Related papers: Demography-adjusted tests of neutrality based on g…
Many scientific applications involve testing theories that are only partially specified. This task often amounts to testing the goodness-of-fit of a candidate distribution while allowing for reasonable deviations from it. The tolerant…
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…
When mutation rates are low, natural selection remains effective, and increasing the mutation rate can give rise to an increase in adaptation rate. When mutation rates are high to begin with, however, increasing the mutation rate may have a…
We consider testing statistical hypotheses about densities of signals in deconvolution models. A new approach to this problem is proposed. We constructed score tests for the deconvolution with the known noise density and efficient score…
We study the evolution of gene frequencies in a population living in $\mathbb{R}^d$, modelled by the spatial Lambda Fleming-Viot process with natural selection (Barton, Etheridge and Veber, 2010 and Etheridge, Veber and Yu, 2014). We…
Biometric recognition is used across a variety of applications from cyber security to border security. Recent research has focused on ensuring biometric performance (false negatives and false positives) is fair across demographic groups.…
Classical population genetics a priori assigns fitness to alleles without considering molecular or functional properties of proteins that these alleles encode. Here we study population dynamics in a model where fitness can be inferred from…
The Central Limit Theorem provides a foundation for inferential statistics and hypothesis testing. It describes how standardized statistics behave under repeated sampling from large populations. However, if the size of the sample (n)…
Randomization testing is a fundamental method in statistics, enabling inferential tasks such as testing for (conditional) independence of random variables, constructing confidence intervals in semiparametric location models, and…
New automated and high-throughput methods allow the manipulation and selection of numerous bacterial populations. In this manuscript we are interested in the neutral diversity patterns that emerge from such a setup in which many bacterial…
We consider a model of asexually reproducing individuals with random mutations and selection. The rate of mutations is proportional to the population size, $N$. The mutations may be either beneficial or deleterious. In a paper by Yu,…
The investigation of allele frequency trajectories in populations evolving under controlled environmental pressures has become a popular approach to study evolutionary processes on the molecular level. Statistical models based on…
We consider the Moran model of population genetics with two types, mutation, and selection, and investigate the line of descent of a randomly-sampled individual from a contemporary population. We trace this ancestral line back into the…
A forward diffusion equation describing the evolution of the allele frequency spectrum is presented. The influx of mutations is accounted for by imposing a suitable boundary condition. For a Wright-Fisher diffusion with or without selection…
Standing genetic variation provides a rich reservoir of potentially useful mutations facilitating the adaptation to novel environments. Experimental evolution studies have demonstrated that rapid and strong phenotypic responses to selection…
The standard paradigm for the analysis of genome-wide association studies involves carrying out association tests at both typed and imputed SNPs. These methods will not be optimal for detecting the signal of association at SNPs that are not…
We study how environmental stochasticity influences the long-term population size in certain one- and two-species models. The difficulty is that even when one can prove that there is persistence, it is usually impossible to say anything…
We simulate the evolution of model protein sequences subject to mutations. A mutation is considered neutral if it conserves 1) the structure of the ground state, 2) its thermodynamic stability and 3) its kinetic accessibility. All other…
In large populations, multiple beneficial mutations may be simultaneously spreading. In asexual populations, these mutations must either arise on the same background or compete against each other. In sexual populations, recombination can…
Testing for association or dependence between pairs of random variables is a fundamental problem in statistics. In some applications, data are subject to selection bias that causes dependence between observations even when it is absent from…