-
1
-
-
1942443733
-
Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons
-
Acinas, S. G., Marcelino, L. A., Klepac-Ceraj, V. & Polz, M. F. (2004). Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons. J Bacteriol 186, 2629-2635.
-
(2004)
J Bacteriol
, vol.186
, pp. 2629-2635
-
-
Acinas, S.G.1
Marcelino, L.A.2
Klepac-Ceraj, V.3
Polz, M.F.4
-
2
-
-
0025875752
-
Comparative analysis of Bacillus anthracis, Bacillus cereus, and related species on the basis of reverse transcriptase sequencing of 16S rRNA
-
Ash, C., Farrow, J. A. E., Dorsch, M., Stackebrandt, E. & Collins, M. D. (1991). Comparative analysis of Bacillus anthracis, Bacillus cereus, and related species on the basis of reverse transcriptase sequencing of 16S rRNA. Int J Syst Bacteriol 41, 343-346.
-
(1991)
Int J Syst Bacteriol
, vol.41
, pp. 343-346
-
-
Ash, C.1
Farrow, J.A.E.2
Dorsch, M.3
Stackebrandt, E.4
Collins, M.D.5
-
3
-
-
84872836707
-
Defining bacterial species in the genomic era: Insights from the genus Acinetobacter
-
Chan, J. Z. M., Halachev, M. R., Loman, N. J., Constantinidou, C. & Pallen, M. J. (2012). Defining bacterial species in the genomic era: insights from the genus Acinetobacter. BMC Microbiol 12, 302.
-
(2012)
BMC Microbiol
, vol.12
, pp. 302
-
-
Chan, J.Z.M.1
Halachev, M.R.2
Loman, N.J.3
Constantinidou, C.4
Pallen, M.J.5
-
4
-
-
35648991375
-
EzTaxon: A web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences
-
Chun, J., Lee, J. H., Jung, Y., Kim, M., Kim, S., Kim, B. K. & Lim, Y. W. (2007). EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int J Syst Evol Microbiol 57, 2259-2261.
-
(2007)
Int J Syst Evol Microbiol
, vol.57
, pp. 2259-2261
-
-
Chun, J.1
Lee, J.H.2
Jung, Y.3
Kim, M.4
Kim, S.5
Kim, B.K.6
Lim, Y.W.7
-
5
-
-
58149178756
-
Intraspecific polymorphism of 16S rRNA genes in two halophilic archaeal genera, Haloarcula and Halomicrobium
-
Cui, H. L., Zhou, P. J., Oren, A. & Liu, S. J. (2009). Intraspecific polymorphism of 16S rRNA genes in two halophilic archaeal genera, Haloarcula and Halomicrobium. Extremophiles 13, 31-37.
-
(2009)
Extremophiles
, vol.13
, pp. 31-37
-
-
Cui, H.L.1
Zhou, P.J.2
Oren, A.3
Liu, S.J.4
-
6
-
-
58149527706
-
A genomic distance based on MUM indicates discontinuity between most bacterial species and genera
-
Deloger, M., El Karoui, M. & Petit, M. A. (2009). A genomic distance based on MUM indicates discontinuity between most bacterial species and genera. J Bacteriol 191, 91-99.
-
(2009)
J Bacteriol
, vol.191
, pp. 91-99
-
-
Deloger, M.1
El Karoui, M.2
Petit, M.A.3
-
7
-
-
0025296904
-
Diversity and origin of Desulfovibrio species: Phylogenetic definition of a family
-
Devereux, R., He, S. H., Doyle, C. L., Orkland, S., Stahl, D. A., LeGall, J. & Whitman, W. B. (1990). Diversity and origin of Desulfovibrio species: phylogenetic definition of a family. J Bacteriol 172, 3609-3619.
-
(1990)
J Bacteriol
, vol.172
, pp. 3609-3619
-
-
Devereux, R.1
He, S.H.2
Doyle, C.L.3
Orkland, S.4
Stahl, D.A.5
LeGall, J.6
Whitman, W.B.7
-
8
-
-
23944437942
-
Opinion: Re-evaluating prokaryotic species
-
Gevers, D., Cohan, F. M., Lawrence, J. G., Spratt, B. G., Coenye, T., Feil, E. J., Stackebrandt, E., Van de Peer, Y., Vandamme, P. & other authors (2005). Opinion: re-evaluating prokaryotic species. Nat Rev Microbiol 3, 733-739.
-
(2005)
Nat Rev Microbiol
, vol.3
, pp. 733-739
-
-
Gevers, D.1
Cohan, F.M.2
Lawrence, J.G.3
Spratt, B.G.4
Coenye, T.5
Feil, E.J.6
Stackebrandt, E.7
Van de Peer, Y.8
Vandamme, P.9
-
9
-
-
33846555715
-
DNA-DNA hybridization values and their relationship to whole-genome sequence similarities
-
Goris, J., Konstantinidis, K. T., Klappenbach, J. A., Coenye, T., Vandamme, P. & Tiedje, J. M. (2007). DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57, 81-91.
-
(2007)
Int J Syst Evol Microbiol
, vol.57
, pp. 81-91
-
-
Goris, J.1
Konstantinidis, K.T.2
Klappenbach, J.A.3
Coenye, T.4
Vandamme, P.5
Tiedje, J.M.6
-
10
-
-
84878358647
-
Pan-genome analysis of the emerging foodborne pathogen Cronobacter spp. suggests a species-level bidirectional divergence driven by niche adaptation
-
Grim, C. J., Kotewicz, M. L., Power, K. A., Gopinath, G., Franco, A. A., Jarvis, K. G., Yan, Q. Q., Jackson, S. A., Sathyamoorthy, V. & other authors (2013). Pan-genome analysis of the emerging foodborne pathogen Cronobacter spp. suggests a species-level bidirectional divergence driven by niche adaptation. BMC Genomics 14, 366.
-
(2013)
BMC Genomics
, vol.14
, pp. 366
-
-
Grim, C.J.1
Kotewicz, M.L.2
Power, K.A.3
Gopinath, G.4
Franco, A.A.5
Jarvis, K.G.6
Yan, Q.Q.7
Jackson, S.A.8
Sathyamoorthy, V.9
-
11
-
-
77952697494
-
Comparative genomic analysis reveals evidence of two novel Vibrio species closely related to V. cholerae
-
Haley, B. J., Grim, C. J., Hasan, N. A., Choi, S. Y., Chun, J., Brettin, T. S., Bruce, D. C., Challacombe, J. F., Detter, J. C. & other authors (2010). Comparative genomic analysis reveals evidence of two novel Vibrio species closely related to V. cholerae. BMC Microbiol 10, 154.
-
(2010)
BMC Microbiol
, vol.10
, pp. 154
-
-
Haley, B.J.1
Grim, C.J.2
Hasan, N.A.3
Choi, S.Y.4
Chun, J.5
Brettin, T.S.6
Bruce, D.C.7
Challacombe, J.F.8
Detter, J.C.9
-
12
-
-
19544379902
-
Whole-genome prokaryotic phylogeny
-
Henz, S. R., Huson, D. H., Auch, A. F., Nieselt-Struwe, K. & Schuster, S. C. (2005). Whole-genome prokaryotic phylogeny. Bioinformatics 21, 2329-2335.
-
(2005)
Bioinformatics
, vol.21
, pp. 2329-2335
-
-
Henz, S.R.1
Huson, D.H.2
Auch, A.F.3
Nieselt-Struwe, K.4
Schuster, S.C.5
-
13
-
-
0035070157
-
Relationship of 16S rRNA sequence similarity to DNA hybridization in prokaryotes
-
Keswani, J. & Whitman, W. B. (2001). Relationship of 16S rRNA sequence similarity to DNA hybridization in prokaryotes. Int J Syst Evol Microbiol 51, 667-678.
-
(2001)
Int J Syst Evol Microbiol
, vol.51
, pp. 667-678
-
-
Keswani, J.1
Whitman, W.B.2
-
14
-
-
84863230041
-
Introducing EzTaxon-e: A prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species
-
Kim, O. S., Cho, Y. J., Lee, K., Yoon, S. H., Kim, M., Na, H., Park, S. C., Jeon, Y. S., Lee, J. H. & other authors (2012). Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62, 716-721.
-
(2012)
Int J Syst Evol Microbiol
, vol.62
, pp. 716-721
-
-
Kim, O.S.1
Cho, Y.J.2
Lee, K.3
Yoon, S.H.4
Kim, M.5
Na, H.6
Park, S.C.7
Jeon, Y.S.8
Lee, J.H.9
-
15
-
-
14044262978
-
Genomic insights that advance the species definition for prokaryotes
-
Konstantinidis, K. T. & Tiedje, J. M. (2005). Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci U S A 102, 2567-2572.
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, pp. 2567-2572
-
-
Konstantinidis, K.T.1
Tiedje, J.M.2
-
16
-
-
33751217150
-
The bacterial species definition in the genomic era
-
Konstantinidis, K. T., Ramette, A. & Tiedje, J. M. (2006). The bacterial species definition in the genomic era. Philos Trans R Soc Lond B Biol Sci 361, 1929-1940.
-
(2006)
Philos Trans R Soc Lond B Biol Sci
, vol.361
, pp. 1929-1940
-
-
Konstantinidis, K.T.1
Ramette, A.2
Tiedje, J.M.3
-
17
-
-
84863288435
-
Using the RDP classifier to predict taxonomic novelty and reduce the search space for finding novel organisms
-
Lan, Y. M., Wang, Q., Cole, J. R. & Rosen, G. L. (2012). Using the RDP classifier to predict taxonomic novelty and reduce the search space for finding novel organisms. PLoS ONE 7, e32491.
-
(2012)
PLoS ONE
, vol.7
-
-
Lan, Y.M.1
Wang, Q.2
Cole, J.R.3
Rosen, G.L.4
-
18
-
-
80052290460
-
rRNASelector: A computer program for selecting ribosomal RNA encoding sequences from metagenomic and metatranscriptomic shotgun libraries
-
Lee, J. H., Yi, H. & Chun, J. (2011). rRNASelector: a computer program for selecting ribosomal RNA encoding sequences from metagenomic and metatranscriptomic shotgun libraries. J Microbiol 49, 689-691.
-
(2011)
J Microbiol
, vol.49
, pp. 689-691
-
-
Lee, J.H.1
Yi, H.2
Chun, J.3
-
19
-
-
0348212231
-
An approach to the measurement of genetic relatedness among organisms
-
McCarthy, B. J. & Bolton, E. T. (1963). An approach to the measurement of genetic relatedness among organisms. Proc Natl Acad Sci U S A 50, 156-164.
-
(1963)
Proc Natl Acad Sci U S A
, vol.50
, pp. 156-164
-
-
McCarthy, B.J.1
Bolton, E.T.2
-
20
-
-
84857122937
-
An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea
-
McDonald, D., Price, M. N., Goodrich, J., Nawrocki, E. P., DeSantis, T. Z., Probst, A., Andersen, G. L., Knight, R. & Hugenholtz, P. (2012). An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J 6, 610-618.
-
(2012)
ISME J
, vol.6
, pp. 610-618
-
-
McDonald, D.1
Price, M.N.2
Goodrich, J.3
Nawrocki, E.P.4
DeSantis, T.Z.5
Probst, A.6
Andersen, G.L.7
Knight, R.8
Hugenholtz, P.9
-
21
-
-
84874011652
-
Genome sequence-based species delimitation with confidence intervals and improved distance functions
-
Meier-Kolthoff, J. P., Auch, A. F., Klenk, H. P. & Göker, M. (2013). Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14, 60.
-
(2013)
BMC Bioinformatics
, vol.14
, pp. 60
-
-
Meier-Kolthoff, J.P.1
Auch, A.F.2
Klenk, H.P.3
Göker, M.4
-
22
-
-
84883464181
-
Accurate and universal delineation of prokaryotic species
-
Mende, D. R., Sunagawa, S., Zeller, G. & Bork, P. (2013). Accurate and universal delineation of prokaryotic species. Nat Methods 10, 881-884.
-
(2013)
Nat Methods
, vol.10
, pp. 881-884
-
-
Mende, D.R.1
Sunagawa, S.2
Zeller, G.3
Bork, P.4
-
23
-
-
77953646161
-
Diversity of 16S rRNA genes within individual prokaryotic genomes
-
Pei, A. Y., Oberdorf, W. E., Nossa, C. W., Agarwal, A., Chokshi, P., Gerz, E. A., Jin, Z., Lee, P., Yang, L. & other authors (2010). Diversity of 16S rRNA genes within individual prokaryotic genomes. Appl Environ Microbiol 76, 3886-3897.
-
(2010)
Appl Environ Microbiol
, vol.76
, pp. 3886-3897
-
-
Pei, A.Y.1
Oberdorf, W.E.2
Nossa, C.W.3
Agarwal, A.4
Chokshi, P.5
Gerz, E.A.6
Jin, Z.7
Lee, P.8
Yang, L.9
-
24
-
-
83155175374
-
Classifier chains for multi-label classification
-
Read, J., Pfahringer, B., Holmes, G. & Frank, E. (2011). Classifier chains for multi-label classification. Mach Learn 85, 333-359.
-
(2011)
Mach Learn
, vol.85
, pp. 333-359
-
-
Read, J.1
Pfahringer, B.2
Holmes, G.3
Frank, E.4
-
25
-
-
73149098333
-
Shifting the genomic gold standard for the prokaryotic species definition
-
Richter, M. & Rosselló-Móra, R. (2009). Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 106, 19126-19131.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 19126-19131
-
-
Richter, M.1
Rosselló-Móra, R.2
-
27
-
-
85025353793
-
The formation of hybrid DNA molecules and their use in studies of DNA homologies
-
Schildkraut, C. L., Marmur, J. & Doty, P. (1961). The formation of hybrid DNA molecules and their use in studies of DNA homologies. J Mol Biol 3, 595-617.
-
(1961)
J Mol Biol
, vol.3
, pp. 595-617
-
-
Schildkraut, C.L.1
Marmur, J.2
Doty, P.3
-
28
-
-
33947302827
-
Taxonomic parameters revisited: Tarnished gold standards
-
Stackebrandt, E. & Ebers, J. (2006). Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 33, 152-155.
-
(2006)
Microbiol Today
, vol.33
, pp. 152-155
-
-
Stackebrandt, E.1
Ebers, J.2
-
29
-
-
0028028182
-
Taxonomic note: A place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology
-
Stackebrandt, E. & Goebel, B. M. (1994). Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44, 846-849.
-
(1994)
Int J Syst Bacteriol
, vol.44
, pp. 846-849
-
-
Stackebrandt, E.1
Goebel, B.M.2
-
30
-
-
0035989633
-
Report of the ad hoc committee for the reevaluation of the species definition in bacteriology
-
Stackebrandt, E., Frederiksen, W., Garrity, G. M., Grimont, P. A. D., Kämpfer, P., Maiden, M. C., Nesme, X., Rosselló-Mora, R., Swings, J. & other authors (2002). Report of the ad hoc committee for the reevaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52, 1043-1047.
-
(2002)
Int J Syst Evol Microbiol
, vol.52
, pp. 1043-1047
-
-
Stackebrandt, E.1
Frederiksen, W.2
Garrity, G.M.3
Grimont, P.A.D.4
Kämpfer, P.5
Maiden, M.C.6
Nesme, X.7
Rosselló-Mora, R.8
Swings, J.9
-
31
-
-
76849088617
-
Notes on the characterization of prokaryote strains for taxonomic purposes
-
Tindall, B. J., Rosselló-Móra, R., Busse, H. J., Ludwig, W. & Kämpfer, P. (2010). Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 60, 249-266.
-
(2010)
Int J Syst Evol Microbiol
, vol.60
, pp. 249-266
-
-
Tindall, B.J.1
Rosselló-Móra, R.2
Busse, H.J.3
Ludwig, W.4
Kämpfer, P.5
-
33
-
-
0000770675
-
Report of the ad hoc committee on reconciliation of approaches to bacterial systematics
-
Wayne, L. G., Brenner, D. J., Colwell, R. R., Grimont, P. A. D., Kandler, O., Krichevsky, M. I., Moore, L. H., Moore, W. E. C., Murray, R. G. E. & other authors (1987). Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37, 463-464.
-
(1987)
Int J Syst Bacteriol
, vol.37
, pp. 463-464
-
-
Wayne, L.G.1
Brenner, D.J.2
Colwell, R.R.3
Grimont, P.A.D.4
Kandler, O.5
Krichevsky, M.I.6
Moore, L.H.7
Moore, W.E.C.8
Murray, R.G.E.9
-
34
-
-
84857234269
-
Comparative genomics of Neisseria weaveri clarifies the taxonomy of this species and identifies genetic determinants that may be associated with virulence
-
Yi, H., Cho, Y. J., Yoon, S. H., Park, S. C. & Chun, J. (2012). Comparative genomics of Neisseria weaveri clarifies the taxonomy of this species and identifies genetic determinants that may be associated with virulence. FEMS Microbiol Lett 328, 100-105.
-
(2012)
FEMS Microbiol Lett
, vol.328
, pp. 100-105
-
-
Yi, H.1
Cho, Y.J.2
Yoon, S.H.3
Park, S.C.4
Chun, J.5
|