相关论文: The adaptive filter of the yeast galactose pathway
The yeast galactose network has provided many insights into how eukaryotic gene circuits regulate metabolic function. However, there is currently no consensus model of the network that incorporates protein dilution due to cellular growth.…
The galactose network is a complex system responsible for galactose metabolism. It has been extensively studied experimentally and mathematically at the unicellular level to broaden our understanding of its regulatory mechanisms at higher…
The Leloir galactose utilization or GAL pathway of budding yeasts, including that of the baker's yeast Saccharomyces cerevisiae and the opportunistic human pathogen Candida albicans, breaks down the sugar galactose for energy and biomass…
The molecular network in an organism consists of transcription/translation regulation, protein-protein interactions/modifications and a metabolic network, together forming a system that allows the cell to respond sensibly to the multiple…
Translation is a key step in the synthesis of proteins. Accordingly, cells have evolved an intricate array of control mechanisms to regulate this process. By constructing a multi-component mathematical framework for translation we uncover…
The mating pathway in \emph{Saccharomyces cerevisiae} is one of the best understood signal transduction pathways in eukaryotes. It transmits the mating signal from plasma membrane into the nucleus through the G-protein coupled receptor and…
Gene regulatory networks constitute the first layer of the cellular computation for cell adaptation and surveillance. In these webs, a set of causal relations is built up from thousands of interactions between transcription factors and…
Gene expression dynamics satisfying given input-output relationships were investigated by evolving the networks for an optimal response. We found three types of networks and corresponding dynamics, depending on the sensitivity of gene…
Synthesizing high-fidelity complex images from text is challenging. Based on large pretraining, the autoregressive and diffusion models can synthesize photo-realistic images. Although these large models have shown notable progress, there…
We investigate the structural and dynamical properties of the transcriptional regulatory network of the yeast {\it Saccharomyces cerevisiae} and compare it with two unbiased ensembles: one obtained by reshuffling the edges and the other…
The biological processes that execute complex multiple functions, such as cell cycle, must ensure the order of sequential events and keep the dynamic robustness against various fluctuations. Here, we examine the dynamic mechanism and the…
BACKGROUND. Signal recognition and information processing is a fundamental cellular function, which in part involves comprehensive transcriptional regulatory (TR) mechanisms carried out in response to complex environmental signals in the…
The chemotactic pathway allows bacteria to respond and adapt to environmental changes, by tuning the tumbling and running motions that are due to clockwise and counterclockwise rotations of their flagella. The pathway is tightly regulated…
Gene regulatory dynamics is governed by molecular processes and therefore exhibits an inherent stochasticity. However, for the survival of an organism it is a strict necessity that this intrinsic noise does not prevent robust functioning of…
Generative Adversarial Networks (GANs) represent an attractive and novel approach to generate realistic data, such as genes, proteins, or drugs, in synthetic biology. Here, we apply GANs to generate synthetic DNA sequences encoding for…
Gene expression is a stochastic process governed by the presence of specific transcription factors. Here we study the dynamics of gene expression in the presence of feedback, where a gene regulates its own expression. The nonlinear coupling…
We present a comparative analysis of large-scale topological and evolutionary properties of transcription networks in three species, the two distant bacteria E. coli and B. subtilis, and the yeast S. cerevisiae. The study focuses on the…
The receptive fields of simple cells in the visual cortex can be understood as linear filters. These filters can be modelled by Gabor functions, or by Gaussian derivatives. Gabor functions can also be combined in an `energy model' of the…
Construction of synthetic genetic networks requires the assembly of DNA fragments encoding functional biological parts in a defined order. Yet this may become a time-consuming procedure. To address this technical bottleneck, we have created…
A substantial focus of research in molecular biology are gene regulatory networks: the set of transcription factors and target genes which control the involvement of different biological processes in living cells. Previous statistical…