Understanding pneumococcal serotype 1 biology through population genomic analysis
暂无分享,去创建一个
Cheryl P. Andam | J. Corander | W. Hanage | J. Parkhill | S. Bentley | S. Harris | N. French | R. Heyderman | B. Sigaúque | A. Kiran | J. Collard | A. Kadioglu | G. Pluschke | M. Antonio | P. Turner | A. von Gottberg | L. McGee | K. Klugman | D. Everett | M. du Plessis | Laura Bricio-Moreno | J. Cornick | Marie Yang | C. Chaguza | S. Ousmane | Chinelo Ebruke | Feyruz Yalçin | Madikay Senghore | Shanil Govindpersad
[1] Cheryl P. Andam,et al. Recombination in Streptococcus pneumoniae Lineages Increase with Carriage Duration and Size of the Polysaccharide Capsule , 2016, mBio.
[2] Julian Parkhill,et al. Robust high-throughput prokaryote de novo assembly and improvement pipeline for Illumina data , 2016, bioRxiv.
[3] S. Bentley,et al. Phylogenetic Analysis of Invasive Serotype 1 Pneumococcus in South Africa, 1989 to 2013 , 2016, Journal of Clinical Microbiology.
[4] S. Madhi,et al. Epidemiology of Serotype 1 Invasive Pneumococcal Disease, South Africa, 2003–2013 , 2016, Emerging infectious diseases.
[5] Simon R. Harris,et al. SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments , 2016, bioRxiv.
[6] Julian Parkhill,et al. Population genomic datasets describing the post-vaccine evolutionary epidemiology of Streptococcus pneumoniae , 2015, Scientific Data.
[7] S. Bentley,et al. Region-specific diversification of the highly virulent serotype 1 Streptococcus pneumoniae , 2015, Microbial genomics.
[8] Andrew J. Page,et al. Roary: rapid large-scale prokaryote pan genome analysis , 2015, bioRxiv.
[9] B. Gessner,et al. Streptococcus pneumoniae Serotype 1 Burden in the African Meningitis Belt: Exploration of Functionality in Specific Antibodies , 2015, Clinical and Vaccine Immunology.
[10] M. Nahm,et al. Genetic, Biochemical, and Serological Characterization of a New Pneumococcal Serotype, 6H, and Generation of a Pneumococcal Strain Producing Three Different Capsular Repeat Units , 2015, Clinical and Vaccine Immunology.
[11] Jacqueline A. Keane,et al. Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins , 2014, Nucleic acids research.
[12] A. von Gottberg,et al. Population Snapshot of Streptococcus pneumoniae Causing Invasive Disease in South Africa Prior to Introduction of Pneumococcal Conjugate Vaccines , 2014, PloS one.
[13] Torsten Seemann,et al. Prokka: rapid prokaryotic genome annotation , 2014, Bioinform..
[14] L. Hammitt,et al. Population effect of 10-valent pneumococcal conjugate vaccine on nasopharyngeal carriage of Streptococcus pneumoniae and non-typeable Haemophilus influenzae in Kilifi, Kenya: findings from cross-sectional carriage studies , 2014, The Lancet. Global health.
[15] A. Tomasz,et al. Variable recombination dynamics during the emergence, transmission and ‘disarming’ of a multidrug-resistant pneumococcal clone , 2014, BMC Biology.
[16] Jukka Corander,et al. Dense genomic sampling identifies highways of pneumococcal recombination , 2014, Nature Genetics.
[17] Koichiro Tamura,et al. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. , 2013, Molecular biology and evolution.
[18] T. Feltwell,et al. Dominant Role of Nucleotide Substitution in the Diversification of Serotype 3 Pneumococci over Decades and during a Single Infection , 2013, PLoS Genetics.
[19] M. Nahm,et al. Discovery of Streptococcus pneumoniae Serotype 6 Variants with Glycosyltransferases Synthesizing Two Differing Repeating Units* , 2013, The Journal of Biological Chemistry.
[20] M. Lipsitch,et al. Population genomics of post-vaccine changes in pneumococcal epidemiology , 2013, Nature Genetics.
[21] Jukka Corander,et al. Hierarchical and Spatially Explicit Clustering of DNA Sequences with BAPS Software , 2013, Molecular biology and evolution.
[22] A. Hakansson,et al. High Levels of Genetic Recombination during Nasopharyngeal Carriage and Biofilm Formation in Streptococcus pneumoniae , 2012, mBio.
[23] J. Parkhill,et al. Genetic Characterisation of Malawian Pneumococci Prior to the Roll-Out of the PCV13 Vaccine Using a High-Throughput Whole Genome Sequencing Approach , 2012, PloS one.
[24] Marc Lipsitch,et al. Rates of Acquisition and Clearance of Pneumococcal Serotypes in the Nasopharynges of Children in Kilifi District, Kenya , 2012, The Journal of infectious diseases.
[25] Thomas R Larson,et al. Biochemical, Genetic, and Serological Characterization of Two Capsule Subtypes among Streptococcus pneumoniae Serotype 20 Strains , 2012, The Journal of Biological Chemistry.
[26] Liam J. Revell,et al. phytools: an R package for phylogenetic comparative biology (and other things) , 2012 .
[27] M. Suchard,et al. Bayesian Phylogenetics with BEAUti and the BEAST 1.7 , 2012, Molecular biology and evolution.
[28] Christophe Fraser,et al. Inferring pandemic growth rates from sequence data , 2012, Journal of The Royal Society Interface.
[29] K. O'Brien,et al. Impact of more than a decade of pneumococcal conjugate vaccine use on carriage and invasive potential in Native American communities. , 2012, The Journal of infectious diseases.
[30] S. Clarke,et al. 13-valent pneumococcal conjugate vaccine (PCV13) , 2011, Human vaccines.
[31] Peer Bork,et al. Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy , 2011, Nucleic Acids Res..
[32] M. Molyneux,et al. Ten Years of Surveillance for Invasive Streptococcus pneumoniae during the Era of Antiretroviral Scale-Up and Cotrimoxazole Prophylaxis in Malawi , 2011, PloS one.
[33] W. Pirovano,et al. Scaffolding pre-assembled contigs using SSPACE , 2011, Bioinform..
[34] J. Burton,et al. Rapid Pneumococcal Evolution in Response to Clinical Interventions , 2011, Science.
[35] K. O'Brien,et al. Systematic Evaluation of Serotypes Causing Invasive Pneumococcal Disease among Children Under Five: The Pneumococcal Global Serotype Project , 2010, PLoS medicine.
[36] M. DePristo,et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.
[37] C. Orihuela,et al. The Pneumococcal Serine-Rich Repeat Protein Is an Intra-Species Bacterial Adhesin That Promotes Bacterial Aggregation In Vivo and in Biofilms , 2010, PLoS pathogens.
[38] M. Nahm,et al. A new pneumococcal serotype, 11E, has a variably inactivated wcjE gene. , 2010, The Journal of infectious diseases.
[39] R. Rappuoli,et al. Molecular architecture of Streptococcus pneumoniae TIGR4 pili , 2009, The EMBO journal.
[40] F. Kong,et al. First report of putative Streptococcus pneumoniae serotype 6D among nasopharyngeal isolates from Fijian children. , 2009, The Journal of infectious diseases.
[41] T. Cherian,et al. Burden of disease caused by Streptococcus pneumoniae in children younger than 5 years: global estimates , 2009, The Lancet.
[42] C. Orihuela,et al. The Streptococcus pneumoniae adhesin PsrP binds to Keratin 10 on lung cells , 2009, Molecular microbiology.
[43] Jukka Corander,et al. Hyper-Recombination, Diversity, and Antibiotic Resistance in Pneumococcus , 2009, Science.
[44] J. Galagan,et al. Pneumococcal Capsular Polysaccharide Structure Predicts Serotype Prevalence , 2009, PLoS pathogens.
[45] Richard Durbin,et al. Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .
[46] Bartek Wilczynski,et al. Biopython: freely available Python tools for computational molecular biology and bioinformatics , 2009, Bioinform..
[47] Martin Antonio,et al. Seasonality and outbreak of a predominant Streptococcus pneumoniae serotype 1 clone from The Gambia: Expansion of ST217 hypervirulent clonal complex in West Africa , 2008, BMC Microbiology.
[48] E. Birney,et al. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. , 2008, Genome research.
[49] Jeffrey N. Weiser,et al. The role of Streptococcus pneumoniae virulence factors in host respiratory colonization and disease , 2008, Nature Reviews Microbiology.
[50] R. Rappuoli,et al. Pneumococcal Pili Are Composed of Protofilaments Exposing Adhesive Clusters of Rrg A , 2008, PLoS pathogens.
[51] A. Rambaut,et al. BEAST: Bayesian evolutionary analysis by sampling trees , 2007, BMC Evolutionary Biology.
[52] R. Rappuoli,et al. RrgA is a pilus-associated adhesin in Streptococcus pneumoniae , 2007, Molecular microbiology.
[53] In Ho Park,et al. Discovery of a New Capsular Serotype (6C) within Serogroup 6 of Streptococcus pneumoniae , 2007, Journal of Clinical Microbiology.
[54] Alexandros Stamatakis,et al. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models , 2006, Bioinform..
[55] B. Gessner,et al. Epidemiological and molecular characteristics of a highly lethal pneumococcal meningitis epidemic in Burkina Faso. , 2006, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.
[56] R. Gertz,et al. Sequential multiplex PCR approach for determining capsular serotypes of Streptococcus pneumoniae isolates. , 2006, Journal of clinical microbiology.
[57] S. Ho,et al. Relaxed Phylogenetics and Dating with Confidence , 2006, PLoS biology.
[58] Julian Parkhill,et al. Genetic Analysis of the Capsular Biosynthetic Locus from All 90 Pneumococcal Serotypes , 2006, PLoS genetics.
[59] R. Rappuoli,et al. A pneumococcal pilus influences virulence and host inflammatory responses. , 2006, Proceedings of the National Academy of Sciences of the United States of America.
[60] Matthew Berriman,et al. ACT: the Artemis comparison tool , 2005, Bioinform..
[61] G. Pluschke,et al. An outbreak of serotype 1 Streptococcus pneumoniae meningitis in northern Ghana with features that are characteristic of Neisseria meningitidis meningitis epidemics. , 2005, The Journal of infectious diseases.
[62] O. Pybus,et al. Bayesian coalescent inference of past population dynamics from molecular sequences. , 2005, Molecular biology and evolution.
[63] Jun Yu,et al. VFDB: a reference database for bacterial virulence factors , 2004, Nucleic Acids Res..
[64] B. Spratt,et al. Geographic Distribution and Clonal Diversity of Streptococcus pneumoniae Serotype 1 Isolates , 2003, Journal of Clinical Microbiology.
[65] G. Pozzi,et al. The three extra-cellular zinc metalloproteinases of Streptococcus pneumoniae have a different impact on virulence in mice , 2003, BMC Microbiology.
[66] B. Spratt,et al. Clonal relationships between invasive and carriage Streptococcus pneumoniae and serotype- and clone-specific differences in invasive disease potential. , 2003, The Journal of infectious diseases.
[67] J. Weiser,et al. Antibody-enhanced pneumococcal adherence requires IgA1 protease , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[68] B. Spratt,et al. A multilocus sequence typing scheme for Streptococcus pneumoniae: identification of clones associated with serious invasive disease. , 1998, Microbiology.
[69] M. Achtman,et al. Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. , 1998, Proceedings of the National Academy of Sciences of the United States of America.
[70] Thomas L. Madden,et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.
[71] Ziheng Yang. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods , 1994, Journal of Molecular Evolution.
[72] P. Ayoubi,et al. Tn5253, the pneumococcal omega (cat tet) BM6001 element, is a composite structure of two conjugative transposons, Tn5251 and Tn5252 , 1991, Journal of bacteriology.
[73] T. Mitchell,et al. What is different about serotype 1 pneumococci? , 2012, Future microbiology.
[74] H. Kishino,et al. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA , 2005, Journal of Molecular Evolution.
[75] M. Sillanpää,et al. Bayesian analysis of genetic differentiation between populations. , 2003, Genetics.