相关论文: Information-theoretic View of Sequence Organizatio…

We introduce an improved version of RECKONER, an error corrector for Illumina whole genome sequencing data. By modifying its workflow we reduce the computation time even 10 times. We also propose a new method of determination of $k$-mer…

Rich information on the prebiotic evolution is still stored in contemporary genomic data. The statistical mechanism at the sequence level may play a significant role in the prebiotic evolution. Based on statistical analysis of genome…

We introduce a class of stochastic integer sequences. In these sequences, every element is a sum of two previous elements, at least one of which is chosen randomly. The interplay between randomness and memory underlying these sequences…

In this article, we review existing probabilistic models for modeling abundance of fixed-length strings (k-mers) in DNA sequencing data. These models capture dependence of the abundance on various phenomena, such as the size and repeat…

The question how complex systems become more organized and efficient with time is open. Examples are, the formation of elementary particles from pure energy, the formation of atoms from particles, the formation of stars and galaxies, the…

We propose a new interpretation of measures of information and disorder by connecting these concepts to group theory in a new way. Entropy and group theory are connected here by their common relation to sets of permutations. A combinatorial…

Sequences have become first class citizens in supervised learning thanks to the resurgence of recurrent neural networks. Many complex tasks that require mapping from or to a sequence of observations can now be formulated with the…

During evolution of microorganisms genomes underwork have different changes in their lengths, gene orders, and gene contents. Investigating these structural rearrangements helps to understand how genomes have been modified over time. Some…

The problem of differentiating the informational content of coding (exons) and non-coding (introns) regions of a DNA sequence is one of the central problems of genomics. The introns are estimated to be nearly 95% of the DNA and since they…

The main statistical distributions applicable to the analysis of genome architecture and genome tracks are briefly discussed and critically assessed. Although the observed features in distributions of element lengths can be equally well…

Various approaches to alignment-free sequence comparison are based on the length of exact or inexact word matches between two input sequences. Haubold {\em et al.} (2009) showed how the average number of substitutions between two DNA…

The ``comma sequence'' starts with 1 and is defined by the property that if k and k' are consecutive terms, the two-digit number formed from the last digit of k and the first digit of k' is equal to the difference k'-k. If there is more…

It is known that the majority of the human genome consists of repeated sequences. Furthermore, it is believed that a significant part of the rest of the genome also originated from repeated sequences and has mutated to its current form. In…

The implications of large-scale coherence in biological systems and possible links to quantum theory are only beginning to be explored. Whether quantum-like coherent phenomena are relevant, or even possible at all, at the high temperatures…

We study information scrambling -- a spread of initially localized quantum information into the system's many degree of freedom -- in discrete-time quantum walks. We consider out-of-time-ordered correlators (OTOC) and K-complexity as a…

This article discusses the properties of extremes of degree sequences calculated from network data. We introduce the notion of a normalized degree, in order to permit a comparison of degree sequences between networks with differing numbers…

Background: With the fast development of next generation sequencing technologies, increasing numbers of genomes are being de novo sequenced and assembled. However, most are in fragmental and incomplete draft status, and thus it is often…

A measure called Physical Complexity is established and calculated for a population of sequences, based on statistical physics, automata theory, and information theory. It is a measure of the quantity of information in an organism's genome.…

In this work, the dynamics of fluctuations in gene expression time series is investigated. By using collected data of gene expression from yeast and human organisms, we found that the fluctuations of gene expression level and its average…

Genetic sequences are known to possess non-trivial composition together with symmetries in the frequencies of their components. Recently, it has been shown that symmetry and structure are hierarchically intertwined in DNA, suggesting a…