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LIMIX: genetic analysis of multiple traits

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/s00439-006-0240-zopenalex-snapshot

Bias, precision and heritability of self-reported and clinically measured height in Australian twins

inferredcites →https://doi.org/10.1007/s00439-012-1220-0openalex-snapshot

Pleiotropy and allelic heterogeneity in the TOMM40-APOE genomic region related to clinical and metabolic features of hepatitis C infection

inferredcites →https://doi.org/10.1016/j.ajhg.2011.05.029openalex-snapshot

Rare-Variant Association Testing for Sequencing Data with the Sequence Kernel Association Test

inferredcites →https://doi.org/10.1016/s0925-2312(97)90018-7openalex-snapshot

Advances in neural information processing systems 7

inferredcites →https://doi.org/10.1038/nature08872openalex-snapshot

Understanding mechanisms underlying human gene expression variation with RNA sequencing

inferredcites →https://doi.org/10.1038/nature12531openalex-snapshot

Transcriptome and genome sequencing uncovers functional variation in humans

inferredcites →https://doi.org/10.1038/nature12772openalex-snapshot

The effects of genetic variation on gene expression dynamics during development

inferredcites →https://doi.org/10.1038/ng.2310openalex-snapshot

Genome-wide efficient mixed-model analysis for association studies

inferredcites →https://doi.org/10.1038/ng.2314openalex-snapshot

An efficient multi-locus mixed-model approach for genome-wide association studies in structured populations

inferredcites →https://doi.org/10.1038/ng.2376openalex-snapshot

A mixed-model approach for genome-wide association studies of correlated traits in structured populations

inferredcites →https://doi.org/10.1038/ng.271openalex-snapshot

Genome-wide association analysis of metabolic traits in a birth cohort from a founder population

inferredcites →https://doi.org/10.1038/ng.546openalex-snapshot

Mixed linear model approach adapted for genome-wide association studies

inferredcites →https://doi.org/10.1038/ng.548openalex-snapshot

Variance component model to account for sample structure in genome-wide association studies

inferredcites →https://doi.org/10.1038/ng.608openalex-snapshot

Common SNPs explain a large proportion of the heritability for human height

inferredcites →https://doi.org/10.1038/ng.823openalex-snapshot

Genome partitioning of genetic variation for complex traits using common SNPs

inferredcites →https://doi.org/10.1038/nmeth.1681openalex-snapshot

FaST linear mixed models for genome-wide association studies

inferredcites →https://doi.org/10.1038/nmeth.2848openalex-snapshot

Efficient multivariate linear mixed model algorithms for genome-wide association studies

inferredcites →https://doi.org/10.1073/pnas.1002425107openalex-snapshot

Correction for hidden confounders in the genetic analysis of gene expression

inferredcites →https://doi.org/10.1073/pnas.1530509100openalex-snapshot

Statistical significance for genomewide studies

inferredcites →https://doi.org/10.1093/bioinformatics/bts260openalex-snapshot

Identifying differentially expressed transcripts from RNA-seq data with biological variation

inferredcites →https://doi.org/10.1093/bioinformatics/btt177openalex-snapshot

A powerful and efficient set test for genetic markers that handles confounders

inferredcites →https://doi.org/10.1093/biomet/58.3.545openalex-snapshot

Recovery of Inter-Block Information when Block Sizes are Unequal

inferredcites →https://doi.org/10.1093/emboj/17.24.7170openalex-snapshot

Yeast mitochondrial F1F0‐ATP synthase exists as a dimer: identification of three dimer‐specific subunits

inferredcites →https://doi.org/10.1093/genetics/140.3.1111openalex-snapshot

Multiple trait analysis of genetic mapping for quantitative trait loci.

inferredcites →https://doi.org/10.1093/nar/27.1.29openalex-snapshot

KEGG: Kyoto Encyclopedia of Genes and Genomes

inferredcites →https://doi.org/10.1093/nar/28.1.27openalex-snapshot

KEGG: Kyoto Encyclopedia of Genes and Genomes

inferredcites →https://doi.org/10.1111/1467-9868.00196openalex-snapshot

Probabilistic Principal Component Analysis

inferredcites →https://doi.org/10.1161/atvbaha.109.201020openalex-snapshot

Genetic Variants Influencing Circulating Lipid Levels and Risk of Coronary Artery Disease

inferredcites →https://doi.org/10.1186/1297-9686-23-1-67openalex-snapshot

Estimating variances and covariances for multivariate animal models by restricted maximum likelihood

inferredcites →https://doi.org/10.1186/gb-2009-10-3-r25openalex-snapshot

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

inferredcites →https://doi.org/10.1214/009053607000000758openalex-snapshot

Regularized estimation of large covariance matrices

inferredcites →https://doi.org/10.1214/ss/1177011926openalex-snapshot

That BLUP is a Good Thing: The Estimation of Random Effects

inferredcites →https://doi.org/10.1371/journal.pbio.0060083openalex-snapshot

Gene–Environment Interaction in Yeast Gene Expression

inferredcites →https://doi.org/10.1371/journal.pcbi.1000770openalex-snapshot

A Bayesian Framework to Account for Complex Non-Genetic Factors in Gene Expression Levels Greatly Increases Power in eQTL Studies

inferredcites →https://doi.org/10.1371/journal.pcbi.1002330openalex-snapshot

Joint Modelling of Confounding Factors and Prominent Genetic Regulators Provides Increased Accuracy in Genetical Genomics Studies

inferredcites →https://doi.org/10.1371/journal.pgen.0030161openalex-snapshot

Capturing Heterogeneity in Gene Expression Studies by Surrogate Variable Analysis

inferredcites →https://doi.org/10.1371/journal.pgen.1001276openalex-snapshot

Joint Genetic Analysis of Gene Expression Data with Inferred Cellular Phenotypes

inferredcites →https://doi.org/10.1371/journal.pgen.1001317openalex-snapshot

Single-Tissue and Cross-Tissue Heritability of Gene Expression Via Identity-by-Descent in Related or Unrelated Individuals

inferredcites →https://doi.org/10.1371/journal.pgen.1003396openalex-snapshot

Robust Prediction of Expression Differences among Human Individuals Using Only Genotype Information

inferredcites →https://doi.org/10.1371/journal.pgen.1003491openalex-snapshot

Effectively Identifying eQTLs from Multiple Tissues by Combining Mixed Model and Meta-analytic Approaches

inferredcites →https://doi.org/10.1371/journal.pgen.1003608openalex-snapshot

Prediction of Complex Human Traits Using the Genomic Best Linear Unbiased Predictor

inferredcites →https://doi.org/10.1371/journal.pgen.1004022openalex-snapshot

Meta-Analysis Identifies Gene-by-Environment Interactions as Demonstrated in a Study of 4,965 Mice

inferredcites →https://doi.org/10.1534/genetics.109.113381openalex-snapshot

Better Estimates of Genetic Covariance Matrices by “Bending” Using Penalized Maximum Likelihood

inferredcites →https://doi.org/10.2307/2529430openalex-snapshot

Best Linear Unbiased Estimation and Prediction under a Selection Model

inferredcites →https://doi.org/10.7551/mitpress/3206.001.0001openalex-snapshot

Gaussian Processes for Machine Learning

What points at this work

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

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Powerful rare variant association testing in a copula‐based joint analysis of multiple phenotypes

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Advances in Maize Genomics

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Biological Pathway Identification

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Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients

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Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions

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Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters

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Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells

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Recurrent inversion polymorphisms in humans associate with genetic instability and genomic disorders

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Modeling Cell-Cell Interactions from Spatial Molecular Data with Spatial Variance Component Analysis

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Genetic mapping of quantitative trait loci in crops

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Functional interrogation of twenty type 2 diabetes-associated genes using isogenic human embryonic stem cell-derived β-like cells

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SNPs, short tandem repeats, and structural variants are responsible for differential gene expression across C57BL/6 and C57BL/10 substrains

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Introduction to Machine Learning in Digital Healthcare Epidemiology

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Genetic variants regulating expression levels and isoform diversity during embryogenesis

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Common genetic variation drives molecular heterogeneity in human iPSCs

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Predicting quantitative traits from genome and phenome with near perfect accuracy

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Powerful decomposition of complex traits in a diploid model

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A random forest approach to capture genetic effects in the presence of population structure

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Promoter shape varies across populations and affects promoter evolution and expression noise

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Genome-wide association mapping for grain manganese in rice (Oryza sativa L.) using a multi-experiment approach

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Revisiting a GWAS peak in Arabidopsis thaliana reveals possible confounding by genetic heterogeneity

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The germline genetic component of drug sensitivity in cancer cell lines

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GSNOR provides plant tolerance to iron toxicity via preventing iron-dependent nitrosative and oxidative cytotoxicity

inferred← citeshttps://doi.org/10.1038/s41467-020-16482-4openalex-snapshot

Properties of structural variants and short tandem repeats associated with gene expression and complex traits

inferred← citeshttps://doi.org/10.1038/s41467-021-22548-8openalex-snapshot

Genetic perturbation of PU.1 binding and chromatin looping at neutrophil enhancers associates with autoimmune disease

inferred← citeshttps://doi.org/10.1038/s41467-025-61327-7openalex-snapshot

Suppression of gut colonization by multidrug-resistant Escherichia coli clinical isolates through cooperative niche exclusion

inferred← citeshttps://doi.org/10.1038/s41467-025-66105-zopenalex-snapshot

Genetic architecture and mechanisms of host-microbiome interactions from a multi-cohort analysis of outbred laboratory rats

inferred← citeshttps://doi.org/10.1038/s41477-025-02148-wopenalex-snapshot

Major alleles of CDCA7 shape CG methylation in Arabidopsis thaliana

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Genomic basis for RNA alterations in cancer

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Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation

inferred← citeshttps://doi.org/10.1038/s41588-024-01702-0openalex-snapshot

Cell-type-specific and disease-associated expression quantitative trait loci in the human lung

inferred← citeshttps://doi.org/10.1038/s41591-021-01441-3openalex-snapshot

Mitochondrial DNA variants modulate N-formylmethionine, proteostasis and risk of late-onset human diseases

inferred← citeshttps://doi.org/10.1038/s41598-022-15058-0openalex-snapshot

DNA methylation fingerprint of hepatocellular carcinoma from tissue and liquid biopsies

inferred← citeshttps://doi.org/10.1093/bioinformatics/btac369openalex-snapshot

transferGWAS: GWAS of images using deep transfer learning

inferred← citeshttps://doi.org/10.1093/bioinformatics/btac455openalex-snapshot

Efficient permutation-based genome-wide association studies for normal and skewed phenotypic distributions

inferred← citeshttps://doi.org/10.1093/femsec/fiaa202openalex-snapshot

Massive rhizobial genomic variation associated with partner quality in Lotus–Mesorhizobium symbiosis

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The Carbon Footprint of Bioinformatics

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Metabolome plasticity in 241Arabidopsis thalianaaccessions reveals evolutionary cold adaptation processes

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A genome-wide association study identifies Arabidopsis thaliana genes that contribute to differences in the outcome of infection with two Turnip mosaic potyvirus strains that differ in their evolutionary history and degree of host specialization

inferred← citeshttps://doi.org/10.1099/mgen.0.001349openalex-snapshot

microGWAS: a computational pipeline to perform large-scale bacterial genome-wide association studies

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Genomic basis for RNA alterations revealed by whole-genome analyses of 27 cancer types

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Haplotype-resolved inversion landscape reveals hotspots of mutational recurrence associated with genomic disorders

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Cell type-specific and disease-associated eQTL in the human lung

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Major alleles of CDCA7α shape CG-methylation in Arabidopsis thaliana

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High cell-type specificity of eQTLs revealed by single-nucleus analyses of brain and blood

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Variation in PU.1 binding and chromatin looping at neutrophil enhancers influences autoimmune disease susceptibility

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Genomic properties of structural variants and short tandem repeats that impact gene expression and complex traits in humans

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Multi-trait multi-locus SEM model discriminates SNPs of different effects

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Modelling local gene networks increases power to detect trans-acting genetic effects on gene expression

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SCANPY: large-scale single-cell gene expression data analysis

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"Missing" G x E Variation Controls Flowering Time in Arabidopsis thaliana

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Joint genetic analysis using variant sets reveals polygenic gene-context interactions

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Common alleles of CMT2 and NRPE1 are major determinants of CHH methylation variation in Arabidopsis thaliana

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Conditional GWAS of non-CG transposon methylation in Arabidopsis thaliana reveals major polymorphisms in five genes

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On the causes of gene-body methylation variation in Arabidopsis thaliana

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The bacterial genetic determinants of Escherichia coli capacity to cause bloodstream infections in humans

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The maternal environment interacts with genetic variation in regulating seed dormancy in Swedish Arabidopsis thaliana

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Interactions between genetic variation and cellular environment in skeletal muscle gene expression

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Investigating the effect of dependence between conditions with Bayesian Linear Mixed Models for motif activity analysis

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The impact of the genetic background on gene deletion phenotypes in Saccharomyces cerevisiae

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Drug mechanism‐of‐action discovery through the integration of pharmacological and CRISPR screens

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Predictive features of gene expression variation reveal mechanistic link with differential expression

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CellRegMap: a statistical framework for mapping context‐specific regulatory variants using scRNA‐seq

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GWAS with Heterogeneous Data: Estimating the Fraction of Phenotypic Variation Mediated by Gene Expression Data

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Connecting phenotype to genotype: PheWAS-inspired analysis of autism spectrum disorder

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TorchLIMIX: GPU-accelerated multivariate genome-wide association studies

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Elucidating the genetic basis of variation in populations by large scale phenomics and genomics

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Combining Association and Haplotype Studies Towards the Improvement of Fruit Quality in Tomato

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DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation

inferred← citeshttps://doi.org/10.7554/elife.57390openalex-snapshot

Population-scale proteome variation in human induced pluripotent stem cells

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Pneumococcal genetic variability in age-dependent bacterial carriage

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Genetic basis of Arabidopsis thaliana responses to infection by naïve and adapted isolates of turnip mosaic virus

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Genetic basis of Arabidopsis thaliana responses to infection by naïve and adapted isolates of turnip mosaic virus

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