Ahsan Sanaullah

The paper introduces ms2, a suite of algorithms for efficiently computing matching statistics and SMEMs in compressed pangenome indexes, achieving significant speedups over existing methods.

This paper develops efficient algorithms for detecting long exact matches between genome assemblies in compressed space and sublinear time, revealing novel structural variations in centromeres.

The paper introduces algorithms for constructing RLBWT-based compressed full text indexes in compressed space, reducing memory usage for large-scale pangenome analysis.

This paper introduces SLAB, an algorithm for identifying haplotype block cores using PBWT, and applies it to UK Biobank data to detect selection signals.

The paper introduces HP-PBWT, a parallel PBWT algorithm for efficient haplotype matching in large biobank datasets, achieving significant speed-ups in both IO-included and IO-excluded benchmarks.

This paper introduces Dynamic μ-PBWT, a memory-efficient data structure for dynamic updates of haplotype panels, supporting efficient queries and reducing memory usage compared to existing methods.

This paper defines haplotype matches in pangenome graphs and provides efficient algorithms for querying them using GBWT and related data structures.

The paper introduces the MPSC problem as an alternative to the LS model for haplotype threading, enabling efficient haplotype reconstruction on large panels.

The paper introduces d-PBWT, a dynamic version of the PBWT data structure, enabling efficient insertion and deletion of haplotypes while maintaining PBWT functionality.