Related papers: Discovering functional DNA elements using populati…
Methods to effectively detect multi-locus genetic association are becoming increasingly relevant in the genetic dissection of complex trait in humans. Current approaches typically consider a limited number of hypotheses, most of which are…
Since the completion of the human genome sequencing project in 2001, significant progress has been made in areas such as gene regulation editing and protein structure prediction. However, given the vast amount of genomic data, the segments…
Population genomic studies have shown that genetic draft and background selection can profoundly affect the genome-wide patterns of molecular variation. We performed forward simulations under realistic gene-structure and selection scenarios…
The detection of molecular signatures of selection is one of the major concerns of modern population genetics. A widely used strategy in this context is to compare samples from several populations, and to look for genomic regions with…
Most of the DNA that composes a complex organism is non-coding and defined as junk. Even the coding part is composed of genes that affect the phenotype differently. Therefore, a random mutation has an effect on the specimen fitness that…
Each human genome is a 3 billion base pair set of encoding instructions. Decoding the genome using deep learning fundamentally differs from most tasks, as we do not know the full structure of the data and therefore cannot design…
Evolutionary dynamics and patterns of molecular evolution are strongly influenced by selection on linked regions of the genome, but our quantitative understanding of these effects remains incomplete. Recent work has focused on predicting…
With the development of high-throughput technologies, genomics datasets rapidly grow in size, including functional genomics data. This has allowed the training of large Deep Learning (DL) models to predict epigenetic readouts, such as…
Population diversity is crucial in evolutionary algorithms to enable global exploration and to avoid poor performance due to premature convergence. This book chapter reviews runtime analyses that have shown benefits of population diversity,…
There are many instances in genetics in which we wish to determine whether two candidate populations are distinguishable on the basis of their genetic structure. Examples include populations which are geographically separated, case--control…
Recent advances in high-throughput genomics technologies have resulted in the sequencing of large numbers of (near) complete genomes. These genome sequences are being mined for important functional elements, such as genes. They are also…
We updated the agent based Monte Carlo code HERITAGE that simulates human evolution within restrictive environments such as interstellar, sub-light speed spacecraft in order to include the effects of population genetics. We incorporated a…
Elucidating the genetic basis of human diseases is a central goal of genetics and molecular biology. While traditional linkage analysis and modern high-throughput techniques often provide long lists of tens or hundreds of disease gene…
Molecular phenotypes are important links between genomic information and organismic functions, fitness, and evolution. Complex phenotypes, which are also called quantitative traits, often depend on multiple genomic loci. Their evolution…
The methylation of DNA regulates gene expression. On cell division the methylation state of the DNA is typically inherited from parent to daughter cells. While the chemical bond between the methyl group and the DNA is very strong, changes…
This manuscript delves into the intersection of genomics and phenotypic prediction, focusing on the statistical innovation required to navigate the complexities introduced by noisy covariates and confounders. The primary emphasis is on the…
We investigate a continuous time, probability measure-valued dynamical system that describes the process of mutation-selection balance in a context where the population is infinite, there may be infinitely many loci, and there are weak…
We discuss two different ways of chromosomes' and genomes' evolution. Purifying selection dominates in large panmictic populations, where Mendelian law of independent gene assortment is valid. If the populations are small, recombination…
Motivation: DNA methylation is an intensely studied epigenetic mark, yet its functional role is incompletely understood. Attempts to quantitatively associate average DNA methylation to gene expression yield poor correlations outside of the…
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…