Calibrating a coalescent simulation of human genome sequence variation

scientific article published on November 2005

Calibrating a coalescent simulation of human genome sequence variation is …
instance of (P31):
scholarly articleQ13442814

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P356DOI10.1101/GR.3709305
P932PMC publication ID1310645
P698PubMed publication ID16251467
P5875ResearchGate publication ID7516121

P50authorDavid AltshulerQ5230746
David ReichQ5238967
Stacey GabrielQ32649203
Stephen F SchaffnerQ37366508
Mark Joseph DalyQ39071290
P2093author name stringCatherine Foo
P2860cites workPopulation history and natural selection shape patterns of genetic variation in 132 genesQ21146407
Detecting recent positive selection in the human genome from haplotype structureQ22122511
Selection versus demography: a multilocus investigation of the domestication process in maizeQ48201320
Chromosome-wide distribution of haplotype blocks and the role of recombination hot spotsQ56879657
Recombination hotspots rather than population history dominate linkage disequilibrium in the MHC class II regionQ78685657
Evidence for substantial fine-scale variation in recombination rates across the human genomeQ80174941
The structure of haplotype blocks in the human genomeQ27860500
Intensely punctate meiotic recombination in the class II region of the major histocompatibility complexQ28190352
A map of human genome sequence variation containing 1.42 million single nucleotide polymorphismsQ28203288
Crossover clustering and rapid decay of linkage disequilibrium in the Xp/Yp pseudoautosomal gene SHOXQ28207843
A DNA polymorphism discovery resource for research on human genetic variationQ28292727
Generating samples under a Wright-Fisher neutral model of genetic variationQ29547168
A high-resolution recombination map of the human genomeQ29547815
Linkage disequilibrium in the human genomeQ29616097
Linkage disequilibrium in humans: models and dataQ30654298
Theory of the effects of population structure and sampling on patterns of linkage disequilibrium applied to genomic data from humansQ30813006
The allele frequency spectrum in genome-wide human variation data reveals signals of differential demographic history in three large world populationsQ30912371
Assessing the performance of the haplotype block model of linkage disequilibriumQ33906300
Population-genetic basis of haplotype blocks in the 5q31 regionQ33909547
Gene conversion and different population histories may explain the contrast between polymorphism and linkage disequilibrium levelsQ34020571
The discovery of single-nucleotide polymorphisms--and inferences about human demographic historyQ34044860
Human genome sequence variation and the influence of gene history, mutation and recombinationQ34142742
The fine-scale structure of recombination rate variation in the human genomeQ34315919
Patterns of linkage disequilibrium in the human genomeQ34609904
Testing models of selection and demography in Drosophila simulansQ34615919
A coalescent model of recombination hotspotsQ34617535
Haplotype blocks and linkage disequilibrium in the human genomeQ35191477
High-resolution patterns of meiotic recombination across the human major histocompatibility complexQ37202950
P433issue11
P407language of work or nameEnglishQ1860
P304page(s)1576-1583
P577publication date2005-11-01
P1433published inGenome ResearchQ5533485
P1476titleCalibrating a coalescent simulation of human genome sequence variation
P478volume15

Reverse relations

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Q46523768Recombination rates in admixed individuals identified by ancestry-based inference
Q39496810Refining the Use of Linkage Disequilibrium as a Robust Signature of Selective Sweeps
Q57278407Refining the impact of TCF7L2 gene variants on type 2 diabetes and adaptive evolution
Q41963101Replication of genetic associations as pseudoreplication due to shared genealogy
Q53392505Reproducible simulations of realistic samples for next-generation sequencing studies using Variant Simulation Tools.
Q36702004Reproduction and immunity-driven natural selection in the human WFDC locus
Q34400818Resurrecting surviving Neandertal lineages from modern human genomes
Q90573058Retrospective Association Analysis of Longitudinal Binary Traits Identifies Important Loci and Pathways in Cocaine Use
Q30992447Reveel: large-scale population genotyping using low-coverage sequencing data
Q35748549Robust and Powerful Affected Sibpair Test for Rare Variant Association
Q40235180Sampling ARG of multiple populations under complex configurations of subdivision and admixture
Q24676642Scan of human genome reveals no new Loci under ancient balancing selection
Q36017094Scan-statistic approach identifies clusters of rare disease variants in LRP2, a gene linked and associated with autism spectrum disorders, in three datasets
Q37318455Scanning for genomic regions subject to selective sweeps using SNP-MaP strategy.
Q50631433Searching for signals of evolutionary selection in 168 genes related to immune function.
Q37076975Selection and explosive growth alter genetic architecture and hamper the detection of causal rare variants
Q34462822Selection and reduced population size cannot explain higher amounts of Neandertal ancestry in East Asian than in European human populations
Q42684890SeqSIMLA2: simulating correlated quantitative traits accounting for shared environmental effects in user-specified pedigree structure
Q40377156SeqSIMLA2_exact: simulate multiple disease sites in large pedigrees with given disease status for diseases with low prevalence
Q34778042SeqSIMLA: a sequence and phenotype simulation tool for complex disease studies
Q35982039Sequence Kernel Association Analysis of Rare Variant Set Based on the Marginal Regression Model for Binary Traits
Q36494204Sequence Kernel Association Test of Multiple Continuous Phenotypes
Q36909285Sequence kernel association tests for the combined effect of rare and common variants
Q33559782Sequence variation and genetic evolution at the human F12 locus: mapping quantitative trait nucleotides that influence FXII plasma levels
Q42854796Sequence-level population simulations over large genomic regions
Q50707628SequenceLDhot: detecting recombination hotspots.
Q24630443Shared and unique components of human population structure and genome-wide signals of positive selection in South Asia
Q24651949Signals of recent positive selection in a worldwide sample of human populations
Q34153592Signatures of positive selection apparent in a small sample of human exomes
Q33862553Similarity in recombination rate estimates highly correlates with genetic differentiation in humans
Q35898620Similarity-based multimarker association tests for continuous traits.
Q31125474Simulating association studies: a data-based resampling method for candidate regions or whole genome scans
Q34590469Simulating gene trees under the multispecies coalescent and time-dependent migration
Q33546641Simulating gene-environment interactions in complex human diseases
Q37480771Simulation of genomes: a review.
Q33354962Simultaneous analysis of all SNPs in genome-wide and re-sequencing association studies
Q35862959Small Sample Kernel Association Tests for Human Genetic and Microbiome Association Studies
Q24678953Statistical evaluation of alternative models of human evolution
Q35919633Strong Selection at MHC in Mexicans since Admixture
Q34569870Sum of parts is greater than the whole: inference of common genetic history of populations
Q36202029Systematic underestimation of the age of selected alleles
Q24678506TLR4 polymorphisms, infectious diseases, and evolutionary pressure during migration of modern humans
Q31115682Tag SNP selection for candidate gene association studies using HapMap and gene resequencing data
Q36010533Testing Rare-Variant Association without Calling Genotypes Allows for Systematic Differences in Sequencing between Cases and Controls
Q50968371Testing the effect of rare compound-heterozygous and recessive mutations in case--parent sequencing studies.
Q37025075The Complex Admixture History and Recent Southern Origins of Siberian Populations
Q21090229The case for selection at CCR5-Delta32
Q37636303The deleterious mutation load is insensitive to recent population history
Q30577440The effect of genomic inversions on estimation of population genetic parameters from SNP data
Q33895392The effect of recent admixture on inference of ancient human population history
Q47335562The effective size of the Icelandic population and the prospects for LD mapping: inference from unphased microsatellite markers
Q30853607The effects of demography and long-term selection on the accuracy of genomic prediction with sequence data
Q35514258The genetic legacy of the expansion of Turkic-speaking nomads across Eurasia
Q60046260The impact of a fine-scale population stratification on rare variant association test results
Q37628796The impact of accelerating faster than exponential population growth on genetic variation
Q46816983The impact of natural selection on an ABCC11 SNP determining earwax type.
Q36935092The impact of natural selection on health and disease: uses of the population genetics approach in humans
Q42118230The light skin allele of SLC24A5 in South Asians and Europeans shares identity by descent
Q41809234The promise and limitations of population exomics for human evolution studies
Q21145001The role of geography in human adaptation
Q36993031The signature of long-standing balancing selection at the human defensin beta-1 promoter.
Q24599166The timing of pigmentation lightening in Europeans
Q42135854The value of statistical or bioinformatics annotation for rare variant association with quantitative trait
Q42369086To identify associations with rare variants, just WHaIT: Weighted haplotype and imputation-based tests
Q46650409Tracing genetic history of modern humans using X-chromosome lineages
Q26828744Two-phase and family-based designs for next-generation sequencing studies
Q38606760Unified Sequence-Based Association Tests Allowing for Multiple Functional Annotations and Meta-Analysis of Noncoding Variation in Metabochip Data
Q43731365Using maximal segmental score in genome-wide association studies
Q34000914Utilizing population controls in rare-variant case-parent association tests
Q53093415Variants in SNAP25 are targets of natural selection and influence verbal performances in women.
Q28603568Whole-genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection
Q35927954Widely distributed noncoding purifying selection in the human genome
Q37119639Widespread balancing selection and pathogen-driven selection at blood group antigen genes
Q91639265metaFARVAT: An Efficient Tool for Meta-Analysis of Family-Based, Case-Control, and Population-Based Rare Variant Association Studies
Q51927442msHOT: modifying Hudson's ms simulator to incorporate crossover and gene conversion hotspots.

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