12 Result(s)
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Pier Francesco Palamara
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Article
Open AccessHaplotype-based inference of recent effective population size in modern and ancient DNA samples
Individuals sharing recent ancestors are likely to co-inherit large identical-by-descent (IBD) genomic regions. The distribution of these IBD segments in a population may be used to reconstruct past demographi...
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Article
Open AccessBiobank-scale inference of ancestral recombination graphs enables genealogical analysis of complex traits
Genome-wide genealogies compactly represent the evolutionary history of a set of genomes and inferring them from genetic data has the potential to facilitate a wide range of analyses. We introduce a method, AR...
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Article
Open AccessIdentity-by-descent detection across 487,409 British samples reveals fine scale population structure and ultra-rare variant associations
Detection of Identical-By-Descent (IBD) segments provides a fundamental measure of genetic relatedness and plays a key role in a wide range of analyses. We develop FastSMC, an IBD detection algorithm that comb...
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Article
Author Correction: Linkage disequilibrium–dependent architecture of human complex traits shows action of negative selection
In the version of the paper initially published, information on competing interests for author Benjamin M. Neale was missing. The ‘Competing interests' statement should have included the sentence ‘B.M.N. is on...
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Article
Detecting genome-wide directional effects of transcription factor binding on polygenic disease risk
Biological interpretation of genome-wide association study data frequently involves assessing whether SNPs linked to a biological process, for example, binding of a transcription factor, show unsigned enrichme...
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Article
High-throughput inference of pairwise coalescence times identifies signals of selection and enriched disease heritability
Interest in reconstructing demographic histories has motivated the development of methods to estimate locus-specific pairwise coalescence times from whole-genome sequencing data. Here we introduce a powerful n...
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Article
Insights into clonal haematopoiesis from 8,342 mosaic chromosomal alterations
The selective pressures that shape clonal evolution in healthy individuals are largely unknown. Here we investigate 8,342 mosaic chromosomal alterations, from 50 kb to 249 Mb long, that we uncovered in blood-d...
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Article
Linkage disequilibrium–dependent architecture of human complex traits shows action of negative selection
Steven Gazal, Alkes Price and colleagues extend stratified LD score regression to continuous annotations. They analyze summary statistics from 56 complex diseases and traits and find that SNPs with low levels ...
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Article
Reference-based phasing using the Haplotype Reference Consortium panel
Po-Ru Loh, Alkes Price and colleagues present Eagle2, a reference-based phasing algorithm that allows for highly accurate and efficient phasing of genotypes across a broad range of cohort sizes. They demonstra...
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Article
Fast and accurate long-range phasing in a UK Biobank cohort
Po-Ru Loh, Pier Francesco Palamara and Alkes Price develop a new long-range phasing method, Eagle, that harnesses long, shared identical-by-descent tracts and can be applied to large outbred populations. They ...
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Article
Open AccessA minimal descriptor of an ancestral recombinations graph
Ancestral Recombinations Graph (ARG) is a phylogenetic structure that encodes both duplication events, such as mutations, as well as genetic exchange events, such as recombinations: this captures the (genetic)...
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Chapter and Conference Paper
Teamwork Design Based on Petri Net Plans
This paper presents a design of cooperative behaviors through Petri Net Plans, based on the principles provided by Cohen and Levesque’s Joint Commitments Theory. Petri Net Plans are a formal tool that has prov...
