Results 21 to 30 of about 283,425 (262)
The third moments of the site frequency spectrum [PDF]
Theoretical Population Biology, 2017 Abstract The analysis of patterns of segregating (i.e. polymorphic) sites in aligned sequences is routine in population genetics. Quantities of interest include the total number of segregating sites and the number of sites with mutations of different frequencies, the so-called site frequency spectrum
Klassmann, A., Ferretti, L.
openaire +3 more sources
The site frequency spectrum of dispensable genes [PDF]
Theoretical Population Biology, 2015 The differences between DNA-sequences within a population are the basis to infer the ancestral relationship of the individuals. Within the classical infinitely many sites model, it is possible to estimate the mutation rate based on the site frequency spectrum, which is comprised by the numbers $C_1,...,C_{n-1}$, where n is the sample size and $C_s$ is ...
Franz Baumdicker
exaly +6 more sources
An accurate approximation for the expected site frequency spectrum in a Galton-Watson process under an infinite sites mutation model. [PDF]
Theor Popul Biol, 2019 If viruses or other pathogens infect a single host, the outcome of infection often hinges on the fate of the initial invaders. The initial basic reproduction number R0, the expected number of cells infected by a single infected cell, helps determine whether the initial viruses can establish a successful beachhead.
Spouge JL.
europepmc +3 more sources
Accuracy of Demographic Inferences from the Site Frequency Spectrum: The Case of the Yoruba Population. [PDF]
Genetics, 2017 Abstract Some methods for demographic inference based on the observed genetic diversity of current populations rely on the use of summary statistics such as the Site Frequency Spectrum (SFS). Demographic models can be either model-constrained with numerous parameters such as growth rates, timing of demographic events ...
Lapierre M, Lambert A, Achaz G.
europepmc +4 more sources
Limit theorems for the site frequency spectrum of neutral mutations in an exponentially growing population. [PDF]
Stoch Process Their ApplThe site frequency spectrum (SFS) is a widely used summary statistic of genomic data. Motivated by recent evidence for the role of neutral evolution in cancer, we investigate the SFS of neutral mutations in an exponentially growing population. Using branching process techniques, we establish (first-order) almost sure convergence results for the SFS of ...
Gunnarsson EB, Leder K, Zhang X.
europepmc +6 more sources
Non-parametric estimation of population size changes from the site frequency spectrum [PDF]
Statistical Applications in Genetics and Molecular Biology, 2017 Abstract The variability in population size is a key quantity for understanding the evolutionary history of a species. We present a new method, CubSFS, for estimating the changes in population size of a panmictic population from the site frequency spectrum.
Waltoft, Berit Lindum, Hobolth, Asger
core +7 more sources
The impact of sampling schemes on the site frequency spectrum in nonequilibrium subdivided populations. [PDF]
Genetics, 2009 Abstract Using coalescent simulations, we study the impact of three different sampling schemes on patterns of neutral diversity in structured populations. Specifically, we are interested in two summary statistics based on the site frequency spectrum as a function of migration rate, demographic history of the entire substructured ...
Städler T +4 more
europepmc +6 more sources
Site Frequency Spectrum in stationary branching populations [PDF]
This paper explores the Site Frequency Spectrum (SFS) in stationary branching populations. We derive estimates for the SFS associated with a sample from a continuous-state branching process conditioned to never go extinct, utilizing a quadratic branching mechanism.
Abraham, Romain +2 more
core +7 more sources
Spec-RWKV: A Spectrum-Guided Multi-Scale Recurrent Modeling Framework for Multi-Center Resting-State fMRI-Assisted Diagnosis [PDF]
Brain SciencesBackground: Multi-center resting-state functional magnetic resonance imaging (rs-fMRI) is important for neurodevelopmental disorder diagnosis, but cross-site differences in repetition time (TR) can cause temporal feature misalignment.
Sihang Peng, Qi Xu
doaj +2 more sources
The site frequency spectrum for coalescing Brownian motion [PDF]
Stochastic Processes and their Applications, 2023 We consider an expanding population on the plane. The genealogy of a sample from the population is modelled by coalescing Brownian motion on the circle. We establish a weak law of large numbers for the site frequency spectrum in this model. A parallel result holds for a localized version where the genealogy is modelled by coalescing Brownian motion on ...
Shuai, Yubo
openaire +4 more sources