Leena Salmela

The paper introduces a contig assembler that provides correctness guarantees by modeling misassembly probabilities in de Bruijn graph assemblies.

GraphChainer improves alignment of erroneous long reads to acyclic variation graphs, aligning more reads and total read length than existing tools.

This paper defines contigs for variable-order de Bruijn graphs and presents an algorithm to improve genome assembly contiguity using PacBio HiFi data.

This paper introduces DynamicBOSS, a succinct dynamic de Bruijn graph representation that supports unlimited additions and deletions of nodes and edges, outperforming existing methods for large-scale datasets.

The paper introduces cOMet, an error correction method for optical mapping data, which improves the accuracy of Rmap data and enhances genome assembly quality.

The paper compares finite-state machines and position weight matrices for modeling sequence motifs, finding FSMs provide better discrimination of positive and negative sequences.

The paper disentangles de Bruijn graphs using optical maps to improve long-read assembly efficiency and accuracy.