Daniel Doerr

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

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 introduces a grammar-based compression method for GFA haplotype paths, improving storage efficiency and runtime for pangenome graph analyses.

Panacus quantifies core genome size and pangenome growth from pangenome graphs, processing large datasets efficiently.

The paper introduces a computational model to study allelic and non-allelic homologous recombination by representing genomes as graphs and solving founder set problems.

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 improves the assembly of two ancient Yersinia pestis genomes using an optimization-based gap-filling method, resulting in highly supported assemblies with 95% ancient read coverage.