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We introduce a model for simulating mutation of prokaryote DNA sequences. Using that model we can then evaluated traditional techniques like parsimony and maximum likelihood methods for computing phylogenetic relationships. We also use the…
Consider a supercritical birth and death process where the children acquire mutations. We study the mutation rates along the ancestral lineages in a sample of size $n$ from the population at time $T$. The mutation rate is time-inhomogenous…
Tools that effectively analyze and compare sequences are of great importance in various areas of applied computational research, especially in the framework of molecular biology. In the present paper, we introduce simple geometric criteria…
Comment on "Fluctuations in the DNA double helix: A critical review" by Frank-Kamenetskii and Prakash
We introduce a complexity measure for symbolic sequences. Starting from a segmentation procedure of the sequence, we define its complexity as the entropy of the distribution of lengths of the domains of relatively uniform composition in…
The distribution of bases spacing in human genome was investigated. An analysis of the frequency of occurrence in the human genome of different sequence lengths flanked by one type of nucleotide was carried out showing that the distribution…
Transcription is the first step of gene expression, in which a particular segment of DNA is copied to RNA by the enzyme RNA polymerase (RNAP). Despite many details of the complex interactions between DNA and RNA synthesis disclosed…
Reticulate evolutionary processes result in phylogenetic histories that cannot be modeled using a tree topology. Here, we apply methods from topological data analysis to molecular sequence data with reticulations. Using a simple example, we…
Protein folding and evolution are intimately linked phenomena. Here, we revisit the concept of exons as potential protein folding modules across 38 abundant and conserved protein families. Taking advantage of genomic exon-intron…
Periodic patterns play the important regulatory and structural roles in genomic DNA sequences. Commonly, the underlying periodicities should be understood in a broad statistical sense, since the corresponding periodic patterns have been…
We provide an overview of current approaches to DNA-based storage system design and accompanying synthesis, sequencing and editing methods. We also introduce and analyze a suite of new constrained coding schemes for both archival and random…
Charge transfer along the base-pair stack in DNA is modeled in terms of thermally-assisted tunneling between adjacent base pairs. Central to our approach is the notion that tunneling between fluctuating pairs is rate-limited by the…
Given a set of species whose evolution is represented by a species tree, a gene family is a group of genes having evolved from a single ancestral gene. A gene family evolves along the branches of a species tree through various mechanisms,…
Intermittent density fluctuations of nucleotide molecules (adenine, guanine, cytosine and thymine) along DNA sequences are studied in the framework of a hierarchical structure (HS) model originally proposed for the study of fully developed…
DNA denaturation has long been a subject of intense study due to its relationship to DNA transcription and its fundamental importance as a nonlinear, structural transition. Many aspects of this phenomenon, however, remain poorly understood.…
Protein evolution involves mutations occurring across a wide range of time scales. In analogy with disordered systems in statistical physics, this dynamical heterogeneity suggests strong correlations between mutations happening at distinct…
Transcriptomic analysis are characterized by being not directly quantitative and only providing relative measurements of expression levels up to an unknown individual scaling factor. This difficulty is enhanced for differential expression…
Complexity metrics and machine learning (ML) models have been utilized to analyze the lengths of segmental genomic entities like: exons, introns, intergenic and repeat/unique DNA sequences, in each of the 22 human chromosomes. The purpose…
By using the Jensen-Shannon divergence, genomic DNA can be divided into compositionally distinct domains through a standard recursive segmentation procedure. Each domain, while significantly different from its neighbours, may however share…
We consider inference about the history of a sample of DNA sequences, conditional upon the haplotype counts and the number of segregating sites observed at the present time. After deriving some theoretical results in the coalescent setting,…