Related papers: Gene-history correlation and population structure
Identifying drivers of complex traits from the noisy signals of genetic variation obtained from high throughput genome sequencing technologies is a central challenge faced by human geneticists today. We hypothesize that the variants…
Genome-wide association studies (GWAS) have emerged as a rich source of genetic clues into disease biology, and they have revealed strong genetic correlations among many diseases and traits. Some of these genetic correlations may reflect…
Supergenes are genomic regions containing sets of tightly linked loci that control multi-trait phenotypic polymorphisms under balancing selection. Recent advances in genomics have uncovered significant variation in both the genomic…
Genetic data are frequently categorical and have complex dependence structures that are not always well understood. For this reason, clustering and classification based on genetic data, while highly relevant, are challenging statistical…
Gene interaction graphs aim to capture various relationships between genes and can represent decades of biology research. When trying to make predictions from genomic data, those graphs could be used to overcome the curse of dimensionality…
A structural genetic model incorporating a modern understanding of the genome and common practice in genome-wide association studies is derived mathematically. The model shows the Haldane map distance as a direct consequence of the…
We linked names and contact information to publicly available profiles in the Personal Genome Project. These profiles contain medical and genomic information, including details about medications, procedures and diseases, and demographic…
Single-cell experiments have revealed cell-to-cell variability in generation times and growth rates for genetically identical cells. Theoretical models relating the fluctuating generation times of single cells to the population growth rate…
It is widely acknowledged that there is a diversity problem in genomics stemming from the vast underrepresentation of non-European genetic ancestry populations. While many challenges exist to address this gap, a major complicating factor is…
Modern population genetics studies typically involve genome-wide genotyping of individuals from a diverse network of ancestries. An important, unsolved problem is how to formulate and estimate probabilistic models of observed genotypes that…
Combining genome-wide structural models with phenomenological data is at the forefront of efforts to understand the organizational principles regulating the human genome. Here, we use chromosome-chromosome contact data as knowledge-based…
Heterozygote disadvantage is potentially a potent driver of population genetic divergence. Also referred to as underdominance, this phenomena describes a situation where a genetic heterozygote has a lower overall fitness than either…
Human aging is a process controlled by both genetics and environment. Many studies have been conducted to identify a subset of genes related to aging from the human genome. Biologists implicitly categorize age-related genes into genes that…
People tend to have their social interactions with members of their own community. Such group-structured interactions can have a profound impact on the behaviors that evolve. Group structure affects the way people cooperate, and how they…
The prediction of phenotypic traits using high-density genomic data has many applications such as the selection of plants and animals of commercial interest; and it is expected to play an increasing role in medical diagnostics. Statistical…
We present a data structure called a history graph that offers a practical basis for the analysis of genome evolution. It conceptually simplifies the study of parsimonious evolutionary histories by representing both substitutions and double…
A pedigree is a directed graph that describes how individuals are related through ancestry in a sexually-reproducing population. In this paper we explore the question of whether one can reconstruct a pedigree by just observing sequence data…
Genealogical networks (i.e. family trees) are of growing interest, with the largest known data sets now including well over one billion individuals. Interest in family history also supports an 8.5 billion dollar industry whose size is…
Reconstruction of population histories is a central problem in population genetics. Existing coalescent-based methods, like the seminal work of Li and Durbin (Nature, 2011), attempt to solve this problem using sequence data but have no…
In the analysis of complex traits, genetic effects are frequently modelled as either fixed or random effects. Such assumptions serve as a foundation of defining heritability and relatedness using genome-wide single nucleotide polymorphism…