Alexander G. Ioannidis

A high-resolution human pangenome structural variant resource for improved disease association

The paper constructs a high-resolution human pangenome structural variant resource, identifies disease-associated SVs, and demonstrates its utility in filtering variants from probands and associating SVs with traits in a large cohort.

Multi-ancestry admixture mapping reveals ancestry-associated disease loci in the UK Biobank

This study uses multi-ancestry admixture mapping in the UK Biobank to identify ancestry-associated disease loci, finding 13 genome-wide significant associations and four novel risk loci.

High Resolution Ancestry Deconvolution for Next Generation Genomic Data

This paper introduces Gnomix, a high-resolution ancestry deconvolution method for next-generation genomic data, achieving higher accuracy and faster performance than existing methods.

ADAMIXTURE: Adaptive First-Order Optimization for Biobank-Scale Genetic Clustering

ADAMIXTURE improves genetic clustering for large datasets by combining EM with Adam optimization, achieving faster runtime and scalability without sacrificing accuracy.

ARGformer: learning on ancestral recombination graphs with transformers

ARGformer uses transformers to learn embeddings from ancestral recombination graphs, enabling population structure analysis and ancestry inference without genotype data.

Non-Parametric Ancestry Adjustment for Polygenic Scores

This paper introduces non-parametric methods to adjust polygenic scores for ancestry bias, improving accuracy for non-European populations using the UK Biobank.

Graph transformer for ancient ancestry inference

ARGMix uses a graph transformer to infer local ancestry from ancient DNA, showing continuity between Otzi the Iceman and present-day Europeans.

The diploid reference genome of a human embryonic stem cell line

The paper presents the first telomere-to-telomere diploid reference genome of the human embryonic stem cell line H9, revealing genomic features and ancestry.

Point cloud local ancestry inference (PCLAI): continuous coordinate-based ancestry along the genome

PCLAI infers continuous genetic ancestry across the genome using a point cloud representation, enabling time-stratified geographic insights from ancient samples.

Sex Checking by Zygosity Distributions

Zigo is a reference-free, ML-based method for verifying sex concordance using genotype data, achieving high accuracy across different data modalities without manual tuning.

Biobank-Scale Polygenic Prediction in Admixed Populations Using Local Ancestry via the Group Lasso

This paper introduces Combine, a framework for polygenic prediction in admixed populations using local ancestry and group lasso, showing improved performance over existing methods.

snputils: A High-Performance Python Library for Genetic Variation and Population Structure

snputils provides a high-performance Python library for handling genetic variation and population structure data, improving efficiency and integration in genomic research.

Deep Variational Autoencoders for Population Genetics

This paper applies variational autoencoders to genomic data to capture population structure, enable dimensionality reduction, and improve data compression across diverse populations.

Analysis of a deeply-phenotyped familial hypercholesterolemia cohort from Mexico shows a role for both rare and common alleles across known dyslipidemia genes and reveals structural variation in a novel locus.

The paper analyzes a Mexican FH cohort to show rare and common alleles in FH genes and a novel locus contribute to disease risk, with replication in UK Biobank.

Present-day admixed genomes reveal prehistoric adaptation to cold, maritime diet, and local pathogens in Patagonia

The paper analyzes genome-wide data from Indigenous Patagonians to uncover genetic adaptations to cold, maritime diet, and pathogens, revealing prehistoric selection signals and admixture patterns.

Pan-African metapopulation model explains Homo sapiens genetic and morphological evolution

The paper models Homo sapiens evolution as a Pan-African metapopulation, showing how climate and connectivity shaped genetic and morphological diversity over 200,000 years.

Polygenic risk score portability for common diseases across genetically diverse populations

This study evaluates polygenic risk score (PRS) performance across four ancestry groups for 14 diseases, finding that ancestry-specific PRS models improve accuracy and identifying cross-trait interactions.

PopGenAdapt: Semi-Supervised Domain Adaptation for Genotype-to-Phenotype Prediction in Underrepresented Populations

PopGenAdapt improves genotype-to-phenotype prediction in underrepresented populations using semi-supervised domain adaptation, outperforming supervised methods in Nigerian, Sri Lankan, and Hawaiian populations.

Machine Learning Strategies for Improved Phenotype Prediction in Underrepresented Populations

This paper introduces a machine learning toolkit to improve phenotype prediction accuracy for underrepresented populations using SNP data from diverse genomic datasets.

Nationwide genomic biobank in Mexico unravels demographic history and complex trait architecture from 6,057 individuals

Neural ADMIXTURE: rapid population clustering with autoencoders

Neural ADMIXTURE uses an autoencoder to rapidly cluster large genetic datasets, reducing computation time compared to traditional methods like ADMIXTURE.

Demographic history and genetic structure in pre-Hispanic Central Mexico

The paper analyzes pre-Hispanic genetic data from Mexico to show population continuity despite climate change and identifies an ancient unsampled ghost population's contribution.

Adversarial Attacks on Genotype Sequences

The paper demonstrates how adversarial attacks can corrupt genomic analyses and explores machine learning techniques to detect such manipulations.

Meta-analysis fine-mapping is often miscalibrated at single-variant resolution

This paper shows that meta-analysis fine-mapping is often miscalibrated due to cohort heterogeneity and introduces a QC method to identify suspicious loci.

Global Biobank Meta-analysis Initiative: powering genetic discovery across human diseases

Meta-analysis of harmonized GWAS from up to 18 biobanks (six ancestry groups) across 14 endpoints replicated 320 known loci and identified 188 apparently novel loci.

Validating and automating learning of cardiometabolic polygenic risk scores from direct-to-consumer genetic and phenotypic data: implications for scaling precision health research.

This study validates and automates polygenic risk score (PRS) development for cardiometabolic diseases using direct-to-consumer genetic and phenotypic data, showing comparable performance to larger clinical datasets.

Deconvoluting complex correlates of COVID19 severity with local ancestry inference and viral phylodynamics: Results of a multiomic pandemic tracking strategy

The paper integrates multi-omic data to identify genetic and microbiome factors associated with severe COVID-19, independent of ancestry and social factors.

Archetypal Analysis for Population Genetics

This paper introduces Archetypal Analysis for efficient genetic clustering, showing it outperforms ADMIXTURE in speed and interpretability across human and canid datasets.

Predicting Dog Phenotypes from Genotypes

This paper predicts dog phenotypes (breed, height, weight) from genotypes using linear and non-linear methods, showing that linear methods outperform non-linear for breed classification but not for height and weight regression.

Generative Moment Matching Networks for Genotype Simulation

This paper uses Generative Moment Matching Networks to simulate SNP sequences and introduces training improvements and evaluation metrics.