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Browse publications attributed to Doherty Institute researchers

Overview

Research publications at the Doherty Institute

Our commitment to advancing knowledge in infectious diseases and immunology is reflected in a growing body of peer-reviewed research. This page provides access to published studies from our world-class scientists and collaborators, showcasing breakthroughs that inform policy, improve clinical practice, and drive innovation to improve health outcomes. Browse our collection to stay informed on the latest scientific insights shaping the future.

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Showing publications from Dr Michael Hall (118)

Kraken2 Human Pangenome Reference Consortium Release 2 database

2025 · data-set
A kraken2 database built from the genome assemblies generated in the second release of the Human Pangenome Reference Consortium (https://projects.ensembl.org/hprc/).…

NanoVarBench variant truthset files

2025 · data-set
These tarballs contain the variant truthsets used for each sample in our paper “Benchmarking reveals superiority of deep learning variant…

Clockwork database

2025 · data-set
This database (clockwork) contains common sputum contaminants along with a selection of NTM genomes and H37Rv – as used in…

Clockwork database

2025 · data-set
This database (clockwork) contains common sputum contaminants along with a selection of NTM genomes and H37Rv – as used in…

Kraken2 Human Pangenome Reference Consortium database

2025 · data-set
A kraken2 database built from the genome assemblies used by the Human Pangenome Reference Consortium (https://projects.ensembl.org/hprc/). This archive contains the…

Kraken2 Human Pangenome Reference Consortium database

2025 · data-set
A kraken2 database built from the genome assemblies used by the Human Pangenome Reference Consortium (https://projects.ensembl.org/hprc/). This archive contains the…

Kraken2 Human database

2025 · data-set
A kraken2 database built from just the Human library on 29/06/2023. This archive contains just the three files required by…

Kraken2 Human database

2025 · data-set
A kraken2 database built from just the Human library on 29/06/2023. This archive contains just the three files required by…

Mycobacterium genus database

2025 · data-set
The database is built as a Mycobacterium-specific one. For this database, we used genome_updater.sh (v0.6.3; https://github.com/pirovc/genome_updater) genome_updater.sh -d “refseq” -g…

Mycobacterium genus database

2025 · data-set
The database is built as a Mycobacterium-specific one. For this database, we used genome_updater.sh (v0.6.3; https://github.com/pirovc/genome_updater) genome_updater.sh -d “refseq” -g…

Mycobacterium representative kraken2 database

2025 · data-set
A kraken2 database built from the a representative Mycobacterium set of genomes. This archive contains the three files required by…

Mycobacterium representative kraken2 database

2025 · data-set
A kraken2 database built from the a representative Mycobacterium set of genomes. This archive contains the three files required by…

Mycobacterium tuberculosis database

2025 · data-set
This database contains the M. tuberculosis H37Rv reference genome (RefSeq accession GCF_000195955.2), plus 17 high-quality M. tuberculosis references from lineages…

Mycobacterium tuberculosis database

2025 · data-set
This database contains the M. tuberculosis H37Rv reference genome (RefSeq accession GCF_000195955.2), plus 17 high-quality M. tuberculosis references from lineages…

Simulated Illumina metagenomic reads

2025 · data-set
We simulated metagenomic Illumina sequencing reads to a mixture ratio that approximates that found in patient sputa, albeit with a…

Simulated Illumina metagenomic reads

2025 · data-set
We simulated metagenomic Illumina sequencing reads to a mixture ratio that approximates that found in patient sputa, albeit with a…
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