Benchmarking of long-read assemblers for prokaryote whole genome sequencing [version 4; peer review: 4 approved]

by Ryan R. Wick, Kathryn E. Holt
Published 2021-02-01

Benchmarking of long-read assemblers for prokaryote whole genome sequencing [version 1; peer review: 2 approved]

by Ryan R. Wick, Kathryn E. Holt
Published 2019-12-01

The impact of genomics on precision public health: beyond the pandemic

by Muin J. Khoury, Kathryn E. Holt
Published 2021-04-01

Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks.

by Ryan R Wick, Louise M Judd, Kathryn E Holt
Published 2018-11-01

Performance of neural network basecalling tools for Oxford Nanopore sequencing

by Ryan R. Wick, Louise M. Judd, Kathryn E. Holt
Published 2019-06-01

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads.

by Ryan R Wick, Louise M Judd, Claire L Gorrie, Kathryn E Holt
Published 2017-06-01

Genomic Diversity and Antimicrobial Resistance of <named-content content-type="genus-species">Haemophilus</named-content> Colonizing the Airways of Young Children with Cystic Fibro...

by Stephen C. Watts, Louise M. Judd, Rosemary Carzino, Sarath Ranganathan, Kathryn E. Holt
Published 2021-03-01

Impact of insertion sequences on convergent evolution of Shigella species.

by Jane Hawkey, Jonathan M Monk, Helen Billman-Jacobe, Bernhard Palsson, Kathryn E Holt
Published 2020-07-01

GeneMates: an R package for detecting horizontal gene co-transfer between bacteria using gene-gene associations controlled for population structure

by Yu Wan, Ryan R. Wick, Justin Zobel, Danielle J. Ingle, Michael Inouye, Kathryn E. Holt
Published 2020-09-01

Elucidation of pathways driving asthma pathogenesis: Development of a systems-level analytic strategy

by Michael L Walker, Kathryn E Holt, Kathryn E Holt, Gary Peter Anderson, Shu Mei Teo, Shu Mei Teo, Peter D Sly, Patrick G Holt, Patrick G Holt, Michael eInouye, Michael eInouye
Published 2014-09-01

Inferring demographic parameters in bacterial genomic data using Bayesian and hybrid phylogenetic methods

by Sebastian Duchene, David A. Duchene, Jemma L. Geoghegan, Zoe A. Dyson, Jane Hawkey, Kathryn E. Holt
Published 2018-06-01

Empirical ways to identify novel Bedaquiline resistance mutations in AtpE.

by Malancha Karmakar, Carlos H M Rodrigues, Kathryn E Holt, Sarah J Dunstan, Justin Denholm, David B Ascher
Published 2019-01-01

The inflated mitochondrial genomes of siphonous green algae reflect processes driving expansion of noncoding DNA and proliferation of introns

by Sonja I. Repetti, Christopher J. Jackson, Louise M. Judd, Ryan R. Wick, Kathryn E. Holt, Heroen Verbruggen
Published 2020-01-01

Direct Nanopore Sequencing of mRNA Reveals Landscape of Transcript Isoforms in Apicomplexan Parasites

by V. Vern Lee, Louise M. Judd, Aaron R. Jex, Kathryn E. Holt, Christopher J. Tonkin, Stuart A. Ralph
Published 2021-04-01

A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex

by Margaret M. C. Lam, Ryan R. Wick, Stephen C. Watts, Louise T. Cerdeira, Kelly L. Wyres, Kathryn E. Holt
Published 2021-07-01

Z/I1 Hybrid Virulence Plasmids Carrying Antimicrobial Resistance genes in <i>S.</i> Typhimurium from Australian Food Animal Production

by Ethan R. Wyrsch, Jane Hawkey, Louise M. Judd, Ruth Haites, Kathryn E. Holt, Steven P. Djordjevic, Helen Billman-Jacobe
Published 2019-08-01

Tracking key virulence loci encoding aerobactin and salmochelin siderophore synthesis in Klebsiella pneumoniae

by Margaret M. C. Lam, Kelly L. Wyres, Louise M. Judd, Ryan R. Wick, Adam Jenney, Sylvain Brisse, Kathryn E. Holt
Published 2018-10-01

Trycycler: consensus long-read assemblies for bacterial genomes

by Ryan R. Wick, Louise M. Judd, Louise T. Cerdeira, Jane Hawkey, Guillaume Méric, Ben Vezina, Kelly L. Wyres, Kathryn E. Holt
Published 2021-09-01

Population structure and antimicrobial resistance patterns of Salmonella Typhi isolates in urban Dhaka, Bangladesh from 2004 to 2016.

by Sadia Isfat Ara Rahman, Zoe A Dyson, Elizabeth J Klemm, Farhana Khanam, Kathryn E Holt, Emran Kabir Chowdhury, Gordon Dougan, Firdausi Qadri
Published 2020-02-01

A Salmonella Typhimurium-Typhi genomic chimera: a model to study Vi polysaccharide capsule function in vivo.

by Angela M Jansen, Lindsay J Hall, Simon Clare, David Goulding, Kathryn E Holt, Andrew J Grant, Piero Mastroeni, Gordon Dougan, Robert A Kingsley
Published 2011-07-01