Related papers: Long-range correlation in the whole human genome
Recently, scientists from The Craig J. Venter Institute reported construction of very long DNA molecules using a variety of experimental procedures adopting a number of working hypotheses. Finding a mathematical rule for generation of such…
Estimating the phylogeny of the genus Homo is entering a new phase of vastly improved data and methodology. There is increasing evidence of 6 to 10 competing species/lineages at any point in the last half million years, making the…
The crucial aspect of this demonstration is the discovery of renewal events, hidden in the computed dynamics of a multifractal metronome, which enables the replacement of the phenomenon of strong anticipation with a time delayed…
A behaviour of molecular cluster with Lennard-Jones potential of interactions as Hamiltonian system is studied by computer simulation (molecular dynamics method). It is shown that complex periodic oscillations of the cluster as a whole are…
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…
Much of interesting complex biological behaviour arises from collective properties. Important information about collective behaviour lies in the time and space structure of fluctuations around average properties, and two-point correlation…
With the number of fully-sequenced genomes now well over a hundred it has become possible to start investigating if there are any quantitative regularities in the genetic make-up of genomes. In (physics/0307001), I originally showed that…
Chromosomal rearrangements, which shuffle DNA throughout the genome, are an important source of divergence across taxa. Using a paired-end read approach with Illumina sequence data for archaic humans, I identify changes in genome structure…
We determine the Renyi entropies K_q of symbol sequences generated by human chromosomes. These exhibit nontrivial behaviour as a function of the scanning parameter q. In the thermodynamic formalism, there are phase transition-like phenomena…
We introduce a method to estimate the complexity function of symbolic dynamical systems from a finite sequence of symbols. We test such complexity estimator on several symbolic dynamical systems whose complexity functions are known exactly.…
{\bf Background}: Several features are known to correlate with the GC-content in the human genome, including recombination rate, gene density and distance to telomere. However, by testing for pairwise correlation only, it is impossible to…
To support comparative genomics, population genetics, and medical genetics, we propose that a reference genome should come with a scheme for mapping each base in any DNA string to a position in that reference genome. We refer to a…
We study the role of phylogenetic trees on correlations in mutation processes. Generally, correlations decay exponentially with the generation number. We find that two distinct regimes of behavior exist. For mutation rates smaller than a…
A theory of additive Markov chains with long-range memory, proposed earlier in Phys. Rev. E 68, 06117 (2003), is developed and used to describe statistical properties of long-range correlated systems. The convenient characteristics of such…
The periodic transference of nucleotide strings in bacterial and archaeal complete genomes is investigated by using the metric representation and the recurrence plot method. The generated periodic correlation structures exhibit four kinds…
We show the existence of a high interrelation between the different loops that may appear in a DNA segment. Conformational changes in a chain segment caused by the formation of a particular loop may either promote or prevent the appearance…
Evolution has fascinated quantitative and physical scientists for decades: how can the random process of mutation, recombination, and duplication of genetic information generate the diversity of life? What determines the rate of evolution?…
Many natural, engineered, and social systems can be represented using the framework of a layered network, where each layer captures a different type of interaction between the same set of nodes. The study of such multiplex networks is a…
High-dimensional phenotypes hold promise for richer findings in association studies, but testing of several phenotype traits aggravates the grand challenge of association studies, that of multiple testing. Several methods have recently been…
With the number of sequenced genomes now over one hundred, and the availability of rough functional annotations for a substantial proportion of their genes, it has become possible to study the statistics of gene content across genomes. Here…