Published in BMC Bioinformatics on February 06, 2017
Complete Genome Analysis of Thermus parvatiensis and Comparative Genomics of Thermus spp. Provide Insights into Genetic Variability and Evolution of Natural Competence as Strategic Survival Attributes. Front Microbiol (2017) 0.75
Restriction-modification mediated barriers to exogenous DNA uptake and incorporation employed by Prevotella intermedia. PLoS One (2017) 0.75
TopHat: discovering splice junctions with RNA-Seq. Bioinformatics (2009) 81.13
MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics (2004) 50.89
Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res (1999) 49.21
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics (2006) 43.68
CRISPR provides acquired resistance against viruses in prokaryotes. Science (2007) 29.74
Small CRISPR RNAs guide antiviral defense in prokaryotes. Science (2008) 17.79
Evolution and classification of the CRISPR-Cas systems. Nat Rev Microbiol (2011) 17.11
Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proc Natl Acad Sci U S A (2012) 16.48
CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res (2007) 15.56
FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol (2009) 15.15
Identification of genes that are associated with DNA repeats in prokaryotes. Mol Microbiol (2002) 14.67
The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature (2010) 14.21
Phage response to CRISPR-encoded resistance in Streptococcus thermophilus. J Bacteriol (2007) 13.67
HMMER web server: interactive sequence similarity searching. Nucleic Acids Res (2011) 13.00
A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. PLoS Comput Biol (2005) 11.82
CRISPR-Cas systems in bacteria and archaea: versatile small RNAs for adaptive defense and regulation. Annu Rev Genet (2011) 9.88
Bacteriophage resistance mechanisms. Nat Rev Microbiol (2010) 7.38
The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. BMC Bioinformatics (2007) 7.34
Diversity, activity, and evolution of CRISPR loci in Streptococcus thermophilus. J Bacteriol (2007) 7.00
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
NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res (2016) 5.40
A putative viral defence mechanism in archaeal cells. Archaea (2006) 4.84
PILER-CR: fast and accurate identification of CRISPR repeats. BMC Bioinformatics (2007) 4.28
FragGeneScan: predicting genes in short and error-prone reads. Nucleic Acids Res (2010) 4.16
An updated evolutionary classification of CRISPR-Cas systems. Nat Rev Microbiol (2015) 3.74
Prediction of effective genome size in metagenomic samples. Genome Biol (2007) 3.73
Phage genomics: small is beautiful. Cell (2002) 3.26
Timescales of genetic and epigenetic inheritance. Cell (2007) 3.10
CRISPR-Cas systems: Prokaryotes upgrade to adaptive immunity. Mol Cell (2014) 2.87
Identification of new noncoding RNAs in Listeria monocytogenes and prediction of mRNA targets. Nucleic Acids Res (2007) 2.75
A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair. Mol Microbiol (2010) 2.70
Self-targeting by CRISPR: gene regulation or autoimmunity? Trends Genet (2010) 2.62
Cas1-Cas2 complex formation mediates spacer acquisition during CRISPR-Cas adaptive immunity. Nat Struct Mol Biol (2014) 2.21
Diverse CRISPRs evolving in human microbiomes. PLoS Genet (2012) 2.20
CRISPR-Cas immunity in prokaryotes. Nature (2015) 1.75
CRISPR-based technologies: prokaryotic defense weapons repurposed. Trends Genet (2014) 1.60
A very early-branching Staphylococcus aureus lineage lacking the carotenoid pigment staphyloxanthin. Genome Biol Evol (2011) 1.51
Programmable RNA shredding by the type III-A CRISPR-Cas system of Streptococcus thermophilus. Mol Cell (2014) 1.30
Genome reduction and co-evolution between the primary and secondary bacterial symbionts of psyllids. Mol Biol Evol (2012) 1.23
Modulation of CRISPR locus transcription by the repeat-binding protein Cbp1 in Sulfolobus. Nucleic Acids Res (2011) 1.16
CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems. Nucleic Acids Res (2013) 1.16
Identification of a new repetitive element in Staphylococcus aureus. Infect Immun (2000) 1.10
Essential requirements for the detection and degradation of invaders by the Haloferax volcanii CRISPR/Cas system I-B. RNA Biol (2013) 1.01
Evidence for the widespread distribution of CRISPR-Cas system in the Phylum Cyanobacteria. RNA Biol (2013) 0.99
The role of variable DNA tandem repeats in bacterial adaptation. FEMS Microbiol Rev (2013) 0.97
An evolutionary link between natural transformation and CRISPR adaptive immunity. MBio (2012) 0.94
CRISPRDetect: A flexible algorithm to define CRISPR arrays. BMC Genomics (2016) 0.86
Expanding the catalog of cas genes with metagenomes. Nucleic Acids Res (2013) 0.85
Accurate computational prediction of the transcribed strand of CRISPR non-coding RNAs. Bioinformatics (2014) 0.84
Comparative Analysis of the Orphan CRISPR2 Locus in 242 Enterococcus faecalis Strains. PLoS One (2015) 0.82
RNA-Seq reveals differential gene expression in Staphylococcus aureus with single-nucleotide resolution. PLoS One (2013) 0.80
RNA-Seq analyses reveal CRISPR RNA processing and regulation patterns. Biochem Soc Trans (2013) 0.78
Variation in the genomic locations and sequence conservation of STAR elements among staphylococcal species provides insight into DNA repeat evolution. BMC Genomics (2012) 0.76