Santiago Marco‐Sola

Theseus provides a fast and optimal affine-gap sequence-to-graph alignment algorithm, outperforming existing methods in speed while maintaining optimality.

Singletrack improves memory efficiency and performance for gap-affine sequence alignment without sacrificing accuracy.

This paper introduces adaptive tracepoints for compressing pangenome alignments, achieving significant compression ratios while maintaining alignment accuracy.

QuickEd improves sequence alignment speed for long reads by using a bound-and-align strategy, achieving faster performance than existing tools while maintaining accuracy.

This paper introduces PGGB, a pipeline for building pangenome graphs that includes all variation without bias, enabling variation detection, conservation measurement, recombination event detection, and phylogenetic inference.

BIMSA accelerates long sequence alignment using Processing-In-Memory, achieving significant speedups over existing PIM and CPU implementations.

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 presents a draft human pangenome reference that improves variant discovery and structural variant detection compared to existing references.

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

This paper introduces BiWFA, an algorithm that performs gap-affine sequence alignment in O(s) memory while maintaining O(ns) time complexity, improving memory efficiency for large-scale alignments.

This paper introduces ILVES-PC, an algorithm for accurately and efficiently imposing constraints in molecular dynamics simulations, achieving significant speedups and improved accuracy over existing methods.

This paper introduces WFA-GPU, a GPU-accelerated tool for exact gap-affine sequence alignment, showing significant speed improvements over CPU and other GPU implementations.

AnchorWave improves genome alignment for genomes with high diversity, structural polymorphism, and whole-genome duplication by using a duplication-informed algorithm and gap cost strategy.

The paper introduces GEMBS, a high-throughput processing tool for DNA methylation data from WGBS, aiming to improve efficiency for large datasets.