Related papers: Intracellular delay limits cyclic changes in gene …
Modern time series gene expression and other omics data sets have enabled unprecedented resolution of the dynamics of cellular processes such as cell cycle and response to pharmaceutical compounds. In anticipation of the proliferation of…
Intrinsic transcriptional noise induced by operator fluctuations is investigated with a simple spin like stochastic model. The effects of transcriptional fluctuations in protein synthesis is probed by coupling transcription and translation…
All stem cell fate transitions, including the metabolic reprogramming of stem cells and the somatic reprogramming of fibroblasts into pluripotent stem cells, can be understood from a unified theoretical model of cell fates. Each cell fate…
It is well-known that gene activation/deactivation dynamics may be a major source of randomness in genetic networks, also in the case of large concentrations of the transcription factors. In this work, we investigate the effect of realistic…
Genes are connected in complex networks of interactions where often the product of one gene is a transcription factor that alters the expression of another. Many of these networks are based on a few fundamental motifs leading to switches…
Gene regulatory networks, i.e. DNA segments in a cell which interact with each other indirectly through their RNA and protein products, lie at the heart of many important intracellular signal transduction processes. In this paper we analyse…
Recent whole genome polymerase binding assays have shown that a large proportion of unexpressed genes have pre-assembled RNA pol II transcription initiation complex stably bound to their promoters. Some such promoter proximally paused genes…
Transcription factors are proteins that regulate gene activity by activating or repressing gene transcription. A special class of transcriptional repressors operates via a short-range mechanism, making local DNA regions inaccessible to…
Synaptic, dendritic and single-cell kinetics generate significant time delays that shape the dynamics of large networks of spiking neurons. Previous work has shown that such effective delays can be taken into account with a rate model…
Existence of a new type of oscillating synchronization that oscillates between three different types of synchronizations (anticipatory, complete and lag synchronizations) is identified in unidirectionally coupled nonlinear time-delay…
We derive exact solutions of simplified models for the temporal evolution of the protein concentration within a cell population arbitrarily far from the stationary state. We show that monitoring the dynamics can assist in modeling and…
We analyze the stabilization of unstable steady states by delayed feedback control with a periodic time-varying delay in the regime of a high-frequency modulation of the delay. The average effect of the delayed feedback term in the control…
In 2000, Elowitz and Leibler introduced the repressilator--a synthetic gene circuit with three genes that cyclically repress transcription of the next gene--as well as a corresponding mathematical model. Experimental data and model…
In this research, we present a generalized quasispecies model in which population growth is governed by an arbitrary nonlinear function incorporating time delays. We begin by demonstrating that, under the constant population constraint, the…
We train a neural network to predict distributional responses in gene expression following genetic perturbations. This is an essential task in early-stage drug discovery, where such responses can offer insights into gene function and inform…
This paper is devoted to the study of the stability of limit cycles of a nonlinear delay differential equation with a distributed delay. The equation arises from a model of population dynamics describing the evolution of a pluripotent stem…
From the response to external stimuli to cell division and death, the dynamics of living cells is based on the expression of specific genes at specific times. The decision when to express a gene is implemented by the binding and unbinding…
Eukaryotic DNA replication follows a specific temporal program, with some genomic regions consistently replicating earlier than others, yet what determines this program is largely unknown. Highly transcribed regions have been observed to…
Quasispecies theory provides the conceptual and theoretical bases for describing the dynamics of biological information of replicators subject to large mutation rates. This theory, initially conceived within the framework of prebiotic…
The regulation of cellular function is often controlled at the level of gene transcription. Such genetic regulation usually consists of interacting networks, whereby gene products from a single network can act to control their own…