Publications

For a full list of publications visit GoogleScholar. Recent highlights are listed below.

Helena B. Cooper, Ben Vezina, Jane Hawkey, Virginie Passet, Sebastián López-Fernández, Jonathan M. Monk, Sylvain Brisse, Kathryn E. Holt, Kelly L. Wyres. 2024. A validated pangenome-scale metabolic model for the Klebsiella pneumoniae species complex. Microbial Genomics doi: https://doi.org/10.1099/mgen.0.001206
Ben Vezina, Stephen C. Watts, Jane Hawkey, Helena B. Cooper, Louise M. Judd, Adam Jenney, Jonathan M. Monk, Kathryn E. Holt, Kelly L. Wyres. 2023. Bactabolize is a tool for high-throughput generation of bacterial strain-specific metabolic models. eLife doi: https://doi.org/10.7554/eLife.87406.3
Jane Hawkey, Ben Vezina, Jonathan M. Monk, Louise M. Judd, Taylor Harshegyi, Sebastien Lopez-Fernandez, Carla Rodrigues C, Sylvain Brisse, Katheyn E. Holt and Kelly L. Wyres. 2022. A curated collection of Klebsiella metabolic models reveals variable substrate usage and gene essentiality. Genome Research 32 1004-1014 doi: https://doi.org/10.1101/gr.276289.121.
Margaret M.C. Lam, Ryan R. Wick, Kathryn E. Holt and Kelly L Wyres. 2022. Kaptive 2.0: Updated capsule and LPS locus typing from Klebsiella whole genome sequences. Microbial Genomics 8:3 doi: https://doi.org/10.1099/mgen.0.000800.
Margaret M.C. Lam, Ryan R. Wick, Stephen C. Watts, Louise T. Cerdeira, Kelly L. Wyres and Kathryn E. Holt. 2021. A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex. Nature Communications 12: 4188 doi: https://doi.org/10.1038/s41467-021-24448-3.
Kelly L. Wyres, Margaret M.C. Lam and Kathryn E. Holt. 2020. Population genomics of Klebsiella pneumoniae. Nature Reviews Microbiology doi: https://doi.org/10.1038/s41579-019-0315-1.
Kelly L. Wyres, To N. T. Nguyen, Margaret M. C. Lam, Louise M. Judd, Nguyen van Vinh Chau, David A. B. Dance, Margaret Ip, Abhilasha Karkey, Clare L. Ling, Thyl Miliya, Paul N. Newton, Nguyen Phu Huong Lan, Amphone Sengduangphachanh, Paul Turner, Balaji Veeraraghavan, Phat Voong Vinh, Manivanh Vongsouvath, Nicholas R. Thomson, Stephen Baker and Kathryn E. Holt. 2020. Genomic surveillance for hypervirulence and multi-drug resistance in invasive Klebsiella pneumoniae from south and southeast Asia. Genome Medicine 12:1-16 doi: https://doi.org/10.1186/s13073-019-0706-y.