Estimation of Allele Frequencies From High-Coverage Genome-Sequencing Projects

No abstract is available for this paper.

• Publication year

  2009

• Venue

  Genetics

• Publication date

  2009-05-01

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1534/genetics.109.100479PMID 19293142PMCID PMC2674824
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Population Genetic Inference From Resequencing Data

  2009cited by this paper
• Estimation of nucleotide diversity, disequilibrium coefficients, and mutation rates from high-coverage genome-sequencing projects.

  2008cited by this paper
• Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals.

  2008cited by this paper
• DNA from Pre-Clovis Human Coprolites in Oregon, North America

  2008cited by this paper
• Recurrent positive selection of the Drosophila hybrid incompatibility gene Hmr.

  2008cited by this paper
• Accuracy and quality of massively parallel DNA pyrosequencing

  2007cited by this paper
• The Structure of Linkage Disequilibrium Around a Selective Sweep

  2007cited by this paper
• Joint Inference of the Distribution of Fitness Effects of Deleterious Mutations and Population Demography Based on Nucleotide Polymorphism Frequencies

  2007cited by this paper
• Patterns of damage in genomic DNA sequences from a Neandertal

  2007cited by this paper
• Accounting for bias from sequencing error in population genetic estimates.

  2007cited by this paper
• The Origins of Genome Architecture

  2007influential reference
• Genetic relatedness analysis: modern data and new challenges

  2006cited by this paper
• Genetics and analysis of quantitative traits

  1999cited by this paper
• Base-calling of automated sequencer traces using phred. II. Error probabilities.

  1998cited by this paper
• Statistical methods employed in evaluation of single-locus probe results in criminal identity cases.

  1998cited by this paper
• Base-calling of automated sequencer traces using phred. I. Accuracy assessment.

  1998cited by this paper
• Genetic Data Analysis II.

  1997cited by this paper
• Genetic data analysis II

  1997cited by this paper
• Genetics and Analysis of Quantitative Traits

  1996cited by this paper
• Genetic Data Analysis II . By Bruce S. Weir, Sunderland, Massachusetts. Sinauer Associates, Inc.445 pages. ISBN 0-87893-902-4.

  1996cited by this paper
• The neutral theory of molecular evolution.

  1983cited by this paper
• Mathematical population genetics

  1981cited by this paper
• Estimation of average heterozygosity and genetic distance from a small number of individuals.

  1978cited by this paper

• Speciation with gene flow in an island endemic hummingbird

  2025cites this paper
• β2 and β3a regulatory subunits can coassemble in the same BK channels

  2025cites this paper
• β2 and β3a regulatory subunits can coassemble in the same BK channels

  2025cites this paper
• Assessing the sensitivity of divergence time estimates to locus sampling, calibration points, and model priors in a RAD‐seq phylogeny of Carex section Schoenoxiphium

  2021cites this paper
• Appropriate Use of Bifactor Analysis in Psychopathology Research: Appreciating Benefits and Limitations.

  2020cites this paper
• Stacks 2: Analytical Methods for Paired-end Sequencing Improve RADseq-based Population Genomics

  2019cites this paper
• Distance analysis among northern and southern European legume accessions using next-generation sequencing reveal discrepancies between geographic and genetic origins

  2019cites this paper
• Genetic structure and biogeographic history of the Bicknell's Thrush/Gray-cheeked Thrush species complex

  2019cites this paper
• Phenotypic and genetic introgression across a moving woodpecker hybrid zone

  2019cites this paper
• Genetic diversity among cultivated beets (Beta vulgaris) assessed via population-based whole genome sequences

  2019cites this paper
• Efficient genome-wide genotyping strategies and data integration in crop plants

  2018cites this paper
• Isolation by distance, not incipient ecological speciation, explains genetic differentiation in an Andean songbird (Aves: Furnariidae: Cranioleuca antisiensis, Line‐cheeked Spinetail) despite near threefold body size change across an environmental gradient

  2018cites this paper
• Genotype Calling from Population-Genomic Sequencing Data

  2017cites this paper
• Analyse de la variation nucléotidique et structurale chez le soja par une approche de re-séquençage

  2017cites this paper
• Fast-GBS: a new pipeline for the efficient and highly accurate calling of SNPs from genotyping-by-sequencing data

  2017cites this paper
• Cross‐platform compatibility of de novo‐aligned SNPs in a nonmodel butterfly genus

  2017cites this paper
• Patterns of Diversification in a Neotropical Radiation of Birds (Aves: Furnariidae)

  2017cites this paper
• Bioinformatic processing of RAD‐seq data dramatically impacts downstream population genetic inference

  2017cites this paper
• Population Genomics of Paramecium Species

  2017cites this paper
• Conservation genomics reveals multiple evolutionary units within Bell’s Vireo (Vireo bellii)

  2016cites this paper
• From next-generation resequencing reads to a high-quality variant data set

  2016cites this paper
• Ecological population genomics in the marine environment.

  2016cites this paper
• Can Evolutionary Rate Matrices be Estimated from Allele Frequencies?

  2015cites this paper
• Genotype-Frequency Estimation from High-Throughput Sequencing Data

  2015influential citation
• Estimating error models for whole genome sequencing using mixtures of Dirichlet-multinomial distributions

  2015cites this paper
• Hybridization in headwater regions, and the role of rivers as drivers of speciation in Amazonian birds

  2015cites this paper
• Comparative Population Genomics of Neotropical Forest Birds

  2015cites this paper
• Addressing challenges for population genetic inference from next-generation sequencing

  2014cites this paper
• Climate-mediated movement of an avian hybrid zone.

  2014cites this paper
• Genome Informatics for High-Throughput Sequencing Data Analysis: Methods and Applications

  2014cites this paper
• Genome-wide variant discovery using sequence assembly, mapping and population-wide analysis

  2014cites this paper
• Genome-Wide Estimation of Linkage Disequilibrium from Population-Level High-Throughput Sequencing Data

  2014cites this paper
• Spatiotemporally consistent genomic signatures of reproductive isolation in a moving hybrid zone

  2014cites this paper
• Characterizing bias in population genetic inferences from low-coverage sequencing data.

  2014cites this paper
• Resequencing studies of nonmodel organisms using closely related reference genomes: optimal experimental designs and bioinformatics approaches for population genomics

  2014cites this paper
• The impact of whole-genome sequencing on the reconstruction of human population history

  2014cites this paper
• So , you want to use next-generation sequencing in marine systems ? Insight from the Pan-Pacific Advanced

  2014cites this paper
• So, You Want to Use Next Generation Sequencing In Marine Systems? Insight from the Pan Pacific Advanced Studies Institute

  2014cites this paper
• Genomic variation in a widespread Neotropical bird (Xenops minutus) reveals divergence, population expansion, and gene flow.

  2014cites this paper
• GENOMIC AND MORPHOLOGICAL ANALYSIS OF A SEMIPERMEABLE AVIAN HYBRID ZONE SUGGESTS ASYMMETRICAL INTROGRESSION OF A SEXUAL SIGNAL

  2014cites this paper
• Recent progress and challenges in population genetics of polyploid organisms: an overview of current state‐of‐the‐art molecular and statistical tools

  2014cites this paper
• On Combining Reference Data to Improve Imputation Accuracy

  2013cites this paper
• Parallel tagged amplicon sequencing reveals major lineages and phylogenetic structure in the North American tiger salamander (Ambystoma tigrinum) species complex

  2013cites this paper
• Sequence Capture versus Restriction Site Associated DNA Sequencing for Shallow Systematics.

  2013cites this paper
• Assessing the Effect of Sequencing Depth and Sample Size in Population Genetics Inferences

  2013cites this paper
• Stacks: an analysis tool set for population genomics

  2013cites this paper
• Applications of next-generation sequencing to phylogeography and phylogenetics.

  2013cites this paper
• Robust Demographic Inference from Genomic and SNP Data

  2013cites this paper
• Quantifying Population Genetic Differentiation from Next-Generation Sequencing Data

  2013cites this paper
• Theoretical framework of population genetics with somatic mutations taken into account: application to copy number variations in humans

  2013cites this paper
• Integrating phylogenetics, phylogeography and population genetics through genomes and evolutionary theory.

  2013cites this paper
• Adaptive evolution during an ongoing range expansion: the invasive bank vole (Myodes glareolus) in Ireland

  2013cites this paper
• On Estimation of Allele Frequencies via Next-Generation DNA Resequencing with Barcoding

  2013cites this paper
• Population Genetics and Parasite Diversity

  2013cites this paper
• Application of Next-Generation Sequencing Technologies for Genetic Diversity Analysis in Cereals

  2013cites this paper
• Single Nucleotide Polymorphism (SNP) Detection and Genotype Calling from Massively Parallel Sequencing (MPS) Data

  2012cites this paper
• Joint genotyping on the fly: Identifying variation among a sequenced panel of inbred lines

  2012cites this paper
• How to infer reliable diploid genotypes from NGS or traditional sequence data: from basic probability to experimental optimization

  2012cites this paper
• Population genomic analysis of model and nonmodel organisms using sequenced RAD tags.

  2012cites this paper
• Experimental Analysis of Sources of Error in Evolutionary Studies Based on Roche/454 Pyrosequencing of Viral Genomes

  2012cites this paper
• The Population Genomics of a Fast Evolver: High Levels of Diversity, Functional Constraint, and Molecular Adaptation in the Tunicate Ciona intestinalis

  2012cites this paper
• Adaptive mechanisms in pathogens: universal aneuploidy in Leishmania.

  2012cites this paper
• Quantitative trait locus analysis for next-generation sequencing with the functional linear models

  2012cites this paper
• jPopGen Suite: population genetic analysis of DNA polymorphism from nucleotide sequences with errors

  2012cites this paper
• Family-based association studies for next-generation sequencing.

  2012cites this paper
• Assessing the Accuracy and Power of Population Genetic Inference from Low-Pass Next-Generation Sequencing Data

  2012influential citation
• Differential expression--the next generation and beyond.

  2012cites this paper
• The Application of Pooled DNA Sequencing in Disease Association Study

  2012cites this paper
• Empirical Validation of Pooled Whole Genome Population Re-Sequencing in Drosophila melanogaster

  2012cites this paper
• Data Production and Analysis in Population Genomics

  2012cites this paper
• Transcriptome Analysis and SNP Development Can Resolve Population Differentiation of Streblospio benedicti, a Developmentally Dimorphic Marine Annelid

  2012cites this paper
• The simple fool's guide to population genomics via RNA‐Seq: an introduction to high‐throughput sequencing data analysis

  2012cites this paper
• Allele identification in assembled genomic sequence datasets.

  2012cites this paper
• Computational analysis of high throughput sequencing data.

  2011cites this paper
• Bayesian estimation of genomic clines

  2011cites this paper
• Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing

  2011cites this paper
• Genomic diversity in switchgrass (Panicum virgatum): from the continental scale to a dune landscape

  2011cites this paper
• Estimation of allele frequency and association mapping using next-generation sequencing data

  2011influential citation
• Two Evolutionary Histories in the Genome of Rice: the Roles of Domestication Genes

  2011cites this paper
• A Hierarchical Bayesian Model for Next-Generation Population Genomics

  2011cites this paper
• Genetic Diversity Analysis with 454 Pyrosequencing and Genomic Reduction Confirmed the Eastern and Western Division in the Cultivated Barley Gene Pool

  2011cites this paper
• Genome-wide genetic marker discovery and genotyping using next-generation sequencing

  2011cites this paper
• Study of the rate and spectrum of spontaneous mutations

  2011cites this paper
• Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance.

  2011cites this paper
• Association studies for next-generation sequencing.

  2011cites this paper
• Inference of Site Frequency Spectra From High-Throughput Sequence Data: Quantification of Selection on Nonsynonymous and Synonymous Sites in Humans

  2011cites this paper
• Alignment-free estimation of nucleotide diversity

  2011cites this paper
• Estimation of population divergence times from non-overlapping genomic sequences: examples from dogs and wolves.

  2011cites this paper
• SNP discovery and genotyping for evolutionary genetics using RAD sequencing.

  2011cites this paper
• Demographic history and rare allele sharing among human populations

  2011cites this paper
• Applications of next generation sequencing in molecular ecology of non-model organisms

  2011cites this paper
• Using Population Genomics to Detect Selection in Natural Populations: Key Concepts and Methodological Considerations

  2010cites this paper
• Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants

  2010cites this paper
• MASSIVELY PARALLEL SEQUENCING OF POOLED DNA SAMPLES-THE NEXT GENERATION OF MOLECULAR MARKERS

  2010cites this paper
• Population genetic inference from genomic sequence variation.

  2010cites this paper
• Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags

  2010cites this paper
• mlRho – a program for estimating the population mutation and recombination rates from shotgun‐sequenced diploid genomes

  2010cites this paper
• Estimating population genetic parameters and comparing model goodness-of-fit using DNA sequences with error.

  2010influential citation
• To Pool, or Not to Pool?

  2010cites this paper
• Bayesian analysis of molecular variance in pyrosequences quantifies population genetic structure across the genome of Lycaeides butterflies

  2010cites this paper