Kathryn Holt
Kathryn Holt
Monash University & LSHTM
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
12232017
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
8602013
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
5882014
Bandage: interactive visualization of de novo genome assemblies
RR Wick, MB Schultz, J Zobel, KE Holt
Bioinformatics 31 (20), 3350-2, 2015
5852015
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
5572015
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
5142015
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
5022008
Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4
New England Journal of Medicine 365 (8), 718-724, 2011
4962011
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
4632009
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
3522010
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
3252005
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
3182015
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
2392012
Completing bacterial genome assemblies with multiplex MinION sequencing
RR Wick, LM Judd, CL Gorrie, KE Holt
Microbial Genomics, 2017
1832017
Pseudogene accumulation in the evolutionary histories of Salmonella enterica serovars Paratyphi A and Typhi
K Holt, N Thomson, J Wain, G Langridge, R Hasan, Z Bhutta, M Quail, ...
BMC genomics 10 (1), 36, 2009
1672009
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
1582016
Typhoid in Kenya is associated with a dominant multidrug-resistant Salmonella enterica serovar Typhi haplotype that is also widespread in Southeast Asia
S Kariuki, G Revathi, J Kiiru, DM Mengo, J Mwituria, J Muyodi, A Munyalo, ...
Journal of clinical microbiology 48 (6), 2171, 2010
1562010
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
1452017
Performance of neural network basecalling tools for Oxford Nanopore sequencing
RR Wick, LM Judd, KE Holt
Genome Biology 20 (1), 129, 2019
1382019
Genome-scale rates of evolutionary change in bacteria
S Duchêne, KE Holt, FX Weill, S Le Hello, J Hawkey, DJ Edwards, ...
Microbial Genomics 2 (11), 2016
1282016
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