-
1
-
-
31344459549
-
Antimicrobial-resistant bacteria in the community setting
-
Furuya EY, Lowy FD: Antimicrobial-resistant bacteria in the community setting. Nat Rev Microbiol 2006, 4:36-45.
-
(2006)
Nat Rev Microbiol
, vol.4
, pp. 36-45
-
-
Furuya, E.Y.1
Lowy, F.D.2
-
2
-
-
57849137502
-
CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA
-
Marraffini LA, Sontheimer EJ: CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA. Science 2008, 322:1843-1845.
-
(2008)
Science
, vol.322
, pp. 1843-1845
-
-
Marraffini, L.A.1
Sontheimer, E.J.2
-
3
-
-
79955795335
-
CRISPR inhibition of prophage acquisition in Streptococcus pyogenes
-
Nozawa T, Furukawa N, Aikawa C, Watanabe T, Haobam B, Kurokawa K, Maruyama F, Nakagawa I: CRISPR inhibition of prophage acquisition in Streptococcus pyogenes. PLoS One 2011, 6:e19543.
-
(2011)
PLoS One
, vol.6
-
-
Nozawa, T.1
Furukawa, N.2
Aikawa, C.3
Watanabe, T.4
Haobam, B.5
Kurokawa, K.6
Maruyama, F.7
Nakagawa, I.8
-
4
-
-
79952168979
-
Multidrug-resistant enterococci lack CRISPR-cas
-
Palmer KL, Gilmore MS: Multidrug-resistant enterococci lack CRISPR-cas. MBio 2010, 1(pii):e00227-10.
-
(2010)
MBio
, vol.1
-
-
Palmer, K.L.1
Gilmore, M.S.2
-
5
-
-
77954761569
-
Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow
-
Wozniak RA, Waldor MK: Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow. Nat Rev Microbiol 2010, 8:552-563.
-
(2010)
Nat Rev Microbiol
, vol.8
, pp. 552-563
-
-
Wozniak, R.A.1
Waldor, M.K.2
-
6
-
-
2442449227
-
Genomic islands in pathogenic and environmental microorganisms
-
Dobrindt U, Hochhut B, Hentschel U, Hacker J: Genomic islands in pathogenic and environmental microorganisms. Nat Rev Microbiol 2004, 2:414-424.
-
(2004)
Nat Rev Microbiol
, vol.2
, pp. 414-424
-
-
Dobrindt, U.1
Hochhut, B.2
Hentschel, U.3
Hacker, J.4
-
7
-
-
60149088444
-
Genomic islands: tools of bacterial horizontal gene transfer and evolution
-
Juhas M, van der Meer JR, Gaillard M, Harding RM, Hood DW, Crook DW: Genomic islands: tools of bacterial horizontal gene transfer and evolution. FEMS Microbiol Rev 2009, 33:376-393.
-
(2009)
FEMS Microbiol Rev
, vol.33
, pp. 376-393
-
-
Juhas, M.1
van der Meer, J.R.2
Gaillard, M.3
Harding, R.M.4
Hood, D.W.5
Crook, D.W.6
-
8
-
-
74249095519
-
CRISPR/Cas, the immune system of bacteria and archaea
-
Horvath P, Barrangou R: CRISPR/Cas, the immune system of bacteria and archaea. Science 2010, 327:167-170.
-
(2010)
Science
, vol.327
, pp. 167-170
-
-
Horvath, P.1
Barrangou, R.2
-
9
-
-
34047118522
-
CRISPR provides acquired resistance against viruses in prokaryotes
-
Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, Romero DA, Horvath P: CRISPR provides acquired resistance against viruses in prokaryotes. Science 2007, 315:1709-1712.
-
(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
Romero, D.A.7
Horvath, P.8
-
10
-
-
78149261827
-
The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA
-
Garneau JE, Dupuis ME, Villion M, Romero DA, Barrangou R, Boyaval P, Fremaux C, Horvath P, Magadan AH, Moineau S: The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature 2010, 468:67-71.
-
(2010)
Nature
, vol.468
, pp. 67-71
-
-
Garneau, J.E.1
Dupuis, M.E.2
Villion, M.3
Romero, D.A.4
Barrangou, R.5
Boyaval, P.6
Fremaux, C.7
Horvath, P.8
Magadan, A.H.9
Moineau, S.10
-
11
-
-
77249170201
-
CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea
-
Marraffini LA, Sontheimer EJ: CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea. Nat Rev Genet 2010, 11:181-190.
-
(2010)
Nat Rev Genet
, vol.11
, pp. 181-190
-
-
Marraffini, L.A.1
Sontheimer, E.J.2
-
12
-
-
79959963663
-
Interference by clustered regularly interspaced short palindromic repeat (CRISPR) RNA is governed by a seed sequence
-
Semenova E, Jore MM, Datsenko KA, Semenova A, Westra ER, Wanner B, van der Oost J, Brouns SJ, Severinov K: Interference by clustered regularly interspaced short palindromic repeat (CRISPR) RNA is governed by a seed sequence. Proc Natl Acad Sci USA 2011, 108:10098-10103.
-
(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
van der Oost, J.7
Brouns, S.J.8
Severinov, K.9
-
13
-
-
39149142575
-
CRISPR-a widespread system that provides acquired resistance against phages in bacteria and archaea
-
Sorek R, Kunin V, Hugenholtz P: CRISPR-a widespread system that provides acquired resistance against phages in bacteria and archaea. Nat Rev Microbiol 2008, 6:181-186.
-
(2008)
Nat Rev Microbiol
, vol.6
, pp. 181-186
-
-
Sorek, R.1
Kunin, V.2
Hugenholtz, P.3
-
14
-
-
68249102788
-
CRISPR-based adaptive and heritable immunity in prokaryotes
-
van der Oost J, Jore MM, Westra ER, Lundgren M, Brouns SJ: CRISPR-based adaptive and heritable immunity in prokaryotes. Trends Biochem Sci 2009, 34:401-407.
-
(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
-
15
-
-
0036267740
-
Identification of genes that are associated with DNA repeats in prokaryotes
-
Jansen R, Embden JD, Gaastra W, Schouls LM: Identification of genes that are associated with DNA repeats in prokaryotes. Mol Microbiol 2002, 43:1565-1575.
-
(2002)
Mol Microbiol
, vol.43
, pp. 1565-1575
-
-
Jansen, R.1
Embden, J.D.2
Gaastra, W.3
Schouls, L.M.4
-
16
-
-
84969323736
-
-
CRISPRs web server. [http://crispr.u-psud.fr/crispr/].
-
-
-
-
17
-
-
84873729095
-
Multiplex genome engineering using CRISPR/Cas systems
-
Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA, Zhang F: Multiplex genome engineering using CRISPR/Cas systems. Science 2013, 339:819-823.
-
(2013)
Science
, vol.339
, pp. 819-823
-
-
Cong, L.1
Ran, F.A.2
Cox, D.3
Lin, S.4
Barretto, R.5
Habib, N.6
Hsu, P.D.7
Wu, X.8
Jiang, W.9
Marraffini, L.A.10
Zhang, F.11
-
18
-
-
84873734105
-
RNA-Guided human genome engineering via Cas9
-
Mali P, Yang L, Esvelt KM, Aach J, Guell M, Dicarlo JE, Norville JE, Church GM: RNA-Guided human genome engineering via Cas9. Science 2013, 339:823-826.
-
(2013)
Science
, vol.339
, pp. 823-826
-
-
Mali, P.1
Yang, L.2
Esvelt, K.M.3
Aach, J.4
Guell, M.5
Dicarlo, J.E.6
Norville, J.E.7
Church, G.M.8
-
19
-
-
84876575031
-
Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems
-
Dicarlo JE, Norville JE, Mali P, Rios X, Aach J, Church GM: Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems. Nucleic Acids Res 2013, 41:4336-4343.
-
(2013)
Nucleic Acids Res
, vol.41
, pp. 4336-4343
-
-
Dicarlo, J.E.1
Norville, J.E.2
Mali, P.3
Rios, X.4
Aach, J.5
Church, G.M.6
-
20
-
-
84876409836
-
Genome editing with RNA-guided Cas9 nuclease in Zebrafish embryos
-
Chang N, Sun C, Gao L, Zhu D, Xu X, Zhu X, Xiong JW, Xi JJ: Genome editing with RNA-guided Cas9 nuclease in Zebrafish embryos. Cell Res 2013, 23:465-472.
-
(2013)
Cell Res
, vol.23
, pp. 465-472
-
-
Chang, N.1
Sun, C.2
Gao, L.3
Zhu, D.4
Xu, X.5
Zhu, X.6
Xiong, J.W.7
Xi, J.J.8
-
21
-
-
84874687019
-
Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression
-
Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, Lim WA: Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 2013, 152:1173-1183.
-
(2013)
Cell
, vol.152
, pp. 1173-1183
-
-
Qi, L.S.1
Larson, M.H.2
Gilbert, L.A.3
Doudna, J.A.4
Weissman, J.S.5
Arkin, A.P.6
Lim, W.A.7
-
22
-
-
79953250082
-
CRISPR RNA maturation by transencoded small RNA and host factor RNase III
-
Deltcheva E, Chylinski K, Sharma CM, Gonzales K, Chao Y, Pirzada ZA, Eckert MR, Vogel J, Charpentier E: CRISPR RNA maturation by transencoded small RNA and host factor RNase III. Nature 2011, 471:602-607.
-
(2011)
Nature
, vol.471
, pp. 602-607
-
-
Deltcheva, E.1
Chylinski, K.2
Sharma, C.M.3
Gonzales, K.4
Chao, Y.5
Pirzada, Z.A.6
Eckert, M.R.7
Vogel, J.8
Charpentier, E.9
-
23
-
-
38949123143
-
Phage response to CRISPR-encoded resistance in Streptococcus thermophilus
-
Deveau H, Barrangou R, Garneau JE, Labonte J, Fremaux C, Boyaval P, Romero DA, Horvath P, Moineau S: Phage response to CRISPR-encoded resistance in Streptococcus thermophilus. J Bacteriol 2008, 190:1390-1400.
-
(2008)
J Bacteriol
, vol.190
, pp. 1390-1400
-
-
Deveau, H.1
Barrangou, R.2
Garneau, J.E.3
Labonte, J.4
Fremaux, C.5
Boyaval, P.6
Romero, D.A.7
Horvath, P.8
Moineau, S.9
-
24
-
-
78651482834
-
Analysis of streptococcal CRISPRs from human saliva reveals substantial sequence diversity within and between subjects over time
-
Pride DT, Sun CL, Salzman J, Rao N, Loomer P, Armitage GC, Banfield JF, Relman DA: Analysis of streptococcal CRISPRs from human saliva reveals substantial sequence diversity within and between subjects over time. Genome Res 2011, 21:126-136.
-
(2011)
Genome Res
, vol.21
, pp. 126-136
-
-
Pride, D.T.1
Sun, C.L.2
Salzman, J.3
Rao, N.4
Loomer, P.5
Armitage, G.C.6
Banfield, J.F.7
Relman, D.A.8
-
25
-
-
84861539064
-
Bacterial 'immunity' against bacteriophages
-
Abedon ST: Bacterial 'immunity' against bacteriophages. Bacteriophage 2012, 2:50-54.
-
(2012)
Bacteriophage
, vol.2
, pp. 50-54
-
-
Abedon, S.T.1
-
27
-
-
0026903941
-
Different bacteriophage resistance mechanisms in Streptococcus salivarius subsp. thermophilus
-
Larbi D, Decaris B, Simonet JM: Different bacteriophage resistance mechanisms in Streptococcus salivarius subsp. thermophilus. J Dairy Res 1992, 59:349-357.
-
(1992)
J Dairy Res
, vol.59
, pp. 349-357
-
-
Larbi, D.1
Decaris, B.2
Simonet, J.M.3
-
28
-
-
0034198173
-
Protection against bacteriophage contamination in industrial fermentation processes-investigation and applications of phage resistance mechanisms in bacteria
-
Ogata S, Eguchi T, Doi K: Protection against bacteriophage contamination in industrial fermentation processes-investigation and applications of phage resistance mechanisms in bacteria. Uirusu 2000, 50:17-26.
-
(2000)
Uirusu
, vol.50
, pp. 17-26
-
-
Ogata, S.1
Eguchi, T.2
Doi, K.3
-
29
-
-
44449133775
-
Virus population dynamics and acquired virus resistance in natural microbial communities
-
Andersson AF, Banfield JF: Virus population dynamics and acquired virus resistance in natural microbial communities. Science 2008, 320:1047-1050.
-
(2008)
Science
, vol.320
, pp. 1047-1050
-
-
Andersson, A.F.1
Banfield, J.F.2
-
30
-
-
84855271565
-
Phage-bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome
-
Berg Miller ME, Yeoman CJ, Chia N, Tringe SG, Angly FE, Edwards RA, Flint HJ, Lamed R, Bayer EA, White BA: Phage-bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome. Environ Microbiol 2012, 14:207-227.
-
(2012)
Environ Microbiol
, vol.14
, pp. 207-227
-
-
Berg Miller, M.E.1
Yeoman, C.J.2
Chia, N.3
Tringe, S.G.4
Angly, F.E.5
Edwards, R.A.6
Flint, H.J.7
Lamed, R.8
Bayer, E.A.9
White, B.A.10
-
31
-
-
84859885188
-
Evidence of a robust resident bacteriophage population revealed through analysis of the human salivary virome
-
Pride DT, Salzman J, Haynes M, Rohwer F, Davis-Long C, White RA III, Loomer P, Armitage GC, Relman DA: Evidence of a robust resident bacteriophage population revealed through analysis of the human salivary virome. ISME J 2012, 6:915-926.
-
(2012)
ISME J
, vol.6
, pp. 915-926
-
-
Pride, D.T.1
Salzman, J.2
Haynes, M.3
Rohwer, F.4
Davis-Long, C.5
White, R.A.6
Loomer, P.7
Armitage, G.C.8
Relman, D.A.9
-
32
-
-
77954627922
-
Viruses in the faecal microbiota of monozygotic twins and their mothers
-
Reyes A, Haynes M, Hanson N, Angly FE, Heath AC, Rohwer F, Gordon JI: Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature 2010, 466:334-338.
-
(2010)
Nature
, vol.466
, pp. 334-338
-
-
Reyes, A.1
Haynes, M.2
Hanson, N.3
Angly, F.E.4
Heath, A.C.5
Rohwer, F.6
Gordon, J.I.7
-
33
-
-
84865795822
-
Comparisons of clustered regularly interspaced short palindromic repeats and viromes in human saliva reveal bacterial adaptations to salivary viruses
-
Pride DT, Salzman J, Relman DA: Comparisons of clustered regularly interspaced short palindromic repeats and viromes in human saliva reveal bacterial adaptations to salivary viruses. Environ Microbiol 2012, 14:2564-2576.
-
(2012)
Environ Microbiol
, vol.14
, pp. 2564-2576
-
-
Pride, D.T.1
Salzman, J.2
Relman, D.A.3
-
34
-
-
84865169354
-
CRISPR targeting reveals a reservoir of common phages associated with the human gut microbiome
-
Stern A, Mick E, Tirosh I, Sagy O, Sorek R: CRISPR targeting reveals a reservoir of common phages associated with the human gut microbiome. Genome Res 2012, 22:1985-1994.
-
(2012)
Genome Res
, vol.22
, pp. 1985-1994
-
-
Stern, A.1
Mick, E.2
Tirosh, I.3
Sagy, O.4
Sorek, R.5
-
35
-
-
84862276328
-
Structure, function and diversity of the healthy human microbiome
-
Human Microbiome Project Consortium: Structure, function and diversity of the healthy human microbiome. Nature 2012, 486:207-214.
-
(2012)
Nature
, vol.486
, pp. 207-214
-
-
-
36
-
-
84862286169
-
A framework for human microbiome research
-
Human Microbiome Project Consortium: A framework for human microbiome research. Nature 2012, 486:215-221.
-
(2012)
Nature
, vol.486
, pp. 215-221
-
-
-
37
-
-
84864042533
-
Diverse CRISPRs evolving in human microbiomes
-
Rho M, Wu YW, Tang H, Doak TG, Ye Y: Diverse CRISPRs evolving in human microbiomes. PLoS Genet 2012, 8:e1002441.
-
(2012)
PLoS Genet
, vol.8
-
-
Rho, M.1
Wu, Y.W.2
Tang, H.3
Doak, T.G.4
Ye, Y.5
-
38
-
-
33745634395
-
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
-
Li W, Godzik A: Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 2006, 22:1658-1659.
-
(2006)
Bioinformatics
, vol.22
, pp. 1658-1659
-
-
Li, W.1
Godzik, A.2
-
39
-
-
77955085897
-
Self-targeting by CRISPR: gene regulation or autoimmunity?
-
Stern A, Keren L, Wurtzel O, Amitai G, Sorek R: Self-targeting by CRISPR: gene regulation or autoimmunity?. Trends Genet 2010, 26:335-340.
-
(2010)
Trends Genet
, vol.26
, pp. 335-340
-
-
Stern, A.1
Keren, L.2
Wurtzel, O.3
Amitai, G.4
Sorek, R.5
-
40
-
-
84969317703
-
-
ICTV website. [http://www.ictvdb.org].
-
-
-
-
41
-
-
75549086985
-
ACLAME: a CLAssification of Mobile genetic Elements, update 2010
-
Leplae R, Lima-Mendez G, Toussaint A: ACLAME: a CLAssification of Mobile genetic Elements, update 2010. Nucleic Acids Res 2010, 38:D57-61.
-
(2010)
Nucleic Acids Res
, vol.38
, pp. D57-D61
-
-
Leplae, R.1
Lima-Mendez, G.2
Toussaint, A.3
-
42
-
-
84969321715
-
-
DACC website. [http://www.hmpdacc.org/].
-
-
-
-
43
-
-
78651326786
-
FragGeneScan: predicting genes in short and errorprone reads
-
Rho M, Tang H, Ye Y: FragGeneScan: predicting genes in short and errorprone reads. Nucleic Acids Res 2010, 38:e191.
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Rho, M.1
Tang, H.2
Ye, Y.3
-
44
-
-
61449201423
-
IslandViewer: an integrated interface for computational identification and visualization of genomic islands
-
Langille MG, Brinkman FS: IslandViewer: an integrated interface for computational identification and visualization of genomic islands. Bioinformatics 2009, 25:664-665.
-
(2009)
Bioinformatics
, vol.25
, pp. 664-665
-
-
Langille, M.G.1
Brinkman, F.S.2
-
45
-
-
50149094265
-
Evaluation of genomic island predictors using a comparative genomics approach
-
Langille MG, Hsiao WW, Brinkman FS: Evaluation of genomic island predictors using a comparative genomics approach. BMC Bioinformatics 2008, 9:329.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 329
-
-
Langille, M.G.1
Hsiao, W.W.2
Brinkman, F.S.3
-
46
-
-
33745828696
-
Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models
-
Waack S, Keller O, Asper R, Brodag T, Damm C, Fricke WF, Surovcik K, Meinicke P, Merkl R: Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models. BMC Bioinformatics 2006, 7:142.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 142
-
-
Waack, S.1
Keller, O.2
Asper, R.3
Brodag, T.4
Damm, C.5
Fricke, W.F.6
Surovcik, K.7
Meinicke, P.8
Merkl, R.9
-
47
-
-
0345237922
-
IslandPath: aiding detection of genomic islands in prokaryotes
-
Hsiao W, Wan I, Jones SJ, Brinkman FS: IslandPath: aiding detection of genomic islands in prokaryotes. Bioinformatics 2003, 19:418-420.
-
(2003)
Bioinformatics
, vol.19
, pp. 418-420
-
-
Hsiao, W.1
Wan, I.2
Jones, S.J.3
Brinkman, F.S.4
-
48
-
-
84969326100
-
-
IslandViewer server. [http://www.pathogenomics.sfu.ca/islandviewer/genome_submit.php].
-
-
-
-
49
-
-
60349094186
-
Atypical association of DDE transposition with conjugation specifies a new family of mobile elements
-
Brochet M, Da Cunha V, Couve E, Rusniok C, Trieu-Cuot P, Glaser P: Atypical association of DDE transposition with conjugation specifies a new family of mobile elements. Mol Microbiol 2009, 71:948-959.
-
(2009)
Mol Microbiol
, vol.71
, pp. 948-959
-
-
Brochet, M.1
Da Cunha, V.2
Couve, E.3
Rusniok, C.4
Trieu-Cuot, P.5
Glaser, P.6
-
50
-
-
79959979274
-
PHAST: a fast phage search tool
-
Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS: PHAST: a fast phage search tool. Nucleic Acids Res 2011, 39:W347-352.
-
(2011)
Nucleic Acids Res
, vol.39
, pp. W347-W352
-
-
Zhou, Y.1
Liang, Y.2
Lynch, K.H.3
Dennis, J.J.4
Wishart, D.S.5
-
51
-
-
64049118040
-
Short motif sequences determine the targets of the prokaryotic CRISPR defence system
-
Mojica FJ, Diez-Villasenor C, Garcia-Martinez J, Almendros C: Short motif sequences determine the targets of the prokaryotic CRISPR defence system. Microbiology 2009, 155:733-740.
-
(2009)
Microbiology
, vol.155
, pp. 733-740
-
-
Mojica, F.J.1
Diez-Villasenor, C.2
Garcia-Martinez, J.3
Almendros, C.4
-
52
-
-
84857097177
-
RNA-guided genetic silencing systems in bacteria and archaea
-
Wiedenheft B, Sternberg SH, Doudna JA: RNA-guided genetic silencing systems in bacteria and archaea. Nature 2012, 482:331-338.
-
(2012)
Nature
, vol.482
, pp. 331-338
-
-
Wiedenheft, B.1
Sternberg, S.H.2
Doudna, J.A.3
-
53
-
-
34248400310
-
A guild of 45 CRISPRassociated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes
-
Haft DH, Selengut J, Mongodin EF, Nelson KE: A guild of 45 CRISPRassociated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. PLoS Comput Biol 2005, 1:e60.
-
(2005)
PLoS Comput Biol
, vol.1
-
-
Haft, D.H.1
Selengut, J.2
Mongodin, E.F.3
Nelson, K.E.4
-
54
-
-
35748974534
-
Evolutionary conservation of sequence and secondary structures in CRISPR repeats
-
Kunin V, Sorek R, Hugenholtz P: Evolutionary conservation of sequence and secondary structures in CRISPR repeats. Genome Biol 2007, 8:R61.
-
(2007)
Genome Biol
, vol.8
, pp. R61
-
-
Kunin, V.1
Sorek, R.2
Hugenholtz, P.3
-
55
-
-
35748931450
-
Identification of compositionally distinct regions in genomes using the centroid method
-
Rajan I, Aravamuthan S, Mande SS: Identification of compositionally distinct regions in genomes using the centroid method. Bioinformatics 2007, 23:2672-2677.
-
(2007)
Bioinformatics
, vol.23
, pp. 2672-2677
-
-
Rajan, I.1
Aravamuthan, S.2
Mande, S.S.3
-
56
-
-
31544472392
-
A novel strategy for the identification of genomic islands by comparative analysis of the contents and contexts of tRNA sites in closely related bacteria
-
Ou HY, Chen LL, Lonnen J, Chaudhuri RR, Thani AB, Smith R, Garton NJ, Hinton J, Pallen M, Barer MR, Rajakumar K: A novel strategy for the identification of genomic islands by comparative analysis of the contents and contexts of tRNA sites in closely related bacteria. Nucleic Acids Res 2006, 34:e3.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Ou, H.Y.1
Chen, L.L.2
Lonnen, J.3
Chaudhuri, R.R.4
Thani, A.B.5
Smith, R.6
Garton, N.J.7
Hinton, J.8
Pallen, M.9
Barer, M.R.10
Rajakumar, K.11
-
57
-
-
84872607723
-
Bacteriophage genes that inactivate the CRISPR/Cas bacterial immune system
-
Bondy-Denomy J, Pawluk A, Maxwell KL, Davidson AR: Bacteriophage genes that inactivate the CRISPR/Cas bacterial immune system. Nature 2013, 493:429-432.
-
(2013)
Nature
, vol.493
, pp. 429-432
-
-
Bondy-Denomy, J.1
Pawluk, A.2
Maxwell, K.L.3
Davidson, A.R.4
-
58
-
-
84861117236
-
Persisting viral sequences shape microbial CRISPR-based immunity
-
Weinberger AD, Sun CL, Plucinski MM, Denef VJ, Thomas BC, Horvath P, Barrangou R, Gilmore MS, Getz WM, Banfield JF: Persisting viral sequences shape microbial CRISPR-based immunity. PLoS Comput Biol 2012, 8: e1002475.
-
(2012)
PLoS Comput Biol
, vol.8
-
-
Weinberger, A.D.1
Sun, C.L.2
Plucinski, M.M.3
Denef, V.J.4
Thomas, B.C.5
Horvath, P.6
Barrangou, R.7
Gilmore, M.S.8
Getz, W.M.9
Banfield, J.F.10
-
59
-
-
84969313349
-
-
NCBI ftp site. [http://www.ncbi.nlm.nih.gov/genomes/GenomesGroup.cgi?taxid=10239].
-
-
-
-
60
-
-
84861898310
-
IMG: the Integrated Microbial Genomes database and comparative analysis system
-
Markowitz VM, Chen IM, Palaniappan K, Chu K, Szeto E, Grechkin Y, Ratner A, Jacob B, Huang J, Williams P, Huntemann M, Anderson I, Mavromatis K, Ivanova NN, Kyrpides NC: IMG: the Integrated Microbial Genomes database and comparative analysis system. Nucleic Acids Res 2012, 40:D115-122.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. D115-D122
-
-
Markowitz, V.M.1
Chen, I.M.2
Palaniappan, K.3
Chu, K.4
Szeto, E.5
Grechkin, Y.6
Ratner, A.7
Jacob, B.8
Huang, J.9
Williams, P.10
Huntemann, M.11
Anderson, I.12
Mavromatis, K.13
Ivanova, N.N.14
Kyrpides, N.C.15
-
61
-
-
84862100340
-
ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria
-
Bi D, Xu Z, Harrison EM, Tai C, Wei Y, He X, Jia S, Deng Z, Rajakumar K, Ou HY: ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria. Nucleic Acids Res 2012, 40:D621-626.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. D621-D626
-
-
Bi, D.1
Xu, Z.2
Harrison, E.M.3
Tai, C.4
Wei, Y.5
He, X.6
Jia, S.7
Deng, Z.8
Rajakumar, K.9
Ou, H.Y.10
-
62
-
-
84969325481
-
-
ICEberg server. [http://http:db-mml.sjtu.edu.cn/ICEberg/].
-
-
-
-
63
-
-
0030854739
-
tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence
-
Lowe TM, Eddy SR: tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997, 25:955-964.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 955-964
-
-
Lowe, T.M.1
Eddy, S.R.2
-
64
-
-
84969322213
-
-
ACLAME database. [http://aclame.ulb.ac.be/].
-
-
-
-
65
-
-
84969313347
-
-
PFAM ftp site. [ftp://ftp.sanger.ac.uk/pub/databases/Pfam/].
-
-
-
-
66
-
-
75549085495
-
eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations
-
Muller J, Szklarczyk D, Julien P, Letunic I, Roth A, Kuhn M, Powell S, von Mering C, Doerks T, Jensen LJ, Bork P: eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations. Nucleic Acids Res 2010, 38:D190-195.
-
(2010)
Nucleic Acids Res
, vol.38
, pp. D190-D195
-
-
Muller, J.1
Szklarczyk, D.2
Julien, P.3
Letunic, I.4
Roth, A.5
Kuhn, M.6
Powell, S.7
von Mering, C.8
Doerks, T.9
Jensen, L.J.10
Bork, P.11
-
67
-
-
0042902833
-
The COG database: an updated version includes eukaryotes
-
Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA: The COG database: an updated version includes eukaryotes. BMC Bioinformatics 2003, 4:41.
-
(2003)
BMC Bioinformatics
, vol.4
, pp. 41
-
-
Tatusov, R.L.1
Fedorova, N.D.2
Jackson, J.D.3
Jacobs, A.R.4
Kiryutin, B.5
Koonin, E.V.6
Krylov, D.M.7
Mazumder, R.8
Mekhedov, S.L.9
Nikolskaya, A.N.10
Rao, B.S.11
Smirnov, S.12
Sverdlov, A.V.13
Vasudevan, S.14
Wolf, Y.I.15
Yin, J.J.16
Natale, D.A.17
-
68
-
-
13244255415
-
MUSCLE: a multiple sequence alignment method with reduced time and space complexity
-
Edgar RC: MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 2004, 5:113.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 113
-
-
Edgar, R.C.1
-
69
-
-
77952988108
-
A new generation of homology search tools based on probabilistic inference
-
Eddy SR: A new generation of homology search tools based on probabilistic inference. Genome Inform 2009, 23:205-211.
-
(2009)
Genome Inform
, vol.23
, pp. 205-211
-
-
Eddy, S.R.1
-
70
-
-
84855167751
-
RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data
-
Zhao Y, Tang H, Ye Y: RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data. Bioinformatics 2012, 28:125-126.
-
(2012)
Bioinformatics
, vol.28
, pp. 125-126
-
-
Zhao, Y.1
Tang, H.2
Ye, Y.3
-
71
-
-
2142738304
-
WebLogo: a sequence logo generator
-
Crooks GE, Hon G, Chandonia JM, Brenner SE: WebLogo: a sequence logo generator. Genome Res 2004, 14:1188-1190.
-
(2004)
Genome Res
, vol.14
, pp. 1188-1190
-
-
Crooks, G.E.1
Hon, G.2
Chandonia, J.M.3
Brenner, S.E.4
-
72
-
-
84969321700
-
-
Weblogo server. [http://weblogo.berkeley.edu/].
-
-
-
-
73
-
-
67849122320
-
MEME SUITE: tools for motif discovery and searching
-
Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS: MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res 2009, 37:W202-208.
-
(2009)
Nucleic Acids Res
, vol.37
, pp. W202-W208
-
-
Bailey, T.L.1
Boden, M.2
Buske, F.A.3
Frith, M.4
Grant, C.E.5
Clementi, L.6
Ren, J.7
Li, W.W.8
Noble, W.S.9
-
74
-
-
33749431828
-
Prophage Finder: a prophage loci prediction tool for prokaryotic genome sequences
-
Bose M, Barber RD: Prophage Finder: a prophage loci prediction tool for prokaryotic genome sequences. In Silico Biol 2006, 6:223-227.
-
(2006)
In Silico Biol
, vol.6
, pp. 223-227
-
-
Bose, M.1
Barber, R.D.2
-
75
-
-
84969317699
-
-
Prophage Finder server. [http://bioinformatics.uwp.edu/~phage/help.htm].
-
-
-
-
76
-
-
84969323747
-
-
PHAST server. [http://phast.wishartlab.com/].
-
-
-
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