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RCandy: an R package for visualizing homologous recombinations in bacterial genomes.
- Published in:
- Bioinformatics, 2022, v. 38, n. 5, p. 1450, doi. 10.1093/bioinformatics/btab814
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- Article
The MITRE trial protocol: a study to evaluate the microbiome as a biomarker of efficacy and toxicity in cancer patients receiving immune checkpoint inhibitor therapy.
- Published in:
- 2022
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- Publication type:
- journal article
Distribution and Spread of Susceptible and Resistant Neisseria gonorrhoeae Across Demographic Groups in a Major Metropolitan Center.
- Published in:
- Clinical Infectious Diseases, 2021, v. 73, n. 9, p. e3146, doi. 10.1093/cid/ciaa1229
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- Article
A community-driven resource for genomic epidemiology and antimicrobial resistance prediction of Neisseria gonorrhoeae at Pathogenwatch.
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- Genome Medicine, 2021, v. 13, n. 1, p. 1, doi. 10.1186/s13073-021-00858-2
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- Article
Adaptation to the cervical environment is associated with increased antibiotic susceptibility in Neisseria gonorrhoeae.
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- Nature Communications, 2020, v. 11, n. 1, p. N.PAG, doi. 10.1038/s41467-020-17980-1
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- Article
Genomic evolution of Neisseria gonorrhoeae since the preantibiotic era (1928–2013): antimicrobial use/misuse selects for resistance and drives evolution.
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- BMC Genomics, 2020, v. 21, n. 1, p. 1, doi. 10.1186/s12864-020-6511-6
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- Article
Genetic variation associated with infection and the environment in the accidental pathogen Burkholderia pseudomallei.
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- Communications Biology, 2019, v. 2, n. 1, p. N.PAG, doi. 10.1038/s42003-019-0678-x
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- Article
Genetic variation regulates the activation and specificity of Restriction-Modification systems in Neisseria gonorrhoeae.
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- Scientific Reports, 2019, v. 9, n. 1, p. N.PAG, doi. 10.1038/s41598-019-51102-2
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- Article
Genome-wide epistasis and co-selection study using mutual information.
- Published in:
- Nucleic Acids Research, 2019, v. 47, n. 18, p. e112, doi. 10.1093/nar/gkz656
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- Article
Evaluation of parameters affecting performance and reliability of machine learning-based antibiotic susceptibility testing from whole genome sequencing data.
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- PLoS Computational Biology, 2019, v. 15, n. 9, p. 1, doi. 10.1371/journal.pcbi.1007349
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- Article
Molecular epidemiology and whole genome sequencing analysis of clinical Mycobacterium bovis from Ghana.
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- PLoS ONE, 2019, v. 14, n. 3, p. 1, doi. 10.1371/journal.pone.0209395
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- Article
Bayesian inference of ancestral dates on bacterial phylogenetic trees.
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- Nucleic Acids Research, 2018, v. 46, n. 22, p. e134, doi. 10.1093/nar/gky783
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- Article
Loss of Genomic Diversity in a Neisseria meningitidis Clone Through a Colonization Bottleneck.
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- Genome Biology & Evolution, 2018, v. 10, n. 8, p. 2102, doi. 10.1093/gbe/evy152
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- Article
Global Scale Dissemination of ST93: A Divergent <italic>Staphylococcus aureus</italic> Epidemic Lineage That Has Recently Emerged From Remote Northern Australia.
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- Frontiers in Microbiology, 2018, p. N.PAG, doi. 10.3389/fmicb.2018.01453
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- Article
Phandango: an interactive viewer for bacterial population genomics.
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- Bioinformatics, 2018, v. 34, n. 2, p. 292, doi. 10.1093/bioinformatics/btx610
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- Article
Correction: Dynamics and impact of homologous recombination on the evolution of Legionella pneumophila.
- Published in:
- 2017
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- Correction Notice
Evolution of mobile genetic element composition in an epidemic methicillinresistant Staphylococcus aureus: temporal changes correlated with frequent loss and gain events.
- Published in:
- BMC Genomics, 2017, v. 18, p. 1, doi. 10.1186/s12864-017-4065-z
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- Article
Dynamics and impact of homologous recombination on the evolution of Legionella pneumophila.
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- PLoS Genetics, 2017, v. 13, n. 6, p. 1, doi. 10.1371/journal.pgen.1006855
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- Article
Seeding and Establishment of Legionella pneumophila in Hospitals: Implications for Genomic Investigations of Nosocomial Legionnaires' Disease.
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- Clinical Infectious Diseases, 2017, v. 64, n. 9, p. 1251, doi. 10.1093/cid/cix153
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- Article
Using whole genome sequencing to investigate transmission in a multi-host system: bovine tuberculosis in New Zealand.
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- BMC Genomics, 2017, v. 18, p. 1, doi. 10.1186/s12864-017-3569-x
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- Article
Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis.
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- PLoS Genetics, 2017, v. 13, n. 2, p. 1, doi. 10.1371/journal.pgen.1006508
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- Article
The First population structure and comparative genomics analysis of Mycobacterium africanum strains from Ghana reveals higher diversity of Lineage 5.
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- International Journal of Mycobacteriology, 2016, v. 5, p. S80, doi. 10.1016/j.ijmyco.2016.09.051
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- Article
Genomic variations leading to alterations in cell morphology of Campylobacter spp.
- Published in:
- Scientific Reports, 2016, p. 38303, doi. 10.1038/srep38303
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- Article
Genomic Epidemiology of Gonococcal Resistance to Extended-Spectrum Cephalosporins, Macrolides, and Fluoroquinolones in the United States, 2000-2013.
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- 2016
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- Publication type:
- journal article
Understanding pneumococcal serotype 1 biology through population genomic analysis.
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- BMC Infectious Diseases, 2016, v. 16, p. 1, doi. 10.1186/s12879-016-1987-z
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- Article
Understanding pneumococcal serotype 1 biology through population genomic analysis.
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- 2016
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- Publication type:
- journal article
The novel 2016 WHO Neisseria gonorrhoeae reference strains for global quality assurance of laboratory investigations: phenotypic, genetic and reference genome characterization.
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- 2016
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- journal article
Whole Genome Sequence Analysis of a Large Isoniazid-Resistant Tuberculosis Outbreak in London: A Retrospective Observational Study.
- Published in:
- 2016
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- Publication type:
- journal article
Acquisition and loss of virulence-associated factors during genome evolution and speciation in three clades of Bordetella species.
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- BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-3112-5
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- Article
Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes.
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- Nature Communications, 2016, v. 7, n. 9, p. 12797, doi. 10.1038/ncomms12797
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- Article
Spatiotemporal Co-existence of Two Mycobacterium ulcerans Clonal Complexes in the Offin River Valley of Ghana.
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- PLoS Neglected Tropical Diseases, 2016, v. 10, n. 7, p. 1, doi. 10.1371/journal.pntd.0004856
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- Article
Microevolution of Monophasic Salmonella Typhimurium during Epidemic, United Kingdom, 2005-2010.
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- 2016
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- journal article
Phylogeny, resistome and mobile genetic elements of emergent OXA-48 and OXA-245 Klebsiella pneumoniae clones circulating in Spain.
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- 2016
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- journal article
The Ess/Type VII secretion system of Staphylococcus aureus shows unexpected genetic diversity.
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- BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2426-7
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- Article
Chlamydia trachomatis from Australian Aboriginal people with trachoma are polyphyletic composed of multiple distinctive lineages.
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- Nature Communications, 2016, v. 7, n. 2, p. 10688, doi. 10.1038/ncomms10688
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- Article
Phylogenomic exploration of the relationships between strains of Mycobacterium avium subspecies paratuberculosis.
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- BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-015-2234-5
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- Article
The effect of genetic structure on molecular dating and tests for temporal signal.
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- Methods in Ecology & Evolution, 2016, v. 7, n. 1, p. 80, doi. 10.1111/2041-210X.12466
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- Article
Circlator: automated circularization of genome assemblies using long sequencing reads.
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- Genome Biology, 2015, v. 16, p. 294, doi. 10.1186/s13059-015-0849-0
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- Article
Early insights into the potential of the Oxford Nanopore MinION for the detection of antimicrobial resistance genes.
- Published in:
- 2015
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- Publication type:
- journal article
Genomic Analysis of Isolates From the United Kingdom 2012 Pertussis Outbreak Reveals That Vaccine Antigen Genes Are Unusually Fast Evolving.
- Published in:
- Journal of Infectious Diseases, 2015, v. 212, n. 2, p. 294, doi. 10.1093/infdis/jiu665
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- Article
Correction: Signatures of Adaptation in Human Invasive Salmonella Typhimurium ST313 Populations from Sub-Saharan Africa.
- Published in:
- 2015
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- Correction Notice
Locally Confined Clonal Complexes of Mycobacterium ulcerans in Two Buruli Ulcer Endemic Regions of Cameroon.
- Published in:
- PLoS Neglected Tropical Diseases, 2015, v. 9, n. 6, p. 1, doi. 10.1371/journal.pntd.0003802
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- Publication type:
- Article
Locally Confined Clonal Complexes of Mycobacterium ulcerans in Two Buruli Ulcer Endemic Regions of Cameroon.
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- PLoS Neglected Tropical Diseases, 2015, v. 9, n. 6, p. 1, doi. 10.1371/journal.pntd.0003802
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- Publication type:
- Article
Correction: Signatures of Adaptation in Human Invasive Salmonella Typhimurium ST313 Populations from Sub-Saharan Africa.
- Published in:
- 2015
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- Publication type:
- Correction Notice
Single-molecule sequencing reveals the molecular basis of multidrug-resistance in ST772 methicillin-resistant Staphylococcus aureus.
- Published in:
- BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1599-9
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- Publication type:
- Article
Evolutionary dynamics of methicillin-resistant Staphylococcus aureus within a healthcare system.
- Published in:
- Genome Biology, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s13059-015-0643-z
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- Publication type:
- Article
Signatures of Adaptation in Human Invasive Salmonella Typhimurium ST313 Populations from Sub-Saharan Africa.
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- PLoS Neglected Tropical Diseases, 2015, v. 9, n. 3, p. 1, doi. 10.1371/journal.pntd.0003611
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- Publication type:
- Article
A high-resolution genomic analysis of multidrug-resistant hospital outbreaks of Klebsiella pneumoniae.
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- EMBO Molecular Medicine, 2015, v. 7, n. 3, p. 227, doi. 10.15252/emmm.201404767
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- Article
Capturing the cloud of diversity reveals complexity and heterogeneity of MRSA carriage, infection and transmission.
- Published in:
- Nature Communications, 2015, v. 6, n. 3, p. 6560, doi. 10.1038/ncomms7560
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- Publication type:
- Article
Signatures of Adaptation in Human Invasive Salmonella Typhimurium ST313 Populations from Sub-Saharan Africa.
- Published in:
- PLoS Neglected Tropical Diseases, 2015, v. 9, n. 3, p. 1, doi. 10.1371/journal.pntd.0003611
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- Publication type:
- Article