Published in BMC Bioinformatics on January 20, 2007
RNA-guided genetic silencing systems in bacteria and archaea. Nature (2012) 17.12
CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res (2007) 15.56
The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. BMC Bioinformatics (2007) 7.34
IMG 4 version of the integrated microbial genomes comparative analysis system. Nucleic Acids Res (2013) 6.14
Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System. Cell (2015) 5.97
CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics (2007) 5.84
Evolutionary conservation of sequence and secondary structures in CRISPR repeats. Genome Biol (2007) 5.40
IMG/M 4 version of the integrated metagenome comparative analysis system. Nucleic Acids Res (2013) 2.99
The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4). Stand Genomic Sci (2015) 2.55
Diverse CRISPRs evolving in human microbiomes. PLoS Genet (2012) 2.20
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A bacterial metapopulation adapts locally to phage predation despite global dispersal. Genome Res (2007) 1.85
CRISPI: a CRISPR interactive database. Bioinformatics (2009) 1.63
CRISPR targeting reveals a reservoir of common phages associated with the human gut microbiome. Genome Res (2012) 1.52
Comparison of single-molecule sequencing and hybrid approaches for finishing the genome of Clostridium autoethanogenum and analysis of CRISPR systems in industrial relevant Clostridia. Biotechnol Biofuels (2014) 1.47
The intracellular sRNA transcriptome of Listeria monocytogenes during growth in macrophages. Nucleic Acids Res (2011) 1.47
CRISPRTarget: bioinformatic prediction and analysis of crRNA targets. RNA Biol (2013) 1.46
Reassessment of the Listeria monocytogenes pan-genome reveals dynamic integration hotspots and mobile genetic elements as major components of the accessory genome. BMC Genomics (2013) 1.43
Draft genome sequence of Bacillus azotoformans MEV2011, a (Co-) denitrifying strain unable to grow with oxygen. Stand Genomic Sci (2015) 1.39
The complete genome and proteome of Laribacter hongkongensis reveal potential mechanisms for adaptations to different temperatures and habitats. PLoS Genet (2009) 1.38
Multiscale model of CRISPR-induced coevolutionary dynamics: diversification at the interface of Lamarck and Darwin. Evolution (2012) 1.21
Viral diversity threshold for adaptive immunity in prokaryotes. MBio (2012) 1.17
Comparative genomics and transcriptomics of lineages I, II, and III strains of Listeria monocytogenes. BMC Genomics (2012) 1.16
CRISPR-mediated phage resistance and the ghost of coevolution past. Proc Biol Sci (2010) 1.14
The elusive object of desire--interactions of bacteriophages and their hosts. Curr Opin Microbiol (2008) 1.14
Metagenomics: tools and insights for analyzing next-generation sequencing data derived from biodiversity studies. Bioinform Biol Insights (2015) 1.13
Evolutionary dynamics of clustered irregularly interspaced short palindromic repeat systems in the ocean metagenome. Appl Environ Microbiol (2010) 1.12
Sequencing of seven haloarchaeal genomes reveals patterns of genomic flux. PLoS One (2012) 1.07
Genomic analysis of "Elusimicrobium minutum," the first cultivated representative of the phylum "Elusimicrobia" (formerly termite group 1). Appl Environ Microbiol (2009) 1.07
The Human Skin Double-Stranded DNA Virome: Topographical and Temporal Diversity, Genetic Enrichment, and Dynamic Associations with the Host Microbiome. MBio (2015) 1.02
Complete genome sequence of DSM 30083(T), the type strain (U5/41(T)) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy. Stand Genomic Sci (2014) 0.99
Crass: identification and reconstruction of CRISPR from unassembled metagenomic data. Nucleic Acids Res (2013) 0.98
Diversity and evolution of class 2 CRISPR-Cas systems. Nat Rev Microbiol (2017) 0.90
The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4). Stand Genomic Sci (2016) 0.88
Reconstruction of novel cyanobacterial siphovirus genomes from Mediterranean metagenomic fosmids. Appl Environ Microbiol (2012) 0.88
CRISPRDetect: A flexible algorithm to define CRISPR arrays. BMC Genomics (2016) 0.86
Comparative genomics of Lactobacillus crispatus suggests novel mechanisms for the competitive exclusion of Gardnerella vaginalis. BMC Genomics (2014) 0.86
Draft genome of the Arabidopsis thaliana phyllosphere bacterium, Williamsia sp. ARP1. Stand Genomic Sci (2016) 0.84
MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems. PLoS One (2014) 0.84
Phage resistance of a marine bacterium, Roseobacter denitrificans OCh114, as revealed by comparative proteomics. Curr Microbiol (2010) 0.83
Extensive genome rearrangements and multiple horizontal gene transfers in a population of pyrococcus isolates from Vulcano Island, Italy. Appl Environ Microbiol (2008) 0.83
Complete genome sequence of 'Halanaeroarchaeum sulfurireducens' M27-SA2, a sulfur-reducing and acetate-oxidizing haloarchaeon from the deep-sea hypersaline anoxic lake Medee. Stand Genomic Sci (2016) 0.82
Metagenomes of tropical soil-derived anaerobic switchgrass-adapted consortia with and without iron. Stand Genomic Sci (2013) 0.82
Elemental sulfur and acetate can support life of a novel strictly anaerobic haloarchaeon. ISME J (2015) 0.81
Comparative analysis of CRISPR cassettes from the human gut metagenomic contigs. BMC Genomics (2014) 0.81
Virulence related sequences; insights provided by comparative genomics of Streptococcus uberis of differing virulence. BMC Genomics (2015) 0.81
Two Novel Myoviruses from the North of Iraq Reveal Insights into Clostridium difficile Phage Diversity and Biology. Viruses (2016) 0.80
Genome sequence of the reddish-pigmented Rubellimicrobium thermophilum type strain (DSM 16684(T)), a member of the Roseobacter clade. Stand Genomic Sci (2013) 0.80
High quality draft genome sequence of Janthinobacterium psychrotolerans sp. nov., isolated from a frozen freshwater pond. Stand Genomic Sci (2017) 0.79
The complete genome sequence and analysis of a plasmid-bearing myxobacterial strain Myxococcus fulvus 124B02 (M 206081). Stand Genomic Sci (2016) 0.78
Complete genome sequence of Thioalkalivibrio paradoxus type strain ARh 1(T), an obligately chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacterium isolated from a Kenyan soda lake. Stand Genomic Sci (2015) 0.78
Genome sequence of the Litoreibacter arenae type strain (DSM 19593(T)), a member of the Roseobacter clade isolated from sea sand. Stand Genomic Sci (2013) 0.78
Metagenome sequencing and 98 microbial genomes from Juan de Fuca Ridge flank subsurface fluids. Sci Data (2017) 0.77
RiTE database: a resource database for genus-wide rice genomics and evolutionary biology. BMC Genomics (2015) 0.77
A Comprehensive Curation Shows the Dynamic Evolutionary Patterns of Prokaryotic CRISPRs. Biomed Res Int (2016) 0.77
Metabolic characteristics of dominant microbes and key rare species from an acidic hot spring in Taiwan revealed by metagenomics. BMC Genomics (2015) 0.76
Draft genome sequence of Francisella tularensis subsp. holarctica BD11-00177. Stand Genomic Sci (2013) 0.76
Draft genome sequence of Bacillus azotoformans MEV2011, a (Co-) denitrifying strain unable to grow with oxygen. Stand Genomic Sci (2015) 0.76
An Enrichment of CRISPR and Other Defense-Related Features in Marine Sponge-Associated Microbial Metagenomes. Front Microbiol (2016) 0.76
Comparative Genomics Analysis of Streptomyces Species Reveals Their Adaptation to the Marine Environment and Their Diversity at the Genomic Level. Front Microbiol (2016) 0.76
Viruses in the Oceanic Basement. MBio (2017) 0.75
RGFA: powerful and convenient handling of assembly graphs. PeerJ (2016) 0.75
Regulated CRISPR Modules Exploit a Dual Defense Strategy of Restriction and Abortive Infection in a Model of Prokaryote-Phage Coevolution. PLoS Comput Biol (2015) 0.75
CRISPRdigger: detecting CRISPRs with better direct repeat annotations. Sci Rep (2016) 0.75
Complete Genome Sequence of Mycobacterium avium, Isolated from Commercial Domestic Pekin Ducks (Anas platyrhynchos domestica), Determined Using PacBio Single-Molecule Real-Time Technology. Genome Announc (2016) 0.75
The invasive Neisseria meningitidis MenC CC103 from Brazil is characterized by an accessory gene repertoire. Sci Rep (2017) 0.75
Not all predicted CRISPR-Cas systems are equal: isolated cas genes and classes of CRISPR like elements. BMC Bioinformatics (2017) 0.75
Genome sequence of the pink to light reddish-pigmented Rubellimicrobium mesophilum type strain (DSM 19309(T)), a representative of the Roseobacter group isolated from soil, and emended description of the species. Stand Genomic Sci (2014) 0.75
Genome sequence of Prevotella intermedia SUNY aB G8-9K-3, a biofilm forming strain with drug-resistance. Braz J Microbiol (2016) 0.75
Complete genome sequence and characterization of avian pathogenic Escherichia coli field isolate ACN001. Stand Genomic Sci (2016) 0.75
CRF: detection of CRISPR arrays using random forest. PeerJ (2017) 0.75
High quality permanent draft genome sequence of Phaseolibacter flectens ATCC 12775(T), a plant pathogen of French bean pods. Stand Genomic Sci (2016) 0.75
Draft Genome Sequences of Three Novel Clostridium Isolates from Northern Iraq. Genome Announc (2016) 0.75
Complete genome sequence of Pseudomonas citronellolis P3B5, a candidate for microbial phyllo-remediation of hydrocarbon-contaminated sites. Stand Genomic Sci (2016) 0.75
Permanent Draft Genome Sequence of Desulfurococcus amylolyticus Strain Z-533(T), a Peptide and Starch Degrader Isolated from Thermal Springs in the Kamchatka Peninsula and Kunashir Island, Russia. Genome Announc (2017) 0.75
Permanent draft genome sequence of Desulfurococcus mobilis type strain DSM 2161, a thermoacidophilic sulfur-reducing crenarchaeon isolated from acidic hot springs of Hveravellir, Iceland. Stand Genomic Sci (2016) 0.75
The CRISPR Spacer Space Is Dominated by Sequences from Species-Specific Mobilomes. MBio (2017) 0.75
Complete Genome Sequence of a Novel Bioflocculant-Producing Strain, Microbacterium paludicola CC3. Genome Announc (2017) 0.75
Genome Sequencing of Ralstonia solanacearum CQPS-1, a Phylotype I Strain Collected from a Highland Area with Continuous Cropping of Tobacco. Front Microbiol (2017) 0.75
Recruitment of CRISPR-Cas systems by Tn7-like transposons. Proc Natl Acad Sci U S A (2017) 0.75
MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res (2004) 168.89
MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics (2004) 50.89
Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science (1996) 41.35
Identification of genes that are associated with DNA repeats in prokaryotes. Mol Microbiol (2002) 14.67
A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. PLoS Comput Biol (2005) 11.82
A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action. Biol Direct (2006) 11.31
CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies. Microbiology (2005) 9.83
REPuter: fast computation of maximal repeats in complete genomes. Bioinformatics (1999) 6.15
Biological significance of a family of regularly spaced repeats in the genomes of Archaea, Bacteria and mitochondria. Mol Microbiol (2000) 5.46
The repetitive DNA elements called CRISPRs and their associated genes: evidence of horizontal transfer among prokaryotes. J Mol Evol (2006) 5.37
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Efficient q-gram filters for finding all epsilon-matches over a given length. J Comput Biol (2006) 4.24
PILER: identification and classification of genomic repeats. Bioinformatics (2005) 3.99
Identification of a novel family of sequence repeats among prokaryotes. OMICS (2002) 3.94
Chromosome evolution in the Thermotogales: large-scale inversions and strain diversification of CRISPR sequences. J Bacteriol (2006) 1.57
MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res (2004) 168.89
A comparison of scoring functions for protein sequence profile alignment. Bioinformatics (2004) 6.44
Local homology recognition and distance measures in linear time using compressed amino acid alphabets. Nucleic Acids Res (2004) 6.42
COACH: profile-profile alignment of protein families using hidden Markov models. Bioinformatics (2004) 6.22
PILER: identification and classification of genomic repeats. Bioinformatics (2005) 3.99
Multiple sequence alignment. Curr Opin Struct Biol (2006) 2.93
Quality measures for protein alignment benchmarks. Nucleic Acids Res (2010) 2.23
Optimizing substitution matrix choice and gap parameters for sequence alignment. BMC Bioinformatics (2009) 0.96