| BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis R Bouckaert, TG Vaughan, J Barido-Sottani, S Duchêne, M Fourment, ... PLoS computational biology 15 (4), e1006650, 2019 | 3237 | 2019 |
| PoPoolation: a toolbox for population genetic analysis of next generation sequencing data from pooled individuals R Kofler, P Orozco-terWengel, N De Maio, RV Pandey, V Nolte, A Futschik, ... PloS one 6 (1), e15925, 2011 | 619 | 2011 |
| Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic Y Turakhia, B Thornlow, AS Hinrichs, N De Maio, L Gozashti, R Lanfear, ... Nature genetics 53 (6), 809-816, 2021 | 313 | 2021 |
| Evolutionary history of the global emergence of the Escherichia coli epidemic clone ST131 N Stoesser, AE Sheppard, L Pankhurst, N De Maio, CE Moore, R Sebra, ... MBio 7 (2), 10.1128/mbio. 02162-15, 2016 | 312 | 2016 |
| Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes N De Maio, LP Shaw, A Hubbard, S George, ND Sanderson, J Swann, ... Microbial genomics 5 (9), e000294, 2019 | 249 | 2019 |
| New routes to phylogeography: a Bayesian structured coalescent approximation N De Maio, CH Wu, KM O’Reilly, D Wilson PLoS genetics 11 (8), e1005421, 2015 | 248 | 2015 |
| SCOTTI: efficient reconstruction of transmission within outbreaks with the structured coalescent N De Maio, CH Wu, DJ Wilson PLoS computational biology 12 (9), e1005130, 2016 | 134 | 2016 |
| Issues with SARS-CoV-2 sequencing data N De Maio, C Walker, R Borges, L Weilguny, G Slodkowicz, N Goldman | 130 | 2020 |
| Genomic diversity affects the accuracy of bacterial single-nucleotide polymorphism–calling pipelines SJ Bush, D Foster, DW Eyre, EL Clark, N De Maio, LP Shaw, N Stoesser, ... Gigascience 9 (2), giaa007, 2020 | 115 | 2020 |
| Mutation rates and selection on synonymous mutations in SARS-CoV-2 N De Maio, CR Walker, Y Turakhia, R Lanfear, R Corbett-Detig, ... Genome biology and evolution 13 (5), evab087, 2021 | 111 | 2021 |
| Want to track pandemic variants faster? Fix the bioinformatics bottleneck EB Hodcroft, N De Maio, R Lanfear, DR MacCannell, BQ Minh, ... Nature 591 (7848), 30-33, 2021 | 107 | 2021 |
| VARIATION IN THERMAL PERFORMANCE AND REACTION NORMS AMONG POPULATIONS OF DROSOPHILA MELANOGASTER P Klepsatel, M Gáliková, N De Maio, CD Huber, C Schlötterer, T Flatt Evolution 67 (12), 3573-3587, 2013 | 107 | 2013 |
| Covert dissemination of carbapenemase-producing Klebsiella pneumoniae (KPC) in a successfully controlled outbreak: long- and short-read whole-genome … J Martin, HTT Phan, J Findlay, N Stoesser, L Pankhurst, I Navickaite, ... Journal of Antimicrobial Chemotherapy 72 (11), 3025-3034, 2017 | 106 | 2017 |
| Stability of SARS-CoV-2 phylogenies Y Turakhia, N De Maio, B Thornlow, L Gozashti, R Lanfear, CR Walker, ... PLoS genetics 16 (11), e1009175, 2020 | 105 | 2020 |
| Combining genomics and epidemiology to analyse bi-directional transmission of Mycobacterium bovis in a multi-host system J Crispell, CH Benton, D Balaz, N De Maio, A Ahkmetova, A Allen, R Biek, ... Elife 8, e45833, 2019 | 95 | 2019 |
| A phylodynamic workflow to rapidly gain insights into the dispersal history and dynamics of SARS-CoV-2 lineages S Dellicour, K Durkin, SL Hong, B Vanmechelen, J Martí-Carreras, MS Gill, ... Molecular biology and evolution 38 (4), 1608-1613, 2021 | 94 | 2021 |
| The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples HS Gweon, LP Shaw, J Swann, N De Maio, M AbuOun, R Niehus, ... Environmental Microbiome 14 (1), 1-15, 2019 | 93 | 2019 |
| Pandemic-scale phylogenomics reveals the SARS-CoV-2 recombination landscape Y Turakhia, B Thornlow, A Hinrichs, J McBroome, N Ayala, C Ye, K Smith, ... Nature 609 (7929), 994-997, 2022 | 92 | 2022 |
| Genomic reconstruction of the SARS-CoV-2 epidemic in England HS Vöhringer, T Sanderson, M Sinnott, N De Maio, T Nguyen, R Goater, ... Nature 600 (7889), 506-511, 2021 | 91 | 2021 |
| PoMo: an allele frequency-based approach for species tree estimation N De Maio, D Schrempf, C Kosiol Systematic biology 64 (6), 1018-1031, 2015 | 88 | 2015 |
Daniel J WilsonUniversity of OxfordVerified email at bdi.ox.ac.uk
