Related papers: Expectation of the Site Frequency Spectrum
We derive on the level of quantum optics expressions for the uncertainty of the photocount in a multi-mode multi-frequency setup. The result depends on the quantum correlations of the individual modes and the frequency spectrum of the…
Fluctuations in the measured mRNA levels of unperturbed cells under fixed conditions have often been viewed as an impediment to the extraction of information from expression profiles. Here, we argue that such expression fluctuations should…
We define and study a numerical-range analogue of the notion of spectral set. Among the results obtained are a positivity criterion and a dilation theorem, analogous to those already known for spectral sets. An important difference from the…
Power spectra of human DNA base C+G frequency distribution in all available contiguous sections exhibit the universal inverse power law form of the statistical normal distribution for the 24 chromosomes. Inverse power law form for power…
Assume that individuals alive at time $t$ in some population can be ranked in such a way that the coalescence times between consecutive individuals are i.i.d. The ranked sequence of these branches is called a coalescent point process. We…
Genotype networks are a method used in systems biology to study the "innovability" of a set of genotypes having the same phenotype. In the past they have been applied to determine the genetic heterogeneity, and stability to mutations, of…
Estimation of Distribution Algorithms (EDAs) are one branch of Evolutionary Algorithms (EAs) in the broad sense that they evolve a probabilistic model instead of a population. Many existing algorithms fall into this category. Analogous to…
We study a minimal model for genome evolution whose elementary processes are single site mutation, duplication and deletion of sequence regions and insertion of random segments. These processes are found to generate long-range correlations…
In sexual populations, selection operates neither on the whole genome, which is repeatedly taken apart and reassembled by recombination, nor on individual alleles that are tightly linked to the chromosomal neighborhood. The resulting…
Latent periodic elements in genomes play important roles in genomic functions. Many complex periodic elements in genomes are difficult to be detected by commonly used digital signal processing (DSP). We present a novel method to compute the…
This paper considers estimation of a univariate density from an individual numerical sequence. It is assumed that (i) the limiting relative frequencies of the numerical sequence are governed by an unknown density, and (ii) there is a known…
In order to analyze data from cancer genome sequencing projects, we need to be able to distinguish causative, or "driver," mutations from "passenger" mutations that have no selective effect. Toward this end, we prove results concerning the…
The most general exclusion single species reaction-diffusion models with nearest-neighbor interactions one a one dimensional lattice are investigated, for which the evolution of full intervals are closed. Using a generating function method,…
Biological systems have evolved to amazingly complex states, yet we do not understand in general how evolution operates to generate increasing genetic and functional complexity. Molecular recognition sites are short genome segments or…
The DNA storage channel is considered, in which a codeword is comprised of $M$ unordered DNA molecules. At reading time, $N$ molecules are sampled with replacement, and then each molecule is sequenced. A coded-index concatenated-coding…
This technical note is on digital filters for the high-fidelity estimation of a sinusoidal signal's frequency in the presence of additive noise. The complex noise is assumed to be white (i.e. uncorrelated) however it need not be Gaussian.…
Genetic sequences are known to possess non-trivial composition together with symmetries in the frequencies of their components. Recently, it has been shown that symmetry and structure are hierarchically intertwined in DNA, suggesting a…
We analyze spectral properties of a quantum graph in the form of a ring chain with a $\delta$ coupling in the vertices exposed to a homogeneous magnetic field perpendicular to the graph plane. We find the band spectrum in the case when the…
Selective sweeps are typically associated with a local reduction of genetic diversity around the adaptive site. However, selective sweeps can also quickly carry neutral mutations to observable population frequencies if they arise early in a…
The $\Delta_3(L)$ statistic characterizes the fluctuations of the number of levels as a function of the length of the spectral interval. It is studied as a possible tool to indicate the regular or chaotic nature of underlying dynamics,…