Related papers: Optimizing information flow in small genetic netwo…
The dynamics of gene regulatory networks is governed by the interaction between deterministic biochemical reactions and molecular noise. To understand how gene regulatory networks process information during cell state transitions, we study…
Positive feedback regulation is ubiquitous in cell signaling networks, often leading to binary outcomes in response to graded stimuli. However, the role of such feedbacks in clustering, and in spatial spreading of activated molecules, has…
The functioning of a living cell is largely determined by the structure of its regulatory network, comprising non-linear interactions between regulatory genes. An important factor for the stability and evolvability of such regulatory…
Living organisms must respond to environmental changes. Generally, accurate and rapid responses are provided by simple, unidirectional networks that connect inputs with outputs. Besides accuracy and speed, biological responses should also…
Identity, response to external stimuli, and spatial architecture of a living system are central topics of molecular biology. Presently, they are largely seen as a result of the interplay between a gene repertoire and the regulatory…
We show how to construct a reduced description of interacting genes in noisy, small regulatory networks using coupled binary "spin" variables. Treating both the protein number and gene expression state variables stochastically and on equal…
Experiments show that the movement of eukaryotic cells is regulated by a process of phase separation of two competing enzymes on the cell membrane, that effectively amplifies shallow external gradients of chemical attractant. Notably, the…
Understanding the rules underlying organismal development is a major unsolved problem in biology. Each cell in a developing organism responds to signals in its local environment by dividing, excreting, consuming, or reorganizing, yet how…
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…
In order to respond to environmental signals, cells often use small molecular circuits to transmit information about their surroundings. Recently, motivated by concrete examples in signaling and gene regulation, a body of work has focused…
Cells use temporal dynamical patterns to transmit information via signaling pathways. As optimality with respect to the environment plays a fundamental role in biological systems, organisms have evolved optimal ways to transmit information.…
Understanding the relationship between spontaneous stochastic fluctuations and the topology of the underlying gene regulatory network is of fundamental importance for the study of single-cell stochastic gene expression. Here by solving the…
The propagation of noise through parallel regulatory pathways is a characteristic feature of feed-forward loops in genetic networks. Although the contributions of the direct and indirect regulatory pathways of feed-forward loops to output…
Many biological regulatory systems process signals out of steady state and respond with a physiological delay. A simple model of regulation which respects these features shows how the ability of a delayed output to transmit information is…
Stochasticity (or noise) at cellular and molecular levels has been observed extensively as a universal feature for living systems. However, how living systems deal with noise while performing desirable biological functions remains a major…
Recent massive numerical simulations have shown that the response of a "stochastic resonator" is enhanced as a consequence of spatial coupling. Similar results have been analytically obtained in a reaction-diffusion model, using…
Gene regulatory networks must relay information from extracellular signals to downstream genes in an efficient, timely and coherent manner. Many complex functional tasks such as the immune response require system-wide broadcasting of…
The spatial structure of the cell is highly organized at all levels: from small complexes and assemblies, to local nano- and micro-clusters, to global, micrometer scales across and between cells. We suggest that this multiscale spatial cell…
Populations of cells regulate gene expression in response to external signals, but their ability to make reliable collective decisions is limited by both intrinsic noise in molecular signaling and variability between individual cells. In…
Exchange of molecules allows cells to exchange information. How robust is the information to changes in cell parameters? We use a mapping between the stochastic dynamics of two cells sharing a stimulatory molecule, and parameters akin to an…