相关论文: Attenuation Regulation as a Term Rewriting System

Gene assembly is an intricate biological process that has been studied formally and modeled through string and graph rewriting systems. Recently, a restriction of the general (intramolecular) model, called simple gene assembly, has been…

We consider a simplified model for gene regulation, where gene expression is regulated by transcription factors (TFs), which are single proteins or protein complexes. Proteins are in turn synthesised from expressed genes, creating a…

We present a novel classification-based method for learning to predict gene regulatory response. Our approach is motivated by the hypothesis that in simple organisms such as Saccharomyces cerevisiae, we can learn a decision rule for…

Current biocomputing approaches predominantly rely on engineered circuits with fixed logic, offering limited stability and reliability under diverse environmental conditions. Here, we use the GRNN framework introduced in our previous work…

Term rewriting has a significant presence in various areas, not least in automated theorem proving where it is used as a proof technique. Many theorem provers employ specialised proof tactics for rewriting. This results in an interleaving…

Characterization of pluripotent states, in which cells can both self-renew and differentiate, and the irreversible loss of pluripotency are important research areas in developmental biology. In particular, an understanding of these…

Antiterminators are essential components of bacterial transcriptional regulation, allowing the control of gene expression in response to fluctuating environmental conditions. Among them, RNA-binding antiterminator proteins play a major role…

The formation of DNA loops by proteins and protein complexes that bind at distal DNA sites plays a central role in many cellular processes, such as transcription, recombination, and replication. Here we review the basic thermodynamic…

Genetic algorithms are a well-known example of bio-inspired heuristic methods. They mimic natural selection by modeling several operators such as mutation, crossover, and selection. Recent discoveries about Epigenetics regulation processes…

Rewriting is a formalism widely used in computer science and mathematical logic. The classical formalism has been extended, in the context of functional languages, with an order over the rules and, in the context of rewrite based languages,…

Cellular phenotypes are determined by the dynamical activity of networks of co-regulated genes. Elucidating such networks is crucial for the understanding of normal cell physiology as well as for the dissection of complex pathologic…

Gene regulation in higher eukaryotes involves a complex interplay between the gene proximal promoter and distal genomic elements (such as enhancers) which work in concert to drive spatio-temporal expression. The experimental…

Many biological processes have been the source of inspiration for heuristic methods that generate high-quality solutions to solve optimization and search problems. This thesis presents an epigenetic technique for Evolutionary Algorithms,…

In medical fields, text classification is one of the most important tasks that can significantly reduce human workload through structured information digitization and intelligent decision support. Despite the popularity of learning-based…

We study the termination problem for probabilistic term rewrite systems. We prove that the interpretation method is sound and complete for a strengthening of positive almost sure termination, when abstract reduction systems and term rewrite…

Expression of cellular genes is regulated by binding of transcription factors to their promoter, either activating or inhibiting transcription of a gene. Particularly interesting is the case when the expressed protein regulates its own…

Gene regulation is a complex process involving the role of several genomic elements which work in concert to drive spatio-temporal expression. The experimental characterization of gene regulatory elements is a very complex and…

On the topic of probabilistic rewriting, there are several works studying both termination and confluence of different systems. While working with a lambda calculus modelling quantum computation, we found a system with probabilistic…

Gene expression analysis aims at identifying the genes able to accurately predict biological parameters like, for example, disease subtyping or progression. While accurate prediction can be achieved by means of many different techniques,…

Small non-coding RNAs can exert significant regulatory activity on gene expression in bacteria. In recent years, substantial progress has been made in understanding bacterial gene expression by sRNAs. However, recent findings that…