Floris P Barthel

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

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

This study shows that telomere dysfunction in human astrocytes leads to acrocentric chromosome instability and nucleolar reorganization through a combination of cytogenetic, imaging, and chromatin-contact analyses.

KaryoScope annotates genome assemblies at base-pair resolution across multiple feature classes quickly and without alignment, revealing structural variation in centromeres and subtelomeres.

This paper presents near-complete, haplotype-resolved assemblies of a pancreatic cancer genome and normal tissue, identifying extensive somatic variants and epigenetic changes in previously excluded regions.

The paper constructs an atlas of telomere variation across humans using long-read sequencing and reveals heritable telomere variant repeats and telomerase-independent extension mechanisms.

This study uses long-read sequencing to show that telomere length differences between chromosome arms influence structural genome changes in IDH-mutant astrocytomas.

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 introduces HKS, a method for exact hierarchical k-mer annotation with variable-length queries, achieving high concordance in human genome assemblies.

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.

DeepSomatic is a deep learning method for detecting somatic variants from short-read and long-read sequencing data, outperforming existing callers, especially for indels.

The paper introduces Telomere-C, a method to map telomeric 3D interactions, revealing ultra-long-range contacts and repetitive element hubs linked to telomere maintenance.

This study shows that cell-free DNA (cfDNA) can track glioblastoma tumor burden and treatment response over time using in vitro models.

The paper presents diploid genome assemblies for two human fibroblast cell lines, enabling clone-specific variant calling, improved read mapping, and accurate phasing.

The paper identifies three span intervals of tandem duplications in TDP tumors and links them to specific gene mutations and pathways, showing TP53 and BRCA1 loss drives short-span TDPs.