相关论文: Metabolic plasticity in synthetic lethal mutants: …

We unravel how functional plasticity and redundancy are essential mechanisms underlying the ability to survive of metabolic networks. We perform an exhaustive computational screening of synthetic lethal reaction pairs in Escherichia coli in…

Recent genomic analyses on the cellular metabolic network show that reaction flux across enzymes are diverse and exhibit power-law behavior in its distribution. While one may guess that the reactions with larger fluxes are more likely to be…

Synthetic lethal reaction/gene-sets are sets of reactions/genes where only the simultaneous removal of all reactions/genes in the set abolishes growth of an organism. In silico, synthetic lethal sets can be identified by simulating the…

Synthetic lethality (SL) is a promising concept for novel discovery of anti-cancer drug targets. However, wet-lab experiments for detecting SLs are faced with various challenges, such as high cost, low consistency across platforms or cell…

Synthetic lethality refers to a combination of two or more genetic events (typically affecting different genes) in which the co-occurrence of the events results in cell or organismal lethality, but the cell or organism remains viable when…

Synthetic lethality, the finding that the simultaneous knockout of two or more individually non-essential genes leads to cell or organism death, has offered a systematic framework to explore cellular function, and also offered therapeutic…

Biological networks have evolved to be highly functional within uncertain environments while remaining extremely adaptable. One of the main contributors to the robustness and evolvability of biological networks is believed to be their…

Local perturbations of individual metabolic reactions may result in different levels of lethality, depending on their roles in metabolism and the size of subsequent cascades induced by their failure. Moreover, essentiality of individual…

Metabolic reactions of single-cell organisms are routinely observed to become dispensable or even incapable of carrying activity under certain circumstances. Yet, the mechanisms as well as the range of conditions and phenotypes associated…

An important goal of medical research is to develop methods to recover the loss of cellular function due to mutations and other defects. Many approaches based on gene therapy aim to repair the defective gene or to insert genes with…

The ubiquity of modules in biological networks may result from an evolutionary benefit of a modular organization. For instance, modularity may increase the rate of adaptive evolution, because modules can be easily combined into new…

Metabolic networks have two properties that are generally regarded as unrelated: One, they have metabolic reactions whose single knockout is lethal for the organism, and two, they have correlated sets of reactions forming functional…

Dynamics maintaining diversity of cell types in a multi-cellular system are studied in relationship with the plasticity of cellular states. By adopting a simple theoretical framework for intra-cellular chemical reaction dynamics with…

Under low concentrations of antibiotics causing DNA damage, \textit{Escherichia coli} bacteria can trigger stochastically a stress response known as the SOS response. While the expression of this stress response can make individual cells…

The methylation of DNA regulates gene expression. On cell division the methylation state of the DNA is typically inherited from parent to daughter cells. While the chemical bond between the methyl group and the DNA is very strong, changes…

Translating metabolic networks into dynamic models is difficult if kinetic constants are unknown. Structural Kinetic Modelling (SKM) replaces reaction elasticities by independent random numbers. Here I propose a variant that accounts for…

Metabolic networks play a crucial role in biology since they capture all chemical reactions in an organism. While there are networks of high quality for many model organisms, networks for less studied organisms are often of poor quality and…

Dynamics maintaining diversity of cell types in a multi-cellular system are studied in relationship with the plasticity of cellular states. First, we introduce a new theoretical framework, reaction-diffusion system on `chemical species…

The objective of the paper is to identify laws and mechanisms that allow the creation of more order from disorder using natural means i.e., without the help of conscious beings. While this is not possible for the collection of all dynamical…

Synthetic control (SC) methods have gained rapid popularity in economics recently, where they have been applied in the context of inferring the effects of treatments on standard continuous outcomes assuming linear input-output relations. In…