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Efficient analysis of large-scale genome-wide data with two R packages: bigstatsr and bigsnpr
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Analysis of Genetic Association Studies
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Long-Range LD Can Confound Genome Scans in Admixed Populations
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The Population Reference Sample, POPRES: A Resource for Population, Disease, and Pharmacological Genetics Research
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A Unified Approach to Genotype Imputation and Haplotype-Phase Inference for Large Data Sets of Trios and Unrelated Individuals
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Effective Genetic-Risk Prediction Using Mixed Models
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Modeling Linkage Disequilibrium Increases Accuracy of Polygenic Risk Scores
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Fast Principal-Component Analysis Reveals Convergent Evolution of ADH1B in Europe and East Asia
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Population structure, migration, and diversifying selection in the Netherlands
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Complex disease and phenotype mapping in the domestic dog
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Projecting the performance of risk prediction based on polygenic analyses of genome-wide association studies
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A reference panel of 64,976 haplotypes for genotype imputation
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Multiple common variants for celiac disease influencing immune gene expression
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Principal components analysis corrects for stratification in genome-wide association studies
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Genotype imputation for genome-wide association studies
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PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses
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Rapid and Accurate Haplotype Phasing and Missing-Data Inference for Whole-Genome Association Studies By Use of Localized Haplotype Clustering
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GenABEL: an R library for genome-wide association analysis
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ccSVM: correcting Support Vector Machines for confounding factors in biological data classification
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The variant call format and VCFtools
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A high-performance computing toolset for relatedness and principal component analysis of SNP data
inferredcites →https://doi.org/10.1093/bioinformatics/bts610openalex-snapshot
GWASTools: an R/Bioconductor package for quality control and analysis of genome-wide association studies
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PRSice: Polygenic Risk Score software
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FlashPCA2: principal component analysis of Biobank-scale genotype datasets
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pcadapt : an R package to perform genome scans for selection based on principal component analysis
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Regularization and Variable Selection Via the Elastic Net
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Strong Rules for Discarding Predictors in Lasso-Type Problems
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Regression Shrinkage and Selection Via the Lasso
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Deflation Techniques for an Implicitly Restarted Arnoldi Iteration
inferredcites →https://doi.org/10.1186/1471-2105-11-134openalex-snapshot
ProbABEL package for genome-wide association analysis of imputed data
inferredcites →https://doi.org/10.1186/1471-2105-13-88openalex-snapshot
SparSNP: Fast and memory-efficient analysis of all SNPs for phenotype prediction
inferredcites →https://doi.org/10.1186/1471-2105-14-166openalex-snapshot
GWAS on your notebook: fast semi-parallel linear and logistic regression for genome-wide association studies
inferredcites →https://doi.org/10.1186/1471-2105-9-526openalex-snapshot
SNPFile – A software library and file format for large scale association mapping and population genetics studies
inferredcites →https://doi.org/10.1186/1756-0500-5-404openalex-snapshot
Fast accurate missing SNP genotype local imputation
inferredcites →https://doi.org/10.1186/s13742-015-0047-8openalex-snapshot
Second-generation PLINK: rising to the challenge of larger and richer datasets
inferredcites →https://doi.org/10.1371/journal.pgen.1003348openalex-snapshot
Power and Predictive Accuracy of Polygenic Risk Scores
inferredcites →https://doi.org/10.1371/journal.pgen.1006091openalex-snapshot
Bias Characterization in Probabilistic Genotype Data and Improved Signal Detection with Multiple Imputation
inferredcites →https://doi.org/10.1371/journal.pone.0093766openalex-snapshot
Fast Principal Component Analysis of Large-Scale Genome-Wide Data
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Regularization Paths for Generalized Linear Models via Coordinate Descent
inferredcites →https://doi.org/10.18637/jss.v040.i08openalex-snapshot
Rcpp : Seamless R and C++ Integration
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Scalable Strategies for Computing with Massive Data
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RSpectra: Solvers for Large-Scale Eigenvalue and SVD Problems
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R: A Language and Environment for Statistical Computing
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The biglasso Package: A Memory- and Computation-Efficient Solver for Lasso Model Fitting with Big Data in R
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Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Leveraging both individual-level genetic data and GWAS summary statistics increases polygenic prediction
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Accounting for age of onset and family history improves power in genome-wide association studies
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Whole-exome sequencing in UK Biobank reveals rare genetic architecture for depression
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Intergenerational transmission of polygenic predisposition for neuropsychiatric traits on emotional and behavioural difficulties in childhood
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Large-scale multi-omics analyses in Hispanic/Latino populations identify genes for cardiometabolic traits
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Insights from the Biorepository and Integrative Genomics pediatric resource
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Polygenic risk score and cluster-based analysis suggests links between type 2 diabetes and vascular dementia in the KARE study
inferred← citeshttps://doi.org/10.1038/s41467-025-67235-0openalex-snapshot
Complex genetic effects linked to plasma protein abundance in the UK Biobank
inferred← citeshttps://doi.org/10.1038/s41467-026-69367-3openalex-snapshot
KidneyGenAfrica multi-cohort Genome-wide association study and polygenic prediction of kidney function in 110,000 Africans
inferred← citeshttps://doi.org/10.1038/s41467-026-74461-7openalex-snapshot
PGS Browser: a public platform for personalized polygenic score analysis and interpretation
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Methylation risk scores are associated with a collection of phenotypes within electronic health record systems
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Polygenic scores and their applications in kidney disease
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Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass
inferred← citeshttps://doi.org/10.1038/s41586-022-04965-xopenalex-snapshot
The sequences of 150,119 genomes in the UK Biobank
inferred← citeshttps://doi.org/10.1038/s41586-023-06079-4openalex-snapshot
Polygenic scoring accuracy varies across the genetic ancestry continuum
inferred← citeshttps://doi.org/10.1038/s41586-026-10926-5openalex-snapshot
Family genetic designs in MoBa provide insights into health and functioning
inferred← citeshttps://doi.org/10.1038/s41588-023-01538-0openalex-snapshot
Rare variants with large effects provide functional insights into the pathology of migraine subtypes, with and without aura
inferred← citeshttps://doi.org/10.1038/s41588-023-01560-2openalex-snapshot
Isoform-level transcriptome-wide association uncovers genetic risk mechanisms for neuropsychiatric disorders in the human brain
inferred← citeshttps://doi.org/10.1038/s41588-025-02118-0openalex-snapshot
Family-based genome-wide association study designs for increased power and robustness
inferred← citeshttps://doi.org/10.1038/s41588-025-02140-2openalex-snapshot
Common-variant and rare-variant genetic architecture of heart failure across the allele-frequency spectrum
inferred← citeshttps://doi.org/10.1038/s41588-025-02396-8openalex-snapshot
Genome-wide association analyses identify distinct genetic architectures for early-onset and late-onset depression
inferred← citeshttps://doi.org/10.1038/s41588-025-02398-6openalex-snapshot
African-ancestry-specific variant IKKβ p.Glu502Lys confers high lupus risk
inferred← citeshttps://doi.org/10.1038/s41591-024-03239-5openalex-snapshot
A framework for sharing of clinical and genetic data for precision medicine applications
inferred← citeshttps://doi.org/10.1038/s41592-026-03235-2openalex-snapshot
SPLENDID incorporates continuous genetic ancestry in biobank-scale data to improve polygenic risk prediction across diverse populations
inferred← citeshttps://doi.org/10.1038/s41593-024-01636-0openalex-snapshot
Analysis of gene expression in the postmortem brain of neurotypical Black Americans reveals contributions of genetic ancestry
inferred← citeshttps://doi.org/10.1038/s41596-020-0353-1openalex-snapshot
Tutorial: a guide to performing polygenic risk score analyses
inferred← citeshttps://doi.org/10.1038/s41596-020-0369-6openalex-snapshot
Reference-free deconvolution, visualization and interpretation of complex DNA methylation data using DecompPipeline, MeDeCom and FactorViz
inferred← citeshttps://doi.org/10.1038/s41598-018-31802-xopenalex-snapshot
Genomic analysis reveals genes affecting distinct phenotypes among different Chinese and western pig breeds
inferred← citeshttps://doi.org/10.1038/s41598-020-79720-1openalex-snapshot
Demographic analyses of a new sample of haploid genomes from a Swedish population of Drosophila melanogaster
inferred← citeshttps://doi.org/10.1038/s41598-022-12199-0openalex-snapshot
Development and validation of an RNA-seq-based transcriptomic risk score for asthma
inferred← citeshttps://doi.org/10.1038/s41598-022-18698-4openalex-snapshot
Genome scanning of behavioral selection in a canine olfactory detection breeding cohort
inferred← citeshttps://doi.org/10.1038/s41598-023-38768-5openalex-snapshot
Genome-wide polygenic risk score for type 2 diabetes in Indian population
inferred← citeshttps://doi.org/10.1038/s41598-025-00945-zopenalex-snapshot
Genome-wide association study of post COVID-19 syndrome in a population-based cohort in Germany
inferred← citeshttps://doi.org/10.1038/s41598-025-23377-1openalex-snapshot
Paternal valproate use and impact of shared genetic susceptibility on child neurodevelopment
inferred← citeshttps://doi.org/10.1038/s41598-025-30530-3openalex-snapshot
Modifiable lifestyle factors and genetic risk of obesity in Indians
inferred← citeshttps://doi.org/10.1038/s41598-025-90277-9openalex-snapshot
Association of genetic risk of Alzheimer’s disease and cognitive function in two European populations
inferred← citeshttps://doi.org/10.1038/s41598-026-36286-8openalex-snapshot
Evidence of a genomic basis for growth rate variation in a natural kelp population
inferred← citeshttps://doi.org/10.1038/s41598-026-69619-8openalex-snapshot
Exploring transcriptomic and genomic latent variable correction approaches in differential expression analysis
inferred← citeshttps://doi.org/10.1038/s41698-025-00895-9openalex-snapshot
Multi-omics analysis identifies diagnostic circulating biomarkers and potential therapeutic targets, revealing IQGAP1 as an oncogene in gastric cancer
inferred← citeshttps://doi.org/10.1038/s41746-019-0138-5openalex-snapshot
The medical AI insurgency: what physicians must know about data to practice with intelligent machines
inferred← citeshttps://doi.org/10.1038/s42003-022-03812-zopenalex-snapshot
Non-linear machine learning models incorporating SNPs and PRS improve polygenic prediction in diverse human populations
inferred← citeshttps://doi.org/10.1038/s42003-025-07846-xopenalex-snapshot
Integrative genomics sheds light on the immunogenetics of tuberculosis in cattle
inferred← citeshttps://doi.org/10.1038/s42003-025-09297-wopenalex-snapshot
Deciphering genetic susceptibility to clear cell renal cell carcinoma
inferred← citeshttps://doi.org/10.1038/s43587-023-00536-5openalex-snapshot
Longitudinal machine learning uncouples healthy aging factors from chronic disease risks
inferred← citeshttps://doi.org/10.1038/s43587-026-01232-wopenalex-snapshot
Design and model choices shape inference of age-varying genetic effects on complex traits
inferred← citeshttps://doi.org/10.1038/s44325-025-00049-7openalex-snapshot
Polygenic risk scores improve CAD risk prediction in individuals at borderline and intermediate clinical risk
inferred← citeshttps://doi.org/10.1073/pnas.2105841118openalex-snapshot
False discovery rate control in genome-wide association studies with population structure
inferred← citeshttps://doi.org/10.1073/pnas.2403210121openalex-snapshot
Fast and scalable ensemble learning method for versatile polygenic risk prediction
inferred← citeshttps://doi.org/10.1073/pnas.2416516122openalex-snapshot
Integrating single-cell data with biological variables
inferred← citeshttps://doi.org/10.1073/pnas.2503952122openalex-snapshot
A unified framework for identification of cell-type-specific spatially variable genes in spatial transcriptomic studies
inferred← citeshttps://doi.org/10.1073/pnas.2525790123openalex-snapshot
Quantifying direct genetic signal captured by principal component adjustment
inferred← citeshttps://doi.org/10.1080/01621459.2023.2261669openalex-snapshot
A Regression-Based Approach to Robust Estimation and Inference for Genetic Covariance
inferred← citeshttps://doi.org/10.1080/13811118.2025.2511264openalex-snapshot
Investigating the Relationship Between DNA Methylation, Genetic Variation, and Suicide Attempt in Bipolar Disorder
inferred← citeshttps://doi.org/10.1080/19490976.2025.2559119openalex-snapshot
First insights into microbial changes within an Inflammatory Bowel Disease Family Cohort study
inferred← citeshttps://doi.org/10.1080/19490976.2026.2696645openalex-snapshot
Multi-omic modelling of body mass index response to a dietary weight loss intervention
inferred← citeshttps://doi.org/10.1080/19585969.2026.2702037openalex-snapshot
Genetic liability for morning chronotype interacts with childhood trauma to predict depressive symptoms in women
inferred← citeshttps://doi.org/10.1093/bib/bbac039openalex-snapshot
PGS-server: accuracy, robustness and transferability of polygenic score methods for biobank scale studies
inferred← citeshttps://doi.org/10.1093/bib/bbac043openalex-snapshot
Fully exploiting SNP arrays: a systematic review on the tools to extract underlying genomic structure
inferred← citeshttps://doi.org/10.1093/bib/bbaf672openalex-snapshot
plmmr: an R package to fit penalized linear mixed models for genome-wide association data with complex correlation structure
inferred← citeshttps://doi.org/10.1093/bib/bbz108openalex-snapshot
Genotype imputation and reference panel: a systematic evaluation on haplotype size and diversity
inferred← citeshttps://doi.org/10.1093/bioinformatics/btaa1029openalex-snapshot
LDpred2: better, faster, stronger
inferred← citeshttps://doi.org/10.1093/bioinformatics/btaa520openalex-snapshot
Efficient toolkit implementing best practices for principal component analysis of population genetic data
inferred← citeshttps://doi.org/10.1093/bioinformatics/btab452openalex-snapshot
Fast numerical optimization for genome sequencing data in population biobanks
inferred← citeshttps://doi.org/10.1093/bioinformatics/btab456openalex-snapshot
RápidoPGS: a rapid polygenic score calculator for summary GWAS data without a test dataset
inferred← citeshttps://doi.org/10.1093/bioinformatics/btab519openalex-snapshot
Optimal linkage disequilibrium splitting
inferred← citeshttps://doi.org/10.1093/bioinformatics/btac179openalex-snapshot
MOSS: multi-omic integration with sparse value decomposition
inferred← citeshttps://doi.org/10.1093/bioinformatics/btac348openalex-snapshot
Using the UK Biobank as a global reference of worldwide populations: application to measuring ancestry diversity from GWAS summary statistics
inferred← citeshttps://doi.org/10.1093/bioinformatics/btae551openalex-snapshot
The GenoPred pipeline: a comprehensive and scalable pipeline for polygenic scoring
inferred← citeshttps://doi.org/10.1093/botlinnean/boac012openalex-snapshot
Population structure and signals of local adaptation in Eugenia uniflora (Myrtaceae), a widely distributed species in the Atlantic Forest
inferred← citeshttps://doi.org/10.1093/g3journal/jkab057openalex-snapshot
Estimating the effective sample size in association studies of quantitative traits
inferred← citeshttps://doi.org/10.1093/genetics/iyae086openalex-snapshot
How group structure impacts the numbers at risk for coronary artery disease: polygenic risk scores and nongenetic risk factors in the UK Biobank cohort
inferred← citeshttps://doi.org/10.1093/gpbjnl/qzaf102openalex-snapshot
Association of Multiple-trait Polygenic Risk Score with Obesity and Cardiometabolic Diseases in Korean Population
inferred← citeshttps://doi.org/10.1093/ije/dyag122openalex-snapshot
Quantifying and adjusting for selection biases in the Norwegian Mother, Father and Child Cohort Study using population-wide individual-level registry information
inferred← citeshttps://doi.org/10.1093/jeb/voae048openalex-snapshot
Temporal genomics help in deciphering neutral and adaptive patterns in the contemporary evolution of kelp populations
inferred← citeshttps://doi.org/10.1093/jnci/djae041openalex-snapshot
Multi-tissue transcriptome-wide association studies identified 235 genes for intrinsic subtypes of breast cancer
inferred← citeshttps://doi.org/10.1093/molbev/msaa053openalex-snapshot
Performing Highly Efficient Genome Scans for Local Adaptation with R Package pcadapt Version 4
inferred← citeshttps://doi.org/10.1093/nar/gkab031openalex-snapshot
DeCompress: tissue compartment deconvolution of targeted mRNA expression panels using compressed sensing
inferred← citeshttps://doi.org/10.1093/nar/gkad373openalex-snapshot
Deep integrative models for large-scale human genomics
inferred← citeshttps://doi.org/10.1093/nar/gkaf1494openalex-snapshot
Interpretable trajectory inference with single-cell linear adaptive negative-binomial expression (scLANE) testing
inferred← citeshttps://doi.org/10.1093/nargab/lqaa003openalex-snapshot
JASS: command line and web interface for the joint analysis of GWAS results
inferred← citeshttps://doi.org/10.1093/ndt/gfag041openalex-snapshot
Novel immune-related susceptibility loci associated with pediatric steroid-sensitive nephrotic syndrome identified by a transethnic genome-wide association study
inferred← citeshttps://doi.org/10.1093/plphys/kiae147openalex-snapshot
A maize semi-dwarf mutant reveals a GRAS transcription factor involved in brassinosteroid signaling
inferred← citeshttps://doi.org/10.1093/plphys/kiaf431openalex-snapshot
Natural variation in tetrapyrrole biosynthetic enzymes and their regulation modifies the maize chlorophyll mutant Oy1-N1989
inferred← citeshttps://doi.org/10.1097/cmr.0000000000000896openalex-snapshot
Melanoma risk prediction based on a polygenic risk score and clinical risk factors
inferred← citeshttps://doi.org/10.1097/crd.0000000000000294openalex-snapshot
Machine Intelligence in Cardiovascular Medicine
inferred← citeshttps://doi.org/10.1098/rspb.2022.1573openalex-snapshot
Temperature-associated selection linked to putative chromosomal inversions in king scallop ( Pecten maximus )
inferred← citeshttps://doi.org/10.1101/19013284openalex-snapshot
Schizophrenia polygenic risk score and cannabis use modify psychosis expression in first episode psychosis patients and population controls
inferred← citeshttps://doi.org/10.1101/2020.10.30.362079openalex-snapshot
Fitting penalized regressions on very large genetic data using snpnet and bigstatsr
inferred← citeshttps://doi.org/10.1101/2021.02.02.429297openalex-snapshot
dcHiC: differential compartment analysis of Hi-C datasets
inferred← citeshttps://doi.org/10.1101/2021.02.19.431997openalex-snapshot
quincunx: an R package to query, download and wrangle PGS Catalog data
inferred← citeshttps://doi.org/10.1101/2021.04.04.438381openalex-snapshot
Inter-chromosomal linkage disequilibrium and linked fitness cost loci associated with selection for herbicide resistance
inferred← citeshttps://doi.org/10.1101/2021.08.19.456975openalex-snapshot
Diverse Genotype-by-Weather Interactions in Switchgrass
inferred← citeshttps://doi.org/10.1101/2022.02.17.22271086openalex-snapshot
The combination of autism and exceptional cognitive ability increases risk for suicidal ideation
inferred← citeshttps://doi.org/10.1101/2022.06.26.495014openalex-snapshot
Genotyping, sequencing and analysis of 140,000 adults from the Mexico City Prospective Study
inferred← citeshttps://doi.org/10.1101/2022.08.11.22278618openalex-snapshot
ADuLT: An efficient and robust time-to-event GWAS
inferred← citeshttps://doi.org/10.1101/2022.08.23.22279134openalex-snapshot
Isoform-level transcriptome-wide association uncovers extensive novel genetic risk mechanisms for neuropsychiatric disorders in the human brain
inferred← citeshttps://doi.org/10.1101/2022.08.29.505629openalex-snapshot
Nucleotide and structural polymorphisms of the eastern oyster genome paint a mosaic of divergence, selection, and human impacts
inferred← citeshttps://doi.org/10.1101/2022.09.14.22279940openalex-snapshot
Multi-PGS enhances polygenic prediction: weighting 937 polygenic scores
inferred← citeshttps://doi.org/10.1101/2022.09.21.22280107openalex-snapshot
Pathway analysis identifies novel non-synonymous variants contributing to extreme vascular outcomes in Williams-Beuren syndrome
inferred← citeshttps://doi.org/10.1101/2022.09.28.509988openalex-snapshot
Polygenic scoring accuracy varies across the genetic ancestry continuum in all human populations
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