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Estimating between-country migration in pneumococcal populations.
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- G3: Genes | Genomes | Genetics, 2024, v. 14, n. 6, p. 1, doi. 10.1093/g3journal/jkae058
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- Article
Detecting co-selection through excess linkage disequilibrium in bacterial genomes.
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- NAR Genomics & Bioinformatics, 2024, v. 6, n. 2, p. 1, doi. 10.1093/nargab/lqae061
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- Article
AmiA and AliA peptide ligands, found in Klebsiella pneumoniae, are imported into pneumococci and alter the transcriptome.
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- Scientific Reports, 2024, v. 14, n. 1, p. 1, doi. 10.1038/s41598-024-63217-2
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Klebsiella pneumoniae peptide hijacks a Streptococcus pneumoniae permease to subvert pneumococcal growth and colonization.
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- Communications Biology, 2024, v. 7, n. 1, p. 1, doi. 10.1038/s42003-024-06113-9
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Immune interface interference vaccines: An evolution‐informed approach to anti‐bacterial vaccine design.
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- Microbial Biotechnology, 2024, v. 17, n. 3, p. 1, doi. 10.1111/1751-7915.14446
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- Article
Genomic and panproteomic analysis of the development of infant immune responses to antigenically-diverse pneumococci.
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- Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-023-44584-2
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Diverse regulatory pathways modulate bet hedging of competence induction in epigenetically-differentiated phase variants of Streptococcus pneumoniae.
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- Nucleic Acids Research, 2023, v. 51, n. 19, p. 10375, doi. 10.1093/nar/gkad760
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Pneumococcal capsule expression is controlled through a conserved, distal cis-regulatory element during infection.
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- PLoS Pathogens, 2023, v. 18, n. 1, p. 1, doi. 10.1371/journal.ppat.1011035
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Post-vaccine epidemiology of serotype 3 pneumococci identifies transformation inhibition through prophage-driven alteration of a non-coding RNA.
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- Genome Medicine, 2022, v. 14, n. 1, p. 1, doi. 10.1186/s13073-022-01147-2
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Comparative Genomics of Disease and Carriage Serotype 1 Pneumococci.
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- Genome Biology & Evolution, 2022, v. 14, n. 4, p. 1, doi. 10.1093/gbe/evac052
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RCandy: an R package for visualizing homologous recombinations in bacterial genomes.
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- Bioinformatics, 2022, v. 38, n. 5, p. 1450, doi. 10.1093/bioinformatics/btab814
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Genome-wide association, prediction and heritability in bacteria with application to Streptococcus pneumoniae.
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- NAR Genomics & Bioinformatics, 2022, v. 4, n. 1, p. 1, doi. 10.1093/nargab/lqac011
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Analysing pneumococcal invasiveness using Bayesian models of pathogen progression rates.
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- PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009389
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The role of interspecies recombination in the evolution of antibiotic-resistant pneumococci.
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- eLife, 2021, p. 1, doi. 10.7554/eLife.67113
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Lineage‐specific evolution and gene flow in Listeria monocytogenes are independent of bacteriophages.
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- Environmental Microbiology, 2020, v. 22, n. 12, p. 5058, doi. 10.1111/1462-2920.15111
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Divergent serotype replacement trends and increasing diversity in pneumococcal disease in high income settings reduce the benefit of expanding vaccine valency.
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- Scientific Reports, 2020, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41598-020-75691-5
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Frequency-dependent selection can forecast evolution in Streptococcus pneumoniae.
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- PLoS Biology, 2020, v. 18, n. 10, p. 1, doi. 10.1371/journal.pbio.3000878
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Genome-wide epistasis and co-selection study using mutual information.
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- Nucleic Acids Research, 2019, v. 47, n. 18, p. e112, doi. 10.1093/nar/gkz656
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- Article
Synergistic Activity of Mobile Genetic Element Defences in Streptococcus pneumoniae.
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- Genes, 2019, v. 10, n. 9, p. 707, doi. 10.3390/genes10090707
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Joint sequencing of human and pathogen genomes reveals the genetics of pneumococcal meningitis.
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- Nature Communications, 2019, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41467-019-09976-3
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The Contribution of Genetic Variation of Streptococcus pneumoniae to the Clinical Manifestation of Invasive Pneumococcal Disease.
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- Clinical Infectious Diseases, 2019, v. 68, n. 1, p. 61, doi. 10.1093/cid/ciy417
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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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Excision-reintegration at a pneumococcal phase-variable restriction-modification locus drives within- and between-strain epigenetic differentiation and inhibits gene acquisition.
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- Nucleic Acids Research, 2018, v. 46, n. 21, p. 11438, doi. 10.1093/nar/gky906
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- Article
Transformation Asymmetry and the Evolution of the Bacterial Accessory Genome.
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- Molecular Biology & Evolution, 2018, v. 35, n. 3, p. 575, doi. 10.1093/molbev/msx309
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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
Pneumococcal Capsule Synthesis Locus cps as Evolutionary Hotspot with Potential to Generate Novel Serotypes by Recombination.
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- Molecular Biology & Evolution, 2017, v. 34, n. 10, p. 2537, doi. 10.1093/molbev/msx173
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Efficient Inference of Recent and Ancestral Recombination within Bacterial Populations.
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- Molecular Biology & Evolution, 2017, v. 34, n. 5, p. 1167, doi. 10.1093/molbev/msx066
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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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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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Horizontal DNA Transfer Mechanisms of Bacteria as Weapons of Intragenomic Conflict.
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- PLoS Biology, 2016, v. 14, n. 3, p. 1, doi. 10.1371/journal.pbio.1002394
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Identification of pneumococcal colonization determinants in the stringent response pathway facilitated by genomic diversity.
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- BMC Genomics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12864-015-1573-6
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Stability of the pneumococcal population structure in Massachusetts as PCV13 was introduced
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- BMC Infectious Diseases, 2015, v. 15, n. 1, p. 68, doi. 10.1186/s12879-015-0797-z
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Selective and Genetic Constraints on Pneumococcal Serotype Switching.
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- PLoS Genetics, 2015, v. 11, n. 3, p. 1, doi. 10.1371/journal.pgen.1005095
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Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins.
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- Nucleic Acids Research, 2015, v. 43, n. 3, p. e15, doi. 10.1093/nar/gku1196
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Diversification of bacterial genome content through distinct mechanisms over different timescales.
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- Nature Communications, 2014, v. 5, n. 11, p. 5471, doi. 10.1038/ncomms6471
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Comprehensive Identification of Single Nucleotide Polymorphisms Associated with Beta-lactam Resistance within Pneumococcal Mosaic Genes.
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- PLoS Genetics, 2014, v. 10, n. 8, p. 1, doi. 10.1371/journal.pgen.1004547
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Variable recombination dynamics during the emergence, transmission and 'disarming' of a multidrug-resistant pneumococcal clone.
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- BMC Biology, 2014, v. 12, n. 1, p. 1, doi. 10.1186/1741-7007-12-49
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Evidence for Soft Selective Sweeps in the Evolution of Pneumococcal Multidrug Resistance and Vaccine Escape.
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- Genome Biology & Evolution, 2014, v. 6, n. 7, p. 1589, doi. 10.1093/gbe/evu120
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Heterogeneity in the Frequency and Characteristics of Homologous Recombination in Pneumococcal Evolution.
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- PLoS Genetics, 2014, v. 10, n. 5, p. 1, doi. 10.1371/journal.pgen.1004300
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Impact of 13-Valent Pneumococcal Conjugate Vaccination on Streptococcus pneumoniae Carriage in Young Children in Massachusetts.
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- Journal of the Pediatric Infectious Diseases Society, 2014, v. 3, n. 1, p. 23, doi. 10.1093/jpids/pit057
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Dense genomic sampling identifies highways of pneumococcal recombination.
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- Nature Genetics, 2014, v. 46, n. 3, p. 305, doi. 10.1038/ng.2895
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RNA-seq reveals the RNA binding proteins, Hfq and RsmA, play various roles in virulence, antibiotic production and genomic flux in Serratia sp. ATCC 39006.
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- BMC Genomics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2164-14-822
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Dominant Role of Nucleotide Substitution in the Diversification of Serotype 3 Pneumococci over Decades and during a Single Infection.
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- PLoS Genetics, 2013, v. 9, n. 10, p. 1, doi. 10.1371/journal.pgen.1003868
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Population genomics of post-vaccine changes in pneumococcal epidemiology.
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- Nature Genetics, 2013, v. 45, n. 6, p. 656, doi. 10.1038/ng.2625
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Pneumococcal Capsular Switching: A Historical Perspective.
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- Journal of Infectious Diseases, 2013, v. 207, n. 3, p. 439, doi. 10.1093/infdis/jis703
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The multidrug-resistant PMEN1 pneumococcus is a paradigm for genetic success.
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- Genome Biology, 2012, v. 13, n. 11, p. 1, doi. 10.1186/gb-2012-13-11-r103
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A High-Resolution View of Genome-Wide Pneumococcal Transformation.
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- PLoS Pathogens, 2012, v. 8, n. 6, p. 1, doi. 10.1371/journal.ppat.1002745
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Lineage-specific Virulence Determinants of Haemophilus influenzae Biogroup aegyptius.
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- Emerging Infectious Diseases, 2012, v. 18, n. 3, p. 449, doi. 10.3201/eid1803.110728
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Detection of recombination events in bacterial genomes from large population samples.
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- Nucleic Acids Research, 2012, v. 40, n. 1, p. 1, doi. 10.1093/nar/gkr928
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Sequence-Based Analysis Uncovers an Abundance of Non-Coding RNA in the Total Transcriptome of Mycobacterium tuberculosis.
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- PLoS Pathogens, 2011, v. 7, n. 11, p. 1, doi. 10.1371/journal.ppat.1002342
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