Giulio Ermanno Pibiri

The paper introduces an optimized sparse and skew hashing data structure for efficient k-mer representation, showing improved query speed and space efficiency compared to existing methods.

Kaminari improves approximate k-mer query performance by using k-mer minimizers and integer compression, outperforming Bloom filters in memory and speed with minimal false positive impact.

The paper introduces the open-closed mod-minimizer, a method that improves k-mer sampling density for all k values compared to existing methods.

The paper introduces lossless compression methods for colored de Bruijn graphs, reducing memory usage while maintaining query efficiency.

The paper introduces the mod-minimizer, a sampling algorithm that improves k-mer density over existing methods for large k and w, achieving optimal density as k approaches infinity.

This paper introduces new randstrobe construction methods, identifies biases in previous approaches, and improves accuracy in short-read mapping.

Fulgor is a compact k-mer index for efficient sequence matching and color queries, outperforming existing methods in space and speed.

The paper introduces a new data structure, Mac-dBG, that improves space efficiency for colored de Bruijn graphs by compressing color representations, while maintaining query efficiency.

The paper introduces a method to reduce the space required for reference indexing by using spectrum preserving tilings and sampling schemes, achieving significant space savings with minimal query slowdown.

This paper introduces an improved weighted k-mer dictionary that compresses k-mer counts more efficiently than existing methods.

The paper introduces a compressed k-mer dictionary that improves space/time efficiency using statistical properties of k-mer minimizers.

The paper introduces Matchtigs, a method to compress kmer sets with a polynomial algorithm and greedy heuristic, achieving significant size reduction and performance improvements in downstream applications.