Skip to content
// Publications

Methods and findings

Peer-reviewed work from the lab.

† : (co-) First author, * : (co-) Corresponding author

// 2026 3 papers

  • pansift: a succinct index for population-scale pangenome graphs of vertebrate genomes

    Mateusz Kowalski†, Søren Lindqvist, Ezekiel Holt*

    Nature Methods · 2026 · 2026;23(4):512-521 link DOI description PubMed

  • Graph-aware structural-variant calling in repetitive and nested regions with svhound

    Priya Bhattacharya†, Yusuf Almasi, Ezekiel Holt*

    Genome Research · 2026 · 2026;36(2):241-256 link DOI description PubMed

  • Clinical pangenomes for the HLA region improve concordance of typing across ancestry-stratified cohorts

    Ines Marchetti†, Priya Bhattacharya, Florian Egger, Ezekiel Holt*

    Cell Genomics · 2026 · 2026;6(3):100614 link DOI description PubMed
// 2025 2 papers

  • Pollinator pangenomes reveal cryptic structural variation in Apis mellifera populations across multiple cohorts

    Yusuf Almasi†, Hannah Engel, Søren Lindqvist, Ezekiel Holt*

    Genome Biology · 2025 · 2025;26:189 link DOI description PubMed

  • graphmap2: linear-time alignment of long reads to chromosome-scale pangenome graphs

    Søren Lindqvist†, Mateusz Kowalski, Ezekiel Holt*

    Bioinformatics · 2025 · 2025;41(15):btaf412 link DOI description PubMed
// 2024 2 papers

  • Beyond the linear reference: how pangenomes reshape population genomics

    Ezekiel Holt*

    Nature Computational Science · 2024 · 2024;4(11):812-823 link DOI description PubMed

  • ribbon-bridge: stitching haplotype-resolved assemblies across nanopore signal dropouts

    Hannah Engel†, Søren Lindqvist, Ezekiel Holt*

    Bioinformatics · 2024 · 2024;40(20):btae588 link DOI description PubMed
// 2023 1 paper

  • A reproducible pipeline for haplotype-resolved long-read assembly of mammalian genomes

    Priya Bhattacharya†, Ezekiel Holt*

    Genome Biology · 2023 · 2023;24:241 link DOI description PubMed