Related papers: Expectation of the Site Frequency Spectrum
The number of fixed mutations accumulated in an evolving population often displays a variance that is significantly larger than the mean (the overdispersed molecular clock). By examining a generic evolutionary process on a neutral network…
The purpose of this study is to provide a new methodology of how one can consistently estimate a change-point in time series data. In contrast with previous studies, the suggested methodology employs only the empirical spectral density and…
The LFPs is a broadband signal that captures variations of neural population activity over a wide range of time scales. The range of time scales available in LFPs is particularly interesting from the neural coding point of view because it…
Cells continuously sense their surroundings to detect modifications and generate responses. Very often changes in extracellular concentrations initiate signaling cascades that eventually result in changes in gene expression. Increasing…
In the analysis of variable stars, the problem of sampling is central. This article focusses on the determination of the Nyquist frequency. It is well defined in the case of regular sampling. However, the time series of variable stars…
The speed of site-specific binding of transcription factor (TFs) proteins with genomic DNA seems to be strongly retarded by the randomly occurring sequence traps. Traps are those DNA sequences sharing significant similarity with the…
Parts of DNA sequences known as exons and introns play very different role in coding and storage of genetic information. Here we show that their conducting properties are also very different. Taking into account long-range correlations…
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.…
Variant calling, the problem of estimating whether a position in a DNA sequence differs from a reference sequence, given noisy, redundant, overlapping short sequences that cover that position, is fundamental to genomics. We propose a deep…
We introduce an evolving network model in which a new node attaches to a randomly selected target node and also to each of its neighbors with probability $p$. The resulting network is sparse for $p<\frac{1}{2}$ and dense (average degree…
We investigate through numerical simulations the effect of selection on two summary statistics for nucleotide variation in a sample of two genes from a population of N asexually reproducing haploid individuals. One is the mean time since…
Natural protein sequences contain a record of their history. A common constraint in a given protein family is the ability to fold to specific structures, and it has been shown possible to infer the main native ensemble by analyzing…
Major unresolved questions in evolutionary genetics include determining the contributions of different mutational sources to the total pool of genetic variation in a species, and understanding how these different forms of genetic variation…
In this paper we treat some fractal and statistical features of the DNA sequences. First, a fractal record model of DNA sequence is proposed by mapping DNA sequences to integer sequences, followed by R/S analysis of the model and…
Motivated by the various examples of spatial variability in the power of the acoustic spectrum, we attempted to look for spatial variability in the peak frequency of the spectrum. However, the determination of this peak frequency on a…
The transmissivity of a one-dimensional random system that is periodic on average is studied. It is shown that the transmission coefficient for frequencies corresponding to a gap in the band structure of the average periodic system…
The efficient recognition of pathogens by the adaptive immune system relies on the diversity of receptors displayed at the surface of immune cells. T-cell receptor diversity results from an initial random DNA editing process, called VDJ…
The premise of genetic analysis is that a causal link exists between phenotypic and allelic variation. Yet it has long been documented that mutant phenotypes are not a simple result of a single DNA lesion, but rather are due to interactions…
We consider interstellar scintillations as a cause of intermittency in radio signals from extraterrestrial intelligence (ETI). We demonstrate that scintillations are very likely to allow initial detections of narrowband signals from distant…
A definition of frequency (cycles per unit-time) based on an approximate reconstruction of the phase-space trajectory of an oscillator from a signal is introduced. It is shown to be invariant under linear filtering, and therefore…