Related papers: Spiky oscillations in NF-kB signalling
Oscillatory activities are widely observed in specific frequency bands of recorded field potentials in different brain regions, and play critical roles in processing neural information. Understanding the structure of these oscillatory…
For cellular biochemical reaction systems where the numbers of molecules is small, significant noise is associated with chemical reaction events. This molecular noise can give rise to behavior that is very different from the predictions of…
Gene products (RNAs, proteins) often occur at low molecular counts inside individual cells, and hence are subject to considerable random fluctuations (noise) in copy number over time. Not surprisingly, cells encode diverse regulatory…
Neural oscillations are electrical activities of the brain measurable at different frequencies. This paper studies the interaction between the fast and slow processes in the brain. We recorded signals intracranially from the simple Wistar…
It has long been debated whether information in the brain is coded at the rate of neuronal spiking or at the precise timing of single spikes. Although this issue is essential to the understanding of neural signal processing, it is not…
K-core percolation is a fundamental dynamical process in complex networks with applications that span numerous real-world systems. Earlier studies focus primarily on random networks without spatial constraints and reveal intriguing…
A ubiquitous building block of signaling pathways is a cycle of covalent modification (e.g., phosphorylation and dephosphorylation in MAPK cascades). Our paper explores the kind of information processing and filtering that can be…
Gene expression is a biochemical process, where stochastic binding and un-binding events naturally generate fluctuations and cell-to-cell variability in gene dynamics. These fluctuations typically have destructive consequences for proper…
We study the emergent dynamics of a network of synaptically coupled slow-fast oscillators. Synaptic coupling provides a network-level positive feedback mechanism that cooperates with cellular-level positive feedback to ignite in-phase…
In the simplest view of transcriptional regulation, the expression of a gene is turned on or off by changes in the concentration of a transcription factor (TF). We use recent data on noise levels in gene expression to show that it should be…
It often is emphasized that gene expression is noisy. A seemingly contradictory view is that control mechanisms have been optimized to squeeze as much information as possible out of a limited number of molecules. Here we revisit these…
Determining how synaptic coupling within and between regions is modulated during sensory processing is an important topic in neuroscience. Electrophysiological recordings provide detailed information about neural spiking but have…
Ring topologies of repressing genes have qualitatively different long-term dynamics if the number of genes is odd (they oscillate) or even (they exhibit bistability). However, these attractors may not fully explain the observed behavior in…
The coding properties of cells with different types of receptive fields have been studied for decades. ON-type neurons fire in response to positive fluctuations of the time-dependent stimulus, whereas OFF cells are driven by negative…
The computation of rank ordering plays a fundamental role in cognitive tasks and offers a basic building block for computing arbitrary digital functions. Spiking neural networks have been demonstrated to be capable of identifying the…
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…
The entrainment (or locking) phenomenon, by which an oscillator adapts its natural rhythm to an external periodic signal, is well-known in physics, chemistry, biology, etc.; however, controlling an stochastic nonlinear system with a…
Timing is essential for many cellular processes, from cellular responses to external stimuli to the cell cycle and circadian clocks. Many of these processes are based on gene expression. For example, an activated gene may be required to…
Biochemical oscillation systems often consist of negative feedback loops with repressive transcription regulation. Such systems have distinctive characteristics in comparison with ordinary chemical systems: i) the numbers of molecules…
Our knowledge of the sensory world is encoded by neurons in sequences of discrete, identical pulses termed action potentials or spikes. There is persistent controversy about the extent to which the precise timing of these spikes is relevant…