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Origin, maintenance and spread of antibiotic resistance genes within plasmids and chromosomes of bloodstream isolates of Escherichia coli JOURNAL ARTICLE published 1 April 2020 in Microbial Genomics Research funded by Chief Scientist Office, Scottish Government Health and Social Care Directorate (67365/1) | Chief Scientist Office, Scottish Government Health and Social Care Directorate (67365/1) | Chief Scientist Office, Scottish Government Health and Social Care Directorate (67365/1) |
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Long-range dispersal moved Francisella tularensis into Western Europe from the East JOURNAL ARTICLE published 1 December 2016 in Microbial Genomics |
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Insights on the SARS-CoV-2 genome variability: the lesson learned in Brazil and its impacts on the future of pandemics JOURNAL ARTICLE published 30 November 2021 in Microbial Genomics Research funded by Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (#88881.506794/2020-01) | Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (# 88887.505971/2020-00) | Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (# 88887.571465/2020-00) | Conselho Nacional de Desenvolvimento Científico e Tecnológico (# 142495/2020-4) |
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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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Population genetic structuring of methicillin-resistant Staphylococcus aureus clone EMRSA-15 within UK reflects patient referral patterns JOURNAL ARTICLE published 1 August 2017 in Microbial Genomics |
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Genomic and phenotypic characterization of Salmonella enterica serovar Kentucky JOURNAL ARTICLE published 26 September 2023 in Microbial Genomics Research funded by National Institute of Food and Agriculture (2020-67017-30792) |
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The resistomes of six carbapenem-resistant pathogens – a critical genotype–phenotype analysis JOURNAL ARTICLE published 1 November 2018 in Microbial Genomics |
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Rapid and accurate SNP genotyping of clonal bacterial pathogens with BioHansel JOURNAL ARTICLE published 9 September 2021 in Microbial Genomics Research funded by Genomics Research and Development Initiative (GRDI) of the Government of Canada (Grants ID 2256344 and 2267905) |
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Comparative genomic analysis of obligately piezophilic Moritella yayanosii DB21MT-5 reveals bacterial adaptation to the Challenger Deep, Mariana Trench JOURNAL ARTICLE published 28 July 2021 in Microbial Genomics Research funded by Strategic Priority Research Program of the Chinese Academy of Sciences (XDA19060403) | National Natural Science Foundation of China (NSFC 42076127, 91751108, 91751202 and 41506147) | Key Technologies Research and Development Program (2016YFC0304905-08) | Key Research and Development Project of Hainan Province (ZDKJ2019011) | Sanya City (2018YD01) |
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The Gonococcal Genetic Island defines distinct sub-populations of Neisseria gonorrhoeae JOURNAL ARTICLE published 22 May 2023 in Microbial Genomics Research funded by Foundation for the National Institutes of Health (R01 AI047958; R01 AI113287) | National Science Foundation (DGE-1747503) |
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Prevalence, antibiotic resistance, and genomic characterisation of Campylobacter spp. in retail chicken in Hanoi, Vietnam JOURNAL ARTICLE published 31 January 2024 in Microbial Genomics |
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Genomic and antigenic diversity of colonizing Klebsiella pneumoniae isolates mirrors that of invasive isolates in Blantyre, Malawi JOURNAL ARTICLE published 1 March 2022 in Microbial Genomics Research funded by Wellcome Trust (109105z/15/a) |
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Phylogenomics of Mycobacterium africanum reveals a new lineage and a complex evolutionary history JOURNAL ARTICLE published 1 February 2021 in Microbial Genomics Research funded by Wellcome Trust (097134/Z/11/Z) | Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (310030_188888, IZRJZ3_164171, IZLSZ3_170834 and CRSII5_177163) | Ministerio de Ciencia, Innovación y Universidades (RTI2018-094399-A-I00) | Conselleria d'Educació, Investigació, Cultura i Esport (SEJI/2019/011) | H2020 European Research Council (883582-ECOEVODRTB) | Ministerio de Ciencia, Innovación y Universidades (Ramon y Cajal) |
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Results of the 2020 Genomic Proficiency Test for the network of European Union Reference Laboratory for Antimicrobial Resistance assessing whole-genome-sequencing capacities JOURNAL ARTICLE published 1 August 2023 in Microbial Genomics Research funded by European Commission (Appointed European Union Reference Laboratory for Antimicrobial resistance (EURL-AR)) | The Fleming Fund, UK aid, Department for health and social care (Regional Grant, Round 1, 2.8 Whole Genome Sequencing) |
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Comparative genomics reveals distinct diversification patterns among LysR-type transcriptional regulators in the ESKAPE pathogen Pseudomonas aeruginosa JOURNAL ARTICLE published 29 February 2024 in Microbial Genomics Research funded by Irish Research Council for Science, Engineering and Technology (GOIPG/2021/692) | Science Foundation Ireland (12/RC/2275_2) | Health Research Board (HRB-ILP-POR-2019-004) | Health Research Board (MRCG-2018-16) |
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Erratum: In silico identification of bacterial seaweed-degrading bioplastic producers JOURNAL ARTICLE published 29 February 2024 in Microbial Genomics |
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Transcriptomic analysis of Pseudomonas ogarae F113 reveals the antagonistic roles of AmrZ and FleQ during rhizosphere adaption JOURNAL ARTICLE published 17 January 2022 in Microbial Genomics Research funded by Ministerio de Ciencia, Innovación y Universidades (RTI2018-093991-B-I00) | Ministerio de Educación, Cultura y Deporte (FPU16/05513) |