相关论文: Attenuation Regulation as a Term Rewriting System
Small regulatory RNAs (sRNAs) are short non-coding RNAs in bacteria capable of post-transcriptional regulation. sRNAs have recently gained attention as tools in basic and applied sciences for example to fine-tune genetic circuits or…
Bigraphs are a versatile modelling formalism that allows easy expression of placement and connectivity relations in a graphical format. System evolution is user defined as a set of rewrite rules. This paper presents a practical, yet…
We propose a generalized version of context-sensitivity in term rewriting based on the notion of "forbidden patterns". The basic idea is that a rewrite step should be forbidden if the redex to be contracted has a certain shape and appears…
This paper gives an overview of the use of control systems engineering in synthetic biology, motivated by applications such as cell therapy and cell fate reprogramming for regenerative medicine. A ubiquitous problem in these and other…
In our previous work, we introduced the rule-based Bayesian Regression, a methodology that leverages two concepts: (i) Bayesian inference, for the general framework and uncertainty quantification and (ii) rule-based systems for the…
We consider the problem of predicting gene expressions from DNA sequences. A key challenge of this task is to find the regulatory elements that control gene expressions. Here, we introduce Seq2Exp, a Sequence to Expression network…
The Human Genome Project has led to an exponential increase in data related to the sequence, structure, and function of biomolecules. Bioinformatics is an interdisciplinary research field that primarily uses computational methods to analyze…
We discuss recent developments in the modeling of negative autoregulated genetic networks. In particular, we consider the temporal evolution of the population of mRNA and proteins in simple networks using rate equations. In the limit of low…
A typed model of strategic term rewriting is developed. The key innovation is that generic traversal is covered. To this end, we define a typed rewriting calculus S'_{gamma}. The calculus employs a many-sorted type system extended by…
A transversal topic of my research has been the development and application of computational methods for DNA sequence analysis. The methods I have been developing aim at improving our understanding of the regulation processes happening in…
The solution of high-dimensional inference and prediction problems in computational biology is almost always a compromise between mathematical theory and practical constraints such as limited computational resources. As time progresses,…
Proof terms are syntactic expressions that represent computations in term rewriting. They were introduced by Meseguer and exploited by van Oostrom and de Vrijer to study equivalence of reductions in (left-linear) first-order term rewriting…
Regulatory genes called small RNAs (sRNAs) are known to play critical roles in cellular responses to changing environments. For several sRNAs, regulation is effected by coupled stoichiometric degradation with messenger RNAs (mRNAs). The…
We present a new syntactic criterion for the automatic detection of non-termination in an abstract setting that encompasses a simplified form of term rewriting and logic programming.
Structural and dynamical fingerprints of evolutionary optimization in biological networks are still unclear. We here analyze the dynamics of genetic regulatory networks responsible for the regulation of cell cycle and cell differentiation…
To survive environmental conditions, cells transcribe their response activities into encoded mRNA sequences in order to produce certain amounts of protein concentrations. The external conditions are mapped into the cell through the…
Rewriting is a formalism widely used in computer science and mathematical logic. When using rewriting as a programming or modeling paradigm, the rewrite rules describe the transformations one wants to operate and rewriting strategies are…
According to recent experimental evidence, the architecture of a promoter, defined as the number, strength and regulatory role of the operators that control the promoter, plays a major role in determining the level of cell-to-cell…
Multi-sample microarray experiments have become a standard experimental method for studying biological systems. A frequent goal in such studies is to unravel the regulatory relationships between genes. During the last few years, regression…
Gene expression is a fundamental process in a living system. The small RNAs (sRNAs) is widely observed as a global regulator in gene expression. The inherent nonlinearity in this regulatory process together with the bursty production of…