Tobias Marschall

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.

gaftools provides utilities for processing graph alignments in GAF format, adapting SAMtools functionalities for pangenome analysis.

The paper characterizes mucin VNTR diversity using long-read genomes and identifies disease associations in cystic fibrosis patients.

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 presents T2T reference genomes from a multi-generational pedigree to study genetic and epigenetic inheritance across the complete genome.

This paper introduces Floco, a network flow-based method for copy number calling on genome graphs, improving accuracy by up to 43% compared to read depth estimation.

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.

DiVerG is a scalable data structure and algorithm for efficiently calculating distances in sequence graphs, outperforming PairG in speed and space efficiency for genomic applications.

EpiPAMPAS detects intra-protein epistasis by analyzing multiple sequence alignments and finds interactions with low p-values in simulated and real viral protein data.

The paper develops a Hi-C analysis pipeline to catalog TADs and loops in human genomes and quantifies the impact of SVs on chromatin structure and gene expression.

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

The paper resolves the amylase locus at nucleotide resolution in modern and ancient humans, showing AMY1 copy number variation predated agriculture and was driven by recombination.

Graphasing uses Strand-seq and assembly graphs to produce chromosome-scale haplotypes without parental data or intermediate steps.

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.

This study characterizes structural and genetic diversity in MUC5AC and MUC5B using long-read sequencing, revealing haplotype variation and evolutionary patterns across human and nonhuman primate populations.

Locityper improves variant calling for complex polymorphic genes using short and long-read sequencing, accurately genotyping 194 out of 256 challenging loci.

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

This paper presents a method for haplotype-resolved assembly of a tetraploid potato genome using long reads and low-depth offspring data, achieving high-quality chromosome-level assemblies with haplotype-specific resolution.

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

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 presents long-read assemblies of 43 diverse human Y chromosomes, revealing extensive structural complexity and variation across 180,000 years of evolution.

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

The paper analyzes gaps and structural variants in phased human genome assemblies, identifying issues with contig ends, misorientations, and large-scale insertions and deletions.

PanPA generates and aligns panproteome graphs to improve alignment accuracy in prokaryotic genomes by leveraging amino acid similarity over DNA sequence diversity.

The paper evaluates sequencing and assembly methods to create high-quality diploid human genome assemblies, finding that long reads and haplotype sorting improve accuracy and completeness.

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