Author
Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.
8 papers
Recent·Most cited
Sebastian Duchêne, Kathryn E Holt, François-Xavier Weill, Simon Le Hello, Jane Hawkey, David J Edwards, Mathieu Fourment, Edward C Holmes
The paper estimates genome-scale evolutionary rates in bacteria and finds that rates vary widely, largely due to sampling time, with a strong negative association between time and rate.
bioRxiv · Aug 15, 2016Evolutionary Biology
Duy Pham Thanh, Ha Thanh Tuyen, To Nguyen Thi Nguyen, Hao Chung The, Ryan R Wick, Guy Thwaites, Stephen Baker, Kathryn E Holt
The paper identifies an inactive mcr-1 gene on a plasmid in a 2008 Vietnamese Shigella sonnei isolate, which becomes active under colistin exposure.
Journal of Antimicrobial Chemotherapy · May 30, 2016Peer-reviewedMicrobiology
Hao Chung The, Maia A Rabaa, Duy Pham Thanh, Niall De Lappe, Martin Cormican, Benjamin P Howden, Sonam Wangchuk, Ladaporn Bodhidatta, Carl Jeffries, To Nguyen Thi Nguyen, Duong Vu Thuy, Corinne N Thompson, Nguyen Phu Huong Lan, Phat Voong Vinh, Tuyen Ha Thanh, , Stephen Baker
This study identifies South Asia as the primary source of ciprofloxacin-resistant Shigella sonnei, showing a single clonal emergence event driving global spread.
bioRxiv · Feb 25, 2016Microbiology
Ryan R Wick, Mark B Schultz, Justin Zobel, Kathryn E Holt
Bandage visualizes de novo genome assembly graphs, allowing users to interact with contig connections and perform BLAST searches within the tool.
Bioinformatics · Oct 15, 2015Peer-reviewedBioinformatics
Shu Mei Teo, Danny Mok, Kym Pham, Merci Kusel, Michael Serralha, Niamh Troy, Barbara J Holt, Belinda J Hales, Michael L Walker, Elysia Hollams, Yury H Bochkov, Kristine Grindle, Sebastian L Johnston, James E Gern, Peter D Sly, , Michael Inouye
The paper examines the infant airway microbiome's role in asthma development by analyzing viral and bacterial communities in nasopharyngeal samples from a birth cohort.
Cell Host & Microbe · May 1, 2015Peer-reviewedGenomics
Jane Hawkey, Mohammad Hamidian, Ryan R Wick, David J Edwards, Helen Billman-Jacobe, Ruth M Hall, Kathryn E Holt
ISMapper identifies IS insertion sites in bacterial genomes from short read data with high accuracy across multiple species and conditions.
bioRxiv · Mar 10, 2015Bioinformatics
Kelly L Wyres, Claire Gorrie, David J Edwards, Heiman FL Wertheim, Li Yang Hsu, Nguyen Van Kinh, Ruth Zadoks, Stephen Baker, Kathryn E Holt
This study identifies extensive capsule locus variation and large-scale genomic recombination in K. pneumoniae CC258/11, expanding the complex to include ST395 and revealing 11 distinct cps loci.
bioRxiv · Oct 27, 2014Genomics
Michael Inouye, Harriet Dashnow, Lesley Raven, Mark B Schultz, Bernard J Pope, Takehiro Tomita, Justin Zobel, Kathryn E Holt
SRST2 is a tool for rapid and accurate detection of genes and alleles from whole genome sequencing data, outperforming assembly-based methods in public health and hospital settings.
bioRxiv · Jul 28, 2014Genomics