-
1
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul, S. F., T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
2
-
-
0011215011
-
Classification of prokaryotic organisms and the concept of bacterial speciation
-
D. R. Boone, R. W. Castenholz, and G. M. Garrity (ed.). Springer-Verlag, New York, N.Y.
-
Brenner, D., J. Staley, and N. Krieg. 2000. Classification of prokaryotic organisms and the concept of bacterial speciation, p. 27-31. In D. R. Boone, R. W. Castenholz, and G. M. Garrity (ed.), Bergey's manual of systematic bacteriology, 2nd ed., vol. 1. Springer-Verlag, New York, N.Y.
-
(2000)
Bergey's Manual of Systematic Bacteriology, 2nd Ed.
, vol.1
, pp. 27-31
-
-
Brenner, D.1
Staley, J.2
Krieg, N.3
-
3
-
-
0034942865
-
Universal trees based on large combined protein sequence data sets
-
Brown, J. R., C. J. Douady, M. J. Italia, W. E. Marshall, and M. J. Stanhope. 2001. Universal trees based on large combined protein sequence data sets. Nat. Genet. 28:281-285.
-
(2001)
Nat. Genet.
, vol.28
, pp. 281-285
-
-
Brown, J.R.1
Douady, C.J.2
Italia, M.J.3
Marshall, W.E.4
Stanhope, M.J.5
-
4
-
-
0001892985
-
AL
-
N. R. Krieg, N. and J. G. Holt (ed.). William and Wilkins, Baltimore, Md
-
AL, p. 38-39. In N. R. Krieg, N. and J. G. Holt (ed.), Bergey's manual of systematic bacteriology, vol. 1. William and Wilkins, Baltimore, Md.
-
(1984)
Bergey's Manual of Systematic Bacteriology
, vol.1
, pp. 38-39
-
-
Canale-Parola, E.1
-
5
-
-
10944248427
-
Computing prokaryotic gene ubiquity: Rescuing the core from extinction
-
Charlebois, R. L., and W. F. Doolittle. 2004. Computing prokaryotic gene ubiquity: rescuing the core from extinction. Genome Res. 14:2469-2477.
-
(2004)
Genome Res.
, vol.14
, pp. 2469-2477
-
-
Charlebois, R.L.1
Doolittle, W.F.2
-
6
-
-
0042121237
-
Multiple sequence alignment with the Clustal series of programs
-
Chenna, R., H. Sugawara, T. Koike, R. Lopez, T. J. Gibson, D. G. Higgins, and J. D. Thompson. 2003. Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res. 31:3497-3500.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 3497-3500
-
-
Chenna, R.1
Sugawara, H.2
Koike, T.3
Lopez, R.4
Gibson, T.J.5
Higgins, D.G.6
Thompson, J.D.7
-
7
-
-
0026531177
-
Prochlorococcus marinus nov. gen. Sp.: An oxyphototrophic prokaryote containing divinyl chrolophyll a and b
-
Chisholm, S., S. Frankel, R. Goericke, R. Olson, B. Palenik, B. Waterbury, L. West-Johnrud, and E. Zettler. 1992. Prochlorococcus marinus nov. gen. Sp.: an oxyphototrophic prokaryote containing divinyl chrolophyll a and b. Arch. Microbiol. 157:297-300.
-
(1992)
Arch. Microbiol.
, vol.157
, pp. 297-300
-
-
Chisholm, S.1
Frankel, S.2
Goericke, R.3
Olson, R.4
Palenik, B.5
Waterbury, B.6
West-Johnrud, L.7
Zettler, E.8
-
8
-
-
1542348484
-
Use of the genomic signature in bacterial classification and identification
-
Coenye, T., and P. Vandamme. 2004. Use of the genomic signature in bacterial classification and identification. Syst. Appl. Microbiol. 27:175-185.
-
(2004)
Syst. Appl. Microbiol.
, vol.27
, pp. 175-185
-
-
Coenye, T.1
Vandamme, P.2
-
9
-
-
0037251969
-
The Ribosomal Database Project (RDP-II): Previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy
-
Cole, J. R., B. Chai, T. L. Marsh, R. J. Farris, Q. Wang, S. A. Kulam, S. Chandra, D. M. McGarrell, T. M. Schmidt, G. M. Garrity, and J. M. Tiedje. 2003. The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res. 31:442-443.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 442-443
-
-
Cole, J.R.1
Chai, B.2
Marsh, T.L.3
Farris, R.J.4
Wang, Q.5
Kulam, S.A.6
Chandra, S.7
McGarrell, D.M.8
Schmidt, T.M.9
Garrity, G.M.10
Tiedje, J.M.11
-
10
-
-
0036061865
-
A phylogenomic approach to bacterial phylogeny: Evidence of a core of genes sharing a common history
-
Daubin, V., M. Gouy, and G. Perriere. 2002. A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history. Genome Res. 12:1080-1090.
-
(2002)
Genome Res.
, vol.12
, pp. 1080-1090
-
-
Daubin, V.1
Gouy, M.2
Perriere, G.3
-
11
-
-
0042027842
-
Phylogenetics and the cohesion of bacterial genomes
-
Daubin, V., N. A. Moran, and H. Ochman. 2003. Phylogenetics and the cohesion of bacterial genomes. Science 301:829-832.
-
(2003)
Science
, vol.301
, pp. 829-832
-
-
Daubin, V.1
Moran, N.A.2
Ochman, H.3
-
12
-
-
0033603539
-
Phylogenetic classification and the universal tree
-
Doolittle, W. F. 1999. Phylogenetic classification and the universal tree. Science 284:2124-2129.
-
(1999)
Science
, vol.284
, pp. 2124-2129
-
-
Doolittle, W.F.1
-
14
-
-
0033231209
-
Whole genome-based phylogenetic analysis of free-living microorganisms
-
Fitz-Gibbon, S. T., and C. H. House. 1999. Whole genome-based phylogenetic analysis of free-living microorganisms. Nucleic Acids Res. 27:4218-4222.
-
(1999)
Nucleic Acids Res.
, vol.27
, pp. 4218-4222
-
-
Fitz-Gibbon, S.T.1
House, C.H.2
-
15
-
-
14544295684
-
Weighted genome trees: Refinements and applications
-
Gophna, U., W. F. Doolittle, and R. L. Charlebois. 2005. Weighted genome trees: refinements and applications. J. Bacteriol. 187:1305-1316.
-
(2005)
J. Bacteriol.
, vol.187
, pp. 1305-1316
-
-
Gophna, U.1
Doolittle, W.F.2
Charlebois, R.L.3
-
16
-
-
0036597701
-
Critical issues in bacterial phylogeny
-
Gupta, R. S., and E. Griffiths, 2002. Critical issues in bacterial phylogeny. Theor. Popul. Biol. 61:423-434.
-
(2002)
Theor. Popul. Biol.
, vol.61
, pp. 423-434
-
-
Gupta, R.S.1
Griffiths, E.2
-
17
-
-
4043070854
-
Phylogenetic analysis based on genome-scale metabolic pathway reaction content
-
Hong, S. H., T. Y. Kim, and S. Y. Lee. 2004. Phylogenetic analysis based on genome-scale metabolic pathway reaction content. Appl. Microbiol. Biotechnol. 65:203-210.
-
(2004)
Appl. Microbiol. Biotechnol.
, vol.65
, pp. 203-210
-
-
Hong, S.H.1
Kim, T.Y.2
Lee, S.Y.3
-
18
-
-
14044262978
-
Genomic insights that advance the species definition for prokaryotes
-
Konstantinidis, K. T., and J. M. Tiedje. 2005. Genomic insights that advance the species definition for prokaryotes. Proc. Natl. Acad. Sci. USA 102:2567-2572.
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 2567-2572
-
-
Konstantinidis, K.T.1
Tiedje, J.M.2
-
19
-
-
0041382581
-
On using the manual
-
D. R. Boone, R. W. Castenholz, and G. M. Garrity (ed.). Springer-Verlag, New York, N.Y.
-
Krieg, N., and G. Garrity. 2000. On using the manual, p. 15-19. In D. R. Boone, R. W. Castenholz, and G. M. Garrity (ed.), Bergey's manual of systematic bacteriology, 2nd ed., vol. I. Springer-Verlag, New York, N.Y.
-
(2000)
Bergey's Manual of Systematic Bacteriology, 2nd Ed.
, vol.1
, pp. 15-19
-
-
Krieg, N.1
Garrity, G.2
-
20
-
-
13844306368
-
Measuring genome conservation across taxa: Divided strains and united kingdoms
-
Kunin, V., D. Ahren, L. Goldovsky, P. Janssen, and C. A. Ouzounis. 2005. Measuring genome conservation across taxa: divided strains and united kingdoms. Nucleic Acids Res. 33:616-621.
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 616-621
-
-
Kunin, V.1
Ahren, D.2
Goldovsky, L.3
Janssen, P.4
Ouzounis, C.A.5
-
21
-
-
0242490943
-
Lateral gene transfer: When will adolescence end?
-
Lawrence, J. G., and H. Hendrickson. 2003. Lateral gene transfer: when will adolescence end? Mol. Microbiol. 50:739-749.
-
(2003)
Mol. Microbiol.
, vol.50
, pp. 739-749
-
-
Lawrence, J.G.1
Hendrickson, H.2
-
22
-
-
0002803581
-
Overview: A phylogenetic backbone and taxonomic framework for prokaryotic systematics
-
D. R. Boone, R. W. Castenholz, and G. M. Garrity (ed.). Springer-Verlag, New York, N.Y.
-
Ludwig, W., and H.-P. Klenk. 2000. Overview: a phylogenetic backbone and taxonomic framework for prokaryotic systematics, p. 49-65. In D. R. Boone, R. W. Castenholz, and G. M. Garrity (ed.), Bergey's manual of systematic bacteriology, 2nd ed., vol. 1. Springer-Verlag, New York, N.Y.
-
(2000)
Bergey's Manual of Systematic Bacteriology, 2nd Ed.
, vol.1
, pp. 49-65
-
-
Ludwig, W.1
Klenk, H.-P.2
-
23
-
-
13144252236
-
Multilocus sequence typing: A portable approach to the identification of clones within populations of pathogenic microorganisms
-
Maiden, M. C., J. A. Bygraves, E. Feil, G. Morelli, J. E. Russell, R. Urwin, Q. Zhang, J. Zhou, K. Zurth, D. A. Caugant, I. M. Feavers, M. Achtman, and B. G. Spratt. 1998. Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc. Natl. Acad. Sci. USA 95:3140-3145.
-
(1998)
Proc. Natl. Acad. Sci. USA
, vol.95
, pp. 3140-3145
-
-
Maiden, M.C.1
Bygraves, J.A.2
Feil, E.3
Morelli, G.4
Russell, J.E.5
Urwin, R.6
Zhang, Q.7
Zhou, J.8
Zurth, K.9
Caugant, D.A.10
Feavers, I.M.11
Achtman, M.12
Spratt, B.G.13
-
24
-
-
13244252316
-
Visualization of comparative genomic analyses by BLAST score ratio
-
Rasko, D. A., G. S. Myers, and J. Ravel. 2005. Visualization of comparative genomic analyses by BLAST score ratio. BMC Bioinformatics 6:2.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 2
-
-
Rasko, D.A.1
Myers, G.S.2
Ravel, J.3
-
25
-
-
0032962457
-
Twilight zone of protein sequence alignments
-
Rost, B. 1999. Twilight zone of protein sequence alignments. Protein Eng. 12:85-94.
-
(1999)
Protein Eng.
, vol.12
, pp. 85-94
-
-
Rost, B.1
-
26
-
-
0026030641
-
Database of homology-derived protein structures and the structural meaning of sequence alignment
-
Sander, C., and R. Schneider. 1991. Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins 9:56-68.
-
(1991)
Proteins
, vol.9
, pp. 56-68
-
-
Sander, C.1
Schneider, R.2
-
27
-
-
3042826875
-
Identification and phylogenetic sorting of bacterial lineages with universally conserved genes and proteins
-
Santos, S. R., and H. Ochman. 2004. Identification and phylogenetic sorting of bacterial lineages with universally conserved genes and proteins. Environ. Microbiol. 6:754-759.
-
(2004)
Environ. Microbiol.
, vol.6
, pp. 754-759
-
-
Santos, S.R.1
Ochman, H.2
-
28
-
-
0032900532
-
Genome phylogeny based on gene content
-
Snel, B., P. Bork, and M. A. Huynen. 1999. Genome phylogeny based on gene content. Nat. Genet. 21:108-110.
-
(1999)
Nat. Genet.
, vol.21
, pp. 108-110
-
-
Snel, B.1
Bork, P.2
Huynen, M.A.3
-
29
-
-
0035989633
-
Report of the Ad Hoc Committee for the re-evaluation of the species definition in bacteriology
-
Stackebrandt, E., W. Frederiksen, G. M. Garrity, P. A. Grimont, P. Kampfer, M. C. Maiden, X. Nesme, R. Rossello-Mora, J. Swings, H. G. Truper, L. Vauterin, A. C. Ward, and W. B. Whitman. 2002. Report of the Ad Hoc Committee for the Re-evaluation 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.4
Kampfer, P.5
Maiden, M.C.6
Nesme, X.7
Rossello-Mora, R.8
Swings, J.9
Truper, H.G.10
Vauterin, L.11
Ward, A.C.12
Whitman, W.B.13
-
30
-
-
0000770675
-
Report of the Ad Hoc Committee on reconciliation of approaches to bacterial systematics
-
Wayne, L. G., D. J. Brenner, R. R. Colwell, P. A. D. Grimont, O. Kandler, M. I. Krichevsky, L. H. Moore, W. E. C. Moore, R. G. E. Murray, E. Stackebrandt, M. P. Starr, and H. G. Trüper. 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
Stackebrandt, E.10
Starr, M.P.11
Trüper, H.G.12
-
31
-
-
0348044549
-
Genome trees constructed using five different approaches suggest new major bacterial clades
-
Wolf, Y. I., I. B. Rogozin, N. V. Grishin, R. L. Tatusov, and E. V. Koonin. 2001. Genome trees constructed using five different approaches suggest new major bacterial clades. BMC Evol. Biol. 1:8.
-
(2001)
BMC Evol. Biol.
, vol.1
, pp. 8
-
-
Wolf, Y.I.1
Rogozin, I.B.2
Grishin, N.V.3
Tatusov, R.L.4
Koonin, E.V.5
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