-
1
-
-
0022633244
-
Molecular evolution of bacteriophages: Evidence of selection against the recognition sites of host restriction enzymes
-
PMID:2832688
-
Sharp PM. Molecular evolution of bacteriophages: evidence of selection against the recognition sites of host restriction enzymes. Mol Biol Evol 1986; 3:75-83; PMID:2832688.
-
(1986)
Mol Biol Evol
, vol.3
, pp. 75-83
-
-
Sharp, P.M.1
-
2
-
-
0030740993
-
Avoidance of palindromic words in bacterial and archaeal genomes: A close connection with restriction enzymes
-
PMID:9171096
-
Gelfand MS, Koonin EV. Avoidance of palindromic words in bacterial and archaeal genomes: a close connection with restriction enzymes. Nucleic Acids Res 1997; 25:2430-9; PMID:9171096; http://dx.doi.org/10.1093/nar/25.12.2430.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 2430-2439
-
-
Gelfand, M.S.1
Koonin, E.V.2
-
3
-
-
0034034401
-
Biological significance of a family of regularly spaced repeats in the genomes of Archaea, Bacteria and mitochondria
-
PMID:10760181
-
Mojica FJ, Díez-Villaseñor C, Soria E, Juez G. Biological significance of a family of regularly spaced repeats in the genomes of Archaea, Bacteria and mitochondria. Mol Microbiol 2000; 36:244-6; PMID:10760181; http://dx.doi.org/10.1046/j.1365-2958.2000.01838.x.
-
(2000)
Mol Microbiol
, vol.36
, pp. 244-246
-
-
Mojica, F.J.1
Díez-Villaseñor, C.2
Soria, E.3
Juez, G.4
-
4
-
-
0036408356
-
Identification of a novel family of sequence repeats among prokaryotes
-
PMID:11883425
-
Jansen R, van Embden JD, Gaastra W, Schouls LM. Identification of a novel family of sequence repeats among prokaryotes. OMICS 2002; 6:23-33; PMID:11883425; http://dx.doi.org/10.1089/15362310252780816.
-
(2002)
OMICS
, vol.6
, pp. 23-33
-
-
Jansen, R.1
Van Embden, J.D.2
Gaastra, W.3
Schouls, L.M.4
-
5
-
-
80755187812
-
CRISPR-Cas systems in bacteria and archaea: Versatile small RNAs for adaptive defense and regulation
-
PMID:22060043
-
Bhaya D, Davison M, Barrangou R. CRISPR-Cas systems in bacteria and archaea: versatile small RNAs for adaptive defense and regulation. Annu Rev Genet 2011; 45:273-97; PMID:22060043; http://dx.doi.org/10.1146/annurev-genet- 110410-132430.
-
(2011)
Annu Rev Genet
, vol.45
, pp. 273-297
-
-
Bhaya, D.1
Davison, M.2
Barrangou, R.3
-
6
-
-
0036267740
-
Identification of genes that are associated with DNA repeats in prokaryotes
-
PMID:11952905
-
Jansen R, Embden JD, Gaastra W, Schouls LM. Identification of genes that are associated with DNA repeats in prokaryotes. Mol Microbiol 2002; 43:1565-75; PMID:11952905; http://dx.doi.org/10.1046/j.1365-2958.2002.02839.x.
-
(2002)
Mol Microbiol
, vol.43
, pp. 1565-1575
-
-
Jansen, R.1
Embden, J.D.2
Gaastra, W.3
Schouls, L.M.4
-
7
-
-
79956157571
-
Evolution and classification of the CRISPR-Cas systems
-
PMID:21552286
-
Makarova KS, Haft DH, Barrangou R, Brouns SJ, Charpentier E, Horvath P, et al. Evolution and classification of the CRISPR-Cas systems. Nat Rev Microbiol 2011; 9:467-77; PMID:21552286; http://dx.doi.org/10.1038/nrmicro2577.
-
(2011)
Nat Rev Microbiol
, vol.9
, pp. 467-477
-
-
Makarova, K.S.1
Haft, D.H.2
Barrangou, R.3
Brouns, S.J.4
Charpentier, E.5
Horvath, P.6
-
8
-
-
34047118522
-
CRISPR provides acquired resistance against viruses in prokaryotes
-
PMID:17379808
-
Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, et al. CRISPR provides acquired resistance against viruses in prokaryotes. Science 2007; 315:1709-12; PMID:17379808; http://dx.doi.org/10.1126/science.1138140.
-
(2007)
Science
, vol.315
, pp. 1709-1712
-
-
Barrangou, R.1
Fremaux, C.2
Deveau, H.3
Richards, M.4
Boyaval, P.5
Moineau, S.6
-
9
-
-
68249102788
-
CRISPR-based adaptive and heritable immunity in prokaryotes
-
PMID:19646880
-
van der Oost J, Jore MM, Westra ER, Lundgren M, Brouns SJ. CRISPR-based adaptive and heritable immunity in prokaryotes. Trends Biochem Sci 2009; 34:401-7; PMID:19646880; http://dx.doi.org/10.1016/j.tibs.2009.05.002.
-
(2009)
Trends Biochem Sci
, vol.34
, pp. 401-407
-
-
Van Der Oost, J.1
Jore, M.M.2
Westra, E.R.3
Lundgren, M.4
Brouns, S.J.5
-
10
-
-
74249095519
-
CRISPR/Cas, the immune system of bacteria and archaea
-
PMID:20056882
-
Horvath P, Barrangou R. CRISPR/Cas, the immune system of bacteria and archaea. Science 2010; 327:167-70; PMID:20056882; http://dx.doi.org/10.1126/ science.1179555.
-
(2010)
Science
, vol.327
, pp. 167-170
-
-
Horvath, P.1
Barrangou, R.2
-
11
-
-
78149261827
-
The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA
-
PMID:21048762
-
Garneau JE, Dupuis MÈ, Villion M, Romero DA, Barrangou R, Boyaval P, et al. The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature 2010; 468:67-71; PMID:21048762; http://dx.doi.org/10.1038/ nature09523.
-
(2010)
Nature
, vol.468
, pp. 67-71
-
-
Garneau, J.E.1
Dupuis, M.È.2
Villion, M.3
Romero, D.A.4
Barrangou, R.5
Boyaval, P.6
-
12
-
-
77957935381
-
CRISPR/Cas system and its role in phage-bacteria interactions
-
PMID:20528693
-
Deveau H, Garneau JE, Moineau S. CRISPR/Cas system and its role in phage-bacteria interactions. Annu Rev Microbiol 2010; 64:475-93; PMID:20528693; http://dx.doi.org/10.1146/annurev.micro.112408.134123.
-
(2010)
Annu Rev Microbiol
, vol.64
, pp. 475-493
-
-
Deveau, H.1
Garneau, J.E.2
Moineau, S.3
-
13
-
-
38949123143
-
Phage response to CRISPR-encoded resistance in Streptococcus thermophilus
-
PMID:18065545
-
Deveau H, Barrangou R, Garneau JE, Labonté J, Fremaux C, Boyaval P, et al. Phage response to CRISPR-encoded resistance in Streptococcus thermophilus. J Bacteriol 2008; 190:1390-400; PMID:18065545; http://dx.doi.org/10.1128/JB.01412-07.
-
(2008)
J Bacteriol
, vol.190
, pp. 1390-1400
-
-
Deveau, H.1
Barrangou, R.2
Garneau, J.E.3
Labonté, J.4
Fremaux, C.5
Boyaval, P.6
-
14
-
-
64049118040
-
Short motif sequences determine the targets of the prokaryotic CRISPR defence system
-
PMID:19246744
-
Mojica FJ, Díez-Villaseñor C, García-Martínez J, Almendros C. Short motif sequences determine the targets of the prokaryotic CRISPR defence system. Microbiology 2009; 155:733-40; PMID:19246744; http://dx.doi.org/10.1099/mic.0.023960-0.
-
(2009)
Microbiology
, vol.155
, pp. 733-740
-
-
Mojica, F.J.1
Díez-Villaseñor, C.2
García-Martínez, J.3
Almendros, C.4
-
15
-
-
49649114086
-
Small CRISPR RNAs guide antiviral defense in prokaryotes
-
PMID:18703739
-
Brouns SJ, Jore MM, Lundgren M, Westra ER, Slijkhuis RJ, Snijders AP, et al. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science 2008; 321:960-4; PMID:18703739; http://dx.doi.org/10.1126/science.1159689.
-
(2008)
Science
, vol.321
, pp. 960-964
-
-
Brouns, S.J.1
Jore, M.M.2
Lundgren, M.3
Westra, E.R.4
Slijkhuis, R.J.5
Snijders, A.P.6
-
16
-
-
77956628107
-
Transcription, processing and function of CRISPR cassettes in Escherichia coli
-
PMID:20624226
-
Pougach K, Semenova E, Bogdanova E, Datsenko KA, Djordjevic M, Wanner BL, et al. Transcription, processing and function of CRISPR cassettes in Escherichia coli. Mol Microbiol 2010; 77:1367-79; PMID:20624226; http://dx.doi.org/10.1111/j.1365-2958.2010.07265.x.
-
(2010)
Mol Microbiol
, vol.77
, pp. 1367-1379
-
-
Pougach, K.1
Semenova, E.2
Bogdanova, E.3
Datsenko, K.A.4
Djordjevic, M.5
Wanner, B.L.6
-
17
-
-
79955574254
-
Structural basis for CRISPR RNA-guided DNA recognition by Cascade
-
PMID:21460843
-
Jore MM, Lundgren M, van Duijn E, Bultema JB, Westra ER, Waghmare SP, et al. Structural basis for CRISPR RNA-guided DNA recognition by Cascade. Nat Struct Mol Biol 2011; 18:529-36; PMID:21460843; http://dx.doi.org/10.1038/nsmb. 2019.
-
(2011)
Nat Struct Mol Biol
, vol.18
, pp. 529-536
-
-
Jore, M.M.1
Lundgren, M.2
Van Duijn, E.3
Bultema, J.B.4
Westra, E.R.5
Waghmare, S.P.6
-
18
-
-
80053169737
-
Structures of the RNA-guided surveillance complex from a bacterial immune system
-
PMID:21938068
-
Wiedenheft B, Lander GC, Zhou K, Jore MM, Brouns SJ, van der Oost J, et al. Structures of the RNA-guided surveillance complex from a bacterial immune system. Nature 2011; 477:486-9; PMID:21938068; http://dx.doi.org/10.1038/ nature10402.
-
(2011)
Nature
, vol.477
, pp. 486-489
-
-
Wiedenheft, B.1
Lander, G.C.2
Zhou, K.3
Jore, M.M.4
Brouns, S.J.5
Van Der Oost, J.6
-
19
-
-
79959963663
-
Interference by clustered regularly interspaced short palindromic repeat (CRISPR) RNA is governed by a seed sequence
-
PMID:21646539
-
Semenova E, Jore MM, Datsenko KA, Semenova A, Westra ER, Wanner B, et al. Interference by clustered regularly interspaced short palindromic repeat (CRISPR) RNA is governed by a seed sequence. Proc Natl Acad Sci USA 2011; 108:10098-103; PMID:21646539; http://dx.doi.org/10.1073/pnas.1104144108.
-
(2011)
Proc Natl Acad Sci USA
, vol.108
, pp. 10098-10103
-
-
Semenova, E.1
Jore, M.M.2
Datsenko, K.A.3
Semenova, A.4
Westra, E.R.5
Wanner, B.6
-
20
-
-
84861996069
-
CRISPR immunity relies on the consecutive binding and degradation of negatively supercoiled invader DNA by Cascade and Cas3
-
PMID:22521689
-
Westra ER, van Erp PB, Künne T, Wong SP, Staals RH, Seegers CL, et al. CRISPR immunity relies on the consecutive binding and degradation of negatively supercoiled invader DNA by Cascade and Cas3. Mol Cell 2012; 46:595-605; PMID:22521689; http://dx.doi.org/10.1016/j.molcel.2012.03.018.
-
(2012)
Mol Cell
, vol.46
, pp. 595-605
-
-
Westra, E.R.1
Van Erp, P.B.2
Künne, T.3
Wong, S.P.4
Staals, R.H.5
Seegers, C.L.6
-
21
-
-
79953779608
-
Cas3 is a single-stranded DNA nuclease and ATP-dependent helicase in the CRISPR/ Cas immune system
-
PMID:21343909
-
Sinkunas T, Gasiunas G, Fremaux C, Barrangou R, Horvath P, Siksnys V. Cas3 is a single-stranded DNA nuclease and ATP-dependent helicase in the CRISPR/ Cas immune system. EMBO J 2011; 30:1335-42; PMID:21343909; http://dx.doi.org/ 10.1038/emboj.2011.41.
-
(2011)
EMBO J
, vol.30
, pp. 1335-1342
-
-
Sinkunas, T.1
Gasiunas, G.2
Fremaux, C.3
Barrangou, R.4
Horvath, P.5
Siksnys, V.6
-
22
-
-
38949214103
-
Diversity, activity, and evolution of CRISPR loci in Streptococcus thermophilus
-
PMID:18065539
-
Horvath P, Romero DA, CoÛté-Monvoisin AC, Richards M, Deveau H, Moineau S, et al. Diversity, activity, and evolution of CRISPR loci in Streptococcus thermophilus. J Bacteriol 2008; 190:1401-12; PMID:18065539; http://dx.doi.org/10.1128/JB.01415-07.
-
(2008)
J Bacteriol
, vol.190
, pp. 1401-1412
-
-
Horvath, P.1
Romero, D.A.2
CoÛté-Monvoisin, A.C.3
Richards, M.4
Deveau, H.5
Moineau, S.6
-
23
-
-
77949398275
-
Identification and characterization of E. coli CRISPR-cas promoters and their silencing by H-NS
-
PMID:20132443
-
Pul U, Wurm R, Arslan Z, Geissen R, Hofmann N, Wagner R. Identification and characterization of E. coli CRISPR-cas promoters and their silencing by H-NS. Mol Microbiol 2010; 75:1495-512; PMID:20132443; http://dx.doi.org/10.1111/ j.1365-2958.2010.07073.x.
-
(2010)
Mol Microbiol
, vol.75
, pp. 1495-1512
-
-
Pul, U.1
Wurm, R.2
Arslan, Z.3
Geissen, R.4
Hofmann, N.5
Wagner, R.6
-
24
-
-
0001641514
-
Mutations of Bacteria from Virus Sensitivity to Virus Resistance
-
PMID:17247100
-
Luria SE, Delbrück M. Mutations of Bacteria from Virus Sensitivity to Virus Resistance. Genetics 1943; 28:491-511; PMID:17247100.
-
(1943)
Genetics
, vol.28
, pp. 491-511
-
-
Luria, S.E.1
Delbrück, M.2
-
25
-
-
84864864464
-
Molecular memory of prior infections activates the CRISPR/Cas adaptive bacterial immunity system
-
PMID:22781758
-
Datsenko KA, Pougach K, Tikhonov A, Wanner BL, Severinov K, Semenova E. Molecular memory of prior infections activates the CRISPR/Cas adaptive bacterial immunity system. Nat Commun 2012; 3:945; PMID:22781758; http://dx.doi.org/10. 1038/ncomms1937.
-
(2012)
Nat Commun
, vol.3
, pp. 945
-
-
Datsenko, K.A.1
Pougach, K.2
Tikhonov, A.3
Wanner, B.L.4
Severinov, K.5
Semenova, E.6
-
26
-
-
84860433123
-
CRISPR interference directs strand specific spacer acquisition
-
PMID:22558257
-
Swarts DC, Mosterd C, van Passel MW, Brouns SJ. CRISPR interference directs strand specific spacer acquisition. PLoS One 2012; 7:e35888; PMID:22558257; http://dx.doi.org/10.1371/journal.pone.0035888.
-
(2012)
PLoS One
, vol.7
-
-
Swarts, D.C.1
Mosterd, C.2
Van Passel, M.W.3
Brouns, S.J.4
-
27
-
-
84861639567
-
Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli
-
PMID:22402487
-
Yosef I, Goren MG, Qimron U. Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli. Nucleic Acids Res 2012; 40:5569-76; PMID:22402487; http://dx.doi.org/10.1093/nar/gks216.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 5569-5576
-
-
Yosef, I.1
Goren, M.G.2
Qimron, U.3
-
29
-
-
84866313681
-
Experimental definition of a clustered regularly interspaced short palindromic duplicon in Escherichia coli
-
PMID:22771574
-
Goren MG, Yosef I, Auster O, Qimron U. Experimental definition of a clustered regularly interspaced short palindromic duplicon in Escherichia coli. J Mol Biol 2012; 423:14-6; PMID:22771574; http://dx.doi.org/10.1016/j.jmb.2012. 06.037.
-
(2012)
J Mol Biol
, vol.423
, pp. 14-16
-
-
Goren, M.G.1
Yosef, I.2
Auster, O.3
Qimron, U.4
-
30
-
-
84873571066
-
In vitro reconstitution of Cascade-mediated CRISPR immunity in Streptococcus thermophilus
-
PMID:23334296
-
Sinkunas T, Gasiunas G, Waghmare SP, Dickman MJ, Barrangou R, Horvath P, et al. In vitro reconstitution of Cascade-mediated CRISPR immunity in Streptococcus thermophilus. EMBO J 2013; 32:385-94; PMID:23334296; http://dx.doi.org/10.1038/emboj.2012.352.
-
(2013)
EMBO J
, vol.32
, pp. 385-394
-
-
Sinkunas, T.1
Gasiunas, G.2
Waghmare, S.P.3
Dickman, M.J.4
Barrangou, R.5
Horvath, P.6
-
31
-
-
0030839806
-
An efficient statistic to detect over- and under-represented words in DNA sequences
-
PMID:9228617
-
Schbath S. An efficient statistic to detect over- and under-represented words in DNA sequences. J Comput Biol 1997; 4:189-92; PMID:9228617; http://dx.doi.org/10.1089/cmb.1997.4.189.
-
(1997)
J Comput Biol
, vol.4
, pp. 189-192
-
-
Schbath, S.1
-
32
-
-
0032526323
-
Oligonucleotide bias in Bacillus subtilis: General trends and taxonomic comparisons
-
PMID:9611243
-
Rocha EP, Viari A, Danchin A. Oligonucleotide bias in Bacillus subtilis: general trends and taxonomic comparisons. Nucleic Acids Res 1998; 26:2971-80; PMID:9611243; http://dx.doi.org/10.1093/nar/26.12.2971.
-
(1998)
Nucleic Acids Res
, vol.26
, pp. 2971-2980
-
-
Rocha, E.P.1
Viari, A.2
Danchin, A.3
-
33
-
-
0028028028
-
Computational DNA sequence analysis
-
PMID:7826021
-
Karlin S, Cardon LR. Computational DNA sequence analysis. Annu Rev Microbiol 1994; 48:619-54; PMID:7826021; http://dx.doi.org/10.1146/annurev.mi. 48.100194.003155.
-
(1994)
Annu Rev Microbiol
, vol.48
, pp. 619-654
-
-
Karlin, S.1
Cardon, L.R.2
-
34
-
-
67149084593
-
Analysis of CRISPR system function in plant pathogen Xanthomonas oryzae
-
PMID:19459963
-
Semenova E, Nagornykh M, Pyatnitskiy M, Artamonova II, Severinov K. Analysis of CRISPR system function in plant pathogen Xanthomonas oryzae. FEMS Microbiol Lett 2009; 296:110-6; PMID:19459963; http://dx.doi.org/10.1111/j.1574- 6968.2009.01626.x.
-
(2009)
FEMS Microbiol Lett
, vol.296
, pp. 110-116
-
-
Semenova, E.1
Nagornykh, M.2
Pyatnitskiy, M.3
Artamonova, I.I.4
Severinov, K.5
-
35
-
-
84873129118
-
Phage mutations in response to CRISPR diversification in a bacterial population
-
PMID:23057534
-
Sun CL, Barrangou R, Thomas BC, Horvath P, Fremaux C, Banfield JF. Phage mutations in response to CRISPR diversification in a bacterial population. Environ Microbiol 2013; 15:463-70; PMID:23057534; http://dx.doi.org/10.1111/j. 1462-2920.2012.02879.x.
-
(2013)
Environ Microbiol
, vol.15
, pp. 463-470
-
-
Sun, C.L.1
Barrangou, R.2
Thomas, B.C.3
Horvath, P.4
Fremaux, C.5
Banfield, J.F.6
-
36
-
-
84874619358
-
Strong bias in the bacterial CRISPR elements that confer immunity to phage
-
PMID:23385575
-
Paez-Espino D, Morovic W, Sun CL, Thomas BC, Ueda K, Stahl B, et al. Strong bias in the bacterial CRISPR elements that confer immunity to phage. Nat Commun 2013; 4:1430; PMID:23385575; http://dx.doi.org/10.1038/ncomms2440.
-
(2013)
Nat Commun
, vol.4
, pp. 1430
-
-
Paez-Espino, D.1
Morovic, W.2
Sun, C.L.3
Thomas, B.C.4
Ueda, K.5
Stahl, B.6
-
37
-
-
84870357797
-
Antibiotic resistance plasmids spread among natural isolates of Escherichia coli in spite of CRISPR elements
-
PMID:23059972
-
Touchon M, Charpentier S, Pognard D, Picard B, Arlet G, Rocha EP, et al. Antibiotic resistance plasmids spread among natural isolates of Escherichia coli in spite of CRISPR elements. Microbiology 2012; 158:2997-3004; PMID:23059972; http://dx.doi.org/10.1099/mic.0.060814-0.
-
(2012)
Microbiology
, vol.158
, pp. 2997-3004
-
-
Touchon, M.1
Charpentier, S.2
Pognard, D.3
Picard, B.4
Arlet, G.5
Rocha, E.P.6
-
38
-
-
70349866687
-
ShortRead: A bioconductor package for input, quality assessment and exploration of high-throughput sequence data
-
PMID:19654119
-
Morgan M, Anders S, Lawrence M, Aboyoun P, Pagès H, Gentleman R. ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data. Bioinformatics 2009; 25:2607-8; PMID:19654119; http://dx.doi.org/10.1093/bioinformatics/btp450.
-
(2009)
Bioinformatics
, vol.25
, pp. 2607-2608
-
-
Morgan, M.1
Anders, S.2
Lawrence, M.3
Aboyoun, P.4
Pagès, H.5
Gentleman, R.6
-
39
-
-
84879462012
-
String objects representing biological sequences, and matching algorithms
-
Pages H, Aboyoun P, Gentleman R, DebRoy S. String objects representing biological sequences, and matching algorithms. Biostrings 2:11.
-
Biostrings
, vol.2
, pp. 11
-
-
Pages, H.1
Aboyoun, P.2
Gentleman, R.3
DebRoy, S.4
|