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Kathryn Holt
Kathryn Holt
LSHTM & Monash University
Verified email at lshtm.ac.uk - Homepage
Title
Cited by
Cited by
Year
Unicycler: resolving bacterial genome assemblies from short and long sequencing reads
RR Wick, LM Judd, CL Gorrie, KE Holt
PLOS Computational Biology 13 (6), e1005595, 2017
56622017
Bandage: interactive visualization of de novo genome assemblies
RR Wick, MB Schultz, J Zobel, KE Holt
Bioinformatics 31 (20), 3350-2, 2015
18952015
Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans
I Comas, M Coscolla, T Luo, S Borrell, KE Holt, M Kato-Maeda, J Parkhill, ...
Nature genetics 45 (10), 1176-1182, 2013
12932013
Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health
KE Holt, H Wertheim, RN Zadoks, S Baker, CA Whitehouse, D Dance, ...
Proceedings of the National Academy of Sciences 112 (27), E3574-E3581, 2015
11872015
Performance of neural network basecalling tools for Oxford Nanopore sequencing
RR Wick, LM Judd, KE Holt
Genome Biology 20 (1), 129, 2019
11232019
SRST2: Rapid genomic surveillance for public health and hospital microbiology labs
M Inouye, H Dashnow, LA Raven, MB Schultz, BJ Pope, T Tomita, J Zobel, ...
Genome Medicine 6 (11), 1-16, 2014
10032014
The Infant Nasopharyngeal Microbiome Impacts Severity of Lower Respiratory Infection and Risk of Asthma Development
SM Teo, D Mok, K Pham, M Kusel, M Serralha, N Troy, BJ Holt, BJ Hales, ...
Cell Host and Microbe 17 (5), 704-715, 2015
9382015
Completing bacterial genome assemblies with multiplex MinION sequencing
RR Wick, LM Judd, CL Gorrie, KE Holt
Microbial Genomics, 2017
7332017
Population genomics of Klebsiella pneumoniae
KL Wyres, MMC Lam, KE Holt
Nature Reviews Microbiology 18 (6), 344-359, 2020
6972020
Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype
RA Kingsley, CL Msefula, NR Thomson, S Kariuki, KE Holt, MA Gordon, ...
Genome research 19 (12), 2279-2287, 2009
6312009
High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi
KE Holt, J Parkhill, CJ Mazzoni, P Roumagnac, FX Weill, I Goodhead, ...
Nature genetics 40 (8), 987-993, 2008
5772008
Klebsiella pneumoniae as a key trafficker of drug resistance genes from environmental to clinically important bacteria
KL Wyres, KE Holt
Current opinion in microbiology 45, 131-139, 2018
5062018
Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4
New England Journal of Medicine 365 (8), 718-724, 2011
4962011
A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex
MMC Lam, RR Wick, SC Watts, LT Cerdeira, KL Wyres, KE Holt
Nature communications 12 (1), 4188, 2021
4862021
Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter-and intracontinental transmission events
VK Wong, S Baker, DJ Pickard, J Parkhill, AJ Page, NA Feasey, ...
Nature Genetics 47 (6), 632-639, 2015
4782015
Gastrointestinal carriage is a major reservoir of Klebsiella pneumoniae infection in intensive care patients
CL Gorrie, M Mirčeta, RR Wick, DJ Edwards, NR Thomson, RA Strugnell, ...
Clinical Infectious Diseases 65 (2), 208-215, 2017
4752017
Identification of Klebsiella capsule synthesis loci from whole genome data
K Wyres, RR Wick, C Gorrie, A Jenney, R Follador, NR Thomson, KE Holt
bioRxiv, 071415, 2016
4672016
Evolutionary dynamics of Clostridium difficile over short and long time scales
M He, M Sebaihia, TD Lawley, RA Stabler, LF Dawson, MJ Martin, KE Holt, ...
Proceedings of the National Academy of Sciences 107 (16), 7527, 2010
4272010
An immunoepidemiological approach to asthma: identification of in-vitro T cell response patterns associated with different wheezing phenotypes in children
T Heaton, J Rowe, S Turner, RC Aalberse, N De Klerk, D Suriyaarachchi, ...
The Lancet 365 (9454), 142-149, 2005
3512005
Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe
KE Holt, S Baker, FX Weill, EC Holmes, A Kitchen, J Yu, V Sangal, ...
Nature genetics 44 (9), 1056-1059, 2012
3322012
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