Related papers: Comparative genomics study of inverted repeats in …
Many microbial populations rapidly adapt to changing environments with multiple variants competing for survival. To quantify such complex evolutionary dynamics in vivo, time resolved and genome wide data including rare variants are…
The aim of the study is to analyze viruses using parameters obtained from distributions of nucleotide sequences in the viral RNA. Seeking for the input data homogeneity, we analyze single-stranded RNA viruses only. Two approaches are used…
To regulate a particular gene, a transcription factor (TF) needs to bind a specific genome location. How is this genome address specified amid the presence of ~10^6-10^9 decoy sites? Our analysis of 319 known TF binding motifs clearly…
Exact string matching has been a fundamental problem in computer science for decades because of many practical applications. Some are related to common procedures, such as searching in files and text editors, or, more recently, to more…
Multiple genome alignment remains a challenging problem. Effects of recombination including rearrangement, segmental duplication, gain, and loss can create a mosaic pattern of homology even among closely related organisms. We describe a…
Satellite DNA are long tandemly repeating sequences in a genome and may be organized as high-order repeats (HORs). They are enriched in centromeres and are challenging to assemble. Existing algorithms for identifying satellite repeats…
In this paper we consider the enumeration of orientable and non-orientable chord diagrams. We show that this enumeration is encoded in appropriate expectation values of the $\beta$-deformed Gaussian and RNA matrix models. We evaluate these…
We present COBS, a COmpact Bit-sliced Signature index, which is a cross-over between an inverted index and Bloom filters. Our target application is to index $k$-mers of DNA samples or $q$-grams from text documents and process approximate…
Massively parallel sequencing techniques have revolutionized biological and medical sciences by providing unprecedented insight into the genomes of humans, animals, and microbes. Modern sequencing platforms generate enormous amounts of…
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.…
Microorganisms are found in almost every environment, including the soil, water, air, and inside other organisms, like animals and plants. While some microorganisms cause diseases, most of them help in biological processes such as…
Non protein coding regions of the human genome contain many complex patterns which regulate the cellular activity. Studying the human genome is limited by the lack of understanding of its features and their complex interactions. However,…
Genes with similar transcriptional activation kinetics can display very different temporal mRNA profiles due to differences in transcription time, degradation rate and RNA processing kinetics. Recent studies have shown that a…
This paper develops an analogy between the cycle structure of, on the one hand, random permutations with cycle lengths restricted to lie in an infinite set $S$ with asymptotic density $\sigma$ and, on the other hand, permutations selected…
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…
Many models of genome rearrangement involve operations (e.g. inversions and translocations) that are self-inverse, and hence generate a group acting on the space of genomes. This gives a correspondence between genome arrangements and the…
We have considered as a theoretical possibility for the development of a nanobiochip the operation principle of which is based on measuring conductance in single-stranded and double-stranded DNA. Calculations have demonstrated that in the…
Motivation: New long read sequencers promise to transform sequencing and genome assembly by producing reads tens of kilobases long. However their high error rate significantly complicates assembly and requires expensive correction steps to…
This article presents a physical biology approach to understanding organization and segregation of bacterial chromosomes. The author uses a "piston" analogy for bacterial chromosomes in a cell, which leads to a phase diagram for the…
In this paper, we study a model, which was first presented by Bunte and Lapidoth, that mimics the programming operation of memory cells. Under this paradigm we assume that cells are programmed sequentially and individually. The programming…