相关论文: Two Cellular Resource Based Models Linking Growth …

Experiments in recent years have vividly demonstrated that gene expression can be highly stochastic. How protein concentration fluctuations affect the growth rate of a population of cells, is, however, a wide open question. We present a…

Genotype-to-phenotype maps and the related fitness landscapes that include epistatic interactions are difficult to measure because of their high dimensional structure. Here we construct such a map using the recently collected corpora of…

Gene regulatory networks (GRNs) play a central role in cellular decision-making. Understanding their structure and how it impacts their dynamics constitutes thus a fundamental biological question. GRNs are frequently modeled as Boolean…

Cell division is a process that involves many biochemical steps and complex biophysical mechanisms. To simplify the understanding of what triggers cell division, three basic models that subsume more microscopic cellular processes associated…

Recent experiments have supported the Adder model for E. coli division control. This model posits that bacteria grow, on average, a fixed size before division. It also predicts decorrelation between the noise in the added size and the size…

Cell size is a fundamental determinant of cellular physiology, influencing processes such as growth, division, and function. In this study, we develop a segmented mathematical framework to investigate how different control mechanisms…

Organisms across all domains of life regulate the size of their cells. However, the means by which this is done is poorly understood. We study two abstracted "molecular" models for size regulation: inhibitor dilution and initiator…

Genetic Programming is an evolutionary algorithm that generates computer programs, or mathematical expressions, to solve complex problems. In this Guide, we demonstrate how to use Genetic Programming to develop surrogate models to mitigate…

Promoters and enhancers are cis-regulatory elements (CREs), DNA sequences that bind transcription factor (TF) proteins to up- or down-regulate target genes. Decades-long efforts yielded TF-DNA interaction models that predict how strongly an…

Biological systems are promising substrates for computation because they naturally process environmental information through complex internal dynamics. In this study, we investigate whether bacterial metabolic models can act as physical…

Cell formation is a critical step in the design of cellular manufacturing systems. Recently, it was tackled using a cut-based-graph-partitioning model. This model meets real-life production systems requirements as it uses the actual amount…

Feed-forward dynamics, which is well-known to have several important implications in nonlinear dynamical systems, frequently occurs in gene expression motifs, and has been well explored experimentally and mathematically. However, dependency…

The rate at which individual bacterial cells grow depends on the concentrations of cellular components such as ribosomes and proteins. These concentrations continuously fluctuate over time and are inherited from mother to daughter cells,…

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.…

Growth in bacterial populations generally depends on the environment (availability and quality of nutrients, presence of a toxic inhibitor, product inhibition..). Here, we build a model to describe the action of a bacteriostatic antibiotic,…

Understanding the organization of reaction fluxes in cellular metabolism from the stoichiometry and the topology of the underlying biochemical network is a central issue in systems biology. In this task, it is important to devise reasonable…

Biological genotypes do not code directly for phenotypes; developmental physiology is the control layer that separates genomes from capacities ascertained by selection. A key aspect is competency, as cells are not a passive material but…

Newly-translated glycoproteins in the endoplasmic reticulum (ER) often undergo cycles of chaperone binding and release in order to assist in folding. Quality control is required to distinguish between proteins that have completed native…

We study the evolution of stars that may be the progenitors of long-soft gamma-ray burst (GRBs) -- rotating naked helium stars presumed to have lost their envelopes to winds or companions. Our aim is to investigate the formation and…

Despite recent advances in our ability to detect adaptive evolution involving the cis-regulation of gene expression, our knowledge of the molecular mechanisms underlying these adaptations has lagged far behind. Across all model organisms…