Related papers: A time series model of CDS sequences in complete g…
A time series model based on the global structure of the complete genome is proposed. Three kinds of length sequences of the complete genome are considered. The correlation dimensions and Hurst exponents of the length sequences are…
This paper considers three kinds of length sequences of the complete genome. Detrended fluctuation analysis, spectral analysis, and the mean distance spanned within time $L$ are used to discuss the correlation property of these sequences.…
Previous investigation of coding sequence lengths (CDS) in the bacterial circular chromosome revealed short range correlation in the series of these data. We have further analyzed the averaged periodograms of these series and we found that…
Large-scale dynamical properties of complete chromosome DNA sequences of eukaryotes are considered. By the proposed deterministic models with intermittency and symbolic dynamics we describe a wide spectrum of large-scale patterns inherent…
Herein it is shown that in order to study the statistical properties of DNA sequences in bacterial chromosomes it suffices to consider only one half of the chromosome because they are similar to its corresponding complementary sequence in…
In condensed matter physics, simplified descriptions are obtained by coarse-graining the features of a system at a certain characteristic length, defined as the typical length beyond which some properties are no longer correlated. From a…
We model long range correlations of nucleotides in the human DNA sequence using the long range one dimensional Ising model. We show that for distances between $10^3$ and $10^6$ bp the correlations show an universal behaviour and may be…
This paper introduces the notion of measure representation of DNA sequences. Spectral analysis and multifractal analysis are then performed on the measure representations of a large number of complete genomes. The main aim of this paper is…
A comprehensive approach to cellular differentiation in cyanobacteria is developed. To this aim, the process of heterocyst cell formation is studied under a systems biology point of view. By relying on statistical physics techniques, we…
The coding and noncoding length sequences constructed from a complete genome are characterised by multifractal analysis. The dimension spectrum $D_{q}$ and its derivative, the 'analogous' specific heat $C_{q}$, are calculated for the coding…
Protein distributions measured under a broad set of conditions in bacteria and yeast were shown to exhibit a common skewed shape, with variances depending quadratically on means. For bacteria these properties were reproduced by temporal…
The paper describes an algorithm to compute a consensus sequence from a set of DNA sequences of approximatively identical length generated by 3rd sequencing generation technologies. Its purpose targets DNA storage and is guided by specific…
This paper develops a theory for characterisation of DNA sequences based on their measure representation. The measures are shown to be random cascades generated by an infinitely divisible distribution. This probability distribution is…
Coding information is the main source of heterogeneity (non-randomness) in the sequences of bacterial genomes. This information can be naturally modeled by analysing cluster structures in the "in-phase" triplet distributions of relatively…
Single-cell RNA sequencing (scRNA-seq) is powerful technology that allows researchers to understand gene expression patterns at the single-cell level. However, analysing scRNA-seq data is challenging due to issues and biases in data…
Global transposable characteristics in the complete DNA sequence of the Saccharomyces cevevisiae yeast is determined by using the metric representation and recurrence plot methods. In the form of the correlation distance of nucleotide…
Earlier formulations of the DNA assembly problem were all in the context of perfect assembly; i.e., given a set of reads from a long genome sequence, is it possible to perfectly reconstruct the original sequence? In practice, however, it is…
We introduce a model of DNA sequence evolution which can account for biases in mutation rates that depend on the identity of the neighboring bases. An analytic solution for this class of non-equilibrium models is developed by adopting…
A structural genetic model incorporating a modern understanding of the genome and common practice in genome-wide association studies is derived mathematically. The model shows the Haldane map distance as a direct consequence of the…
This is a review of a set of recent papers with some new data added. After a brief biological introduction a visualization scheme of the string composition of long DNA sequences, in particular, of bacterial complete genomes, will be…