| Convergent regulatory evolution and loss of flight in paleognathous birds TB Sackton, P Grayson, A Cloutier, Z Hu, JS Liu, NE Wheeler, PP Gardner, ... Science 364 (6435), 74-78, 2019 | 214 | 2019 |
| An African Salmonella Typhimurium ST313 sublineage with extensive drug-resistance and signatures of host adaptation S Van Puyvelde, D Pickard, K Vandelannoote, E Heinz, B Barbé, ... Nature communications 10 (1), 4280, 2019 | 98 | 2019 |
| Joint sequencing of human and pathogen genomes reveals the genetics of pneumococcal meningitis JA Lees, B Ferwerda, PHC Kremer, NE Wheeler, MV Serón, NJ Croucher, ... Nature communications 10 (1), 2176, 2019 | 86 | 2019 |
| Evaluation of parameters affecting performance and reliability of machine learning-based antibiotic susceptibility testing from whole genome sequencing data AL Hicks, N Wheeler, L Sánchez-Busó, JL Rakeman, SR Harris, YH Grad PLoS computational biology 15 (9), e1007349, 2019 | 80 | 2019 |
| Machine learning identifies signatures of host adaptation in the bacterial pathogen Salmonella enterica NE Wheeler, PP Gardner, L Barquist PLoS genetics 14 (5), e1007333, 2018 | 71 | 2018 |
| Improved prediction of bacterial genotype-phenotype associations using interpretable pangenome-spanning regressions JA Lees, TT Mai, M Galardini, NE Wheeler, ST Horsfield, J Parkhill, ... MBio 11 (4), 10.1128/mbio. 01344-20, 2020 | 69* | 2020 |
| Adaptation to the cervical environment is associated with increased antibiotic susceptibility in Neisseria gonorrhoeae KC Ma, TD Mortimer, AL Hicks, NE Wheeler, L Sánchez-Busó, ... Nature communications 11 (1), 4126, 2020 | 53* | 2020 |
| Evolution of Salmonella enterica serotype Typhimurium driven by anthropogenic selection and niche adaptation M Bawn, NF Alikhan, G Thilliez, M Kirkwood, NE Wheeler, L Petrovska, ... PLoS genetics 16 (6), e1008850, 2020 | 49 | 2020 |
| Increased power from conditional bacterial genome-wide association identifies macrolide resistance mutations in Neisseria gonorrhoeae KC Ma, TD Mortimer, MA Duckett, AL Hicks, NE Wheeler, L Sánchez-Busó, ... Nature communications 11 (1), 5374, 2020 | 44* | 2020 |
| Robust identification of noncoding RNA from transcriptomes requires phylogenetically-informed sampling S Lindgreen, SU Umu, ASW Lai, H Eldai, W Liu, S McGimpsey, ... PLoS computational biology 10 (10), e1003907, 2014 | 43 | 2014 |
| Whole-genome sequencing as part of national and international surveillance programmes for antimicrobial resistance: A roadmap NIHR Global Health Research Unit on Genomic Surveillance of AMR BMJ Global Health 5 (11), e002244, 2020 | 40 | 2020 |
| Rapid Genomic Characterization and Global Surveillance of Klebsiella Using Pathogenwatch S Argimón, S David, A Underwood, M Abrudan, NE Wheeler, M Kekre, ... Clinical Infectious Diseases 73 (Supplement_4), S325-S335, 2021 | 37 | 2021 |
| Why so narrow: distribution of anti-sense regulated, type I toxin-antitoxin systems compared with type II and type III systems DS Coray, NE Wheeler, JA Heinemann, PP Gardner RNA biology 14 (3), 275-280, 2017 | 33 | 2017 |
| A profile-based method for identifying functional divergence of orthologous genes in bacterial genomes NE Wheeler, L Barquist, RA Kingsley, PP Gardner Bioinformatics 32 (23), 3566-3574, 2016 | 30 | 2016 |
| Tracing outbreaks with machine learning NE Wheeler Nature Reviews Microbiology 17 (5), 269-269, 2019 | 28 | 2019 |
| Gauge your phage: benchmarking of bacteriophage identification tools in metagenomic sequencing data SFS Ho, AD Millard, W van Schaik Microbiome, 2023 | 20* | 2023 |
| Breaking the code of antibiotic resistance SW Lo, N Kumar, NE Wheeler Nature Reviews Microbiology 16 (5), 262-262, 2018 | 16 | 2018 |
| NIHR Global Health Research Unit on Genomic Surveillance of Antimicrobial Resistance. 2021. Rapid genomic characterization and global surveillance of Klebsiella using Pathogenwatch S Argimón, S David, A Underwood, M Abrudan, NE Wheeler, M Kekre, ... Clin Infect Dis 73, S325-S335, 0 | 12 | |
| An African Salmonella Typhimurium ST313 sublineage with extensive drug-resistance and signatures of host adaptation. Nat Commun 10: 4280 S Van Puyvelde, D Pickard, K Vandelannoote, E Heinz, B Barbé, ... | 10 | 2019 |
| Contrasting approaches to genome-wide association studies impact the detection of resistance mechanisms in Staphylococcus aureus NE Wheeler, S Reuter, C Chewapreecha, JA Lees, B Blane, C Horner, ... bioRxiv, 758144, 2019 | 8 | 2019 |
Paul P. GardnerUniversity of Otago, New ZealandVerified email at otago.ac.nz
