Daniel Gibney

This paper introduces a rigorous framework for haplotype-aware long-read error correction, achieving accuracy comparable to existing methods in de novo contexts.

DipGenie improves diploid genome phasing using pangenome graphs, achieving lower error rates and better structural variant detection than existing tools.

The paper introduces an integer programming framework for haplotype-resolved genotyping using pangenome graphs, achieving accurate MHC haplotype inference on low-coverage data.

This paper develops haplotype-aware sequence alignment algorithms for pangenome graphs, showing improved consistency with ground-truth recombinations compared to haplotype-agnostic methods.

This paper presents efficient algorithms for co-linear chaining with anchor overlaps and gap costs, showing strong correlation with edit distance.