize the production of desired compound in a given chemical reaction network by appropriately directing the mass flow through the network. Computationally, this problem is…
Robust advances in interactome analysis demand comprehensive, non-redundant and consistently annotated datasets. By non-redundant, we mean that the accounting of evidence for every interaction should be faithful: each independent…
Cooperative interactions among sensory receptors provide a general mechanism to increase the sensitivity of signal transduction. In particular, bacterial chemotaxis receptors interact cooperatively to produce an ultrasensitive response to…
Theoretical frameworks to estimate the tolerance of metabolic networks to various failures are important to evaluate the robustness of biological complex systems in systems biology. In this paper, we focus on a measure for robustness in…
Oscillation has an important role in bio-dynamical systems such as circadian rhythms and eukaryotic cell cycle. John Tyson et. al. in Nature Review Mol Cell Biol 2008 examined a limited number of network topologies consisting of three nodes…
We consider a chemical reaction network governed by mass action kinetics and composed of N different species which can reversibly form heterodimers. A fast iterative algorithm is introduced to compute the equilibrium concentrations of such…
Understanding relationship between noisy dynamics and biological network architecture is a fundamentally important question, particularly in order to elucidate how cells encode and process information. We analytically and numerically…
Our main tenet argues that the primary role of positive thymic selection and the resulting T cell population is the maintenance of a homeostatic equilibrium with self MHC-self peptide complexes. The homeostatic T cell repertoire can…
Many cellular functions are based on the rhythmic organization of biological processes into self-repeating cascades of events. Some of these periodic processes, such as the cell cycles of several species, exhibit conspicuous irregularities…
Key insights in molecular biology, such as enzyme kinetics, protein allostery and gene regulation emerged from quantitative analysis based on time-scale separation, allowing internal complexity to be eliminated and resulting in the…
Many biochemical processes can successfully be described by dynamical systems allowing some form of switching when, depending on their initial conditions, solutions of the dynamical system end up in different regions of state space…
Phosphorelays are a class of signaling mechanisms used by cells to respond to changes in their environment. Phosphorelays (of which two-component systems constitute a special case) are particularly abundant in prokaryotes and have been…
In complex systems, feedback loops can build intricate emergent phenomena, so that a description of the whole system cannot be easily derived from the properties of the individual parts. Here we propose that inter-molecular frustration…
Mass action type deterministic kinetic models of ion channels are usually constructed in such a way as to obey the principle of detailed balance (or, microscopic reversibility) for two reasons: first, the authors aspire to have models…
We use the Litvinov-Maslov correspondence principle to reduce and hybridize networks of biochemical reactions. We apply this method to a cell cycle oscillator model. The reduced and hybridized model can be used as a hybrid model for the…
Cellular behavior is governed by gene regulatory processes that are intrinsically dynamic and nonlinear, and are subject to non-negligible amounts of random fluctuations. Such conditions are ubiquitous in physical systems, where they have…
We derive a convex optimization problem on a steady-state nonequilibrium network of biochemical reactions, with the property that energy conservation and the second law of thermodynamics both hold at the problem solution. This suggests a…
We describe a large class of chemical reaction networks, those endowed with a subtle structural property called concordance. We show that the class of concordant networks coincides precisely with the class of networks which, when taken with…
Metabolism is a fascinating cell machinery underlying life and disease and genome-scale reconstructions provide us with a captivating view of its complexity. However, deciphering the relationship between metabolic structure and function…