Jens Stoye

On Deriving Synteny Blocks by Compacting Elements

This paper introduces a formal framework for deriving synteny blocks directly from sequence data to better capture genomic rearrangements without obscuring structural variation.

Quantifying the Rearrangement Complexity of Pangenomes

This paper introduces the CARP problem to address limitations in rearrangement analysis of pangenomic data by unifying concepts from comparative genomics and graphical pangenomics.

Panacus: fast and exact pangenome growth and core size estimation

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

Applying rearrangement distances to enable plasmid epidemiology with pling

This paper introduces pling, a tool that uses rearrangement distances to cluster plasmids more accurately by accounting for structural changes and avoiding over-clustering caused by transposable elements.

Revisiting pangenome openness with k-mers

The paper estimates pangenome openness using k-mers instead of genes and compares the results, providing an efficient implementation.

Detecting High Scoring Local Alignments in Pangenome Graphs

The paper introduces a heuristic method for finding high-scoring local alignments of DNA queries to pangenome graphs and demonstrates its scalability and effectiveness.

Reconstructing tumor evolutionary histories and clone trees in polynomial-time with SubMARine

This paper introduces SubMARine, a polynomial-time algorithm for reconstructing tumor clone trees that efficiently captures uncertainty and scales to large datasets.

HASLR: Fast Hybrid Assembly of Long Reads

HASLR is a hybrid assembler that combines second and third generation sequencing reads to generate fast and accurate genome assemblies, outperforming other assemblers in speed and misassembly count.