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2025 Journal Article Genome graphs reveal the importance of structural variation in Mycobacterium tuberculosis evolution and drug resistanceCanalda-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 |
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2025 Journal Article Genome size estimation from long read overlapsHall, 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 |
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2025 Journal Article Sustainable data analysis with SnakemakeMölder, 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 |
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2025 Journal Article TBpore cluster: A novel phylogenetic pipeline for tuberculosis transmission studies using nanopore next-generation sequencing dataGagnon, 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 |
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2024 Journal Article Pseudo-éclosion de Mycobacterium tuberculosis due à une contamination croisée en laboratoire : une investigation d'éclosion en épidémiologie moléculaireLéveillé, 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 |
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2024 Journal Article Mycobacterium tuberculosis pseudo-outbreak due to laboratory cross-contamination: a molecular epidemiology outbreak investigationLéveillé, 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 |
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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 MadagascarAmetepe, 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 |
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2024 Journal Article Benchmarking reveals superiority of deep learning variant callers on bacterial nanopore sequence dataHall, 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 |
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2024 Journal Article Concordance of targeted and whole genome sequencing for Mycobacterium tuberculosis genotypic drug susceptibility testingCloutier 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 |
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2024 Journal Article Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic dataHall, 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 |
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2023 Journal Article Drug resistance prediction for Mycobacterium tuberculosis with reference graphsHall, 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 |
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2023 Journal Article Genomic sequencing from sputum for tuberculosis disease diagnosis, lineage determination, and drug susceptibility predictionNilgiriwala, 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 |
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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 |
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2022 Journal Article Assessment of the 2021 WHO Mycobacterium tuberculosis drug resistance mutation catalogue on an independent datasetHall, 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 |
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2022 Journal Article Minos: variant adjudication and joint genotyping of cohorts of bacterial genomesHunt, 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 |
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2022 Journal Article Rasusa: randomly subsample sequencing reads to a specified coverageHall, Michael (2022). Rasusa: randomly subsample sequencing reads to a specified coverage. Journal of Open Source Software, 7 (69) 3941. doi: 10.21105/joss.03941 |
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2022 Journal Article Whole genome deep sequencing analysis of cell-free DNA in samples with low tumour contentGanesamoorthy, 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 |
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2021 Journal Article Pandora: nucleotide-resolution bacterial pan-genomics with reference graphsColquhoun, 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 |
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2021 Journal Article Drug-resistant tuberculosis in pet ring-tailed lemur, MadagascarLaFleur, 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 |
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2021 Journal Article Freshwater monitoring by nanopore sequencingUrban, 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 |
