MH
Martin Hunt
bioinformaticsSoftwaremicrobiologyMycobacterium tuberculosisGenetic VariationGenome, BacterialGenome, HelminthPhylogenyTranscriptomeAlgorithms
On Valency
published · living versionsW_26xzgw86·v1 · currentpublished
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
with Keith R. Bradnam, Joseph N. Fass, Anton Alexandrov, Paul Baranay +86
1 version
Preprints & journals
47 papers in the corpus · 2011–2026AllTheBacteria: a community resource empowers biology and discovers novel peptide antibiotics.42465405 · Hunt, Martin, Torres, Marcelo D T, Alikhan, Nabil-Fareed et al.2026 · 76 citationsbioRxiv : the preprint server for biology. 2026
Complete genomes reveal a refined map of Mycobacterium tuberculosis genetic diversity across evolutionary scales.42251028 · García-Marín, Ana María, Torres-Puente, Manuela, Martinez-Priego, Llúcia et al.2026 · 2 citationsNature communications. 2026;17(1)
Flex-It: A global standardised genotyping framework for Shigella flexneri10.64898/2026.04.17.719127v1 · Hawkey, J., Nodari, C. S., Iqbal, Z. et al.2026 · 0 citationsbioRxiv
Rate variation and recurrent sequence errors in pandemic-scale phylogenetics.41663576 · De Maio, Nicola, Willemsen, Myrthe, Martin, Samuel et al.2026 · 9 citationsNature methods. 2026;23(3):565-573
Rapidly and reproducibly building a comprehensive catalogueof resistance-associated variants for M. tuberculosis10.1101/2025.10.02.679941v2 · Adlard, D., Malone, K. M., Westhead, J. et al.2025 · 0 citationsbioRxiv
Complete genomes reveal the full extent of Mycobacterium tuberculosis complex diversity across evolutionary scales10.1101/2025.08.05.667821v1 · Garcia-Marin, A. M., Torres-Puente, M., Martinez-Priego, L. et al.2025 · 3 citationsbioRxiv
Typhi Mykrobe: fast and accurate lineage identification and antimicrobial resistance genotyping directly from sequence reads for the typhoid fever agent Salmonella Typhi.40766357 · Ingle, Danielle J, Hawkey, Jane, Hunt, Martin et al.2025 · 11 citationsbioRxiv : the preprint server for biology. 2025
Genomic perspective on the bacillus causing paratyphoid B fever.39658567 · Hawkey, Jane, Frézal, Lise, Tran Dien, Alicia et al.2024 · 5 citationsNature communications. 2024;15(1):10143
MmpR5 protein truncation and bedaquiline resistance in Mycobacterium tuberculosis isolates from South Africa: a genomic analysis.38851206 · Roberts, Leah W, Malone, Kerri M, Hunt, Martin et al.2024 · 10 citationsThe Lancet. Microbe. 2024;5(8):100847
Hostile: accurate decontamination of microbial host sequences.38039142 · Constantinides, Bede, Hunt, Martin, Crook, Derrick W2023 · 69 citationsBioinformatics (Oxford, England). 2023;39(12)
A validated cloud-based genomic platform for co-ordinated, expedient global analysis of SARS-CoV-2 genomic epidemiology10.1101/2023.11.27.23298986v5 · Amoako, D., Anh, N. T., Bastable, J. et al.2023 · 0 citationsmedRxiv
Bedaquiline and clofazimine resistance in Mycobacterium tuberculosis: an in-vitro and in-silico data analysis.37003285 · Sonnenkalb, Lindsay, Carter, Joshua James, Spitaleri, Andrea et al.2023 · 104 citationsThe Lancet. Microbe. 2023;4(5):e358-e368
Repeated evolution of bedaquiline resistance in Mycobacterium tuberculosis is driven by truncation of mmpR510.1101/2022.12.08.519610v1 · Roberts, L. W., Malone, K. M., Hunt, M. et al.2022 · 5 citationsbioRxiv
Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes.35791022 · Hunt, Martin, Letcher, Brice, Malone, Kerri M et al.2022 · 37 citationsGenome biology. 2022;23(1):147
ReadItAndKeep: rapid decontamination of SARS-CoV-2 sequencing reads.35551365 · Hunt, Martin, Swann, Jeremy, Constantinides, Bede et al.2022 · 10 citationsBioinformatics (Oxford, England). 2022;38(12):3291-3293
Correction: MiR-277/4989 regulate transcriptional landscape during juvenile to adult transition in the parasitic helminth Schistosoma mansoni.35666710 · Protasio, Anna V, Dongen, Stijn van, Collins, Julie et al.2022 · 2 citationsPLoS neglected tropical diseases. 2022;16(6):e0010521
The 2021 WHO catalogue of Mycobacterium tuberculosis complex mutations associated with drug resistance: A genotypic analysis.35373160 · Walker, Timothy M, Miotto, Paolo, Köser, Claudio U et al.2022 · 293 citationsThe Lancet. Microbe. 2022;3(4):e265-e273
Exploring bacterial diversity via a curated and searchable snapshot of archived DNA sequences.34752446 · Blackwell, Grace A, Hunt, Martin, Malone, Kerri M et al.2021 · 120 citationsPLoS biology. 2021;19(11):e3001421
Pandora: nucleotide-resolution bacterial pan-genomics with reference graphs.34521456 · Colquhoun, Rachel M, Hall, Michael B, Lima, Leandro et al.2022 · 68 citationsGenome biology. 2021;22(1):267
Gramtools enables multiscale variation analysis with genome graphs.34488837 · Letcher, Brice, Hunt, Martin, Iqbal, Zamin2022 · 33 citationsGenome biology. 2021;22(1):259
Global population structure and genotyping framework for genomic surveillance of the major dysentery pathogen, Shigella sonnei.33976138 · Hawkey, Jane, Paranagama, Kalani, Baker, Kate S et al.2021 · 106 citationsNature communications. 2021;12(1):2684
Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.32055708 · Hunt, Martin, Bradley, Phelim, Lapierre, Simon Grandjean et al.2025 · 197 citationsWellcome open research. 2019;4:191
Genetic variation associated with infection and the environment in the accidental pathogen Burkholderia pseudomallei.31799430 · Chewapreecha, Claire, Mather, Alison E, Harris, Simon R et al.2020 · 32 citationsCommunications biology. 2019;2:428
Exploring Plasmodium falciparum Var Gene Expression to Assess Host Selection Pressure on Parasites During Infancy.31681266 · Kivisi, Cheryl A, Muthui, Michelle, Hunt, Martin et al.2020 · 6 citationsFrontiers in immunology. 2019;10:2328
Inferring synteny between genome assemblies: a systematic evaluation.29382321 · Liu, Dang, Hunt, Martin, Tsai, Isheng J2018 · 146 citationsBMC bioinformatics. 2018;19(1):26
ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads.29177089 · Hunt, Martin, Mather, Alison E, Sánchez-Busó, Leonor et al.2019 · 661 citationsMicrobial genomics. 2017;3(10):e000131
Sharing of carbapenemase-encoding plasmids between Enterobacteriaceae in UK sewage uncovered by MinION sequencing.29026655 · Ludden, Catherine, Reuter, Sandra, Judge, Kim et al.2019 · 54 citationsMicrobial genomics. 2017;3(7):e000114
MiR-277/4989 regulate transcriptional landscape during juvenile to adult transition in the parasitic helminth Schistosoma mansoni.28542189 · Protasio, Anna V, van Dongen, Stijn, Collins, Julie et al.2017 · 34 citationsPLoS neglected tropical diseases. 2017;11(5):e0005559
Comparison of bacterial genome assembly software for MinION data and their applicability to medical microbiology.28348876 · Judge, Kim, Hunt, Martin, Reuter, Sandra et al.2018 · 41 citationsMicrobial genomics. 2016;2(9):e000085
Robust high-throughput prokaryote de novo assembly and improvement pipeline for Illumina data.28348874 · Page, Andrew J, De Silva, Nishadi, Hunt, Martin et al.2018 · 240 citationsMicrobial genomics. 2016;2(8):e000083
A Phylogenetic and Phenotypic Analysis of Salmonella enterica Serovar Weltevreden, an Emerging Agent of Diarrheal Disease in Tropical Regions.26867150 · Makendi, Carine, Page, Andrew J, Wren, Brendan W et al.2016 · 67 citationsPLoS neglected tropical diseases. 2016;10(2):e0004446
Circlator: automated circularization of genome assemblies using long sequencing reads.26714481 · Hunt, Martin, Silva, Nishadi De, Otto, Thomas D et al.2016 · 1,189 citationsGenome biology. 2015;16:294
HPMCD: the database of human microbial communities from metagenomic datasets and microbial reference genomes.26578596 · Forster, Samuel C, Browne, Hilary P, Kumar, Nitin et al.2016 · 67 citationsNucleic acids research. 2016;44(D1):D604-9
Roary: rapid large-scale prokaryote pan genome analysis.26198102 · Page, Andrew J, Cummins, Carla A, Hunt, Martin et al.2016 · 5,720 citationsBioinformatics (Oxford, England). 2015;31(22):3691-3
IVA: accurate de novo assembly of RNA virus genomes.25725497 · Hunt, Martin, Gall, Astrid, Ong, Swee Hoe et al.2016 · 196 citationsBioinformatics (Oxford, England). 2015;31(14):2374-6
A comprehensive evaluation of rodent malaria parasite genomes and gene expression.25359557 · Otto, Thomas D, Böhme, Ulrike, Jackson, Andrew P et al.2015 · 271 citationsBMC biology. 2014;12:86
The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode.24580726 · Cotton, James A, Lilley, Catherine J, Jones, Laura M et al.2015 · 265 citationsGenome biology. 2014;15(3):R43
A comprehensive evaluation of assembly scaffolding tools.24581555 · Hunt, Martin, Newbold, Chris, Berriman, Matthew et al.2015 · 174 citationsGenome biology. 2014;15(3):R42
Summarizing specific profiles in Illumina sequencing from whole-genome amplified DNA.24353264 · Tsai, Isheng J, Hunt, Martin, Holroyd, Nancy et al.2015 · 24 citationsDNA research : an international journal for rapid publication of reports on genes and genomes. 2014;21(3):243-54
The genome and transcriptome of Haemonchus contortus, a key model parasite for drug and vaccine discovery.23985316 · Laing, Roz, Kikuchi, Taisei, Martinelli, Axel et al.2015 · 373 citationsGenome biology. 2013;14(8):R88
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.23870653 · Bradnam, Keith R, Fass, Joseph N, Alexandrov, Anton et al.2014 · 671 citationsGigaScience. 2013;2(1):10
REAPR: a universal tool for genome assembly evaluation.23710727 · Hunt, Martin, Kikuchi, Taisei, Sanders, Mandy et al.2015 · 406 citationsGenome biology. 2013;14(5):R47
Characterization and comparative analysis of the complete Haemonchus contortus β-tubulin gene family and implications for benzimidazole resistance in strongylid nematodes.23416426 · Saunders, Gary Ian, Wasmuth, James David, Beech, Robin et al.2013 · 61 citationsInternational journal for parasitology. 2013;43(6):465-75
Diversity in parasitic nematode genomes: the microRNAs of Brugia pahangi and Haemonchus contortus are largely novel.22216965 · Winter, Alan D, Weir, William, Hunt, Martin et al.2012 · 85 citationsBMC genomics. 2012;13:4
A systematically improved high quality genome and transcriptome of the human blood fluke Schistosoma mansoni.22253936 · Protasio, Anna V, Tsai, Isheng J, Babbage, Anne et al.2012 · 419 citationsPLoS neglected tropical diseases. 2012;6(1):e1455
Genomic insights into the origin of parasitism in the emerging plant pathogen Bursaphelenchus xylophilus.21909270 · Kikuchi, Taisei, Cotton, James A, Dalzell, Jonathan J et al.2012 · 430 citationsPLoS pathogens. 2011;7(9):e1002219
Annotation of two large contiguous regions from the Haemonchus contortus genome using RNA-seq and comparative analysis with Caenorhabditis elegans.21858033 · Laing, Roz, Hunt, Martin, Protasio, Anna V et al.2012 · 24 citationsPloS one. 2011;6(8):e23216
Career total: 125 works. 47 are in this corpus.
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