Efficient Control of Population Structure in Model Organism Association Mapping

No abstract is available for this paper.

• Publication year

  2008

• Venue

  Genetics

• Publication date

  2008-03-01

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1534/genetics.107.080101PMID 18385116PMCID PMC2278096
• 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.

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• Maize association population: a high-resolution platform for quantitative trait locus dissection.

  2005cited by this paper
• Genome-Wide Association Mapping in Arabidopsis Identifies Previously Known Flowering Time and Pathogen Resistance Genes

  2005influential reference
• Strategies for mapping and cloning quantitative trait genes in rodents

  2005cited by this paper
• Uncovering regulatory pathways that affect hematopoietic stem cell function using 'genetical genomics'

  2005cited by this paper
• Evolutionary trees from DNA sequences: A maximum likelihood approach

  2005cited by this paper
• Cis-acting expression quantitative trait loci in mice.

  2005cited by this paper
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  2005cited by this paper
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  2005cited by this paper
• Quantitative Trait Locus Analysis Using Recombinant Inbred Intercrosses

  2005cited by this paper
• A large-sample QTL study in mice: II. Body composition

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• Use of a Dense Single Nucleotide Polymorphism Map for In Silico Mapping in the Mouse

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  2004cited by this paper
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  2004influential reference
• Likelihood ratio tests in linear mixed models with one variance component

  2003cited by this paper
• Statistical significance for genomewide studies

  2003cited by this paper
• Variance Components

  2003cited by this paper
• Arabidopsis Map-Based Cloning in the Post-Genome Era

  2002cited by this paper
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  2002cited by this paper
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  2002cited by this paper
• Quantitative trait loci (QTL) for lean body mass and body length in MRL/MPJ and SJL/J F(2) mice.

  2002cited by this paper
• An estimator for pairwise relatedness using molecular markers.

  2002cited by this paper
• Quantitative trait loci (QTL) for lean body mass and body length in MRL/MPJ and SJL/J F2 mice

  2002cited by this paper
• Linear Mixed Models for Longitudinal Data

  2001cited by this paper
• A comparison of microsatellite‐based pairwise relatedness estimators

  2001cited by this paper
• Quantitative trait loci for body weight in the intercross between SM/J and A/J mice.

  2001cited by this paper
• A quick method for computing approximate thresholds for quantitative trait loci detection.

  2001cited by this paper
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  2000cited by this paper
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• Estimation of pairwise relatedness with molecular markers.

  1999cited by this paper
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  1998cited by this paper
• Multipoint quantitative-trait linkage analysis in general pedigrees.

  1998cited by this paper
• Effect of Within-Strain Sample Size on QTL Detection and Mapping Using Recombinant Inbred Mouse Strains

  1998cited by this paper
• Likelihood Ratio Tests for Fixed Model Terms using Residual Maximum Likelihood

  1997cited by this paper
• Phylogenies and the Comparative Method: A General Approach to Incorporating Phylogenetic Information into the Analysis of Interspecific Data

  1997cited by this paper
• A Hidden Markov Model approach to variation among sites in rate of evolution.

  1996cited by this paper
• Restricted Maximum Likelihood Estimation of Variance Components for Univariate Animal Models Using Sparse Matrix Techniques and Average Information

  1995cited by this paper
• Average information REML: An efficient algorithm for variance parameter estimation in linear mixed models

  1995influential reference
• Estimation of effects of single genes on quantitative traits.

  1992cited by this paper
• Estimation of Genetic Parameters in Non-Linear Models

  1990cited by this paper
• Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea

  1989cited by this paper
• Restricted maximum likelihood to estimate variance components for animal models with several random effects using a derivative-free algorithm

  1989cited by this paper
• Newton-Raphson and EM Algorithms for Linear Mixed-Effects Models for Repeated-Measures Data

  1988cited by this paper
• A Derivative-Free Approach for Estimating Variance Components in Animal Models by Restricted Maximum Likelihood1

  1987cited by this paper
• Phylogenies and the Comparative Method

  1985cited by this paper
• Applications of linear models in animal breeding

  1984cited by this paper
• Estimation in Covariance Components Models

  1981cited by this paper
• Bayesian inference for variance components using only error contrasts

  1974cited by this paper
• F approximations to the distribution of Hotelling's T20

  1974cited by this paper
• Recovery of inter-block information when block sizes are unequal

  1971cited by this paper
• Construction of phylogenetic trees.

  1967cited by this paper
• A Simplex Method for Function Minimization

  1965cited by this paper

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