-
1
-
-
84991018148
-
Characterizing leader sequences of CRISPR loci
-
Alkhnbashi, O. S., Shah, S. A., Garrett, R. A., Saunders, S. J., Costa, F., and Backofen, R. (2016). Characterizing leader sequences of CRISPR loci. Bioinformatics 32, i576-i585. doi: 10.1093/bioinformatics/btw454
-
(2016)
Bioinformatics
, vol.32
, pp. i576-i585
-
-
Alkhnbashi, O.S.1
Shah, S.A.2
Garrett, R.A.3
Saunders, S.J.4
Costa, F.5
Backofen, R.6
-
2
-
-
84934992530
-
Characterisation of a multidrug-resistant Bacteroides fragilis isolate recovered from blood of a patient in Denmark using whole-genome sequencing
-
Ank, N., Sydenham, T. V., Iversen, L. H., Justesen, U. S., and Wang, M. (2015). Characterisation of a multidrug-resistant Bacteroides fragilis isolate recovered from blood of a patient in Denmark using whole-genome sequencing. Int. J. Antimicrob. Agents 46, 117-120. doi: 10.1016/j.ijantimicag.2015.02.024
-
(2015)
Int. J. Antimicrob. Agents
, vol.46
, pp. 117-120
-
-
Ank, N.1
Sydenham, T.V.2
Iversen, L.H.3
Justesen, U.S.4
Wang, M.5
-
3
-
-
40549120596
-
The RAST Server: rapid annotations using subsystems technology
-
Aziz, R., Bartels, D., Best, A., DeJongh, M., Disz, T., Edwards, R., et al. (2008). The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9:75. doi: 10.1186/1471-2164-9-75
-
(2008)
BMC Genomics
, vol.9
, pp. 75
-
-
Aziz, R.1
Bartels, D.2
Best, A.3
DeJongh, M.4
Disz, T.5
Edwards, R.6
-
4
-
-
78651083184
-
A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair
-
Babu, M., Beloglazova, N., Flick, R., Graham, C., Skarina, T., Nocek, B., et al. (2011). A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair. Mol. Microbiol. 79, 484-502. doi: 10.1111/j.1365-2958.2010.07465.x
-
(2011)
Mol. Microbiol
, vol.79
, pp. 484-502
-
-
Babu, M.1
Beloglazova, N.2
Flick, R.3
Graham, C.4
Skarina, T.5
Nocek, B.6
-
5
-
-
65549165914
-
What antimicrobial resistance has taught us about horizontal gene transfer
-
Barlow, M. (2009). What antimicrobial resistance has taught us about horizontal gene transfer. Methods Mol. Biol. 532, 397-411. doi: 10.1007/978-1-60327-853-9_23
-
(2009)
Methods Mol. Biol
, vol.532
, pp. 397-411
-
-
Barlow, M.1
-
6
-
-
84946558100
-
Diversity of CRISPR-Cas immune systems and molecular machines
-
Barrangou, R. (2015). Diversity of CRISPR-Cas immune systems and molecular machines. Genome Biol. 16, 247. doi: 10.1186/s13059-015-0816-9
-
(2015)
Genome Biol
, vol.16
, pp. 247
-
-
Barrangou, R.1
-
7
-
-
34047118522
-
CRISPR provides acquired resistance against viruses in prokaryotes
-
Barrangou, R., Fremaux, C., Deveau, H., Richards, M., Boyaval, P., Moineau, S., et al. (2007). CRISPR provides acquired resistance against viruses in prokaryotes. Science 315, 1709-1712. doi: 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
-
8
-
-
0034559920
-
Analysis of cepA and other Bacteroides fragilis genes reveals a unique promoter structure
-
Bayley, D. P., Rocha, E. R., and Smith, C. J. (2000). Analysis of cepA and other Bacteroides fragilis genes reveals a unique promoter structure. FEMS Microbiol. Lett. 193, 149-154. doi: 10.1111/j.1574-6968.2000.tb09417.x
-
(2000)
FEMS Microbiol. Lett
, vol.193
, pp. 149-154
-
-
Bayley, D.P.1
Rocha, E.R.2
Smith, C.J.3
-
9
-
-
84891797680
-
GenBank
-
Benson, D. A., Clark, K., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J., and Sayers, E. W. (2014). GenBank. Nucleic Acids Res. 42, D32-D37. doi: 10.1093/nar/gkt1030
-
(2014)
Nucleic Acids Res
, vol.42
, pp. D32-D37
-
-
Benson, D.A.1
Clark, K.2
Karsch-Mizrachi, I.3
Lipman, D.J.4
Ostell, J.5
Sayers, E.W.6
-
10
-
-
34447644810
-
CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats
-
Bland, C., Ramsey, T. L., Sabree, F., Lowe, M., Brown, K., Kyrpides, N. C., et al. (2007). CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics 8:209. doi: 10.1186/1471-2105-8-209
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 209
-
-
Bland, C.1
Ramsey, T.L.2
Sabree, F.3
Lowe, M.4
Brown, K.5
Kyrpides, N.C.6
-
11
-
-
48249085658
-
Large scale variation in Enterococcus faecalis illustrated by the genome analysis of strain OG1RF
-
Bourgogne, A., Garsin, D. A., Qin, X., Singh, K. V., Sillanpaa, J., Yerrapragada, S., et al. (2008). Large scale variation in Enterococcus faecalis illustrated by the genome analysis of strain OG1RF. Genome Biol. 9:R110. doi: 10.1186/gb-2008-9-7-r110
-
(2008)
Genome Biol
, vol.9
-
-
Bourgogne, A.1
Garsin, D.A.2
Qin, X.3
Singh, K.V.4
Sillanpaa, J.5
Yerrapragada, S.6
-
12
-
-
84957535039
-
Major bacterial lineages are essentially devoid of CRISPR-Cas viral defence systems
-
Burstein, D., Sun, C. L., Brown, C. T., Sharon, I., Anantharaman, K., Probst, A. J., et al. (2016). Major bacterial lineages are essentially devoid of CRISPR-Cas viral defence systems. Nat. Commun. 7:10613. doi: 10.1038/ncomms10613
-
(2016)
Nat. Commun
, vol.7
, pp. 10613
-
-
Burstein, D.1
Sun, C.L.2
Brown, C.T.3
Sharon, I.4
Anantharaman, K.5
Probst, A.J.6
-
13
-
-
70349785162
-
Horizontal gene transfer in the gut: is it a risk?
-
Capozzi, V., and Spano, G. (2009). Horizontal gene transfer in the gut: is it a risk? Food Res. Int. 42, 1501-1502. doi: 10.1016/j.foodres.2009.08.001
-
(2009)
Food Res. Int
, vol.42
, pp. 1501-1502
-
-
Capozzi, V.1
Spano, G.2
-
14
-
-
84903465255
-
The three major types of CRISPR-Cas systems function independently in CRISPR RNA biogenesis in Streptococcus thermophilus
-
Carte, J., Christopher, R. T., Smith, J. T., Olson, S., Barrangou, R., Moineau, S., et al. (2014). The three major types of CRISPR-Cas systems function independently in CRISPR RNA biogenesis in Streptococcus thermophilus. Mol. Microbiol. 93, 98-112. doi: 10.1111/mmi.12644
-
(2014)
Mol. Microbiol
, vol.93
, pp. 98-112
-
-
Carte, J.1
Christopher, R.T.2
Smith, J.T.3
Olson, S.4
Barrangou, R.5
Moineau, S.6
-
15
-
-
84979026021
-
Viruses infecting a freshwater filamentous Cyanobacterium (Nostoc sp.) encode a functional CRISPR array and a proteobacterial DNA polymerase B
-
Chénard, C., Wirth, J. F., and Suttle, C. A. (2016). Viruses infecting a freshwater filamentous Cyanobacterium (Nostoc sp.) encode a functional CRISPR array and a proteobacterial DNA polymerase B. MBio 7:e00667-16. doi: 10.1128/mBio.00667-16
-
(2016)
MBio
, vol.7
-
-
Chénard, C.1
Wirth, J.F.2
Suttle, C.A.3
-
16
-
-
84878211288
-
The tracrRNA and Cas9 families of type II CRISPR-Cas immunity systems
-
Chylinski, K., Le Rhun, A., and Charpentier, E. (2013). The tracrRNA and Cas9 families of type II CRISPR-Cas immunity systems. RNA Biol. 10, 726-737. doi: 10.4161/rna.24321
-
(2013)
RNA Biol
, vol.10
, pp. 726-737
-
-
Chylinski, K.1
Le Rhun, A.2
Charpentier, E.3
-
17
-
-
84902095351
-
Classification and evolution of type II CRISPR-Cas systems
-
Chylinski, K., Makarova, K. S., Charpentier, E., and Koonin, E. V. (2014). Classification and evolution of type II CRISPR-Cas systems. Nucleic Acids Res. 42, 6091-6105. doi: 10.1093/nar/gku241
-
(2014)
Nucleic Acids Res
, vol.42
, pp. 6091-6105
-
-
Chylinski, K.1
Makarova, K.S.2
Charpentier, E.3
Koonin, E.V.4
-
18
-
-
33845428404
-
Kinase activity of overexpressed HipA is required for growth arrest and multidrug tolerance in Escherichia coli
-
Correia, F. F., D'Onofrio, A., Rejtar, T., Li, L., Karger, B. L., Makarova, K., et al. (2006). Kinase activity of overexpressed HipA is required for growth arrest and multidrug tolerance in Escherichia coli. J. Bacteriol. 188, 8360-8367. doi: 10.1128/JB.01237-06
-
(2006)
J. Bacteriol
, vol.188
, pp. 8360-8367
-
-
Correia, F.F.1
D'Onofrio, A.2
Rejtar, T.3
Li, L.4
Karger, B.L.5
Makarova, K.6
-
19
-
-
84903978009
-
Evidence of extensive DNA transfer between Bacteroidales species within the human gut
-
Coyne, M. J., Zitomersky, N. L., McGuire, A. M., Earl, A. M., and Comstock, L. E. (2014). Evidence of extensive DNA transfer between Bacteroidales species within the human gut. MBio 5, e01305-e01314. doi: 10.1128/mBio.01305-14
-
(2014)
MBio
, vol.5
-
-
Coyne, M.J.1
Zitomersky, N.L.2
McGuire, A.M.3
Earl, A.M.4
Comstock, L.E.5
-
20
-
-
2142738304
-
WebLogo: a sequence logo generator
-
Crooks, G. E., Hon, G., Chandonia, J. M., and Brenner, S. E. (2004). WebLogo: a sequence logo generator. Genome Res. 14, 1188-1190. doi: 10.1101/gr.849004
-
(2004)
Genome Res
, vol.14
, pp. 1188-1190
-
-
Crooks, G.E.1
Hon, G.2
Chandonia, J.M.3
Brenner, S.E.4
-
21
-
-
1842431869
-
Role for cystic fibrosis transmembrane conductance regulator protein in a glutathione response to bronchopulmonary pseudomonas infection
-
Day, B. J., van Heeckeren, A. M., Min, E., and Velsor, L. W. (2004). Role for cystic fibrosis transmembrane conductance regulator protein in a glutathione response to bronchopulmonary pseudomonas infection. Infect. Immun. 72, 2045-2051. doi: 10.1128/IAI.72.4.2045-2051.2004
-
(2004)
Infect. Immun
, vol.72
, pp. 2045-2051
-
-
Day, B.J.1
van Heeckeren, A.M.2
Min, E.3
Velsor, L.W.4
-
22
-
-
23644448438
-
RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble
-
Ding, Y., Chan, C. Y., and Lawrence, C. E. (2005). RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble. RNA 11, 1157-1166. doi: 10.1261/rna.2500605
-
(2005)
RNA
, vol.11
, pp. 1157-1166
-
-
Ding, Y.1
Chan, C.Y.2
Lawrence, C.E.3
-
23
-
-
33744941078
-
The repetitive DNA elements called CRISPRs and their associated genes: evidence of horizontal transfer among prokaryotes
-
Godde, J. S., and Bickerton, A. (2006). The repetitive DNA elements called CRISPRs and their associated genes: evidence of horizontal transfer among prokaryotes. J. Mol. Evol. 62, 718-729. doi: 10.1007/s00239-005-0223-z
-
(2006)
J. Mol. Evol
, vol.62
, pp. 718-729
-
-
Godde, J.S.1
Bickerton, A.2
-
24
-
-
34547579396
-
CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats
-
Grissa, I., Vergnaud, G., and Pourcel, C. (2007). CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res. 35, W52-W57. doi: 10.1093/nar/gkm360
-
(2007)
Nucleic Acids Res
, vol.35
, pp. W52-W57
-
-
Grissa, I.1
Vergnaud, G.2
Pourcel, C.3
-
25
-
-
34248400310
-
A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes
-
Haft, D. H., Selengut, J., Mongodin, E. F., and Nelson, K. E. (2005). A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. PLoS Comput. Biol. 1:e60. doi: 10.1371/journal.pcbi.0010060
-
(2005)
PLoS Comput. Biol
, vol.1
-
-
Haft, D.H.1
Selengut, J.2
Mongodin, E.F.3
Nelson, K.E.4
-
26
-
-
71749099862
-
phyloXML: XML for evolutionary biology and comparative genomics
-
Han, M. V., and Zmasek, C. M. (2009). phyloXML: XML for evolutionary biology and comparative genomics. BMC Bioinformatics 10:356. doi: 10.1186/1471-2105-10-356
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 356
-
-
Han, M.V.1
Zmasek, C.M.2
-
27
-
-
84862505694
-
Regulation of the Escherichia coli HipBA toxin-antitoxin system by proteolysis
-
Hansen, S., Vulic, M., Min, J., Yen, T. J., Schumacher, M. A., Brennan, R. G., et al. (2012). Regulation of the Escherichia coli HipBA toxin-antitoxin system by proteolysis. PLoS ONE 7:e39185. doi: 10.1371/annotation/e608601c-eadd-4c11-adb2-7b605aba9c44
-
(2012)
PLoS ONE
, vol.7
-
-
Hansen, S.1
Vulic, M.2
Min, J.3
Yen, T.J.4
Schumacher, M.A.5
Brennan, R.G.6
-
28
-
-
84924705939
-
Cas9 specifies functional viral targets during CRISPR-Cas adaptation
-
Heler, R., Samai, P., Modell, J. W., Weiner, C., Goldberg, G. W., Bikard, D., et al. (2015). Cas9 specifies functional viral targets during CRISPR-Cas adaptation. Nature 519, 199-202. doi: 10.1038/nature14245
-
(2015)
Nature
, vol.519
, pp. 199-202
-
-
Heler, R.1
Samai, P.2
Modell, J.W.3
Weiner, C.4
Goldberg, G.W.5
Bikard, D.6
-
29
-
-
85035060317
-
Novel large-scale chromosomal transfer in Bacteroides fragilis contributes to its pan-genome and rapid environmental adaptation
-
Husain, F., Tang, K., Yaligara, V., Boente, R., Blakely, G., Patrick, S., et al. (2017). Novel large-scale chromosomal transfer in Bacteroides fragilis contributes to its pan-genome and rapid environmental adaptation. Microb. Genom. 4:e000136. doi: 10.1099/mgen.0.000136
-
(2017)
Microb. Genom
, vol.4
-
-
Husain, F.1
Tang, K.2
Yaligara, V.3
Boente, R.4
Blakely, G.5
Patrick, S.6
-
30
-
-
84965035788
-
The Ellis Island effect: a novel mobile element in a multi-drug resistant Bacteroides fragilis clinical isolate includes a mosaic of resistance genes from Gram-positive bacteria
-
Husain, F., Veeranagouda, Y., Boente, R., Tang, K., Mulato, G., and Wexler, H. M. (2014). The Ellis Island effect: a novel mobile element in a multi-drug resistant Bacteroides fragilis clinical isolate includes a mosaic of resistance genes from Gram-positive bacteria. Mob. Genet. Elem. 4, E29801-E29812. doi: 10.4161/mge.29801
-
(2014)
Mob. Genet. Elem
, vol.4
, pp. E29801-E29812
-
-
Husain, F.1
Veeranagouda, Y.2
Boente, R.3
Tang, K.4
Mulato, G.5
Wexler, H.M.6
-
31
-
-
84881585216
-
Structure and genetic content of the megaplasmids of neurotoxigenic Clostridium butyricum type E strains from Italy
-
Iacobino, A., Scalfaro, C., and Franciosa, G. (2013). Structure and genetic content of the megaplasmids of neurotoxigenic Clostridium butyricum type E strains from Italy. PLoS ONE 8:e71324. doi: 10.1371/journal.pone.0071324
-
(2013)
PLoS ONE
, vol.8
-
-
Iacobino, A.1
Scalfaro, C.2
Franciosa, G.3
-
32
-
-
84958125062
-
Degradation of phage transcripts by CRISPR-associated RNases enables type III CRISPR-Cas immunity
-
Jiang, W., Samai, P., and Marraffini, L. A. (2016). Degradation of phage transcripts by CRISPR-associated RNases enables type III CRISPR-Cas immunity. Cell 164, 710-721. doi: 10.1016/j.cell.2015.12.053
-
(2016)
Cell
, vol.164
, pp. 710-721
-
-
Jiang, W.1
Samai, P.2
Marraffini, L.A.3
-
33
-
-
79955574254
-
Structural basis for CRISPR RNA-guided DNA recognition by Cascade
-
Jore, M. M., Lundgren, M., van Duijn, E., Bultema, J. B., Westra, E. R., Waghmare, S. P., et al. (2011). Structural basis for CRISPR RNA-guided DNA recognition by Cascade. Nat. Struct. Mol. Biol. 18, 529-536. doi: 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
-
34
-
-
84883337744
-
Multidrug-resistant Bacteroides fragilis-Seattle, Washington, 2013
-
Kalapila, A., Pergam, S., Pottinger, P., Butler-Wu, S., Whimbey, E., and Duchin, J. (2013). Multidrug-resistant Bacteroides fragilis-Seattle, Washington, 2013. MMWR Morb. Mortal. Wkly. Rep. 62, 694-696
-
(2013)
MMWR Morb. Mortal. Wkly. Rep
, vol.62
, pp. 694-696
-
-
Kalapila, A.1
Pergam, S.2
Pottinger, P.3
Butler-Wu, S.4
Whimbey, E.5
Duchin, J.6
-
35
-
-
84991929179
-
Functional characterization of IgA-targeted bacterial taxa from undernourished Malawian children that produce diet-dependent enteropathy
-
Kau, A. L., Planer, J. D., Liu, J., Rao, S., Yatsunenko, T., Trehan, I., et al. (2015). Functional characterization of IgA-targeted bacterial taxa from undernourished Malawian children that produce diet-dependent enteropathy. Sci. Transl. Med. 7:276ra224. doi: 10.1126/scitranslmed.aaa4877
-
(2015)
Sci. Transl. Med
, vol.7
-
-
Kau, A.L.1
Planer, J.D.2
Liu, J.3
Rao, S.4
Yatsunenko, T.5
Trehan, I.6
-
36
-
-
35748974534
-
Evolutionary conservation of sequence and secondary structures in CRISPR repeats
-
Kunin, V., Sorek, R., and Hugenholtz, P. (2007). Evolutionary conservation of sequence and secondary structures in CRISPR repeats. Genome Biol. 8:R61. doi: 10.1186/gb-2007-8-4-r61
-
(2007)
Genome Biol
, vol.8
-
-
Kunin, V.1
Sorek, R.2
Hugenholtz, P.3
-
37
-
-
38449088143
-
Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes
-
Kurokawa, K., Itoh, T., Kuwahara, T., Oshima, K., Toh, H., Toyoda, A., et al. (2007). Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res. 14, 169-181. doi: 10.1093/dnares/dsm018
-
(2007)
DNA Res
, vol.14
, pp. 169-181
-
-
Kurokawa, K.1
Itoh, T.2
Kuwahara, T.3
Oshima, K.4
Toh, H.5
Toyoda, A.6
-
38
-
-
6944225464
-
Genomic analysis of Bacteroides fragilis reveals extensive DNA inversions regulating cell surface adaptation
-
Kuwahara, T., Yamashita, A., Hirakawa, H., Nakayama, H., Toh, H., Okada, N., et al. (2004). Genomic analysis of Bacteroides fragilis reveals extensive DNA inversions regulating cell surface adaptation. Proc. Natl. Acad. Sci. U.S.A. 101, 14919-14924. doi: 10.1073/pnas.0404172101
-
(2004)
Proc. Natl. Acad. Sci. U.S.A
, vol.101
, pp. 14919-14924
-
-
Kuwahara, T.1
Yamashita, A.2
Hirakawa, H.3
Nakayama, H.4
Toh, H.5
Okada, N.6
-
39
-
-
84884965371
-
CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems
-
Lange, S. J., Alkhnbashi, O. S., Rose, D., Will, S., and Backofen, R. (2013). CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems. Nucleic Acids Res. 41, 8034-8044. doi: 10.1093/nar/gkt606
-
(2013)
Nucleic Acids Res
, vol.41
, pp. 8034-8044
-
-
Lange, S.J.1
Alkhnbashi, O.S.2
Rose, D.3
Will, S.4
Backofen, R.5
-
40
-
-
84896279030
-
The role of CRISPR-Cas systems in virulence of pathogenic bacteria
-
Louwen, R., Staals, R. H., Endtz, H. P., van Baarlen, P., and van der Oost, J. (2014). The role of CRISPR-Cas systems in virulence of pathogenic bacteria. Microbiol. Mol. Biol. Rev. 78, 74-88. doi: 10.1128/MMBR.00039-13
-
(2014)
Microbiol. Mol. Biol. Rev
, vol.78
, pp. 74-88
-
-
Louwen, R.1
Staals, R.H.2
Endtz, H.P.3
van Baarlen, P.4
van der Oost, J.5
-
41
-
-
34248374277
-
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
-
Makarova, K. S., Grishin, N. V., Shabalina, S. A., Wolf, Y. I., and Koonin, E. V. (2006). 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 1:7. doi: 10.1186/1745-6150-1-7
-
(2006)
Biol. Direct
, vol.1
, pp. 7
-
-
Makarova, K.S.1
Grishin, N.V.2
Shabalina, S.A.3
Wolf, Y.I.4
Koonin, E.V.5
-
42
-
-
79956157571
-
Evolution and classification of the CRISPR-Cas systems
-
Makarova, K. S., Haft, D. H., Barrangou, R., Brouns, S. J., Charpentier, E., Horvath, P., et al. (2011). Evolution and classification of the CRISPR-Cas systems. Nat. Rev. Microbiol. 9, 467-477. doi: 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
-
43
-
-
84944449180
-
An updated evolutionary classification of CRISPR-Cas systems
-
Makarova, K. S., Wolf, Y. I., Alkhnbashi, O. S., Costa, F., Shah, S. A., Saunders, S. J., et al. (2015). An updated evolutionary classification of CRISPR-Cas systems. Nat. Rev. Microbiol. 13, 722-736. doi: 10.1038/nrmicro3569
-
(2015)
Nat. Rev. Microbiol
, vol.13
, pp. 722-736
-
-
Makarova, K.S.1
Wolf, Y.I.2
Alkhnbashi, O.S.3
Costa, F.4
Shah, S.A.5
Saunders, S.J.6
-
44
-
-
84868378578
-
Propionibacterium acnes bacteriophages display limited genetic diversity and broad killing activity against bacterial skin isolates
-
Marinelli, L. J., Fitz-Gibbon, S., Hayes, C., Bowman, C., Inkeles, M., Loncaric, A., et al. (2012). Propionibacterium acnes bacteriophages display limited genetic diversity and broad killing activity against bacterial skin isolates. MBio 3:12. doi: 10.1128/mBio.00279-12
-
(2012)
MBio
, vol.3
, pp. 12
-
-
Marinelli, L.J.1
Fitz-Gibbon, S.2
Hayes, C.3
Bowman, C.4
Inkeles, M.5
Loncaric, A.6
-
45
-
-
84861898310
-
IMG: the Integrated Microbial Genomes database and comparative analysis system
-
Markowitz, V., Chen, I. M., Palaniappan, K., Chu, K., Szeto, E., Grechkin, Y., et al. (2012). IMG: the Integrated Microbial Genomes database and comparative analysis system. Nucleic Acids Res. 40, 22. doi: 10.1093/nar/gkr1044
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 22
-
-
Markowitz, V.1
Chen, I.M.2
Palaniappan, K.3
Chu, K.4
Szeto, E.5
Grechkin, Y.6
-
46
-
-
84943160849
-
CRISPR-Cas immunity in prokaryotes
-
Marraffini, L. A. (2015). CRISPR-Cas immunity in prokaryotes. Nature 526, 55-61. doi: 10.1038/nature15386
-
(2015)
Nature
, vol.526
, pp. 55-61
-
-
Marraffini, L.A.1
-
47
-
-
84938323503
-
Programming a human commensal bacterium, bacteroides thetaiotaomicron, to sense and respond to stimuli in the murine gut microbiota
-
Mimee, M., Tucker, A. C., Voigt, C. A., and Lu, T. K. (2015). Programming a human commensal bacterium, bacteroides thetaiotaomicron, to sense and respond to stimuli in the murine gut microbiota. Cell Syst. 1, 62-71. doi: 10.1016/j.cels.2015.06.001
-
(2015)
Cell Syst
, vol.1
, pp. 62-71
-
-
Mimee, M.1
Tucker, A.C.2
Voigt, C.A.3
Lu, T.K.4
-
48
-
-
84977839343
-
Next generation prokaryotic engineering: the CRISPR-Cas toolkit
-
Mougiakos, I., Bosma, E. F., de Vos, W. M., van Kranenburg, R., and van der Oost, J. (2016). Next generation prokaryotic engineering: the CRISPR-Cas toolkit. Trends Biotechnol. 34, 575-587. doi: 10.1016/j.tibtech.2016.02.004
-
(2016)
Trends Biotechnol
, vol.34
, pp. 575-587
-
-
Mougiakos, I.1
Bosma, E.F.2
de Vos, W.M.3
van Kranenburg, R.4
van der Oost, J.5
-
49
-
-
85008452793
-
Complete genome sequence of an enterotoxigenic Bacteroides fragilis clinical isolate
-
Nikitina, A. S., Kharlampieva, D. D., Babenko, V. V., Shirokov, D. A., Vakhitova, M. T., Manolov, A. I., et al. (2015). Complete genome sequence of an enterotoxigenic Bacteroides fragilis clinical isolate. Genome Announc. 3:e00450-15. doi: 10.1128/genomeA.00450-15
-
(2015)
Genome Announc
, vol.3
-
-
Nikitina, A.S.1
Kharlampieva, D.D.2
Babenko, V.V.3
Shirokov, D.A.4
Vakhitova, M.T.5
Manolov, A.I.6
-
50
-
-
84924664059
-
Integrase-mediated spacer acquisition during CRISPR-Cas adaptive immunity
-
Nuñez, J. K., Lee, A. S., Engelman, A., and Doudna, J. A. (2015). Integrase-mediated spacer acquisition during CRISPR-Cas adaptive immunity. Nature 519, 193-198. doi: 10.1038/nature14237
-
(2015)
Nature
, vol.519
, pp. 193-198
-
-
Nuñez, J.K.1
Lee, A.S.2
Engelman, A.3
Doudna, J.A.4
-
51
-
-
79952168979
-
Multidrug-resistant enterococci lack CRISPR-cas
-
Palmer, K. L., and Gilmore, M. S. (2010). Multidrug-resistant enterococci lack CRISPR-cas. MBio 1:10. doi: 10.1128/mBio.00227-10
-
(2010)
MBio
, vol.1
, pp. 10
-
-
Palmer, K.L.1
Gilmore, M.S.2
-
52
-
-
78049492098
-
Twenty-eight divergent polysaccharide loci specifying within-and amongst-strain capsule diversity in three strains of Bacteroides fragilis
-
Patrick, S., Blakely, G. W., Houston, S., Moore, J., Abratt, V. R., Bertalan, M., et al. (2010). Twenty-eight divergent polysaccharide loci specifying within-and amongst-strain capsule diversity in three strains of Bacteroides fragilis. Microbiology 156(Pt 11), 3255-3269. doi: 10.1099/mic.0.042978-0
-
(2010)
Microbiology
, vol.156
, pp. 3255-3269
-
-
Patrick, S.1
Blakely, G.W.2
Houston, S.3
Moore, J.4
Abratt, V.R.5
Bertalan, M.6
-
53
-
-
84977072563
-
Genomic diversity of enterotoxigenic strains of Bacteroides fragilis
-
Pierce, J. V., and Bernstein, H. D. (2016). Genomic diversity of enterotoxigenic strains of Bacteroides fragilis. PLoS ONE 11:e0158171. doi: 10.1371/journal.pone.0158171
-
(2016)
PLoS ONE
, vol.11
-
-
Pierce, J.V.1
Bernstein, H.D.2
-
54
-
-
0018344383
-
Transfer of multiple antibiotic resistance between subspecies of Bacteroides fragilis
-
Privitera, G. F., Dublanchet, A. F., and Sebald, M. (1979). Transfer of multiple antibiotic resistance between subspecies of Bacteroides fragilis. J. Infect. Dis. 139, 97-101. doi: 10.1093/infdis/139.1.97
-
(1979)
J. Infect. Dis
, vol.139
, pp. 97-101
-
-
Privitera, G.F.1
Dublanchet, A.F.2
Sebald, M.3
-
55
-
-
34547561708
-
BmeRABC5 is a multidrug efflux system that can confer metronidazole resistance in Bacteroides fragilis
-
Pumbwe, L., Chang, A., Smith, R. L., and Wexler, H. M. (2007a). BmeRABC5 is a multidrug efflux system that can confer metronidazole resistance in Bacteroides fragilis. Microb. Drug Resist. 13, 96-101. doi: 10.1089/mdr.2007.719
-
(2007)
Microb. Drug Resist
, vol.13
, pp. 96-101
-
-
Pumbwe, L.1
Chang, A.2
Smith, R.L.3
Wexler, H.M.4
-
56
-
-
33846299874
-
Genetic analysis of mechanisms of multidrug resistance in a clinical isolate of Bacteroides fragilis
-
Pumbwe, L., Wareham, D. W., Aduse-Opoku, J., Brazier, J. S., and Wexler, H. M. (2007b). Genetic analysis of mechanisms of multidrug resistance in a clinical isolate of Bacteroides fragilis. Clin. Microbiol. Infect. 13, 183-189. doi: 10.1111/j.1469-0691.2006.01620.x
-
(2007)
Clin. Microbiol. Infect
, vol.13
, pp. 183-189
-
-
Pumbwe, L.1
Wareham, D.W.2
Aduse-Opoku, J.3
Brazier, J.S.4
Wexler, H.M.5
-
57
-
-
84942079449
-
The CRISPR-Cas immune system: biology, mechanisms and applications
-
Rath, D., Amlinger, L., Rath, A., and Lundgren, M. (2015). The CRISPR-Cas immune system: biology, mechanisms and applications. Biochimie 117, 119-128. doi: 10.1016/j.biochi.2015.03.025
-
(2015)
Biochimie
, vol.117
, pp. 119-128
-
-
Rath, D.1
Amlinger, L.2
Rath, A.3
Lundgren, M.4
-
58
-
-
84991528128
-
A single chromosome assembly of Bacteroides fragilis strain BE1 from Illumina and MinION nanopore sequencing data
-
Risse, J., Thomson, M., Patrick, S., Blakely, G., Koutsovoulos, G., Blaxter, M., et al. (2015). A single chromosome assembly of Bacteroides fragilis strain BE1 from Illumina and MinION nanopore sequencing data. Gigascience 4, 60. doi: 10.1186/s13742-015-0101-6
-
(2015)
Gigascience
, vol.4
, pp. 60
-
-
Risse, J.1
Thomson, M.2
Patrick, S.3
Blakely, G.4
Koutsovoulos, G.5
Blaxter, M.6
-
59
-
-
84938794949
-
A year of infection in the intensive care unit: prospective whole genome sequencing of bacterial clinical isolates reveals cryptic transmissions and novel microbiota
-
Roach, D. J., Burton, J. J., Lee, C., Stackhouse, B., Butler-Wu, S. M., Cookson, B. T., et al. (2015). A year of infection in the intensive care unit: prospective whole genome sequencing of bacterial clinical isolates reveals cryptic transmissions and novel microbiota. PLoS Genet. 11:e1005413. doi: 10.1371/journal.pgen.1005413
-
(2015)
PLoS Genet
, vol.11
-
-
Roach, D.J.1
Burton, J.J.2
Lee, C.3
Stackhouse, B.4
Butler-Wu, S.M.5
Cookson, B.T.6
-
60
-
-
84919622362
-
Characterization of a multidrug-resistant, novel bacteroides genomospecies
-
Salipante, S. J., Kalapila, A., Pottinger, P. S., Hoogestraat, D. R., Cummings, L., Duchin, J. S., et al. (2015). Characterization of a multidrug-resistant, novel bacteroides genomospecies. Emerg. Infect. Dis. 21, 95-98. doi: 10.3201/eid2101.140662
-
(2015)
Emerg. Infect. Dis
, vol.21
, pp. 95-98
-
-
Salipante, S.J.1
Kalapila, A.2
Pottinger, P.S.3
Hoogestraat, D.R.4
Cummings, L.5
Duchin, J.S.6
-
61
-
-
4444382949
-
Human intestinal bacteria as reservoirs for antibiotic resistance genes
-
Salyers, A. A., Gupta, A., and Wang, Y. (2004). Human intestinal bacteria as reservoirs for antibiotic resistance genes. Trends Microbiol. 12, 412-416. doi: 10.1016/j.tim.2004.07.004
-
(2004)
Trends Microbiol
, vol.12
, pp. 412-416
-
-
Salyers, A.A.1
Gupta, A.2
Wang, Y.3
-
62
-
-
84906541312
-
CRISPR-Cas systems: new players in gene regulation and bacterial physiology
-
Sampson, T., and Weiss, D. (2014). CRISPR-Cas systems: new players in gene regulation and bacterial physiology. Front. Cell. Infect. Microbiol. 4:37. doi: 10.3389/fcimb.2014.00037
-
(2014)
Front. Cell. Infect. Microbiol
, vol.4
, pp. 37
-
-
Sampson, T.1
Weiss, D.2
-
63
-
-
84900314611
-
CRISPR-Cas systems for editing, regulating and targeting genomes
-
Sander, J. D., and Joung, J. K. (2014). CRISPR-Cas systems for editing, regulating and targeting genomes. Nat. Biotechnol. 32, 347-355. doi: 10.1038/nbt.2842
-
(2014)
Nat. Biotechnol
, vol.32
, pp. 347-355
-
-
Sander, J.D.1
Joung, J.K.2
-
64
-
-
4644251288
-
Isolation of metronidazole-resistant Bacteroides fragilis carrying the nimA nitroreductase gene from a patient in Washington State
-
Schapiro, J. M., Gupta, R., Stefansson, E., Fang, F. C., and Limaye, A. P. (2004). Isolation of metronidazole-resistant Bacteroides fragilis carrying the nimA nitroreductase gene from a patient in Washington State. J. Clin. Microbiol. 42, 4127-4129. doi: 10.1128/JCM.42.9.4127-4129.2004
-
(2004)
J. Clin. Microbiol
, vol.42
, pp. 4127-4129
-
-
Schapiro, J.M.1
Gupta, R.2
Stefansson, E.3
Fang, F.C.4
Limaye, A.P.5
-
65
-
-
84938812034
-
HipBA-promoter structures reveal the basis of heritable multidrug tolerance
-
Schumacher, M. A., Balani, P., Min, J., Chinnam, N. B., Hansen, S., Vulic, M., et al. (2015). HipBA-promoter structures reveal the basis of heritable multidrug tolerance. Nature 524, 59-64. doi: 10.1038/nature14662
-
(2015)
Nature
, vol.524
, pp. 59-64
-
-
Schumacher, M.A.1
Balani, P.2
Min, J.3
Chinnam, N.B.4
Hansen, S.5
Vulic, M.6
-
66
-
-
85035045826
-
-
Science, U.o.M.S.o.M.I.f.G. (2013). GSCID Genomic Sequencing Center for Infectious Disease [Online]. NCBI. Available online at: http://gscid.igs.umaryland.edu/wp.php?wp=comparative_genomics_of_human_mucosal_isolates_of_the_enterotoxigenic_bacteroides_fragilis_group
-
(2013)
GSCID Genomic Sequencing Center for Infectious Disease [Online]. NCBI
-
-
-
67
-
-
80051951299
-
Multi-drug resistant Bacteroides fragilis recovered from blood and severe leg wounds caused by an improvised explosive device (IED) in Afghanistan
-
Sherwood, J., Fraser, S., Citron, D., Wexler, H., Blakely, G., Jobling, K., et al. (2011). Multi-drug resistant Bacteroides fragilis recovered from blood and severe leg wounds caused by an improvised explosive device (IED) in Afghanistan. Anaerobe 17, 152-155. doi: 10.1016/j.anaerobe.2011.02.007
-
(2011)
Anaerobe
, vol.17
, pp. 152-155
-
-
Sherwood, J.1
Fraser, S.2
Citron, D.3
Wexler, H.4
Blakely, G.5
Jobling, K.6
-
68
-
-
84959419241
-
Direct CRISPR spacer acquisition from RNA by a natural reverse transcriptase-Cas1 fusion protein
-
Silas, S., Mohr, G., Sidote, D. J., Markham, L. M., Sanchez-Amat, A., Bhaya, D., et al. (2016). Direct CRISPR spacer acquisition from RNA by a natural reverse transcriptase-Cas1 fusion protein. Science 351:aad4234. doi: 10.1126/science.aad4234
-
(2016)
Science
, vol.351
-
-
Silas, S.1
Mohr, G.2
Sidote, D.J.3
Markham, L.M.4
Sanchez-Amat, A.5
Bhaya, D.6
-
69
-
-
85011270550
-
Emergence and evolution of an international cluster of MDR Bacteroides fragilis isolates
-
Soki, J., Hedberg, M., Patrick, S., Balint, B., Herczeg, R., Nagy, I., et al. (2016). Emergence and evolution of an international cluster of MDR Bacteroides fragilis isolates. J. Antimicrob. Chemother. 71, 2441-2448. doi: 10.1093/jac/dkw175
-
(2016)
J. Antimicrob. Chemother
, vol.71
, pp. 2441-2448
-
-
Soki, J.1
Hedberg, M.2
Patrick, S.3
Balint, B.4
Herczeg, R.5
Nagy, I.6
-
70
-
-
77951627860
-
Diagnosis and management of complicated intra-abdominal infection in adults and children: guidelines by the Surgical Infection Society and the Infectious Diseases Society of America
-
Solomkin, J. S., Mazuski, J. E., Bradley, J. S., Rodvold, K. A., Goldstein, E. J., Baron, E. J., et al. (2010). Diagnosis and management of complicated intra-abdominal infection in adults and children: guidelines by the Surgical Infection Society and the Infectious Diseases Society of America. Surg. Infect. (Larchmt) 11, 79-109. doi: 10.1089/sur.2009.9930
-
(2010)
Surg. Infect. (Larchmt)
, vol.11
, pp. 79-109
-
-
Solomkin, J.S.1
Mazuski, J.E.2
Bradley, J.S.3
Rodvold, K.A.4
Goldstein, E.J.5
Baron, E.J.6
-
71
-
-
39149142575
-
CRISPR-a widespread system that provides acquired resistance against phages in bacteria and archaea
-
Sorek, R., Kunin, V., and Hugenholtz, P. (2008). CRISPR-a widespread system that provides acquired resistance against phages in bacteria and archaea. Nat. Rev. Microbiol. 6, 181-186. doi: 10.1038/nrmicro1793
-
(2008)
Nat. Rev. Microbiol
, vol.6
, pp. 181-186
-
-
Sorek, R.1
Kunin, V.2
Hugenholtz, P.3
-
72
-
-
77955085897
-
Self-targeting by CRISPR: gene regulation or autoimmunity?
-
Stern, A., Keren, L., Wurtzel, O., Amitai, G., and Sorek, R. (2010). Self-targeting by CRISPR: gene regulation or autoimmunity? Trends Genet. 26, 335-340. doi: 10.1016/j.tig.2010.05.008
-
(2010)
Trends Genet
, vol.26
, pp. 335-340
-
-
Stern, A.1
Keren, L.2
Wurtzel, O.3
Amitai, G.4
Sorek, R.5
-
73
-
-
84922695827
-
Identification of antimicrobial resistance genes in multidrug-resistant clinical Bacteroides fragilis isolates by whole genome shotgun sequencing
-
Sydenham, T. V., Soki, J., Hasman, H., Wang, M., Justesen, U. S., and Esgai A(2015). Identification of antimicrobial resistance genes in multidrug-resistant clinical Bacteroides fragilis isolates by whole genome shotgun sequencing. Anaerobe 31, 59-64. doi: 10.1016/j.anaerobe.2014.10.009
-
(2015)
Anaerobe
, vol.31
, pp. 59-64
-
-
Sydenham, T.V.1
Soki, J.2
Hasman, H.3
Wang, M.4
Justesen, U.S.5
Esgai, A.6
-
74
-
-
35448985445
-
Bacteroides-the good, the bad, and the nitty-gritty
-
Wexler, H. M. (2007). Bacteroides-the good, the bad, and the nitty-gritty. Clin. Microbiol. Rev. 20, 593-621. doi: 10.1128/CMR.00008-07
-
(2007)
Clin. Microbiol. Rev
, vol.20
, pp. 593-621
-
-
Wexler, H.M.1
-
75
-
-
84930257307
-
'The genus Bacteroides,'
-
eds E. Y. Rosenberg, E. F. DeLong, F. Thompson, S. Lory, and E. Stackebrandt (Berlin; Heidelberg: Springer Verlig)
-
Wexler, H. M. (2014). "The genus Bacteroides," in The Prokaryotes: Other major lineages of Bacteria and the Archaea, eds E. Y. Rosenberg, E. F. DeLong, F. Thompson, S. Lory, and E. Stackebrandt (Berlin; Heidelberg: Springer Verlig), 459-484
-
(2014)
The Prokaryotes: Other major lineages of Bacteria and the Archaea
, pp. 459-484
-
-
Wexler, H.M.1
-
76
-
-
84984639985
-
Comparative genomic analysis identifies structural features of CRISPR-Cas systems in Riemerella anatipestifer
-
Zhu, D. K., Yang, X. Q., He, Y., Zhou, W. S., Song, X. H., Wang, J. B., et al. (2016). Comparative genomic analysis identifies structural features of CRISPR-Cas systems in Riemerella anatipestifer. BMC Genomics 17:689. doi: 10.1186/s12864-016-3040-4
-
(2016)
BMC Genomics
, vol.17
, pp. 689
-
-
Zhu, D.K.1
Yang, X.Q.2
He, Y.3
Zhou, W.S.4
Song, X.H.5
Wang, J.B.6
|