Related papers: Attenuation Regulation as a Term Rewriting System
Networks of genetic expression can be modelled by hypergraphs with the additional structure that real coefficients are given to each vertex-edge incidence. The spectra, i.e. the multiset of the eigenvalues, of such hypergraphs, are known to…
We introduce skipping refinement, a new notion of correctness for reasoning about optimized reactive systems. Reasoning about reactive systems using refinement involves defining an abstract, high-level specification system and a concrete,…
Over the past few years, microRNAs (miRNAs) have emerged as a new prominent class of gene regulatory factors that negatively regulate expression of approximately one-third of the genes in animal genomes at post-transcriptional level.…
In this paper I have given a mathematical model of Cell reprogramming from a different contexts. Here I considered there is a delay in differential regulator rate equations due to intermediate regulator's regulations. At first I gave some…
The problem of RNA secondary structure design (also called inverse folding) is the following: given a target secondary structure, one aims to create a sequence that folds into, or is compatible with, a given structure. In several practical…
Rewriting logic is naturally concurrent: several subterms of the state term can be rewritten simultaneously. But state terms are global, which makes compositionality difficult to achieve. Compositionality here means being able to decompose…
Bacteria live in environments that are continuously fluctuating and changing. Exploiting any predictability of such fluctuations can lead to an increased fitness. On longer timescales bacteria can "learn" the structure of these fluctuations…
A crucial step in the regulation of gene expression is binding of transcription factor (TF) proteins to regulatory sites along the DNA. But transcription factors act at nanomolar concentrations, and noise due to random arrival of these…
Essentially, in a reversible programming language, for each forward computation from state $S$ to state $S'$, there exists a constructive method to go backwards from state $S'$ to state $S$. Besides its theoretical interest, reversible…
Topological simplification is the process of reducing complexity of a function while maintaining its essential features. Its goal is to find a new filter function, which reorders cells of the input complex in a way which eliminates some…
Skip-gram (word2vec) is a recent method for creating vector representations of words ("distributed word representations") using a neural network. The representation gained popularity in various areas of natural language processing, because…
The expression of one gene might be regulated by its corresponding protein, which is called autoregulation. Although gene regulation is a central topic in biology, autoregulation is much less studied. In general, it is extremely difficult…
Regular expression is important for many natural language processing tasks especially when used to deal with unstructured and semi-structured data. This work focuses on automatically generating regular expressions and proposes a novel…
Strings are a natural representation of biological data such as DNA, RNA and protein sequences. The problem of finding a string that summarizes a set of sequences has direct application in relative compression algorithms for genome and…
We model the transcription factor based regulation network of yeast using a content-based network model that mimicks the recognition of binding motifs on the regulatory regions of the genes. We are thereby able to faithfully reproduce many…
Oscillations lie at the core of many biological processes, from the cell cycle, to circadian oscillations and developmental processes. Time-keeping mechanisms are essential to enable organisms to adapt to varying conditions in environmental…
RNA secondary structure prediction and classification are two important problems in the field of RNA biology. Here, we propose a new permutation based approach to create logical non-disjoint clusters of different secondary structures of a…
An important occurrence in many cellular contexts is the crossing of a prescribed threshold by a regulatory protein. The timing of such events is stochastic as a consequence of the innate randomness in gene expression. A question of…
An attractive mechanism to specify global constraints in rostering and other domains is via formal languages. For instance, the Regular and Grammar constraints specify constraints in terms of the languages accepted by an automaton and a…
Generative molecular design has moved from proof-of-concept to real-world applicability, as marked by the surge in very recent papers reporting experimental validation. Key challenges in explainability and sample efficiency present…