Dr Michael Hall
Research Fellow
UQ Centre for Clinical Research
Publications
Journal Articles
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Köster, Johannes, Mölder, Felix, Jablonski, Kim Philipp, Letcher, Brice, Hall, Michael B., Tomkins-Tinch, Christopher H., Sochat, Vanessa, Forster, Jan, Lee, Soohyun, Twardziok, Sven O., Kanitz, Alexander, Wilm, Andreas, Holtgrewe, Manuel, Rahmann, Sven and Nahnsen, Sven (2021). Sustainable data analysis with Snakemake. F1000Research, 10 33, 33. doi: 10.12688/f1000research.29032.2
Teng, Haotian, Cao, Minh Duc, Hall, Michael B., Duarte, Tania, Wang, Sheng and Coin, Lachlan J M (2019). Correction to: Chiron: translating nanopore raw signal directly into nucleotide sequence using deep learning. GigaScience, 8 (5). doi: 10.1093/gigascience/giz049
Hunt, Martin, Bradley, Phelim, Lapierre, Simon Grandjean, Heys, Simon, Thomsit, Mark, Hall, Michael B., Malone, Kerri M., Wintringer, Penelope, Walker, Timothy M., Cirillo, Daniela M., Comas, Iñaki, Farhat, Maha R., Fowler, Phillip, Gardy, Jennifer, Ismail, Nazir, Kohl, Thomas A., Mathys, Vanessa, Merker, Matthias, Niemann, Stefan, Omar, Shaheed Vally, Sintchenko, Vitali, Smith, Grace, van Soolingen, Dick, Supply, Philip, Tahseen, Sabira, Wilcox, Mark, Arandjelovic, Irena, Peto, Tim E.A., Crook, Derrick W. and Iqbal, Zamin (2019). Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with mykrobe [version 1; peer review: 2 approved, 1 approved with reservations]. Wellcome Open Research, 4 191, 191. doi: 10.12688/wellcomeopenres.15603.1
Teng, Haotian, Cao, Minh Duc, Hall, Michael B., Duarte, Tania, Wang, Sheng and Coin, Lachlan J. M. (2018). Chiron: Translating nanopore raw signal directly into nucleotide sequence using deep learning. GigaScience, 7 (5). doi: 10.1093/gigascience/giy037