Overview
Availability
- Dr Michael Hall is:
- Available for supervision
Works
Search Professor Michael Hall’s works on UQ eSpace
2025
Journal Article
Genome graphs reveal the importance of structural variation in Mycobacterium tuberculosis evolution and drug resistance
Canalda-Baltrons, Aleix, Silcocks, Matthew, Hall, Michael B., Theys, Derrick, Chang 常戌灵, Xuling, Viberg, Linda T., Sherry, Norelle L., Coin, Lachlan and Dunstan, Sarah J. (2025). Genome graphs reveal the importance of structural variation in Mycobacterium tuberculosis evolution and drug resistance. Nature Communications, 16 (1) 10746, 1-17. doi: 10.1038/s41467-025-65779-9
2025
Journal Article
Genome size estimation from long read overlaps
Hall, Michael B, Zhou, Chenxi and Coin, Lachlan J M (2025). Genome size estimation from long read overlaps. Bioinformatics, 41 (11) btaf593, 11. doi: 10.1093/bioinformatics/btaf593
2025
Journal Article
Sustainable data analysis with Snakemake
Mölder, Felix, Jablonski, Kim Philipp, Letcher, Brice, Hall, Michael B., van Dyken, Peter C., Tomkins-Tinch, Christopher H., Sochat, Vanessa, Forster, Jan, Vieira, Filipe G., Meesters, Christian, Lee, Soohyun, Twardziok, Sven O., Kanitz, Alexander, VanCampen, Jake, Malladi, Venkat, Wilm, Andreas, Holtgrewe, Manuel, Rahmann, Sven, Nahnsen, Sven and Köster, Johannes (2025). Sustainable data analysis with Snakemake. F1000Research, 10 33, 33. doi: 10.12688/f1000research.29032.3
2025
Journal Article
TBpore cluster: A novel phylogenetic pipeline for tuberculosis transmission studies using nanopore next-generation sequencing data
Gagnon, Sophie, Ametepe, Emmanuelle, Point, Floriane, Cloutier Charette, William, Chakravarti, Arpita, Rivest, Paul, Akochy, Pierre-Marie, Soualhine, Hafid, Iqbal, Zamin, Hall, Michael B. and Lapierre, Simon Grandjean (2025). TBpore cluster: A novel phylogenetic pipeline for tuberculosis transmission studies using nanopore next-generation sequencing data. PLoS One, 20 (6) e0325914, 1-7. doi: 10.1371/journal.pone.0325914
2024
Journal Article
Pseudo-éclosion de Mycobacterium tuberculosis due à une contamination croisée en laboratoire : une investigation d'éclosion en épidémiologie moléculaire
Léveillé, Nayla, Point, Floriane, Houde, Josée, Hall, Michael, Souhaline, Hafid, LeBlanc, Marie-Andrée, Akochy, Pierre-Marie and Grandjean Lapierre, Simon (2024). Pseudo-éclosion de Mycobacterium tuberculosis due à une contamination croisée en laboratoire : une investigation d'éclosion en épidémiologie moléculaire. Relevé des maladies transmissibles au Canada, 50 (12), 470-475. doi: 10.14745/ccdr.v50i12da03f
2024
Journal Article
Mycobacterium tuberculosis pseudo-outbreak due to laboratory cross-contamination: a molecular epidemiology outbreak investigation
Léveillé, Nayla, Point, Floriane, Houde, Josée, Hall, Michael, Souhaline, Hafid, Leblanc, Marie-Andrée, Akochy, Pierre-Marie and Lapierre, Simon Grandjean (2024). Mycobacterium tuberculosis pseudo-outbreak due to laboratory cross-contamination: a molecular epidemiology outbreak investigation. Canada communicable disease report, 50 (12), 430-435. doi: 10.14745/ccdr.v50i12da03
2024
Journal Article
Whole genome sequencing of M. tuberculosis for disease control in high-burden settings: study protocol for a cluster randomized controlled trial evaluating different community-wide intervention strategies in rural Madagascar
Ametepe, Emmanuelle Sandra Adjoa, Andriamanoha, Noela, Andrianomanana, Fanantenana Randria, Point, Floriane, Mangahasimbola, Reziky Tiandraza, Dyachenko, Alina, Hall, Michael, Gamana, Theodora Mayouya, Knoblauch, Astrid M., Razafindrasoa, Yemimah Yededyah, Nimalan, Arianminpathy, Behr, Marcel, Durand, Madeleine, Johri, Mira, Iqbal, Zamin, Rakotoarivelo, Andry Rivo, Randremanana, Rindra Vatosoa, Rakotosamimanana, Niaina and Lapierre, Simon Grandjean (2024). Whole genome sequencing of M. tuberculosis for disease control in high-burden settings: study protocol for a cluster randomized controlled trial evaluating different community-wide intervention strategies in rural Madagascar. Trials, 25 (1) 717, 1. doi: 10.1186/s13063-024-08537-4
2024
Journal Article
Benchmarking reveals superiority of deep learning variant callers on bacterial nanopore sequence data
Hall, Michael B., Wick, Ryan R., Judd, Louise M., Nguyen, An N., Steinig, Eike J., Xie, Ouli, Davies, Mark, Seemann, Torsten, Stinear, Timothy P. and Coin, Lachlan (2024). Benchmarking reveals superiority of deep learning variant callers on bacterial nanopore sequence data. eLife, 13 RP98300, 1-23. doi: 10.7554/elife.98300.3
2024
Journal Article
Concordance of targeted and whole genome sequencing for Mycobacterium tuberculosis genotypic drug susceptibility testing
Cloutier Charette, William, Rabodoarivelo, Marie-Sylvianne, Point, Floriane, Knoblauch, Astrid M, Andrianomanana, Fanantenana Randria, Hall, Michael B, Iqbal, Zamin, Supply, Philip, Martin, Anandi, Rakotosamimanana, Niaina and Grandjean Lapierre, Simon (2024). Concordance of targeted and whole genome sequencing for Mycobacterium tuberculosis genotypic drug susceptibility testing. Diagnostic microbiology and infectious disease, 109 (2) 116249, 116249. doi: 10.1016/j.diagmicrobio.2024.116249
2024
Journal Article
Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data
Hall, Michael B. and Coin, Lachlan J. M. (2024). Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data. GigaScience, 13 giae010, 1-10. doi: 10.1093/gigascience/giae010
2023
Journal Article
Drug resistance prediction for Mycobacterium tuberculosis with reference graphs
Hall, Michael B., Lima, Leandro, Coin, Lachlan J. M. and Iqbal, Zamin (2023). Drug resistance prediction for Mycobacterium tuberculosis with reference graphs. Microbial Genomics, 9 (8) 001081, 1-14. doi: 10.1099/mgen.0.001081
2023
Journal Article
Genomic sequencing from sputum for tuberculosis disease diagnosis, lineage determination, and drug susceptibility prediction
Nilgiriwala, Kayzad, Rabodoarivelo, Marie-Sylvianne, Hall, Michael B., Patel, Grishma, Mandal, Ayan, Mishra, Shefali, Andrianomanana, Fanantenana Randria, Dingle, Kate, Rodger, Gillian, George, Sophie, Crook, Derrick W., Hoosdally, Sarah, Mistry, Nerges, Rakotosamimanana, Niaina, Iqbal, Zamin, Grandjean Lapierre, Simon and Walker, Timothy M. (2023). Genomic sequencing from sputum for tuberculosis disease diagnosis, lineage determination, and drug susceptibility prediction. Journal of Clinical Microbiology, 61 (3), 1-13. doi: 10.1128/jcm.01578-22
2023
Journal Article
Correction: Evaluation of Nanopore sequencing for Mycobacterium tuberculosis drug susceptibility testing and outbreak investigation: a genomic analysis (vol 4, pg 84, 2022)
Hall, M. B., Rabodoarivelo, M. S. and Koch, A. (2023). Correction: Evaluation of Nanopore sequencing for Mycobacterium tuberculosis drug susceptibility testing and outbreak investigation: a genomic analysis (vol 4, pg 84, 2022). Lancet Microbe, 4 (2), E72-E72. doi: 10.1016/S2666-5247(22)00381-0
2022
Journal Article
Assessment of the 2021 WHO Mycobacterium tuberculosis drug resistance mutation catalogue on an independent dataset
Hall, Michael B and Coin, Lachlan J M (2022). Assessment of the 2021 WHO Mycobacterium tuberculosis drug resistance mutation catalogue on an independent dataset. The Lancet Microbe, 3 (9), e645-E645. doi: 10.1016/S2666-5247(22)00151-3
2022
Journal Article
Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes
Hunt, Martin, Letcher, Brice, Malone, Kerri M., Nguyen, Giang, Hall, Michael B., Colquhoun, Rachel M., Lima, Leandro, Schatz, Michael C., Ramakrishnan, Srividya and Iqbal, Zamin (2022). Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes. Genome Biology, 23 (1) 147, 1. doi: 10.1186/s13059-022-02714-x
2022
Journal Article
Rasusa: randomly subsample sequencing reads to a specified coverage
Hall, Michael (2022). Rasusa: randomly subsample sequencing reads to a specified coverage. Journal of Open Source Software, 7 (69) 3941. doi: 10.21105/joss.03941
2022
Journal Article
Whole genome deep sequencing analysis of cell-free DNA in samples with low tumour content
Ganesamoorthy, Devika, Robertson, Alan James, Chen, Wenhan, Hall, Michael B., Cao, Minh Duc, Ferguson, Kaltin, Lakhani, Sunil R., Nones, Katia, Simpson, Peter T. and Coin, Lachlan J. M. (2022). Whole genome deep sequencing analysis of cell-free DNA in samples with low tumour content. BMC Cancer, 22 (1) 85, 85. doi: 10.1186/s12885-021-09160-1
2021
Journal Article
Pandora: nucleotide-resolution bacterial pan-genomics with reference graphs
Colquhoun, Rachel M., Hall, Michael B., Lima, Leandro, Roberts, Leah W., Malone, Kerri M., Hunt, Martin, Letcher, Brice, Hawkey, Jane, George, Sophie, Pankhurst, Louise and Iqbal, Zamin (2021). Pandora: nucleotide-resolution bacterial pan-genomics with reference graphs. Genome Biology, 22 (1) 267, 267. doi: 10.1186/s13059-021-02473-1
2021
Journal Article
Drug-resistant tuberculosis in pet ring-tailed lemur, Madagascar
LaFleur, Marni, Reuter, Kim E., Hall, Michael B., Rasoanaivo, Hoby H., McKernan, Stuart, Ranaivomanana, Paulo, Michel, Anita, Rabodoarivelo, Marie Sylvianne, Iqbal, Zamin, Rakotosamimanana, Niaina and Lapierre, Simon Grandjean (2021). Drug-resistant tuberculosis in pet ring-tailed lemur, Madagascar. Emerging Infectious Diseases, 27 (3), 977-979. doi: 10.3201/eid2703.202924
2021
Journal Article
Freshwater monitoring by nanopore sequencing
Urban, Lara, Holzer, Andre, Baronas, J. Jotautas, Hall, Michael B., Braeuninger-Weimer, Philipp, Scherm, Michael J., Kunz, Daniel J., Perera, Surangi N., Martin-Herranz, Daniel E., Tipper, Edward T., Salter, Susannah J. and Stammnitz, Maximilian R. (2021). Freshwater monitoring by nanopore sequencing. eLife, 10 e61504, 1-27. doi: 10.7554/elife.61504
Supervision
Availability
- Dr Michael Hall is:
- Available for supervision
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