Simon J. Puglisi

This paper improves SBWT-based k-mer indexes by making them faster and smaller through batching, prefetching, and orientation optimization, outperforming SSHash in speed and space efficiency.

This paper introduces efficient methods to update colored k-mer indexes without rebuilding them from scratch, enabling dynamic maintenance of large genomic collections.

The paper introduces efficient set operations for SBWT-encoded k-mer spectra, enabling memory-efficient processing of large genomic datasets.

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 introduces faster subset rank data structures for k-mer lookup with reduced space usage, achieving Pareto optimal performance in memory and time.

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 introduces a Monte Carlo algorithm to efficiently construct and compress distinct k-mer color sets in microbial genome indexing, reducing memory usage and improving performance.

This paper introduces a novel algorithm for approximate local alignment search using k-bounded matching statistics, showing it is as fast and accurate as state-of-the-art tools in bacterial genomics tasks.

This paper introduces finimizers, frequency-bounded minimizers for k-mer sets, to address frequent minimizer issues in indexing, showing improved query times with a prototype implementation.

Themisto is a scalable k-mer index for pseudoalignment against bacterial genomes, outperforming existing tools in speed, memory use, and recall.

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 the Spectral Burrows-Wheeler Transform (SBWT) and develops succinct index structures for efficient k-spectrum membership queries in genomic data.

The paper surveys computational methods for indexing and querying large sequencing datasets using k-mer-based data structures.

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