Related papers: An exploratory analysis of combined genome-wide SN…
The genetic structure of human populations is extraordinarily complex and of fundamental importance to studies of anthropology, evolution, and medicine. As increasingly many individuals are of mixed origin, there is an unmet need for tools…
Genetic studies of human traits have revolutionized our understanding of the variation between individuals, and opened the door for numerous breakthroughs in biology, medicine and other scientific fields. And yet, the ultimate promise of…
For the vast majority of genome wide association studies (GWAS) published so far, statistical analysis was performed by testing markers individually. In this article we present some elementary statistical considerations which clearly show…
We generated genome-wide data from 69 Europeans who lived between 8,000-3,000 years ago by enriching ancient DNA libraries for a target set of almost four hundred thousand polymorphisms. Enrichment of these positions decreases the…
Genome-wide association studies, in which as many as a million single nucleotide polymorphisms (SNP) are measured on several thousand samples, are quickly becoming a common type of study for identifying genetic factors associated with many…
Population synthesis is a critical task that involves generating synthetic yet realistic representations of populations. It is a fundamental problem in agent-based modeling (ABM), which has become the standard to analyze intelligent…
When biological populations expand into new territory, the evolutionary outcomes can be strongly influenced by genetic drift, the random fluctuations in allele frequencies. Meanwhile, spatial variability in the environment can also…
Over the past several years, DNA sequencing has emerged as one of the driving forces in life-sciences, paving the way for affordable and accurate whole genome sequencing. As genomes represent the entirety of an organism's hereditary…
We scanned through the genomes of 29,141 African Americans, searching for loci where the average proportion of African ancestry deviates significantly from the genome-wide average. We failed to find any genome-wide significant deviations,…
In this work we seek clusters of genomic words in human DNA by studying their inter-word lag distributions. Due to the particularly spiked nature of these histograms, a clustering procedure is proposed that first decomposes each…
We deal with the study of the evolution of the allelic frequencies, at a single locus, for a population distributed continuously over a bounded habitat. We consider evolution which occurs under the joint action of selection and arbitrary…
Evolution has fascinated quantitative and physical scientists for decades: how can the random process of mutation, recombination, and duplication of genetic information generate the diversity of life? What determines the rate of evolution?…
The sample frequency spectrum (SFS) of DNA sequences from a collection of individuals is a summary statistic which is commonly used for parametric inference in population genetics. Despite the popularity of SFS-based inference methods,…
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…
Machine Learning methods have of late made significant efforts to solving multidisciplinary problems in the field of cancer classification using microarray gene expression data. Feature subset selection methods can play an important role in…
Recent outbreaks of infectious diseases have been monitored closely from an epidemiological and microbiological perspective. Extracting from this wealth of data the information that is relevant for the evolution of the pathogen and predict…
Clonal organisms present a particular challenge in population genetics because, in addition to the possible existence of replicates of the same genotype in a given sample, some of the hypotheses and concepts underlying classical population…
We construct genomic predictors for heritable and extremely complex human quantitative traits (height, heel bone density, and educational attainment) using modern methods in high dimensional statistics (i.e., machine learning). Replication…
Stirling numbers of the first kind are used in the derivation of several population genetics statistics, which in turn are useful for testing evolutionary hypotheses directly from DNA sequences. Here, we explore the cumulative distribution…
Genome-wide association studies (GWAS) are commonly employed to study the genetic basis of complex traits and diseases, and a key question is how much heritability could be explained by all variants in GWAS. One widely used approach that…