Related papers: Reducing pervasive false positive identical-by-des…
Identity-by-descent (IBD) is a fundamental concept in genetics with many applications. In a common definition, two haplotypes are said to contain an IBD segment if they share a segment that is inherited from a recent shared common ancestor…
Recent improvements in high-throughput genotyping and sequencing technologies have afforded the collection of massive, genome-wide datasets of DNA information from hundreds of thousands of individuals. These datasets, in turn, provide…
Reconstruction of family trees, or pedigree reconstruction, for a group of individuals is a fundamental problem in genetics. The problem is known to be NP-hard even for datasets known to only contain siblings. Some recent methods have been…
We propose a new framework for designing test and query functions for complex structures that vary across a given parameter such as genetic marker position. The operations we are interested in include equality testing, set operations,…
Recently, haplo-identical transplantation with multiple HLA mismatches has become a viable option for system cell transplants. Haplotype sharing detection requires imputation of donor and recipient. We show that even in high-resolution…
It is increasingly recognized that participation bias can pose problems for genetic studies. Recently, to overcome the challenge that genetic information of non-participants is unavailable, it is shown that by comparing the IBD (identity by…
Motivation: Recombination rates vary considerably at the fine scale within mammalian genomes, with the majority of recombination occurring within hotspots of ~2 kb in width. We present a method for inferring the location of recombination…
Widespread sharing of long, identical-by-descent (IBD) genetic segments is a hallmark of populations that have experienced recent genetic drift. Detection of these IBD segments has recently become feasible, enabling a wide range of…
Image copy detection (ICD) aims to determine whether a query image is an edited copy of any image from a reference set. Currently, there are very limited public benchmarks for ICD, while all overlook a critical challenge in real-world…
The population density and per-generation dispersal rate of a population are central parameters in the study of evolution and ecology. The distribution of recent coalescent events between individuals in space can be used to estimate such…
The single nucleotide polymorphism (SNP) is the most widely studied type of genetic variation. A haplotype is defined as the sequence of alleles at SNP sites on each haploid chromosome. Haplotype information is essential in unravelling the…
The collection of immunoglobulin genes in an individual's germline, which gives rise to B cell receptors via recombination, is known to vary significantly across individuals. In humans, for example, each individual has only a fraction of…
Inferring the causal relationships among a set of variables in the form of a directed acyclic graph (DAG) is an important but notoriously challenging problem. Recently, advancements in high-throughput genomic perturbation screens have…
We investigate saddlepoint approximations applied to the score test statistic in genome-wide association studies with binary phenotypes. The inaccuracy in the normal approximation of the score test statistic increases with increasing sample…
Accurate identification of haplotypes in sequenced human genomes can provide invaluable information about population demography and fine-scale correlations along the genome, thus empowering both population genomic and medical association…
Feature selection is a critical task in machine learning and statistics. However, existing feature selection methods either (i) rely on parametric methods such as linear or generalized linear models, (ii) lack theoretical false discovery…
Shared genealogies introduce allele dependencies in diploid genotypes, as alleles within an individual or between different individuals will likely match when they originate from a recent common ancestor. At a locus shared by a pair of…
Identity by descent (IBD) tracts and runs of homozygosity (ROH) are related concepts that refer to the autozygosity in chromosome segments. However the formal relationship between their length distributions remains to be established. Here…
We propose a novel approach to effectively detect cloned identities of social-sensor cloud service providers (i.e. social media users) in the face of incomplete non-privacy-sensitive profile data. Named ICD-IPD, the proposed approach first…
Large-scale biobanks are being collected around the world in efforts to better understand human health and risk factors for disease. They often survey hundreds of thousands of individuals, combining questionnaires with clinical, genetic,…