Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads
Wick, Ryan R, Judd, Louise M, Gorrie, Claire L, Holt, Kathryn E
Published in PLoS computational biology (01.06.2017)
Published in PLoS computational biology (01.06.2017)
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Journal Article
Population genomics of Klebsiella pneumoniae
Wyres, Kelly L., Lam, Margaret M. C., Holt, Kathryn E.
Published in Nature reviews. Microbiology (01.06.2020)
Published in Nature reviews. Microbiology (01.06.2020)
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Journal Article
Bandage: interactive visualization of de novo genome assemblies
Wick, Ryan R, Schultz, Mark B, Zobel, Justin, Holt, Kathryn E
Published in Bioinformatics (15.10.2015)
Published in Bioinformatics (15.10.2015)
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Journal Article
FastSpar: rapid and scalable correlation estimation for compositional data
Watts, Stephen C, Ritchie, Scott C, Inouye, Michael, Holt, Kathryn E
Published in Bioinformatics (15.03.2019)
Published in Bioinformatics (15.03.2019)
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Journal Article
Kaptive Web: User-Friendly Capsule and Lipopolysaccharide Serotype Prediction for Klebsiella Genomes
Wick, Ryan R, Heinz, Eva, Holt, Kathryn E, Wyres, Kelly L
Published in Journal of clinical microbiology (01.06.2018)
Published in Journal of clinical microbiology (01.06.2018)
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Journal Article
Trycycler: consensus long-read assemblies for bacterial genomes
Wick, Ryan R, Judd, Louise M, Cerdeira, Louise T, Hawkey, Jane, Méric, Guillaume, Vezina, Ben, Wyres, Kelly L, Holt, Kathryn E
Published in Genome Biology (14.09.2021)
Published in Genome Biology (14.09.2021)
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Journal Article
Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones of Klebsiella pneumoniae
Wyres, Kelly L, Wick, Ryan R, Judd, Louise M, Froumine, Roni, Tokolyi, Alex, Gorrie, Claire L, Lam, Margaret M C, Duchêne, Sebastián, Jenney, Adam, Holt, Kathryn E
Published in PLoS genetics (15.04.2019)
Published in PLoS genetics (15.04.2019)
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Journal Article
The Infant Nasopharyngeal Microbiome Impacts Severity of Lower Respiratory Infection and Risk of Asthma Development
Teo, Shu Mei, Mok, Danny, Pham, Kym, Kusel, Merci, Serralha, Michael, Troy, Niamh, Holt, Barbara J., Hales, Belinda J., Walker, Michael L., Hollams, Elysia, Bochkov, Yury A., Grindle, Kristine, Johnston, Sebastian L., Gern, James E., Sly, Peter D., Holt, Patrick G., Holt, Kathryn E., Inouye, Michael
Published in Cell host & microbe (13.05.2015)
Published in Cell host & microbe (13.05.2015)
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Journal Article
Novel Subclone of Carbapenem-Resistant Klebsiella pneumoniae Sequence Type 11 with Enhanced Virulence and Transmissibility, China
Zhou, Kai, Xiao, Tingting, David, Sophia, Wang, Qin, Zhou, Yanzi, Guo, Lihua, Aanensen, David, Holt, Kathryn E, Thomson, Nicholas R, Grundmann, Hajo, Shen, Ping, Xiao, Yonghong
Published in Emerging infectious diseases (01.02.2020)
Published in Emerging infectious diseases (01.02.2020)
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Journal Article
The genomic signatures of Shigella evolution, adaptation and geographical spread
The, Hao Chung, Thanh, Duy Pham, Holt, Kathryn E., Thomson, Nicholas R., Baker, Stephen
Published in Nature reviews. Microbiology (01.04.2016)
Published in Nature reviews. Microbiology (01.04.2016)
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Journal Article
Mercury methylation by metabolically versatile and cosmopolitan marine bacteria
Lin, Heyu, Ascher, David B., Myung, Yoochan, Lamborg, Carl H., Hallam, Steven J., Gionfriddo, Caitlin M., Holt, Kathryn E., Moreau, John W.
Published in The ISME Journal (01.06.2021)
Published in The ISME Journal (01.06.2021)
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Journal Article
Gastrointestinal Carriage Is a Major Reservoir of Klebsiella pneumoniae Infection in Intensive Care Patients
Gorrie, Claire L., Mirčeta, Mirjana, Wick, Ryan R., Edwards, David J., Thomson, Nicholas R., Strugnell, Richard A., Pratt, Nigel F., Garlick, Jill S., Watson, Kerri M., Pilcher, David V., McGloughlin, Steve A., Spelman, Denis W., Jenney, Adam W. J., Holt, Kathryn E.
Published in Clinical infectious diseases (15.07.2017)
Published in Clinical infectious diseases (15.07.2017)
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Journal Article
Population genomics of hypervirulent Klebsiella pneumoniae clonal-group 23 reveals early emergence and rapid global dissemination
Lam, Margaret M. C., Wyres, Kelly L., Duchêne, Sebastian, Wick, Ryan R., Judd, Louise M., Gan, Yunn-Hwen, Hoh, Chu-Han, Archuleta, Sophia, Molton, James S., Kalimuddin, Shirin, Koh, Tse Hsien, Passet, Virginie, Brisse, Sylvain, Holt, Kathryn E.
Published in Nature communications (13.07.2018)
Published in Nature communications (13.07.2018)
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Journal Article
Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health
Holt, Kathryn E, Wertheim, Heiman, Zadoks, Ruth N, Baker, Stephen, Whitehouse, Chris A, Dance, David, Jenney, Adam, Connor, Thomas R, Hsu, Li Yang, Severin, Juliëtte, Brisse, Sylvain, Cao, Hanwei, Wilksch, Jonathan, Gorrie, Claire, Schultz, Mark B, Edwards, David J, Nguyen, Kinh Van, Nguyen, Trung Vu, Dao, Trinh Tuyet, Mensink, Martijn, Minh, Vien Le, Nhu, Nguyen Thi Khanh, Schultsz, Constance, Kuntaman, Kuntaman, Newton, Paul N, Moore, Catrin E, Strugnell, Richard A, Thomson, Nicholas R
Published in Proceedings of the National Academy of Sciences - PNAS (07.07.2015)
Published in Proceedings of the National Academy of Sciences - PNAS (07.07.2015)
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