Jana Ebler

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

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

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

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.

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

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

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

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.

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.

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.

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

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

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.

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

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

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

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.

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

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

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.

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

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.

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.

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

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.

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.