Related papers: Improved haplotyping of rare variants using next-g…
In this paper, we propose Hard Person Identity Mining (HPIM) that attempts to refine the hard example mining to improve the exploration efficacy in person re-identification. It is motivated by following observation: the more attributes some…
The widely used genetic pleiotropic analysis of multiple phenotypes are often designed for examining the relationship between common variants and a few phenotypes. They are not suited for both high dimensional phenotypes and high…
RNA-Seq technology allows for studying the transcriptional state of the cell at an unprecedented level of detail. Beyond quantification of whole-gene expression, it is now possible to disentangle the abundance of individual alternatively…
Population-scale pangenome analysis increasingly requires representations that unify single-nucleotide and structural variation while remaining scalable across large cohorts. Existing formats are typically sequence-centric, path-centric, or…
Motivated by applications in neuroanatomy, we propose a novel methodology for estimating the heritability which corresponds to the proportion of phenotypic variance which can be explained by genetic factors. Estimating this quantity for…
Background: The learning of genotype-phenotype associations and history of human disease by doing detailed and precise analysis of phenotypic abnormalities can be defined as deep phenotyping. To understand and detect this interaction…
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…
Haplotypes, the global patterns of DNA sequence variation, have important implications for identifying complex traits. Recently, blocks of limited haplotype diversity have been discovered in human chromosomes, intensifying the research on…
With advancements in next generation sequencing technology, a massive amount of sequencing data are generated, offering a great opportunity to comprehensively investigate the role of rare variants in the genetic etiology of complex…
Whole and targeted sequencing of human genomes is a promising, increasingly feasible tool for discovering genetic contributions to risk of complex diseases. A key step is calling an individual's genotype from the multiple aligned short read…
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…
Genetic risk prediction is an important component of individualized medicine, but prediction accuracies remain low for many complex diseases. A fundamental limitation is the sample sizes of the studies on which the prediction algorithms are…
With the recent advances in DNA sequencing, it is now possible to have complete genomes of individuals sequenced and assembled. This rich and focused genotype information can be used to do different population-wide studies, now first time…
Phenotyping is fundamental to rare disease diagnosis, but manual curation of structured phenotypes from clinical notes is labor-intensive and difficult to scale. Existing artificial intelligence approaches typically optimize individual…
High throughput sequencing is a technology that allows for the generation of millions of reads of genomic data regarding a study of interest, and data from high throughput sequencing platforms are usually count compositions. Subsequent…
A protocol for the identification of ancestry informative markers (AIMs) from genome-wide single nucleotide polymorphism (SNP) data is proposed. The protocol consists of three main steps: (a) identification of potential positive selection…
The diversity of virus populations within single infected hosts presents a major difficulty for the natural immune response as well as for vaccine design and antiviral drug therapy. Recently developed pyrophosphate based sequencing…
Affordable, high-quality whole-genome assemblies have made it possible to construct rich pangenomes that capture haplotype diversity across many species. As these datasets grow, they motivate the development of specialized techniques…
Phenotypic heterogeneity is a most fascinating property of a population of cells, which shows the differences among individuals even with the same genetic background and extracellular environmental conditions. However, the lack of…
Reconstructing components of a genomic mixture from data obtained by means of DNA sequencing is a challenging problem encountered in a variety of applications including single individual haplotyping and studies of viral communities.…