Polypolish: Short-read polishing of long-read bacterial genome assemblies von Wick, Ryan R, Holt, Kathryn E

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Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads von Wick, Ryan R, Judd, Louise M, Gorrie, Claire L, Holt, Kathryn E

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Performance of neural network basecalling tools for Oxford Nanopore sequencing von Wick, Ryan R, Judd, Louise M, Holt, Kathryn E

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Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing von Wick, Ryan R, Judd, Louise M, Holt, Kathryn E

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Population genomics of Klebsiella pneumoniae von Wyres, Kelly L., Lam, Margaret M. C., Holt, Kathryn E.

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The Infant Nasopharyngeal Microbiome Impacts Severity of Lower Respiratory Infection and Risk of Asthma Development von 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

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Bandage: interactive visualization of de novo genome assemblies von Wick, Ryan R, Schultz, Mark B, Zobel, Justin, Holt, Kathryn E

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Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones of Klebsiella pneumoniae von 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

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A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex von Lam, Margaret M. C., Wick, Ryan R., Watts, Stephen C., Cerdeira, Louise T., Wyres, Kelly L., Holt, Kathryn E.

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FastSpar: rapid and scalable correlation estimation for compositional data von Watts, Stephen C, Ritchie, Scott C, Inouye, Michael, Holt, Kathryn E

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Trycycler: consensus long-read assemblies for bacterial genomes von Wick, Ryan R, Judd, Louise M, Cerdeira, Louise T, Hawkey, Jane, Méric, Guillaume, Vezina, Ben, Wyres, Kelly L, Holt, Kathryn E

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Kaptive Web: User-Friendly Capsule and Lipopolysaccharide Serotype Prediction for Klebsiella Genomes von Wick, Ryan R, Heinz, Eva, Holt, Kathryn E, Wyres, Kelly L

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Benchmarking of long-read assemblers for prokaryote whole genome sequencing [version 1; peer review: 4 approved] von Wick, Ryan R, Holt, Kathryn E

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Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks von Wick, Ryan R, Judd, Louise M, Holt, Kathryn E

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Novel Subclone of Carbapenem-Resistant Klebsiella pneumoniae Sequence Type 11 with Enhanced Virulence and Transmissibility, China von 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

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Airway Microbiota Dynamics Uncover a Critical Window for Interplay of Pathogenic Bacteria and Allergy in Childhood Respiratory Disease von Teo, Shu Mei, Tang, Howard H.F., Mok, Danny, Judd, Louise M., Watts, Stephen C., Pham, Kym, Holt, Barbara J., Kusel, Merci, Serralha, Michael, Troy, Niamh, Bochkov, Yury A., Grindle, Kristine, Lemanske, Robert F., Johnston, Sebastian L., Gern, James E., Sly, Peter D., Holt, Patrick G., Holt, Kathryn E., Inouye, Michael

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The genomic signatures of Shigella evolution, adaptation and geographical spread von The, Hao Chung, Thanh, Duy Pham, Holt, Kathryn E., Thomson, Nicholas R., Baker, Stephen

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Vitamin D over the first decade and susceptibility to childhood allergy and asthma von Hollams, Elysia M., PhD, Teo, Shu Mei, PhD, Kusel, Merci, MBBS, PhD, Holt, Barbara J., BSc, Holt, Kathryn E., PhD, Inouye, Michael, PhD, De Klerk, Nicholas H., PhD, Zhang, Guicheng, PhD, Sly, Peter D., FRACP, Hart, Prue H., PhD, Holt, Patrick G., DSc

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Mercury methylation by metabolically versatile and cosmopolitan marine bacteria von Lin, Heyu, Ascher, David B., Myung, Yoochan, Lamborg, Carl H., Hallam, Steven J., Gionfriddo, Caitlin M., Holt, Kathryn E., Moreau, John W.

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Gastrointestinal Carriage Is a Major Reservoir of Klebsiella pneumoniae Infection in Intensive Care Patients von 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.

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