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Genome-wide assessment of antimicrobial tolerance in Yersinia pseudotuberculosis under ciprofloxacin stress JOURNAL ARTICLE published 1 November 2019 in Microbial Genomics |
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Emergence of linezolid-resistant Enterococcus faecium in a tertiary hospital in Copenhagen JOURNAL ARTICLE published 6 July 2023 in Microbial Genomics Research funded by Novo Nordisk Fonden (NNF16OC0023482) |
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Independent origins and evolution of the secondary replicons of the class Gammaproteobacteria JOURNAL ARTICLE published 15 May 2023 in Microbial Genomics Research funded by PNRA (PNRA18_00075) |
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How public health authorities can use pathogen genomics in health protection practice: a consensus-building Delphi study conducted in the United Kingdom JOURNAL ARTICLE published 6 February 2023 in Microbial Genomics Research funded by Medical Research Council (MC_PC_19027) |
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Patchy promiscuity: machine learning applied to predict the host specificity of Salmonella enterica and Escherichia coli JOURNAL ARTICLE published 1 October 2017 in Microbial Genomics |
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Expanded roles of pyruvate-sensing PdhR in transcription regulation of the Escherichia coli K-12 genome: fatty acid catabolism and cell motility JOURNAL ARTICLE published 1 October 2020 in Microbial Genomics Research funded by Ministry of Education, Culture, Sports, Science and Technology (19K06618) | Ministry of Education, Culture, Sports, Science and Technology (18310133) | Ministry of Education, Culture, Sports, Science and Technology (25430173) |
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Epidemiological links and antimicrobial resistance of clinical Salmonella enterica ST198 isolates: a nationwide microbial population genomic study in Switzerland JOURNAL ARTICLE published 31 October 2022 in Microbial Genomics |
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Evolution of carbapenem resistance in Acinetobacter baumannii during a prolonged infection JOURNAL ARTICLE published 1 March 2018 in Microbial Genomics |
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On the limits of 16S rRNA gene-based metagenome prediction and functional profiling JOURNAL ARTICLE published 29 February 2024 in Microbial Genomics Research funded by Deutsche Forschungsgemeinschaft (395357507) | Deutsche Forschungsgemeinschaft (395357507) | Deutsche Forschungsgemeinschaft (422216132) | VILLUM Young Investigator Grant (13154) | German Federal Ministry of Education and Research (01IS21079) |
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The rate and role of pseudogenes of the Mycobacterium tuberculosis complex JOURNAL ARTICLE published 31 October 2022 in Microbial Genomics Research funded by Fundação de Amparo à Pesquisa do Estado de São Paulo (2017/20147-7) | Fundação de Amparo à Pesquisa do Estado de São Paulo (2017/04617-3) | Fundação de Amparo à Pesquisa do Estado de São Paulo (2019/03232-6) | Conselho Nacional de Desenvolvimento Científico e Tecnológico (88887.508739/2020-00) | Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (001) | Fundação de Amparo à Pesquisa do Estado de São Paulo (2016/26108-0) | Morris Animal Foundation (D17ZO-307) |
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Detection of plasmid contigs in draft genome assemblies using customized Kraken databases JOURNAL ARTICLE published 22 April 2021 in Microbial Genomics Research funded by Japan Society for the Promotion of Science (JP19K20461) | the National Health and Medical Research Council of Australia (APP1176192) | Bill and Melinda Gates Foundation (OPP1175797) |
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NGMASTER: in silico multi-antigen sequence typing for Neisseria gonorrhoeae JOURNAL ARTICLE published 25 August 2016 in Microbial Genomics |
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Porcine commensal Escherichia coli: a reservoir for class 1 integrons associated with IS26 JOURNAL ARTICLE published 7 December 2017 in Microbial Genomics |
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A chromosome-scale genome assembly of the tomato pathogen Cladosporium fulvum reveals a compartmentalized genome architecture and the presence of a dispensable chromosome JOURNAL ARTICLE published 26 April 2022 in Microbial Genomics Research funded by Directorate for Biological Sciences (1557995) | USDA-NIFA (CA-D-PPA-2185-H) | University of California, Davis (Dean’s Distinguished Graduate Fellowship (DDGF) program) |
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Evolution of a clade of Acinetobacter baumannii global clone 1, lineage 1 via acquisition of carbapenem- and aminoglycoside-resistance genes and dispersion of ISAba1 JOURNAL ARTICLE published 1 January 2019 in Microbial Genomics |
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Genome-wide analysis of fitness-factors in uropathogenic Escherichia coli during growth in laboratory media and during urinary tract infections JOURNAL ARTICLE published 24 December 2021 in Microbial Genomics |
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Optimization of high-throughput 16S rRNA gene amplicon sequencing: an assessment of PCR pooling, mastermix use and contamination JOURNAL ARTICLE published 16 October 2023 in Microbial Genomics Research funded by Wellcome Trust (222903/Z/21/Z) | Wellcome Trust (211864/Z/18/Z) | Wellcome Trust (220540/Z/20/A) |
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Whole-genome sequencing and phylogenetic analysis of coxsackievirus-A16 strains causing hand, foot and mouth disease (HFMD) in India JOURNAL ARTICLE published 31 October 2023 in Microbial Genomics Research funded by ICMR-National Institute of Virology, Pune (EVI2103) |
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The highly diverse plasmid population found in Escherichia coli colonizing travellers to Laos and its role in antimicrobial resistance gene carriage JOURNAL ARTICLE published 12 May 2023 in Microbial Genomics |
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RFPlasmid: predicting plasmid sequences from short-read assembly data using machine learning JOURNAL ARTICLE published 30 November 2021 in Microbial Genomics |