DNA Methylation Assessed by SMRT Sequencing Is Linked to Mutations in Neisseria meningitidis Isolates
暂无分享,去创建一个
Jonas Korlach | Tyson A. Clark | Christoph D. Schmid | J. Korlach | Shrikant Mane | Guilin Wang | G. Pluschke | M. Sater | C. Schmid | A. Lamelas | Guilin Wang | Gerd Pluschke | Shrikant Mane | Katharina Röltgen | Araceli Lamelas | Mohamad R. Abdul Sater | K. Röltgen
[1] Sandip Paul,et al. Accelerated gene evolution through replication–transcription conflicts , 2013, Nature.
[2] J. Casadesús,et al. Epigenetic Gene Regulation in the Bacterial World , 2006, Microbiology and Molecular Biology Reviews.
[3] W Arber,et al. Genetic variation: molecular mechanisms and impact on microbial evolution. , 2000, FEMS microbiology reviews.
[4] M. Marinus,et al. Roles of DNA adenine methylation in host-pathogen interactions: mismatch repair, transcriptional regulation, and more. , 2009, FEMS microbiology reviews.
[5] Aaron R. Quinlan,et al. Bioinformatics Applications Note Genome Analysis Bedtools: a Flexible Suite of Utilities for Comparing Genomic Features , 2022 .
[6] Richard J. Roberts,et al. Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing , 2011, Nucleic acids research.
[7] G. Weinstock,et al. Genome Sequencing Reveals Widespread Virulence Gene Exchange among Human Neisseria Species , 2010, PloS one.
[8] I. Kobayashi,et al. Conflicts Targeting Epigenetic Systems and Their Resolution by Cell Death: Novel Concepts for Methyl-Specific and Other Restriction Systems , 2010, DNA research : an international journal for rapid publication of reports on genes and genomes.
[9] C. V. Jongeneel,et al. Indexing Strategies for Rapid Searches of Short Words in Genome Sequences , 2007, PloS one.
[10] M. Achtman,et al. Clonal Waves of Neisseria Colonisation and Disease in the African Meningitis Belt: Eight- Year Longitudinal Study in Northern Ghana , 2007, PLoS medicine.
[11] B. Greenwood,et al. Epidemic meningitis, meningococcaemia, and Neisseria meningitidis , 2007, The Lancet.
[12] S. Turner,et al. Real-time DNA sequencing from single polymerase molecules. , 2010, Methods in enzymology.
[13] Kira S. Makarova,et al. Comparative genomics of defense systems in archaea and bacteria , 2013, Nucleic acids research.
[14] J. Korlach,et al. The complex methylome of the human gastric pathogen Helicobacter pylori , 2013, Nucleic acids research.
[15] M. Maiden. Editorial Commentary: The Endgame for Serogroup A Meningococcal Disease in Africa? , 2012, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.
[16] Jenny Shu,et al. Efficient and accurate whole genome assembly and methylome profiling of E. coli , 2013, BMC Genomics.
[17] T. Mikkelsen,et al. The NIH Roadmap Epigenomics Mapping Consortium , 2010, Nature Biotechnology.
[18] Zixin Deng,et al. Genomic mapping of phosphorothioates reveals partial modification of short consensus sequences , 2014, Nature Communications.
[19] S. Sugano,et al. Methylome Diversification through Changes in DNA Methyltransferase Sequence Specificity , 2014, PLoS genetics.
[20] S. Salzberg,et al. Repetitive DNA and next-generation sequencing: computational challenges and solutions , 2011, Nature Reviews Genetics.
[21] J. Burton,et al. Rapid Pneumococcal Evolution in Response to Clinical Interventions , 2011, Science.
[22] D. Low,et al. Homologous Recombination Drives Both Sequence Diversity and Gene Content Variation in Neisseria meningitidis , 2013, Genome biology and evolution.
[23] Alexander N Gorban,et al. A random six-phase switch regulates pneumococcal virulence via global epigenetic changes , 2014, Nature Communications.
[24] K. Trivedi,et al. Mechanisms of meningococcal colonisation. , 2011, Trends in microbiology.
[25] Tyson A. Clark,et al. Comprehensive Methylome Characterization of Mycoplasma genitalium and Mycoplasma pneumoniae at Single-Base Resolution , 2013, PLoS genetics.
[26] S. Beatson,et al. Origin of the Diversity in DNA Recognition Domains in Phasevarion Associated modA Genes of Pathogenic Neisseria and Haemophilus influenzae , 2012, PloS one.
[27] Tyson A. Clark,et al. Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing , 2012, Nature Biotechnology.
[28] Tyson A. Clark,et al. Direct detection of DNA methylation during single-molecule, real-time sequencing , 2010, Nature Methods.
[29] S. Salzberg,et al. Versatile and open software for comparing large genomes , 2004, Genome Biology.
[30] K. Seib,et al. Phasevarions Mediate Epigenetic Regulation of Antimicrobial Susceptibility in Neisseria meningitidis , 2014, Antimicrobial Agents and Chemotherapy.
[31] M. Maiden,et al. Population genomics: diversity and virulence in the Neisseria , 2008, Current opinion in microbiology.
[32] P. H. Roy,et al. DNA methylation in Neisseria gonorrhoeae and other Neisseriae. , 1990, Gene.
[33] A. Piekarowicz,et al. Neisseria gonorrhoeae FA1090 Carries Genes Encoding Two Classes of Vsr Endonucleases , 2010, Journal of bacteriology.
[34] J. Wain,et al. High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi , 2008, Nature Genetics.
[35] A. van der Ende,et al. NmeSI Restriction-Modification System Identified by Representational Difference Analysis of a HypervirulentNeisseria meningitidis Strain , 2001, Infection and Immunity.
[36] G. Xu,et al. Cytosine methylation and DNA repair. , 2006, Current topics in microbiology and immunology.
[37] T. Tønjum,et al. Restriction and Sequence Alterations Affect DNA Uptake Sequence-Dependent Transformation in Neisseria meningitidis , 2012, PloS one.
[38] S. Salzberg,et al. Erratum: Repetitive DNA and next-generation sequencing: Computational challenges and solutions (Nature Reviews Genetics (2012) 13 (36-46)) , 2012 .
[39] M. Maiden,et al. Meningococcal carriage and disease—Population biology and evolution , 2009, Vaccine.
[40] Julie C Dunning Hotopp,et al. Neisseria meningitidis is structured in clades associated with restriction modification systems that modulate homologous recombination , 2011, Proceedings of the National Academy of Sciences.
[41] K. Jolley,et al. Dam inactivation in Neisseria meningitidis: prevalence among diverse hyperinvasive lineages , 2004, BMC Microbiology.
[42] S. Grimmond,et al. Phasevarions Mediate Random Switching of Gene Expression in Pathogenic Neisseria , 2009, PLoS pathogens.
[43] E. Rocha. The organization of the bacterial genome. , 2008, Annual review of genetics.
[44] Keith C. Norris,et al. DNA cytosine methylation and heat-induced deamination , 1986, Bioscience reports.
[45] S. Fortune,et al. DNA Methylation Impacts Gene Expression and Ensures Hypoxic Survival of Mycobacterium tuberculosis , 2013, PLoS pathogens.
[46] Jonas Korlach,et al. Enhanced 5-methylcytosine detection in single-molecule, real-time sequencing via Tet1 oxidation , 2012, BMC Biology.
[47] Erik van Nimwegen,et al. Universal patterns of purifying selection at noncoding positions in bacteria. , 2007, Genome research.
[48] Jacqueline A. Keane,et al. Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins , 2014, Nucleic acids research.
[49] Tyson A. Clark,et al. Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases , 2013, Genome research.
[50] Gang Fang,et al. Detecting DNA Modifications from SMRT Sequencing Data by Modeling Sequence Context Dependence of Polymerase Kinetic , 2013, PLoS Comput. Biol..
[51] Haixu Tang,et al. Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing , 2012, Proceedings of the National Academy of Sciences.
[52] Tyson A. Clark,et al. Global methylation state at base-pair resolution of the Caulobacter genome throughout the cell cycle , 2013, Proceedings of the National Academy of Sciences.
[53] Julian Parkhill,et al. Emergence of a New Epidemic Neisseria meningitidis Serogroup A Clone in the African Meningitis Belt: High-Resolution Picture of Genomic Changes That Mediate Immune Evasion , 2014, mBio.
[54] M. Frosch,et al. Differential Distribution of Novel Restriction-Modification Systems in Clonal Lineages ofNeisseria meningitidis , 2000, Journal of bacteriology.
[55] A. Richardson,et al. Mismatch repair and the regulation of phase variation in Neisseria meningitidis , 2001, Molecular microbiology.
[56] Mauricio O. Carneiro,et al. The advantages of SMRT sequencing , 2013, Genome Biology.
[57] Matthieu Legendre,et al. Variable tandem repeats accelerate evolution of coding and regulatory sequences. , 2010, Annual review of genetics.
[58] A. Goesmann,et al. Whole-Genome Sequence of the Transformable Neisseria meningitidis Serogroup A Strain WUE2594 , 2011, Journal of bacteriology.
[59] Tyson A. Clark,et al. Specificity of the ModA11, ModA12 and ModD1 epigenetic regulator N6-adenine DNA methyltransferases of Neisseria meningitidis , 2015, Nucleic acids research.
[60] Richard J. Roberts,et al. REBASE—a database for DNA restriction and modification: enzymes, genes and genomes , 2009, Nucleic Acids Res..
[61] B. Barrell,et al. Complete DNA sequence of a serogroup A strain of Neisseria meningitidis Z2491 , 2000, Nature.
[62] Kelly M. Wetmore,et al. Exploring the Roles of DNA Methylation in the Metal-Reducing Bacterium Shewanella oneidensis MR-1 , 2013, Journal of bacteriology.