Comparative genomics of Campylobacter concisus: Analysis of clinical strains reveals genome diversity and pathogenic potential
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G. Hold | S. Berry | I. Mukhopadhya | M. Gemmell | R. Hansen | H. Nielsen | M. Bajaj‐Elliott | H. Nielsen
[1] X. Zhang,et al. Campylobacter concisus Genomospecies 2 Is Better Adapted to the Human Gastrointestinal Tract as Compared with Campylobacter concisus Genomospecies 1 , 2017, Front. Physiol..
[2] Mark Blaxter,et al. BlobTools: Interrogation of genome assemblies , 2017, F1000Research.
[3] N. French,et al. Complete Genome Sequence of Campylobacter concisus ATCC 33237T and Draft Genome Sequences for an Additional Eight Well-Characterized C. concisus Strains , 2017, Genome Announcements.
[4] A. Pathak,et al. Detection of virulence genes in ESBL producing, quinolone resistant commensal Escherichia coli from rural Indian children. , 2017, Journal of infection in developing countries.
[5] S. Riordan,et al. Erratum: Genome analysis of Campylobacter concisus strains from patients with inflammatory bowel disease and gastroenteritis provides new insights into pathogenicity , 2016, Scientific Reports.
[6] S. Riordan,et al. Genome analysis of Campylobacter concisus strains from patients with inflammatory bowel disease and gastroenteritis provides new insights into pathogenicity , 2016, Scientific Reports.
[7] Dmitry Antipov,et al. plasmidSPAdes: Assembling Plasmids from Whole Genome Sequencing Data , 2016, bioRxiv.
[8] Peer Bork,et al. Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees , 2016, Nucleic Acids Res..
[9] Dmitry Antipov,et al. hybridSPAdes: an algorithm for hybrid assembly of short and long reads , 2016, Bioinform..
[10] M. Kanehisa,et al. BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences. , 2016, Journal of molecular biology.
[11] Jian Yang,et al. VFDB 2016: hierarchical and refined dataset for big data analysis—10 years on , 2015, Nucleic Acids Res..
[12] Evgeny M. Zdobnov,et al. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs , 2015, Bioinform..
[13] S. Riordan,et al. Delineation of genetic relatedness and population structure of oral and enteric Campylobacter concisus strains by analysis of housekeeping genes. , 2015, Microbiology.
[14] Andrew J. Page,et al. Roary: rapid large-scale prokaryote pan genome analysis , 2015, bioRxiv.
[15] Si Ming Man,et al. Role of Emerging Campylobacter Species in Inflammatory Bowel Diseases , 2014, Inflammatory bowel diseases.
[16] A. Quinlan. BEDTools: The Swiss‐Army Tool for Genome Feature Analysis , 2014, Current protocols in bioinformatics.
[17] Torsten Seemann,et al. Prokka: rapid prokaryotic genome annotation , 2014, Bioinform..
[18] T. Coenye,et al. Propionibacterium acnes: from Commensal to Opportunistic Biofilm-Associated Implant Pathogen , 2014, Clinical Microbiology Reviews.
[19] Mikhail Pachkov,et al. Automated Reconstruction of Whole-Genome Phylogenies from Short-Sequence Reads , 2014, Molecular biology and evolution.
[20] Aaron E. Darling,et al. A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data , 2014, Bioinform..
[21] S. B. Peterson,et al. Type VI secretion system effectors: poisons with a purpose , 2014, Nature Reviews Microbiology.
[22] Koichiro Tamura,et al. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. , 2013, Molecular biology and evolution.
[23] S. Riordan,et al. The Prevalence and Polymorphisms of Zonula Occluden Toxin Gene in Multiple Campylobacter concisus Strains Isolated from Saliva of Patients with Inflammatory Bowel Disease and Controls , 2013, PloS one.
[24] M. Wilkins,et al. Comparative genomics of Campylobacter concisus isolates reveals genetic diversity and provides insights into disease association , 2013, BMC Genomics.
[25] Richard A. Moore,et al. Co-occurrence of anaerobic bacteria in colorectal carcinomas , 2013, Microbiome.
[26] Andrew C. Pawlowski,et al. The Comprehensive Antibiotic Resistance Database , 2013, Antimicrobial Agents and Chemotherapy.
[27] Aaron A. Klammer,et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data , 2013, Nature Methods.
[28] H. Nielsen,et al. High incidence of Campylobacter concisus in gastroenteritis in North Jutland, Denmark: a population-based study. , 2013, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.
[29] Alexey A. Gurevich,et al. QUAST: quality assessment tool for genome assemblies , 2013, Bioinform..
[30] B. Stecher,et al. 'Blooming' in the gut: how dysbiosis might contribute to pathogen evolution , 2013, Nature Reviews Microbiology.
[31] N. Kaakoush,et al. Investigation of motility and biofilm formation by intestinal Campylobacter concisus strains , 2012, Gut Pathogens.
[32] W. Pirovano,et al. Toward almost closed genomes with GapFiller , 2012, Genome Biology.
[33] J. Engel,et al. The Second Type VI Secretion System of Pseudomonas aeruginosa Strain PAO1 Is Regulated by Quorum Sensing and Fur and Modulates Internalization in Epithelial Cells* , 2012, The Journal of Biological Chemistry.
[34] Richard Hansen,et al. IBD—what role do Proteobacteria play? , 2012, Nature Reviews Gastroenterology &Hepatology.
[35] M. Wilkins,et al. The Pathogenic Potential of Campylobacter concisus Strains Associated with Chronic Intestinal Diseases , 2011, PloS one.
[36] M. Wilkins,et al. Comparative analyses of Campylobacter concisusstrains reveal the genome of the reference strain BAA-1457 is not representative of the species , 2011, Gut pathogens.
[37] S. Brunak,et al. SignalP 4.0: discriminating signal peptides from transmembrane regions , 2011, Nature Methods.
[38] Sean R. Eddy,et al. Fast filtering for RNA homology search , 2011, Bioinform..
[39] Henrik Nielsen,et al. Oral and Fecal Campylobacter concisus Strains Perturb Barrier Function by Apoptosis Induction in HT-29/B6 Intestinal Epithelial Cells , 2011, PloS one.
[40] E. El-Omar,et al. Detection of Campylobacter concisus and Other Campylobacter Species in Colonic Biopsies from Adults with Ulcerative Colitis , 2011, PloS one.
[41] Robert D. Finn,et al. HMMER web server: interactive sequence similarity searching , 2011, Nucleic Acids Res..
[42] L. Cui,et al. Impact of rpoB Mutations on Reduced Vancomycin Susceptibility in Staphylococcus aureus , 2011, Journal of Clinical Microbiology.
[43] S. Pukatzki,et al. The Vibrio cholerae type VI secretion system displays antimicrobial properties , 2010, Proceedings of the National Academy of Sciences.
[44] S. Riordan,et al. Isolation and Detection of Campylobacter concisus from Saliva of Healthy Individuals and Patients with Inflammatory Bowel Disease , 2010, Journal of Clinical Microbiology.
[45] Si Ming Man,et al. Campylobacter concisus and other Campylobacter species in children with newly diagnosed Crohn's disease , 2010, Inflammatory bowel diseases.
[46] S. Mazmanian,et al. A pathobiont of the microbiota balances host colonization and intestinal inflammation. , 2010, Cell host & microbe.
[47] Si Ming Man,et al. The Internal Transcribed Spacer Region, a New Tool for Use in Species Differentiation and Delineation of Systematic Relationships within the Campylobacter Genus , 2010, Applied and Environmental Microbiology.
[48] S. Mazmanian,et al. The gut microbiota shapes intestinal immune responses during health and disease , 2009, Nature Reviews Immunology.
[49] Cole Trapnell,et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.
[50] C. Schmerk,et al. The Francisella Pathogenicity Island Protein PdpD Is Required for Full Virulence and Associates with Homologues of the Type VI Secretion System , 2008, Journal of bacteriology.
[51] Julian Parkhill,et al. Re-annotation and re-analysis of the Campylobacter jejuni NCTC11168 genome sequence , 2007, BMC Genomics.
[52] Peter F. Hallin,et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes , 2007, Nucleic acids research.
[53] Alexandros Stamatakis,et al. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models , 2006, Bioinform..
[54] Bernhard Hube,et al. From commensal to pathogen: stage- and tissue-specific gene expression of Candida albicans. , 2004, Current opinion in microbiology.
[55] Robert C. Edgar,et al. MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.
[56] Dean Laslett,et al. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. , 2004, Nucleic acids research.
[57] A. Tanner,et al. Campylobacter Species in Health, Gingivitis, and Periodontitis , 2000, Journal of dental research.
[58] J. Kaper,et al. Vibrio cholerae produces a second enterotoxin, which affects intestinal tight junctions. , 1991, Proceedings of the National Academy of Sciences of the United States of America.
[59] S. Socransky,et al. Wolinella gen. nov., Wolinella succinogenes (Vibrio succinogenes Wolin et al.) comb. nov., and Description of Bacteroides gracilis sp. nov., Wolinella recta sp. nov., Campylobacter concisus sp. nov., and Eikenella corrodens from Humans with Periodontal Disease , 1981 .
[60] BlobTools: Interrogation of genome assemblies [version 1; referees: 2 approved with reservations] , 2018 .
[61] M. Berriman,et al. REAPR: a universal tool for genome assembly evaluation. , 2013, Genome biology.
[62] Claude-Alain H. Roten,et al. Fast and accurate short read alignment with Burrows–Wheeler transform , 2009, Bioinform..