Major bacterial lineages are essentially devoid of CRISPR-Cas viral defence systems
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Christine L. Sun | Alexander J Probst | Alexander J. Probst | Karthik Anantharaman | Jillian F Banfield | Brian C Thomas | Itai Sharon | D. Burstein | J. Banfield | Karthik Anantharaman | C. Brown | David Burstein | Christine L Sun | Itai Sharon | Christopher T Brown | B. Thomas | B. Thomas
[1] Brian C. Thomas,et al. Metagenomic analysis of a high carbon dioxide subsurface microbial community populated by chemolithoautotrophs and bacteria and archaea from candidate phyla. , 2016, Environmental microbiology.
[2] R. Gardan,et al. Costs of CRISPR-Cas-mediated resistance in Streptococcus thermophilus , 2015, Proceedings of the Royal Society B: Biological Sciences.
[3] James C. Stegen,et al. The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle , 2015, Front. Microbiol..
[4] Brian C. Thomas,et al. Unusual biology across a group comprising more than 15% of domain Bacteria , 2015, Nature.
[5] Brian C. Thomas,et al. CRISPR Immunity Drives Rapid Phage Genome Evolution in Streptococcus thermophilus , 2015, mBio.
[6] Mike Boots,et al. Parasite Exposure Drives Selective Evolution of Constitutive versus Inducible Defense , 2015, Current Biology.
[7] Asaf Levy,et al. CRISPR adaptation biases explain preference for acquisition of foreign DNA , 2015, Nature.
[8] E. Koonin,et al. Babela massiliensis, a representative of a widespread bacterial phylum with unusual adaptations to parasitism in amoebae , 2015, Biology Direct.
[9] Kenneth H. Williams,et al. Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling , 2015, Current Biology.
[10] Brian C. Thomas,et al. Diverse uncultivated ultra-small bacterial cells in groundwater , 2015, Nature Communications.
[11] R. Sorek,et al. BREX is a novel phage resistance system widespread in microbial genomes , 2015, The EMBO journal.
[12] S. Yooseph,et al. Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle , 2014, Proceedings of the National Academy of Sciences.
[13] Richard J. Roberts,et al. REBASE—a database for DNA restriction and modification: enzymes, genes and genomes , 2009, Nucleic Acids Res..
[14] Kira S. Makarova,et al. Classification and evolution of type II CRISPR-Cas systems , 2014, Nucleic acids research.
[15] Matthew Fraser,et al. InterProScan 5: genome-scale protein function classification , 2014, Bioinform..
[16] Alexandros Stamatakis,et al. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies , 2014, Bioinform..
[17] E. Birney,et al. Pfam: the protein families database , 2013, Nucleic Acids Res..
[18] I-Min A. Chen,et al. IMG 4 version of the integrated microbial genomes comparative analysis system , 2013, Nucleic Acids Res..
[19] Brian C. Thomas,et al. Small Genomes and Sparse Metabolisms of Sediment-Associated Bacteria from Four Candidate Phyla , 2013, mBio.
[20] Natalia N. Ivanova,et al. Insights into the phylogeny and coding potential of microbial dark matter , 2013, Nature.
[21] Eugene V. Koonin,et al. Evolutionary Dynamics of the Prokaryotic Adaptive Immunity System CRISPR-Cas in an Explicit Ecological Context , 2013, Journal of bacteriology.
[22] James E. DiCarlo,et al. RNA-Guided Human Genome Engineering via Cas9 , 2013, Science.
[23] Le Cong,et al. Multiplex Genome Engineering Using CRISPR/Cas Systems , 2013, Science.
[24] K. Katoh,et al. MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability , 2013, Molecular biology and evolution.
[25] Brian C. Thomas,et al. Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization , 2013, Genome research.
[26] Brian C. Thomas,et al. Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla , 2012, Science.
[27] J. Doudna,et al. A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity , 2012, Science.
[28] Siu-Ming Yiu,et al. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth , 2012, Bioinform..
[29] Steven L Salzberg,et al. Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.
[30] Mart Krupovic,et al. Genomics of Bacterial and Archaeal Viruses: Dynamics within the Prokaryotic Virosphere , 2011, Microbiology and Molecular Reviews.
[31] Sean R. Eddy,et al. Accelerated Profile HMM Searches , 2011, PLoS Comput. Biol..
[32] Sagi Snir,et al. Defense Islands in Bacterial and Archaeal Genomes and Prediction of Novel Defense Systems , 2011, Journal of bacteriology.
[33] David S. Wishart,et al. PHAST: A Fast Phage Search Tool , 2011, Nucleic Acids Res..
[34] Stan J. J. Brouns,et al. Evolution and classification of the CRISPR–Cas systems , 2011, Nature Reviews Microbiology.
[35] Robert D. Finn,et al. HMMER web server: interactive sequence similarity searching , 2011, Nucleic Acids Res..
[36] Philippe Horvath,et al. The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA , 2010, Nature.
[37] Zixin Deng,et al. TADB: a web-based resource for Type 2 toxin–antitoxin loci in bacteria and archaea , 2010, Nucleic Acids Res..
[38] Robert C. Edgar,et al. Search and clustering orders of magnitude faster than BLAST , 2010, Bioinform..
[39] Adi Stern,et al. Self-targeting by CRISPR: gene regulation or autoimmunity? , 2010, Trends in genetics : TIG.
[40] Miriam L. Land,et al. Trace: Tennessee Research and Creative Exchange Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification Recommended Citation Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification , 2022 .
[41] Brian C. Thomas,et al. Community-wide analysis of microbial genome sequence signatures , 2009, Genome Biology.
[42] Philippe Horvath,et al. Comparative analysis of CRISPR loci in lactic acid bacteria genomes. , 2009, International journal of food microbiology.
[43] R. Kaul,et al. Genome Sequence of the Fish Pathogen Renibacterium salmoninarum Suggests Reductive Evolution away from an Environmental Arthrobacter Ancestor , 2008, Journal of bacteriology.
[44] V. Kunin,et al. CRISPR — a widespread system that provides acquired resistance against phages in bacteria and archaea , 2008, Nature Reviews Microbiology.
[45] J. Banfield,et al. Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses. , 2007, Environmental microbiology.
[46] Ibtissem Grissa,et al. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats , 2007, Nucleic Acids Res..
[47] Peter B. McGarvey,et al. UniRef: comprehensive and non-redundant UniProt reference clusters , 2007, Bioinform..
[48] R. Barrangou,et al. CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes , 2007, Science.
[49] J. S. Godde,et al. The Repetitive DNA Elements Called CRISPRs and Their Associated Genes: Evidence of Horizontal Transfer Among Prokaryotes , 2006, Journal of Molecular Evolution.
[50] E. Bidnenko,et al. Phage abortive infection in lactococci: variations on a theme. , 2005, Current opinion in microbiology.
[51] Dmitrij Frishman,et al. Illuminating the Evolutionary History of Chlamydiae , 2004, Science.
[52] L. Schouls,et al. Identification of genes that are associated with DNA repeats in prokaryotes , 2002, Molecular microbiology.
[53] P. Wyrick. Intracellular survival by Chlamydia , 2000, Cellular microbiology.
[54] I. Longden,et al. EMBOSS: the European Molecular Biology Open Software Suite. , 2000, Trends in genetics : TIG.
[55] J. M. González,et al. CRISPR elements in the Thermococcales: evidence for associated horizontal gene transfer inPyrococcus furiosus , 2010, Journal of Applied Genetics.
[56] Hiroyuki Ogata,et al. KEGG: Kyoto Encyclopedia of Genes and Genomes , 1999, Nucleic Acids Res..
[57] N. Murray,et al. Restriction and modification systems. , 1991, Annual review of genetics.
[58] Supplemental Information 2: Kyoto Encyclopedia of genes and genomes. , 2022 .