分子网络
We have developed a coarse-grained formulation for modeling the dynamic behavior of cells quantitatively, based on stochasticity and heterogeneity, rather than on biochemical reactions. We treat each reaction as a continuous-time stochastic…
Canalization is a classic concept in Developmental Biology that is thought to be an important feature of evolving systems. In a Boolean network it is a form of network robustness in which a subset of the input signals control the behavior…
We discuss a method of approximate model reduction for networks of biochemical reactions. This method can be applied to networks with polynomial or rational reaction rates and whose parameters are given by their orders of magnitude. In…
A statistically principled way of conducting weighted network analysis is still lacking. Comparison of different populations of weighted networks is hard because topology is inherently dependent on wiring cost, where cost is defined as the…
Here we introduce a new design framework for synthetic biology that exploits the advantages of Bayesian model selection. We will argue that the difference between inference and design is that in the former we try to reconstruct the system…
Cells use genetic switches to shift between alternate gene expression states, e.g., to adapt to new environments or to follow a developmental pathway. Here, we study the dynamics of switching in a generic-feedback on/off switch. Unlike…
A wealth of new research has highlighted the critical roles of small RNAs (sRNAs) in diverse processes such as quorum sensing and cellular responses to stress. The pathways controlling these processes often have a central motif comprising…
In recent years experiments have demonstrated that living cells can measure low chemical concentrations with high precision, and much progress has been made in understanding what sets the fundamental limit to the precision of chemical…
Target identification, one of the steps of drug discovery, aims at identifying biomolecules whose function should be therapeutically altered in order to cure the considered pathology. This work proposes an algorithm for in silico target…
Double phosphorylation of protein kinases is a common feature of signalling cascades. This motif may reduce cross-talk between signalling pathways, as the second phosphorylation site allows for proofreading, especially when phosphorylation…
Complexes of physically interacting proteins constitute fundamental functional units responsible for driving biological processes within cells. A faithful reconstruction of the entire set of complexes is therefore essential to understand…
Integrin signaling regulates cell migration and plays a pivotal role in developmental processes and cancer metastasis. Integrin signaling has been studied extensively and much data is available on pathway components and interactions. Yet…
We study the spatio-temporal dynamics of the generalized repressilator, a system of coupled repressing genes arranged in a directed ring topology, and give analytical conditions for the emergence of a cascade of unstable periodic orbits…
Complex networks can often be decomposed into less complex sub-networks whose structures can give hints about the functional organization of the network as a whole. However, these structural motifs can only tell one part of the functional…
Gene regulation involves a hierarchy of events that extend from specific protein-DNA interactions to the combinatorial assembly of nucleoprotein complexes. The effects of DNA sequence on these processes have typically been studied based…
Michaelis-Menten equation is a basic equation of enzyme kinetics and gives an acceptable approximation of real chemical reaction processes. Analyzing the derivation of this equation yields the fact that its good performance of approximating…
Clinical studies have indicated that in malignant surveillances fluctuations in the population of certain effector T-cell repertoire become suppressed. Motivated by such observations and in an attempt to quantify adaptive human response to…
This paper addresses the statistical significance of structures in random data: Given a set of vectors and a measure of mutual similarity, how likely does a subset of these vectors form a cluster with enhanced similarity among its elements?…
Often questions arise about old or extinct networks. What proteins interacted in a long-extinct ancestor species of yeast? Who were the central players in the Last.fm social network 3 years ago? Our ability to answer such questions has been…
According to recent experimental evidence, the architecture of a promoter, defined as the number, strength and regulatory role of the operators that control the promoter, plays a major role in determining the level of cell-to-cell…