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LiMMBo: a simple, scalable approach for linear mixed models in high-dimensional genetic association studies

https://doi.org/10.1101/255497
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Estimation of high-dimensional prior and posterior covariance matrices in Kalman filter variants
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Voxelwise genome-wide association study (vGWAS)
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A well-conditioned estimator for large-dimensional covariance matrices
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Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines
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Dissection of genetically complex traits with extremely large pools of yeast segregants
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An integrated map of genetic variation from 1,092 human genomes
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Finding the sources of missing heritability in a yeast cross
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Genetic variants regulating expression levels and isoform diversity during embryogenesis
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A rare functional cardioprotective APOC3 variant has risen in frequency in distinct population isolates
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Combining high-throughput phenotyping and genome-wide association studies to reveal natural genetic variation in rice
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A mixed-model approach for genome-wide association studies of correlated traits in structured populations
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Efficient Bayesian mixed-model analysis increases association power in large cohorts
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Promoter shape varies across populations and affects promoter evolution and expression noise
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Mixed linear model approach adapted for genome-wide association studies
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Variance component model to account for sample structure in genome-wide association studies
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A unified mixed-model method for association mapping that accounts for multiple levels of relatedness
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FaST linear mixed models for genome-wide association studies
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Improved linear mixed models for genome-wide association studies
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Efficient multivariate linear mixed model algorithms for genome-wide association studies
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Efficient set tests for the genetic analysis of correlated traits
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The landscape of genetic complexity across 5,700 gene expression traits in yeast
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Pvclust: an R package for assessing the uncertainty in hierarchical clustering
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Estimation of pleiotropy between complex diseases using single-nucleotide polymorphism-derived genomic relationships and restricted maximum likelihood
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Two genes differentially regulated in the cell cycle and by DNA-damaging agents encode alternative regulatory subunits of ribonucleotide reductase.
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Genomewide Linkage Scan for Combined Obesity Phenotypes using Principal Component Analysis
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Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
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Genetic Dissection of Transcriptional Regulation in Budding Yeast
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GCD2, a Translational Repressor of the GCN4 Gene, Has a General Function in the Initiation of Protein Synthesis in Saccharomyces cerevisiae
inferredcites →https://doi.org/10.1145/279232.279236openalex-snapshot
Algorithm 778: L-BFGS-B
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Second-generation PLINK: rising to the challenge of larger and richer datasets
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A Statistical Framework to Infer Functional Gene Relationships From Biologically Interrelated Microarray Experiments
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Regularized estimation of large covariance matrices
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Population Structure and Cryptic Relatedness in Genetic Association Studies
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A Genome-Wide Association Study Identifies Five Loci Influencing Facial Morphology in Europeans
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A Multi-Trait, Meta-analysis for Detecting Pleiotropic Polymorphisms for Stature, Fatness and Reproduction in Beef Cattle
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Modeling 3D Facial Shape from DNA
inferredcites →https://doi.org/10.1371/journal.pgen.1006149openalex-snapshot
Genome-Wide Association Study Reveals Multiple Loci Influencing Normal Human Facial Morphology
inferredcites →https://doi.org/10.1371/journal.pmed.1001779openalex-snapshot
UK Biobank: An Open Access Resource for Identifying the Causes of a Wide Range of Complex Diseases of Middle and Old Age
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inferredcites →https://doi.org/10.2202/1544-6115.1175openalex-snapshot
A Shrinkage Approach to Large-Scale Covariance Matrix Estimation and Implications for Functional Genomics
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PhenotypeSimulator: Flexible Phenotype Simulation from Different Genetic and Noise Models

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1007/978-981-99-8251-6_9openalex-snapshot
Biological Pathway Identification
inferred← citeshttps://doi.org/10.1016/b978-0-443-15750-9.00143-9openalex-snapshot
Multivariate Quantitative Genetics
inferred← citeshttps://doi.org/10.1101/373902openalex-snapshot
Fast and flexible linear mixed models for genome-wide genetics
inferred← citeshttps://doi.org/10.1101/737676openalex-snapshot
Priors, population sizes, and power in genome-wide hypothesis tests
inferred← citeshttps://doi.org/10.11606/t.41.2019.tde-04062019-130253openalex-snapshot
Evolução da covariação genética em caracteres complexos: interação entre o mapa genótipo-fenótipo e seleção natural
inferred← citeshttps://doi.org/10.1186/s12859-023-05261-9openalex-snapshot
Priors, population sizes, and power in genome-wide hypothesis tests
inferred← citeshttps://doi.org/10.1186/s12859-023-05519-2openalex-snapshot
Regularized multi-trait multi-locus linear mixed models for genome-wide association studies and genomic selection in crops
inferred← citeshttps://doi.org/10.1371/journal.pgen.1007978openalex-snapshot
Fast and flexible linear mixed models for genome-wide genetics
inferred← citeshttps://doi.org/10.1534/g3.119.400098openalex-snapshot
Testing Pleiotropy vs. Separate QTL in Multiparental Populations
inferred← citeshttps://doi.org/10.6084/m9.figshare.26585133openalex-snapshot
Additional file 1 of Priors, population sizes, and power in genome-wide hypothesis tests
inferred← citeshttps://doi.org/10.6084/m9.figshare.26585136openalex-snapshot
Additional file 2 of Priors, population sizes, and power in genome-wide hypothesis tests
inferred← citeshttps://doi.org/10.6084/m9.figshare.26585139openalex-snapshot
Additional file 3 of Priors, population sizes, and power in genome-wide hypothesis tests
inferred← citeshttps://doi.org/10.6084/m9.figshare.26585142openalex-snapshot
Additional file 4 of Priors, population sizes, and power in genome-wide hypothesis tests
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