Related papers: Detection of selective sweeps in cattle using geno…
Genetic variation in human populations is influenced by geographic ancestry due to spatial locality in historical mating and migration patterns. Spatial population structure in genetic datasets has been traditionally analyzed using either…
The phenomenon of gene conservation is an interesting evolutionary problem related to speciation and adaptation. Conserved genes are acted upon in evolution in a way that preserves their function despite other structural and functional…
Cryptic genetic sequences have attenuated effects on phenotypes. In the classic view, relaxed selection allows cryptic genetic diversity to build up across individuals in a population, providing alleles that may later contribute to…
High-throughput shotgun sequence data makes it possible in principle to accurately estimate population genetic parameters without confounding by SNP ascertainment bias. One such statistic of interest is the proportion of heterozygous sites…
When an advantageous mutation occurs in a population, the favorable allele may spread to the entire population in a short time, an event known as a selective sweep. As a result, when we sample $n$ individuals from a population and trace…
Detecting genomic footprints of selection is an important step in the understanding of evolution. Accounting for linkage disequilibrium in genome scans allows increasing the detection power, but haplotype-based methods require individual…
The usefulness of a `total-evidence' approach to human population genetics was assessed through a clustering analysis of combined genome-wide SNP datasets. The combination contained only 3146 SNPs. Detailed examination of the results…
Speciation is of fundamental importance to understanding the huge diversity of life on Earth. In contrast to current phenomenological models, we develop a biophysically motivated approach to study speciation involving the co-evolution of…
Genome Wide Association Studies (GWAS) are used to identify statistically significant genetic variants in case-control studies. GWAS typically use a p-value threshold of 5 x 10-8 to identify highly ranked single nucleotide polymorphisms…
Deep learning has revolutionized many industries by enabling models to automatically learn complex patterns from raw data, reducing dependence on manual feature engineering. However, deep learning algorithms are sensitive to input data, and…
Although a number of studies have shown that natural and laboratory populations initially well-adapted to their environment can evolve rapidly when conditions suddenly change, the dynamics of rapid adaptation are not well understood. Here a…
Training datasets are crucial for convolutional neural network-based algorithms, which directly impact their overall performance. As such, using a well-structured dataset that has minimum level of bias is always desirable. In this paper, we…
In this paper we present a method for localisation of facial landmarks on human and sheep. We introduce a new feature extraction scheme called triplet-interpolated feature used at each iteration of the cascaded shape regression framework.…
The neutral mutation rate is known to vary widely along human chromosomes, leading to mutational hot and cold regions. We provide evidence that categories of functionally-related genes reside preferentially in mutationally hot or cold…
Motivation Protein fold recognition is an important problem in structural bioinformatics. Almost all traditional fold recognition methods use sequence (homology) comparison to indirectly predict the fold of a tar get protein based on the…
Buffaloes are farm animals that contribute to food security by providing high quality meat and milk. They can better tolerate the adverse effects of global climate change on their meat and milk production. Despite their advantages,…
Plant breeding and variety trials are usually conducted in multiple environments sampled from a defined target population of environments in order to characterize the performance of breeding lines or varieties. When the population is large…
Motivation: Most existing methods for DNA sequence analysis rely on accurate sequences or genotypes. However, in applications of the next-generation sequencing (NGS), accurate genotypes may not be easily obtained (e.g. multi-sample…
Identifying genes that display spatial patterns is critical to investigating expression interactions within a spatial context and further dissecting biological understanding of complex mechanistic functionality. Despite the increase in…
The aetiology of polygenic obesity is multifactorial, which indicates that life-style and environmental factors may influence multiples genes to aggravate this disorder. Several low-risk single nucleotide polymorphisms (SNPs) have been…