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Nicole E Wheeler
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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
2422019
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
1112019
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
992019
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
882019
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
832018
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
80*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
672020
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
61*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
572021
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
562020
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
49*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
452014
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
352017
Gauge your phage: benchmarking of bacteriophage identification tools in metagenomic sequencing data
SFS Ho, AD Millard, W van Schaik
Microbiome, 2023
32*2023
Tracing outbreaks with machine learning
NE Wheeler
Nature Reviews Microbiology 17 (5), 269-269, 2019
312019
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
312016
NIHR global health research unit on genomic surveillance of antimicrobial resistance 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, 2021
192021
Safety by design: Biosafety and biosecurity in the age of synthetic genomics
SA Hoffmann, J Diggans, D Densmore, J Dai, T Knight, E Leproust, ...
Iscience 26 (3), 2023
182023
Innovations in genomic antimicrobial resistance surveillance
NE Wheeler, V Price, E Cunningham-Oakes, KK Tsang, JG Nunn, ...
The Lancet Microbe 4 (12), e1063-e1070, 2023
172023
Breaking the code of antibiotic resistance
SW Lo, N Kumar, NE Wheeler
Nature Reviews Microbiology 16 (5), 262-262, 2018
172018
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Articles 1–20