Roving methyltransferases generate a mosaic epigenetic landscape and influence evolution in Bacteroides fragilis group

[1]  G. Dantas,et al.  Time for Some Group Therapy: Update on Identification, Antimicrobial Resistance, Taxonomy, and Clinical Significance of the Bacteroides fragilis Group , 2022, Journal of clinical microbiology.

[2]  G. Dantas,et al.  Comparative Genomics of Bacteroides fragilis Group Isolates Reveals Species-Dependent Resistance Mechanisms and Validates Clinical Tools for Resistance Prediction , 2022, mBio.

[3]  Joshua J. Hamilton,et al.  Polysaccharide utilization loci in Bacteroides determine population fitness and community-level interactions. , 2022, Cell host & microbe.

[4]  Peter C. Fineran,et al.  Identification and classification of antiviral defence systems in bacteria and archaea with PADLOC reveals new system types , 2021, Nucleic acids research.

[5]  Z. Baharoglu,et al.  Deficiency in cytosine DNA methylation leads to high chaperonin expression and tolerance to aminoglycosides in Vibrio cholerae , 2021, bioRxiv.

[6]  Sven Rahmann,et al.  Sustainable data analysis with Snakemake , 2021, F1000Research.

[7]  Xue-Song Zhang,et al.  Discovering multiple types of DNA methylation from bacteria and microbiome using nanopore sequencing , 2021, Nature Methods.

[8]  C. Médigue,et al.  panRGP: a pangenome-based method to predict genomic islands and explore their diversity. , 2020, Bioinformatics.

[9]  N. Kyrpides,et al.  CheckV assesses the quality and completeness of metagenome-assembled viral genomes , 2020, Nature Biotechnology.

[10]  Cameron L.M. Gilchrist,et al.  clinker & clustermap.js: Automatic generation of gene cluster comparison figures , 2020, bioRxiv.

[11]  Matthew B. Sullivan,et al.  Cenote-Taker 2 Democratizes Virus Discovery and Sequence Annotation , 2020, bioRxiv.

[12]  K. Seib,et al.  Epigenetic Regulation of Virulence and Immunoevasion by Phase-Variable Restriction-Modification Systems in Bacterial Pathogens. , 2020, Annual review of microbiology.

[13]  G. Fang,et al.  Conserved DNA Methyltransferases: A Window into Fundamental Mechanisms of Epigenetic Regulation in Bacteria. , 2020, Trends in microbiology.

[14]  Narmada Thanki,et al.  CDD/SPARCLE: the conserved domain database in 2020 , 2019, Nucleic Acids Res..

[15]  Donovan H Parks,et al.  GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database , 2019, Bioinform..

[16]  Christophe Ambroise,et al.  PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph , 2019, bioRxiv.

[17]  H. Hasman,et al.  Complete hybrid genome assembly of clinical multidrug-resistant Bacteroides fragilis isolates enables comprehensive identification of antimicrobial-resistance genes and plasmids , 2019, Microbial genomics.

[18]  A. Kasarskis,et al.  Epigenomic characterization of Clostridioides difficile finds a conserved DNA methyltransferase that mediates sporulation and pathogenesis , 2019, Nature Microbiology.

[19]  Rohan B. H. Williams,et al.  Annotated bacterial chromosomes from frame-shift-corrected long-read metagenomic data , 2019, Microbiome.

[20]  Andrew C. Tolonen,et al.  Invertible promoters mediate bacterial phase variation, antibiotic resistance, and host adaptation in the gut , 2019, Science.

[21]  Edoardo Pasolli,et al.  Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle , 2019, Cell.

[22]  E. Schadt,et al.  Deciphering bacterial epigenomes using modern sequencing technologies , 2018, Nature Reviews Genetics.

[23]  James Robertson,et al.  MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies , 2018, Microbial genomics.

[24]  J. Wagenaar,et al.  Plasmids carrying antimicrobial resistance genes in Enterobacteriaceae , 2018, The Journal of antimicrobial chemotherapy.

[25]  R. Morgan,et al.  N4-cytosine DNA methylation regulates transcription and pathogenesis in Helicobacter pylori , 2018, Nucleic acids research.

[26]  Yu Lin,et al.  Assembly of long, error-prone reads using repeat graphs , 2018, Nature Biotechnology.

[27]  R. Roberts,et al.  Comparative genome and methylome analysis reveals restriction/modification system diversity in the gut commensal Bifidobacterium breve , 2017, Nucleic acids research.

[28]  Evan Bolton,et al.  Database resources of the National Center for Biotechnology Information , 2017, Nucleic Acids Res..

[29]  Alexander E. Kel,et al.  cutPrimers: A New Tool for Accurate Cutting of Primers from Reads of Targeted Next Generation Sequencing , 2017, J. Comput. Biol..

[30]  A. Goodman,et al.  An insider's perspective: Bacteroides as a window into the microbiome , 2017, Nature Microbiology.

[31]  S. Koren,et al.  Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation , 2016, bioRxiv.

[32]  Niranjan Nagarajan,et al.  Fast and accurate de novo genome assembly from long uncorrected reads. , 2017, Genome research.

[33]  Raymond Lo,et al.  CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database , 2016, Nucleic Acids Res..

[34]  Yan Li,et al.  SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation , 2016, PloS one.

[35]  Roland Eils,et al.  Complex heatmaps reveal patterns and correlations in multidimensional genomic data , 2016, Bioinform..

[36]  Daniel H. Huson,et al.  MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data , 2016, PLoS Comput. Biol..

[37]  Dongwan D. Kang,et al.  The Epigenomic Landscape of Prokaryotes , 2016, PLoS genetics.

[38]  C. Putnam.  Evolution of the methyl directed mismatch repair system in Escherichia coli. , 2016, DNA repair.

[39]  Jacqueline A. Keane,et al.  Circlator: automated circularization of genome assemblies using long sequencing reads , 2015, Genome Biology.

[40]  Brian D. Ondov,et al.  Mash: fast genome and metagenome distance estimation using MinHash , 2015, Genome Biology.

[41]  Connor T. Skennerton,et al.  CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes , 2015, Genome research.

[42]  Kristian Liland,et al.  micropan: an R-package for microbial pan-genomics , 2015, BMC Bioinformatics.

[43]  Robert Hein,et al.  rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development , 2014, Nucleic Acids Res..

[44]  Christina A. Cuomo,et al.  Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement , 2014, PloS one.

[45]  Chao Xie,et al.  Fast and sensitive protein alignment using DIAMOND , 2014, Nature Methods.

[46]  M. Touchon,et al.  The interplay of restriction-modification systems with mobile genetic elements and their prokaryotic hosts , 2014, Nucleic acids research.

[47]  Torsten Seemann,et al.  Prokka: rapid prokaryotic genome annotation , 2014, Bioinform..

[48]  Alexandros Stamatakis,et al.  RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies , 2014, Bioinform..

[49]  S. Rasmussen,et al.  Identification of acquired antimicrobial resistance genes , 2012, The Journal of antimicrobial chemotherapy.

[50]  Peter A. Jones.  Functions of DNA methylation: islands, start sites, gene bodies and beyond , 2012, Nature Reviews Genetics.

[51]  Sergey I. Nikolenko,et al.  SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing , 2012, J. Comput. Biol..

[52]  M. Sakamoto,et al.  Identification and classification of the genus Bacteroides by multilocus sequence analysis. , 2011, Microbiology.

[53]  Sean R. Eddy,et al.  Accelerated Profile HMM Searches , 2011, PLoS Comput. Biol..

[54]  E. Urbán,et al.  Antimicrobial susceptibility of Bacteroides fragilis group isolates in Europe: 20 years of experience. , 2011, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

[55]  Sylvain Moineau,et al.  Bacteriophage resistance mechanisms , 2010, Nature Reviews Microbiology.

[56]  Ning Ma,et al.  BLAST+: architecture and applications , 2009, BMC Bioinformatics.

[57]  Toni Gabaldón,et al.  trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses , 2009, Bioinform..

[58]  Colin R. Parrish,et al.  Presence and role of cytosine methylation in DNA viruses of animals , 2008, Nucleic acids research.

[59]  Thomas Rattei,et al.  Gepard: a rapid and sensitive tool for creating dotplots on genome scale , 2007, Bioinform..

[60]  Michael B. Stadler,et al.  Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome , 2007, Nature Genetics.

[61]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[62]  P. Shannon,et al.  Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks , 2003 .

[63]  C. Smith,et al.  The Bacteroides mobilizable transposon Tn4555 integrates by a site-specific recombination mechanism similar to that of the gram-positive bacterial element Tn916 , 1997, Journal of bacteriology.

[64]  M. Marinus,et al.  The dam and dcm strains of Escherichia coli--a review. , 1994, Gene.

[65]  L. Blyn,et al.  Regulation of pap pilin phase variation by a mechanism involving differential dam methylation states. , 1990, The EMBO journal.

[66]  H. Flint,et al.  Formation of propionate and butyrate by the human colonic microbiota. , 2017, Environmental microbiology.