| Roary: rapid large-scale prokaryote pan genome analysis AJ Page, CA Cummins, M Hunt, VK Wong, S Reuter, MTG Holden, ... Bioinformatics 31 (22), 3691-3693, 2015 | 4053 | 2015 |
| Circlator: automated circularization of genome assemblies using long sequencing reads M Hunt, ND Silva, TD Otto, J Parkhill, JA Keane, SR Harris Genome biology 16, 1-10, 2015 | 881 | 2015 |
| Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species KR Bradnam, JN Fass, A Alexandrov, P Baranay, M Bechner, I Birol, ... Gigascience 2 (1), 2047-217X-2-10, 2013 | 792 | 2013 |
| ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads M Hunt, AE Mather, L Sánchez-Busó, AJ Page, J Parkhill, JA Keane, ... Microbial genomics 3 (10), e000131, 2017 | 570 | 2017 |
| A Systematically Improved High Quality Genome and Transcriptome of the Human Blood Fluke Schistosoma mansoni AV Protasio, IJ Tsai, A Babbage, S Nichol, M Hunt, MA Aslett, N De Silva, ... PLoS neglected tropical diseases 6 (1), e1455, 2012 | 475 | 2012 |
| REAPR: a universal tool for genome assembly evaluation M Hunt, T Kikuchi, M Sanders, C Newbold, M Berriman, TD Otto Genome biology 14, 1-10, 2013 | 461 | 2013 |
| Genomic Insights into the Origin of Parasitism in the Emerging Plant Pathogen Bursaphelenchus xylophilus T Kikuchi, JA Cotton, JJ Dalzell, K Hasegawa, N Kanzaki, P McVeigh, ... PLoS pathogens 7 (9), e1002219, 2011 | 442 | 2011 |
| The genome and transcriptome of Haemonchus contortus, a key model parasite for drug and vaccine discovery R Laing, T Kikuchi, A Martinelli, IJ Tsai, RN Beech, E Redman, N Holroyd, ... Genome biology 14, 1-16, 2013 | 354 | 2013 |
| Prediction of susceptibility to first-line tuberculosis drugs by DNA sequencing CRyPTIC Consortium and the 100,000 Genomes Project New England Journal of Medicine 379 (15), 1403-1415, 2018 | 320 | 2018 |
| A comprehensive evaluation of rodent malaria parasite genomes and gene expression TD Otto, U Böhme, AP Jackson, M Hunt, B Franke-Fayard, ... BMC biology 12, 1-18, 2014 | 299 | 2014 |
| The genome and life-stage specific transcriptomes of Globodera pallidaelucidate key aspects of plant parasitism by a cyst nematode JA Cotton, CJ Lilley, LM Jones, T Kikuchi, AJ Reid, P Thorpe, IJ Tsai, ... Genome biology 15, 1-17, 2014 | 253 | 2014 |
| Robust high-throughput prokaryote de novo assembly and improvement pipeline for Illumina data AJ Page, N De Silva, M Hunt, MA Quail, J Parkhill, SR Harris, TD Otto, ... Microbial genomics 2 (8), e000083, 2016 | 234 | 2016 |
| A comprehensive evaluation of assembly scaffolding tools M Hunt, C Newbold, M Berriman, TD Otto Genome biology 15, 1-15, 2014 | 228 | 2014 |
| IVA: accurate de novo assembly of RNA virus genomes M Hunt, A Gall, SH Ong, J Brener, B Ferns, P Goulder, E Nastouli, ... Bioinformatics 31 (14), 2374-2376, 2015 | 201 | 2015 |
| The 2021 WHO catalogue of Mycobacterium tuberculosis complex mutations associated with drug resistance: a genotypic analysis TM Walker, P Miotto, CU Köser, PW Fowler, J Knaggs, Z Iqbal, M Hunt, ... The Lancet Microbe 3 (4), e265-e273, 2022 | 137 | 2022 |
| Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe M Hunt, P Bradley, SG Lapierre, S Heys, M Thomsit, MB Hall, KM Malone, ... Wellcome open research 4, 2019 | 117 | 2019 |
| Inferring synteny between genome assemblies: a systematic evaluation D Liu, M Hunt, IJ Tsai BMC bioinformatics 19, 1-13, 2018 | 110 | 2018 |
| Diversity in parasitic nematode genomes: the microRNAs of Brugia pahangi and Haemonchus contortus are largely novel AD Winter, W Weir, M Hunt, M Berriman, JS Gilleard, E Devaney, C Britton BMC genomics 13, 1-19, 2012 | 83 | 2012 |
| HPMCD: the database of human microbial communities from metagenomic datasets and microbial reference genomes SC Forster, HP Browne, N Kumar, M Hunt, H Denise, A Mitchell, RD Finn, ... Nucleic acids research 44 (D1), D604-D609, 2016 | 72 | 2016 |
| Exploring bacterial diversity via a curated and searchable snapshot of archived DNA sequences GA Blackwell, M Hunt, KM Malone, L Lima, G Horesh, BTF Alako, ... PLoS biology 19 (11), e3001421, 2021 | 71 | 2021 |
