Related papers: Statistical analysis of simple repeats in the huma…
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…
We analyzed the periodic patterns in E. coli promoters and compared the distributions of the corresponding patterns in promoters and in the complete genome to elucidate their function. Except the three-base periodicity, coincident with that…
Genome-wide analysis of distributions of densities of long-range interactions of human chromosomes with each other, nucleoli, nuclear lamina, and binding sites of chromatin state regulatory proteins, CTCF and STAT1, identifies non-random…
Recurrent mutations are a common phenomenon in population genetics. They may be at the origin of the fixation of a new genotype, if they give a phenotypic advantage to the carriers of the new mutation. In this paper, we are interested in…
We study the following model for a diploid population of constant size $N$: Every individual carries a random number of (genetic) elements. Upon a reproduction event each of the two parents passes each element independently with probability…
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,…
Tandem duplication is an evolutionary process whereby a segment of DNA is replicated and proximally inserted. The different configurations that can arise from this process give rise to some interesting combinatorial questions. Firstly, we…
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…
Current models for the folding of the human genome see a hierarchy stretching down from chromosome territories, through A/B compartments and TADs (topologically-associating domains), to contact domains stabilized by cohesin and CTCF.…
Genome rearrangements can be modeled as $k$-breaks, which break a genome at k positions and glue the resulting fragments in a new order. In particular, reversals, translocations, fusions, and fissions are modeled as $2$-breaks, and…
DNA storage has emerged as an important area of research. The reliability of DNA storage system depends on designing the DNA strings (called DNA codes) that are sufficiently dissimilar. In this work, we introduce DNA codes that satisfy a…
Zimin words are words that have the same prefix and suffix. They are unavoidable patterns, with all sufficiently large strings encompassing them. Here, we examine for the first time the presence of k-mers not containing any Zimin patterns,…
Much evolutionary information is stored in the fluctuations of protein length distributions. The genome size and non-coding DNA content can be calculated based only on the protein length distributions. So there is intrinsic relationship…
Macromolecular crowding plays a principal role in a wide range of biological processes including gene expression, chromosomal compaction, and viral infection. However, the impact that crowding has on the dynamics of nucleic acids remains a…
Recursive processing in sentence comprehension is considered a hallmark of human linguistic abilities. However, its underlying neural mechanisms remain largely unknown. We studied whether a modern artificial neural network trained with…
DNA as a data storage medium has several advantages, including far greater data density compared to electronic media. We propose that schemes for data storage in the DNA of living organisms may benefit from studying the reconstruction…
The two strands of a DNA molecule with a repetitive sequence can pair into many different basepairing patterns. For perfectly periodic sequences, early bulk experiments of Poerschke indicate the existence of a sliding process, permitting…
Humans have $23$ pairs of homologous chromosomes. The homologous pairs are almost identical pairs of chromosomes. For the most part, differences in homologous chromosome occur at certain documented positions called single nucleotide…
Haplotypes, the global patterns of DNA sequence variation, have important implications for identifying complex traits. Recently, blocks of limited haplotype diversity have been discovered in human chromosomes, intensifying the research on…
Proteins are constructed from a limited alphabet of ~20 amino acids, yet the origins and selection of this specific alphabet are unresolved. One largely overlooked aspect is whether elemental composition constrains the range of viable…