Publications
Journal Articles
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 June) e0325914, e0325914-6. doi: 10.1371/journal.pone.0325914
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
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, 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
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