相关论文: From DNA sequence analysis to modeling replication…
Locations of DNA replication initiation in prokaryotes, called "origins of replication", are well-characterized. However, a mechanistic understanding of the sequence-dependence of the local unzipping of double-stranded DNA, the first step…
The Dissertation is focused on the studies of associations between functional elements in human genome and their nucleotide structure. The asymmetry in nucleotide content (skew, bias) was chosen as the main feature for nucleotide structure.…
Replication of genetic material is an important process for all living organisms. Origins of replication initiate the copying of DNA at many points on a chromosome, and it is the distribution of these points that is relevant here, as it…
This study presents the first global, 1 Mbp level analysis of patterns of nucleotide substitutions along the human lineage. The study is based on the analysis of a large amount of repetitive elements deposited into the human genome since…
Biological cells replicate their genomes in a well-planned manner. The DNA replication program of an organism determines the timing at which different genomic regions are replicated, with fundamental consequences for cell homeostasis and…
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…
The nucleotide composition of human genes with a special emphasis on transcription-related strand asymmetries is analyzed. Such asymmetries may be associated with different mutational rates in two principal factors. The first one is…
Biologists have long sought a way to explain how statistical properties of genetic sequences emerged and are maintained through evolution. On the one hand, non-random structures at different scales indicate a complex genome organisation. On…
Splicing sites provide unique statistics in human genome due to their large number and reasonably complete annotation. Analyses of the cumulative SNPs distribution in splicing sites reveal a few interesting observations. While a degree of…
The human genome contains repetitive DNA at different level of sequence length, number and dispersion. Highly repetitive DNA is particularly rich in homo-- and di--nucleotide repeats, while middle repetitive DNA is rich of families of…
The so called long range correlation properties of DNA sequences are studied using the variance analyses of the density distribution of a single or a group of nucleotides in a model independent way. This new method which was suggested…
The double-helical structure of DNA results from canonical base pairing and stacking interactions. However, variations from steady-state conformations result from mechanical perturbations in cells. These different topologies have…
Background: Duplication of genes is important for evolution of molecular networks. Many authors have therefore considered gene duplication as a driving force in shaping the topology of molecular networks. In particular it has been noted…
About 2% of human genetic polymorphisms have been hypothesized to arise via multinucleotide mutations (MNMs), complex events that generate SNPs at multiple sites in a single generation. MNMs have the potential to accelerate the pace at…
In this paper, we review the literature on statistical long-range correlation in DNA sequences. We examine the current evidence for these correlations, and conclude that a mixture of many length scales (including some relatively long ones)…
It is shown that the nucleotide sequences in DNA molecules have cluster-scaling properties (discovered for the first time in turbulent processes: Sreenivasan and Bershadskii, 2006, J. Stat. Phys., 125, 1141-1153.). These properties are…
Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. Delineating recombination events is important in the study of molecular evolution, as inference of such events provides a clearer…
The recently proposed compressed backbone theory suggested that the intrinsic curvature in DNA can result from a geometric mismatch between the specific backbone length and optimal base stacking orientations. It predicted that the curvature…
Human populations have experienced dramatic growth since the Neolithic revolution. Recent studies that sequenced a very large number of individuals observed an extreme excess of rare variants, and provided clear evidence of recent rapid…
Centromeres are essential for chromosome segregation, yet their DNA sequences evolve rapidly. In most animals and plants that have been studied, centromeres contain megabase-scale arrays of tandem repeats. Despite their importance, very…