Jonas Meisner

A generative model for dimensionality reduction with millions of features and few samples

This paper introduces a deep generative decoder model for dimensionality reduction with millions of features and few samples, showing it outperforms PCA and VAE in tumor classification.

Faroese Whole Genomes Provide Insight into Ancestry and Recent Selection

This study analyzes whole genome sequencing data from the Faroe Islands to explore ancestry, genetic diversity, and signals of recent selection in a North Atlantic founder population.

Accurate and scalable genome-wide ancestry estimation using haplotype clusters

This paper introduces a scalable haplotype cluster-based method for genome-wide ancestry estimation, achieving higher accuracy and speed compared to existing approaches.

Plasma Proteome Variation and its Genetic Determinants in Children and Adolescents

This study identifies genetic determinants of plasma protein levels in children and adolescents using MS-based proteomics, revealing extensive genetic impacts that persist into adulthood.

Leveraging haplotype information in heritability estimation and polygenic prediction

This paper introduces a haplotype-based framework for heritability estimation and reference-free polygenic prediction, showing improved performance over genotype-based methods in depression and schizophrenia.

Faster model-based estimation of ancestry proportions

The paper introduces fastmixture, a model-based ancestry estimation method that is more accurate and faster than existing approaches for large genomic datasets.

Non-linear genetic regulation of the blood plasma proteome

The paper identifies non-linear genetic regulation of plasma proteins using a deep learning method, finding dominance and epistasis effects in large cohorts.

Fast and accurate out-of-core PCA framework for large scale biobank data

PCAone is a fast and memory-efficient PCA framework that outperforms existing methods on large-scale biobank and single-cell RNA sequencing data.

Tracing the evolutionary path of the CCR5delta32 deletion via ancient and modern genomes

The paper traces the evolutionary history of the CCR5delta32 deletion using ancient and modern genomes, finding it originated at least 7,000 years ago in Western Eurasia and underwent positive selection.

Detecting Selection in Low-Coverage High-Throughput Sequencing Data using Principal Component Analysis

The paper introduces two selection statistics for detecting selection signals in low-coverage sequencing data using PCAngsd, showing they control false positives and match results from high-quality genotypes.

Large-scale Inference of Population Structure in Presence of Missingness using PCA

EMU accurately infers population structure from ultra-low coverage sequencing data with missingness, outperforming existing methods on real and simulated datasets.

Haplotype and Population Structure Inference using Neural Networks in Whole-Genome Sequencing Data

HaploNet uses neural networks to infer population structure from whole-genome sequencing data, outperforming standard methods in distinguishing closely related populations.

Genomic diversity and novel genome-wide association with fruit morphology in Capsicum, from 746k polymorphic sites.

The paper identifies 746k polymorphic sites in Capsicum species and finds four novel loci associated with fruit shape, including a mutation in the Longifolia 1-like gene.

Testing for Hardy-Weinberg Equilibrium in Structured Populations using NGS Data

The paper introduces a method to test Hardy-Weinberg Equilibrium in structured populations using NGS data, accounting for population structure to detect deviations caused by factors other than structure.

Inferring Population Structure and Admixture Proportions in Low Depth NGS Data

The paper presents two methods for inferring population structure and admixture proportions in low depth NGS data using PCAngsd framework.