184 research outputs found
The boundary of the orbital beta process
No full textThe unitarily invariant probability measures on infinite Hermitian matrices have been classified by Pickrell and by Olshanski and Vershik. This classification is equivalent to determining the boundary of a certain inhomogeneous Markov chain with given transition probabilities. This formulation of the problem makes sense for general β-ensembles when one takes as the transition probabilities the Dixon–Anderson conditional probability distribution. In this paper we determine the boundary of this Markov chain for any β∈(0,∞], also giving in this way a new proof of the classical β=2 case (Pickrell, Olshanski and Vershik). Finally, as a by-product of our results we obtain alternative proofs of the almost sure convergence of the rescaled Hua–Pickrell and Laguerre β-ensembles to the general β Hua–Pickrell and β Bessel point processes respectively; these results were obtained earlier by Killip and Stoiciu, Valkó and Virág, Ramírez and Rider
The boundary of the orbital beta process
No full textThe unitarily invariant probability measures on infinite Hermitian matrices have been classified by Pickrell and by Olshanski and Vershik. This classification is equivalent to determining the boundary of a certain inhomogeneous Markov chain with given transition probabilities. This formulation of the problem makes sense for general β-ensembles when one takes as the transition probabilities the Dixon–Anderson conditional probability distribution. In this paper we determine the boundary of this Markov chain for any β∈(0,∞], also giving in this way a new proof of the classical β=2 case (Pickrell, Olshanski and Vershik). Finally, as a by-product of our results we obtain alternative proofs of the almost sure convergence of the rescaled Hua–Pickrell and Laguerre β-ensembles to the general β Hua–Pickrell and β Bessel point processes respectively; these results were obtained earlier by Killip and Stoiciu, Valkó and Virág, Ramírez and Rider
Tucson's First Draftees In World War I
No full textThe first contingent called to serve their country in 1917 included: (front row from left) Andrew Martin, Harold Schwalen, Leonard Klein, Howard Moice, William Norton, James Donald Johns, Joseph Norvell and Joseph Roberts; (rear row, from left) Arnold Pixely, Temple Penrod, George Ruskell, Harry Chambers, William Pickrell, J.C. Nevenzel, and Joseph Fox
Detecting Polygenic Adaptation in Admixture Graphs
No full textAbstract
Polygenic adaptation occurs when natural selection changes the average value of a complex trait in a population, via small shifts in allele frequencies at many loci. Here, Racimo, Berg, and Pickrell present a method...
An open question in human evolution is the importance of polygenic adaptation: adaptive changes in the mean of a multifactorial trait due to shifts in allele frequencies across many loci. In recent years, several methods have been developed to detect polygenic adaptation using loci identified in genome-wide association studies (GWAS). Though powerful, these methods suffer from limited interpretability: they can detect which sets of populations have evidence for polygenic adaptation, but are unable to reveal where in the history of multiple populations these processes occurred. To address this, we created a method to detect polygenic adaptation in an admixture graph, which is a representation of the historical divergences and admixture events relating different populations through time. We developed a Markov chain Monte Carlo (MCMC) algorithm to infer branch-specific parameters reflecting the strength of selection in each branch of a graph. Additionally, we developed a set of summary statistics that are fast to compute and can indicate which branches are most likely to have experienced polygenic adaptation. We show via simulations that this method—which we call PolyGraph—has good power to detect polygenic adaptation, and applied it to human population genomic data from around the world. We also provide evidence that variants associated with several traits, including height, educational attainment, and self-reported unibrow, have been influenced by polygenic adaptation in different populations during human evolution.</jats:p
False positive peaks in ChIP-seq and other sequencing-based functional assays caused by unannotated high copy number regions
No full textAbstract
Motivation: Sequencing-based assays such as ChIP-seq, DNase-seq and MNase-seq have become important tools for genome annotation. In these assays, short sequence reads enriched for loci of interest are mapped to a reference genome to determine their origin. Here, we consider whether false positive peak calls can be caused by particular type of error in the reference genome: multicopy sequences which have been incorrectly assembled and collapsed into a single copy.
Results: Using sequencing data from the 1000 Genomes Project, we systematically scanned the human genome for regions of high sequencing depth. These regions are highly enriched for erroneously inferred transcription factor binding sites, positions of nucleosomes and regions of open chromatin. We suggest a simple masking procedure to remove these regions and reduce false positive calls.
Availability: Files for masking out these regions are available at eqtl.uchicago.edu
Contact: [email protected]; [email protected]; [email protected]; [email protected]
Supplementary information: Supplementary data are available at Bioinformatics online.</jats:p
Ancient DNA reveals key stages in the formation of Central European mitochondrial genetic diversity
No full textThe processes that shaped modern European mitochondrial DNA (mtDNA) variation remain unclear. The initial peopling by Palaeolithic hunter-gatherers ~42,000 years ago and the immigration of Neolithic farmers into Europe ~8000 years ago appear to have played important roles but do not explain present-day mtDNA diversity. We generated mtDNA profiles of 364 individuals from prehistoric cultures in Central Europe to perform a chronological study, spanning the Early Neolithic to the Early Bronze Age (5500 to 1550 calibrated years before the common era). We used this transect through time to identify four marked shifts in genetic composition during the Neolithic period, revealing a key role for Late Neolithic cultures in shaping modern Central European genetic diversity.Guido Brandt, Wolfgang Haak, Christina J. Adler, Christina Roth, Anna Szécsényi-Nagy, Sarah Karimnia, Sabine Möller-Rieker, Harald Meller, Robert Ganslmeier, Susanne Friederich, Veit Dresely, Nicole Nicklisch, Joseph K. Pickrell, Frank Sirocko, David Reich, Alan Cooper, Kurt W. Alt, The Genographic Consortiu
Recommended from our members
Conformal Variations of Piecewise Constant Curvature Two and Three Dimensional Manifolds
No full textPiecewise constant curvature manifolds are discrete analogues of Riemannian manifolds in which edge lengths play the role of the metric tensor. These triangulated manifolds are specified by two types of data: 1. Each edge in the triangulation is assigned a real-valued length. 2. For each simplex in the triangulation, there exists an isometric embedding of that simplex into one of three background geometries (Euclidean, hyperbolic, or spherical). In particular, this isometry respects the edge length data. By making the edge lengths functions of scalars, called conformal parameters, that are assigned to the vertices of the triangulation we obtain a conformal structure - that is, a parameterization of a discrete conformal class. We discuss how our definition of conformal structure places several existing notions of a discrete conformal class in a common framework. We then describe discrete analogues of scalar curvature for 2-and 3-manifolds and study how these curvatures depend on the conformal parameters. This leads us to some local rigidity theorems - we identify circumstances in which the mapping from conformal parameters to scalar curvatures is a local diffeomorphism. In three dimensions, we focus on the case of hyperbolic background geometry. We study a discrete analogue of the Einstein-Hilbert (or total scalar curvature) functional and investigate when this functional is locally convex
Joint Analysis of Functional Genomic Data and Genome-wide Association Studies of 18 Human Traits
No full textAnnotations of gene structures and regulatory elements can inform genome-wide association studies (GWASs). However, choosing the relevant annotations for interpreting an association study of a given trait remains challenging. I describe a statistical model that uses association statistics computed across the genome to identify classes of genomic elements that are enriched with or depleted of loci influencing a trait. The model naturally incorporates multiple types of annotations. I applied the model to GWASs of 18 human traits, including red blood cell traits, platelet traits, glucose levels, lipid levels, height, body mass index, and Crohn disease. For each trait, I used the model to evaluate the relevance of 450 different genomic annotations, including protein-coding genes, enhancers, and DNase-I hypersensitive sites in over 100 tissues and cell lines. The fraction of phenotype-associated SNPs influencing protein sequence ranged from around 2% (for platelet volume) up to around 20% (for low-density lipoprotein cholesterol), repressed chromatin was significantly depleted for SNPs associated with several traits, and cell-type-specific DNase-I hypersensitive sites were enriched with SNPs associated with several traits (for example, the spleen in platelet volume). Finally, reweighting each GWAS by using information from functional genomics increased the number of loci with high-confidence associations by around 5%
Corn-Popper
No full textPatent for a corn popper that can also be used for roasting nuts or for general cooking. Illustrations included
- …
