Jana Ebler

GBZ-base and GAF-base: Indexed pangenome file formats

The paper introduces GBZ-base and GAF-base, indexed pangenome file formats for efficient subgraph and alignment extraction.

Population-scale Y chromosome assemblies reveal recurrent remodeling within constrained architectures

The paper presents a population-scale Y chromosome reference panel with 142 assemblies, revealing structural and epigenetic variation across 180,000 years of evolution.

A global view of human centromere variation and evolution

The paper assembles and characterizes 2,110 human centromeres, revealing novel haplotypes, mobile element insertions, and mutation rate variation across chromosomes.

HPRC2: A human pangenome reference with near-complete coverage of common genetic variation

460 haplotypes from 230 genomes, selected to maximize common-variant coverage, capture 99.43% of All of Us common small variants and halve structurally unreliable regions and base errors versus HPRC1.

Pangenome-based human genome analysis improves trait association and genomic prediction

This paper develops a pangenome-based method to improve trait association and genomic prediction by capturing complex genetic variation missed by traditional approaches.

Scalable and rare-variant aware genome inference across the 1kGP cohort

The paper improves genome inference by introducing haplotype sampling and polishing workflows, enhancing variant detection in the 1000 Genomes Project cohort.

Population differences of chromosome 22q11.2 duplication structure predispose differentially to microdeletion and inversion.

The paper analyzes chromosome 22q11.2 haplotypes to show how structural variations in specific regions correlate with microdeletion and inversion risks across populations.

Pangenome discovery of missing autism variants

The paper uses long-read sequencing to identify pathogenic variants in autism cases, finding three pathogenic mutations and nine candidate structural variants missed by short-read sequencing.

Long-read sequencing and structural variant characterization in 1,019 samples from the 1000 Genomes Project

The paper uses long-read sequencing to characterize structural variants in 1,019 samples from the 1000 Genomes Project, identifying 167,291 sequence-resolved SVs and highlighting their genomic and functional implications.

Complex genetic variation in nearly complete human genomes

Hybrid HiFi/ultra-long ONT assemblies of 65 diverse humans yield 130 haplotypes, 1,246 complete centromeres, and a pangenome panel enabling short-read genome inference at median QV 45.

Impact and characterization of serial structural variations across humans and great apes

The paper introduces NAHRwhals, a method to detect serial structural variations in long-read genomes, identifies 37 sSV loci in humans, and shows their relevance to disease.

SVarp: pangenome-based structural variant discovery

SVarp discovers haplotype-resolved structural variants using a pangenome reference and long reads, achieving high recall in simulated and real data.

Whole-genome long-read sequencing downsampling and its effect on variant calling precision and recall

This study compares variant calling precision and recall of Oxford Nanopore and PacBio HiFi platforms across different sequence coverages.

Pangenome Graph Construction from Genome Alignment with Minigraph-Cactus

The paper introduces Minigraph-Cactus, a pangenome pipeline that constructs pangenome graphs directly from whole-genome alignments, demonstrating improved performance in mapping and variant calling across human and Drosophila data.

A Draft Human Pangenome Reference

The paper presents a draft human pangenome reference that improves variant discovery and structural variant detection compared to existing references.

Recombination between heterologous human acrocentric chromosomes

The paper shows recombination between heterologous human acrocentric chromosomes using pangenome data, revealing pseudo-homologous regions linked to Robertsonian translocations.

Inversion polymorphism in a complete human genome assembly

The paper analyzes inversion polymorphisms in a complete human genome assembly, showing improved detection and orientation accuracy with the T2T reference compared to GRCh38.

BubbleGun: Enumerating Bubbles and Superbubbles in Genome Graphs

BubbleGun efficiently detects bubbles and superbubbles in genome graphs, outperforming existing tools on large datasets.

A multi-platform reference for somatic structural variation detection

The paper compiles a comprehensive reference dataset of true somatic structural variations by analyzing melanoma and normal cell lines with multiple sequencing technologies and experimental validation.

Pangenome-based genome inference

PanGenie improves variant calling by using a pangenome reference and k-mer counts, achieving higher accuracy and speed compared to traditional methods.

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

The paper identifies recurrent inversions in human genomes and links them to genomic disorders through mutational recurrence and structural diversity.

Mako: a graph-based pattern growth approach to detect complex structural variants

Mako detects complex structural variants using a graph-based pattern growth approach, achieving 70% validation rate on real data and identifying 15 CSV types including two novel ones.

De novo assembly of 64 haplotype-resolved human genomes of diverse ancestry and integrated analysis of structural variation

The paper presents 64 haplotype-resolved human genomes using long-read sequencing and identifies structural variants, SV-eQTLs, and adaptive selection candidates.

A fully phased accurate assembly of an individual human genome

This paper presents a fully phased de novo genome assembly of an individual using Strand-seq and HiFi reads, achieving high accuracy and contiguity with low switch error rates.

Haplotype Threading: Accurate Polyploid Phasing from Long Reads

This paper introduces a novel two-stage method for polyploid haplotype phasing using long reads, achieving lower error rates than existing methods in challenging regions.

Highly-accurate long-read sequencing improves variant detection and assembly of a human genome

This paper develops a long-read sequencing protocol to improve variant detection and genome assembly in a human genome, achieving high accuracy and contiguity.

Haplotype-aware genotyping from noisy long reads

This paper introduces a haplotype-aware genotyping method for noisy long reads, showing improved accuracy in variant calling using longer reads from Oxford Nanopore and Pacific Biosciences.

Genotyping of Inversions and Tandem Duplications

This paper introduces DIGTYPER, a statistical method for genotyping inversions and duplications from NGS data, showing improved performance over DELLY for duplications and short inversions.