Simon Gravel

BLocPRS: locus-aware ensembles of polygenic scores provide accurate linear prediction

BLocPRS improves polygenic risk score prediction by combining locus-specific weights from different PRSs, achieving higher accuracy in UK Biobank and extending to non-European populations.

Recurrent structural variation and recent turnover at the 17q21.31 locus in humans and great apes

The paper characterizes structural variation at the 17q21.31 locus in humans and great apes, identifying new haplotypes and evolutionary dynamics.

Inferring hominin history with recurrent gene flow from single unphased genomes and a two-locus statistic

This paper develops a method to infer hominin demographic history using two-locus statistics from single unphased genomes, revealing two episodes of gene flow and population structure in ancient Eurasian AMH.

Topological stratification of continuous genetic variation in large biobanks

The paper introduces a topological clustering method for genetic data from biobanks, showing it can reveal population structure and aid in quality control and polygenic score analysis.

A multi-ancestry genetic reference for the Quebec population

The paper constructs a genetic reference panel for the Quebec population using whole-genome sequencing and GWAS to improve phenotype-genotype association discovery.

Aligning gene trees with family trees

The paper introduces an algorithm to align genetic tree sequences with genealogical pedigrees, demonstrating its scalability and application to reconstruct allele inheritance.

Whole-genome sequencing of 3,135 individuals representing the genetic diversity of the Japanese population

The paper sequenced 3,135 Japanese individuals to identify genetic variants and construct a reference haplotype, highlighting the need for diverse population inclusion in genetic catalogs.

A comprehensive genomic framework for identifying genes predisposing to homologous recombination repair deficient breast cancer

The paper develops a genomic framework to identify genes predisposing to homologous recombination repair deficient breast cancer by integrating mutational signatures, exome data, and clinical-genomic analysis.

Sparse Polygenic Risk Score Inference with the Spike-and-Slab LASSO

This paper introduces SSLPRS, a Polygenic Risk Score method using Spike-and-Slab LASSO, showing improved variable selection and prediction accuracy over existing methods.

LD Matrix Approximations for Scalable Analysis of High-dimensional Genetic Data

This paper introduces a method to approximate LD matrices with sparse, banded matrices that are positive semi-definite, improving accuracy over existing methods on large genomic data.

Personalized polygenic risk prediction and assessment with a Mixture-of-Experts framework

The paper introduces MoEPRS, a Mixture-of-Experts framework for personalized polygenic risk prediction, showing modest accuracy improvements over single-source models across diverse biobanks.

Towards whole-genome inference of polygenic scores with fast and memory-efficient algorithms

This paper introduces efficient algorithms for polygenic score inference using large-scale genetic data, achieving significant improvements in speed, memory use, and cross-population transferability.

Using the ancestral recombination graph to study the history of rare variants in founder populations

This paper uses ancestral recombination graphs to impute and trace rare variants in founder populations, showing high accuracy in mutation age and regional frequency estimation.

Slave Trade and Colonial Expansion Resulted in Strong Sex-Biased Admixture in South Africa

The paper uses genetic data to show sex-biased admixture patterns in South Africa due to colonial migration, with European males and Khoe-San females contributing disproportionately to different regions.

On the Genes, Genealogies, and Geographies of Quebec

The paper models French Canadian ancestry using genealogical and genetic data, revealing population structure shaped by geography and migration.

A weakly structured stem for human origins in Africa

The paper infers demographic models of African population history using genomic data, finding a weakly structured stem model explains polymorphism better than archaic introgression.

Fast and Accurate Bayesian Polygenic Risk Modeling with Variational Inference

VIPRS improves polygenic risk prediction using variational inference, achieving high accuracy and efficiency in both simulated and real datasets.

Efficient ancestry and mutation simulation with msprime 1.0

The paper introduces msprime 1.0, a high-performance simulation tool for ancestry and mutation in population genetics, showing it is faster and more memory efficient than existing alternatives.

Assumptions about frequency-dependent architectures of complex traits bias measures of functional enrichment

This study shows that assumptions in LDSC models can bias functional enrichment estimates in GWAS, suggesting the need for better calibration.

Taming Strong Selection with Large Sample Sizes

The paper shows that strong selection and large sample sizes can be used to derive accurate allele frequency distributions beyond the strong selection limit.

Recent fluctuations in Mexican American genomes have altered the genetic architecture of biomedical traits

The paper shows that increased Amerindigenous ancestry in Mexican Americans over time has altered the genetic architecture of traits like height and polygenic risk scores.

Lessons learned from bugs in models of human history

The paper identifies and discusses two bugs in population genetic models implemented with msprime, highlighting their impact on published analyses and offering recommendations to prevent similar errors.

Unbiased estimation of linkage disequilibrium from unphased data

The paper presents unbiased estimators for linkage disequilibrium statistics from unphased data, improving accuracy across populations and LD scales.

Revealing multi-scale population structure in large cohorts

The paper introduces PCA-UMAP for visualizing population structure in large genomic datasets, revealing subpopulations and fine-scale relationships between geography, genotypes, and phenotypes.

Legacy Data Confounds Genomics Studies

The paper identifies a batch effect in 1000 Genomes Project data causing spurious mutation calls and affecting GWAS results, suggesting legacy data may need to be retired or upgraded.

Models of archaic admixture and recent history from two-locus statistics

The paper develops a likelihood-based framework to infer demographic history using two-locus statistics, showing that models including archaic admixture better explain genetic diversity patterns.

Perspective: Genomic inference using diffusion models and the allele frequency spectrum

The paper uses diffusion models and whole-genome sequence data to examine the impact of selection on demographic inference and mutation rate estimates in French Canadian individuals.

On the decidability of population size histories from finite allele frequency spectra

The paper shows that inferring population size histories from finite allele frequency spectra is not uniquely determined, even with reasonable constraints.

Human demographic history impacts genetic risk prediction across diverse populations

This study shows that genetic risk scores from European GWAS are biased when applied to other populations due to demographic history, highlighting the need for more diverse data.

The Great Migration and African-American genomic diversity

This study assesses African-American genomic diversity using cohort data, revealing higher African ancestry in the South and migration patterns linked to the Great Migration.