-
1
-
-
0033515041
-
An Escherichia coli strain with all chromosomal rRNA operons inactivated: complete exchange of rRNA genes between bacteria
-
Asai T., Zaporojets D., Squires C., Squires C.L. An Escherichia coli strain with all chromosomal rRNA operons inactivated: complete exchange of rRNA genes between bacteria. Proc. Natl. Acad. Sci. U.S.A. 1999, 96:1971-1976.
-
(1999)
Proc. Natl. Acad. Sci. U.S.A.
, vol.96
, pp. 1971-1976
-
-
Asai, T.1
Zaporojets, D.2
Squires, C.3
Squires, C.L.4
-
2
-
-
0004318743
-
-
Bergey's Manual Trust, Springer-Verlag, New York
-
Bergey's Manual Trust Bergey's Manual of Systematic Bacteriology, vol. 1-5 2001-2009, Springer-Verlag, New York. 2nd ed.
-
(2001)
Bergey's Manual of Systematic Bacteriology
, vol.1-5
-
-
-
3
-
-
33646797802
-
Origin and phylogeny of chloroplasts revealed by a simple correlation analysis of complete genomes
-
Chu K.H., Qi J., Yu Z.G., Anh V. Origin and phylogeny of chloroplasts revealed by a simple correlation analysis of complete genomes. Mol. Biol. Evol. 2004, 28:70-76.
-
(2004)
Mol. Biol. Evol.
, vol.28
, pp. 70-76
-
-
Chu, K.H.1
Qi, J.2
Yu, Z.G.3
Anh, V.4
-
4
-
-
0028791864
-
Life with 482 genes
-
Coffeau A. Life with 482 genes. Science 1995, 276:445-446.
-
(1995)
Science
, vol.276
, pp. 445-446
-
-
Coffeau, A.1
-
5
-
-
77956012995
-
-
PHYLIP (Phylogeny Inference Package) ver. 3.68. Available from .
-
Felsenstein, J., 2008. PHYLIP (Phylogeny Inference Package) ver. 3.68. Available from http://evolution.genetics.washington.edu/phylip.html.
-
(2008)
-
-
Felsenstein, J.1
-
6
-
-
34648815169
-
Prokaryote phylogeny meets taxonomy: an exhaustive comparison of composition vector trees with systematic bacteriology
-
Gao L., Qi J., Sun J.D., Hao B.L. Prokaryote phylogeny meets taxonomy: an exhaustive comparison of composition vector trees with systematic bacteriology. Sci. Chin. Ser. C-Life Sci. 2007, 50:587-599.
-
(2007)
Sci. Chin. Ser. C-Life Sci.
, vol.50
, pp. 587-599
-
-
Gao, L.1
Qi, J.2
Sun, J.D.3
Hao, B.L.4
-
7
-
-
1242268097
-
Molecular phylogeny of coronaviruses including human SARS-CoV
-
Gao L., Qi J., Wei H.B., Sun Y.G., Hao B.L. Molecular phylogeny of coronaviruses including human SARS-CoV. Chin. Sci. Bull. 2003, 48:1170-1174.
-
(2003)
Chin. Sci. Bull.
, vol.48
, pp. 1170-1174
-
-
Gao, L.1
Qi, J.2
Wei, H.B.3
Sun, Y.G.4
Hao, B.L.5
-
8
-
-
34047110724
-
Whole genome molecular phylogeny of large dsDNA viruses using composition vector method
-
Gao L., Qi J. Whole genome molecular phylogeny of large dsDNA viruses using composition vector method. BMC Evol. Biol. 2007, 7:41. 10.1086/1471-2148/7/41.
-
(2007)
BMC Evol. Biol.
, vol.7
, pp. 41
-
-
Gao, L.1
Qi, J.2
-
9
-
-
0012172988
-
-
Springer, New York
-
Garrity G.M., Johnson K.L., Bell J.A., Searles D.B. Taxonomic Outline of the Procaryotes, Bergey's Manual of Systematic Bacteriology, Rel. 3.0 2002, Springer, New York. 2nd Ed., 10.1007/bergeysoutline200210.
-
(2002)
Taxonomic Outline of the Procaryotes, Bergey's Manual of Systematic Bacteriology, Rel. 3.0
-
-
Garrity, G.M.1
Johnson, K.L.2
Bell, J.A.3
Searles, D.B.4
-
10
-
-
0012172988
-
-
Springer, New York
-
Garrity G.M., Bell J.A., Lilburn T.G. Taxonomic Outline of the Procaryotes, Bergey's Manual of Systematic Bacteriology, Rel. 4.0 2003, Springer, New York. 2nd Ed., 10.1007/bergeysoutline200310.
-
(2003)
Taxonomic Outline of the Procaryotes, Bergey's Manual of Systematic Bacteriology, Rel. 4.0
-
-
Garrity, G.M.1
Bell, J.A.2
Lilburn, T.G.3
-
11
-
-
0012172988
-
-
Springer, New York
-
Garrity G.M., Bell J.A., Lilburn T.G. Taxonomic Outline of the Procaryotes, Bergey's Manual of Systematic Bacteriology, Rel. 5.0 2004, Springer, New York. 2nd Ed., 10.1007/bergeysoutline200405.
-
(2004)
Taxonomic Outline of the Procaryotes, Bergey's Manual of Systematic Bacteriology, Rel. 5.0
-
-
Garrity, G.M.1
Bell, J.A.2
Lilburn, T.G.3
-
12
-
-
77956011667
-
-
Taxonomic Outline of Bacteria and Archaea (TOBA), Rel.7.7, Michigan State University, available from .
-
Garrity, G.M., Lilburn, T.G., Cole, J.R., Harrison, S.H., Euzéby, J., Tindall, B.J., 2007. Taxonomic Outline of Bacteria and Archaea (TOBA), Rel.7.7, Michigan State University, available from http://www.taxonomicoutline.org/.
-
(2007)
-
-
Garrity, G.M.1
Lilburn, T.G.2
Cole, J.R.3
Harrison, S.H.4
Euzéby, J.5
Tindall, B.J.6
-
13
-
-
3242889314
-
Prokaryote phylogeny without sequence alignment: from avoidance signature to composition distance
-
Hao B.L., Qi J. Prokaryote phylogeny without sequence alignment: from avoidance signature to composition distance. J. Bioinform. Comput. Biol. 2004, 2:1-19.
-
(2004)
J. Bioinform. Comput. Biol.
, vol.2
, pp. 1-19
-
-
Hao, B.L.1
Qi, J.2
-
15
-
-
0000298267
-
Lateral gene transfer, genome surveys, and the phylogeny of prokaryotes
-
Hyunen M., Snel B., Bork P. Lateral gene transfer, genome surveys, and the phylogeny of prokaryotes. Science 1999, 286:1443a.
-
(1999)
Science
, vol.286
-
-
Hyunen, M.1
Snel, B.2
Bork, P.3
-
16
-
-
24944587193
-
Towards a genome-based taxonomy for prokaryotes
-
Konstantinidis K.T., Tiedje K.V. Towards a genome-based taxonomy for prokaryotes. J. Bacteriol. 2005, 187:6258-6264.
-
(2005)
J. Bacteriol.
, vol.187
, pp. 6258-6264
-
-
Konstantinidis, K.T.1
Tiedje, K.V.2
-
18
-
-
43649097637
-
Finite automaton for testing composition-based reconstructibility of sequences
-
Li Q., Xie H.M. Finite automaton for testing composition-based reconstructibility of sequences. J. Comput. Syst. Sci. 2008, 74:870-874.
-
(2008)
J. Comput. Syst. Sci.
, vol.74
, pp. 870-874
-
-
Li, Q.1
Xie, H.M.2
-
19
-
-
77951246352
-
Revised road map to the phylum Firmicutes
-
Springer Verlag, New York
-
Ludwig W., Schleifer K.-H., Whitman W.B. Revised road map to the phylum Firmicutes. Bergey's Manual of Systematic Bacteriology, vol. 3 (The Firmicutes) 2009, Springer Verlag, New York. 2nd Ed.
-
(2009)
Bergey's Manual of Systematic Bacteriology, vol. 3 (The Firmicutes)
-
-
Ludwig, W.1
Schleifer, K.-H.2
Whitman, W.B.3
-
20
-
-
37649023694
-
Parallel genomic evolution and metabolic interdependence in an encient symbiosis
-
McCutcheon J.P., Moran N.A. Parallel genomic evolution and metabolic interdependence in an encient symbiosis. Proc. Natl. Acad. Sci. U.S.A. 2007, 104:19392-19397.
-
(2007)
Proc. Natl. Acad. Sci. U.S.A.
, vol.104
, pp. 19392-19397
-
-
McCutcheon, J.P.1
Moran, N.A.2
-
21
-
-
33749987465
-
The 160-kilobase genome of the bacterial endosymbiont Carsonella
-
Nakabachi A., Yamashita A., Toh H., Ishikawa H., Dunbar H.E., Moran N.A., Hattori M. The 160-kilobase genome of the bacterial endosymbiont Carsonella. Science 2006, 31:267.
-
(2006)
Science
, vol.31
, pp. 267
-
-
Nakabachi, A.1
Yamashita, A.2
Toh, H.3
Ishikawa, H.4
Dunbar, H.E.5
Moran, N.A.6
Hattori, M.7
-
22
-
-
77956010475
-
-
NCBI, The NCBI FTP site: .
-
NCBI, 2009. The NCBI FTP site: ftp://ftp.ncbi.nih.gov/genomes/Bacteria/.
-
(2009)
-
-
-
24
-
-
27744441025
-
Phylogenomics
-
Philippe H., Delsuc F., Brinkmann H., Lartillot N. Phylogenomics. Annu. Rev. Ecol. Evol. Syst. 2005, 76:541-562.
-
(2005)
Annu. Rev. Ecol. Evol. Syst.
, vol.76
, pp. 541-562
-
-
Philippe, H.1
Delsuc, F.2
Brinkmann, H.3
Lartillot, N.4
-
25
-
-
3242890106
-
CVTree: a phylogenetic tree reconstruction tool based on whole genomes
-
Web Server Issue, W45-W47
-
Qi J., Luo H., Hao B.L. CVTree: a phylogenetic tree reconstruction tool based on whole genomes. Nucl. Acids Res. 2004, 32. Web Server Issue, W45-W47.
-
(2004)
Nucl. Acids Res.
, vol.32
-
-
Qi, J.1
Luo, H.2
Hao, B.L.3
-
26
-
-
1242335920
-
Whole-proteome prokaryote phylogeny without sequence alignment: a K-string composition approach
-
Qi J., Wang B., Hao B.L. Whole-proteome prokaryote phylogeny without sequence alignment: a K-string composition approach. J. Mol. Evol. 2004, 58:1-11.
-
(2004)
J. Mol. Evol.
, vol.58
, pp. 1-11
-
-
Qi, J.1
Wang, B.2
Hao, B.L.3
-
27
-
-
0023375195
-
The neighbor-joining method: a new method for reconstructing phylogenetic tress
-
Saitou N., Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic tress. Mol. Biol. Evol. 1987, 4:406-425.
-
(1987)
Mol. Biol. Evol.
, vol.4
, pp. 406-425
-
-
Saitou, N.1
Nei, M.2
-
28
-
-
33846676442
-
Decomposition and reconstruction of protein sequences: the problem of uniqueness and factorizable language
-
Shi X.L., Xie H.M., Zhang S.Y., Hao B.L. Decomposition and reconstruction of protein sequences: the problem of uniqueness and factorizable language. J. Korean Phys. Soc. 2007, 50:118-123.
-
(2007)
J. Korean Phys. Soc.
, vol.50
, pp. 118-123
-
-
Shi, X.L.1
Xie, H.M.2
Zhang, S.Y.3
Hao, B.L.4
-
30
-
-
33751258603
-
The bacterial species dilemma and the genomic-phylogenetic species concept
-
Staley J.T. The bacterial species dilemma and the genomic-phylogenetic species concept. Phil. Trans. R. Soc. B 2006, 361:1899-1909.
-
(2006)
Phil. Trans. R. Soc. B
, vol.361
, pp. 1899-1909
-
-
Staley, J.T.1
-
31
-
-
84880804685
-
-
in press,doi:10.1007/s11434-010-0008-7
-
Sun, J.D., Xu, Z., Hao, B.L., in press. Whole-genome based archaea phylogeny and taxonomy: a composition vector approach. Chin. Sci. Bull., doi:10.1007/s11434-010-0008-7.
-
Chin. Sci. Bull.
-
-
Sun, J.D.1
Xu, Z.2
Hao, B.L.3
-
32
-
-
0033043696
-
Is there a phylogenetic signal in prokaryote proteins?
-
Teichmann A.A., Mitchison G. Is there a phylogenetic signal in prokaryote proteins?. J. Mol. Evol. 1999, 49:98-107.
-
(1999)
J. Mol. Evol.
, vol.49
, pp. 98-107
-
-
Teichmann, A.A.1
Mitchison, G.2
-
33
-
-
69949152972
-
A fungal phylogeny based on 82 complete genomes using the composition vector method
-
Wang H., Xu Z., Hao B.L. A fungal phylogeny based on 82 complete genomes using the composition vector method. BMC Evol. Biol. 2009, 9:195.
-
(2009)
BMC Evol. Biol.
, vol.9
, pp. 195
-
-
Wang, H.1
Xu, Z.2
Hao, B.L.3
-
34
-
-
0001271789
-
Phylogenetic structure of the prokaryotic domain: the primary kingdoms
-
Woese C.R., Fox G.E. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc. Natl. Acad. Sci. U.S.A. 1977, 74:5088-5090.
-
(1977)
Proc. Natl. Acad. Sci. U.S.A.
, vol.74
, pp. 5088-5090
-
-
Woese, C.R.1
Fox, G.E.2
-
35
-
-
0034053846
-
Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process
-
Woese C.R., Olsen G.J., Ibba M., Söll D. Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process. Microbiol. Mol. Biol. Rev. 2000, 64:202-236.
-
(2000)
Microbiol. Mol. Biol. Rev.
, vol.64
, pp. 202-236
-
-
Woese, C.R.1
Olsen, G.J.2
Ibba, M.3
Söll, D.4
-
36
-
-
0022379296
-
A phylogenetic definition of the major eubacterial taxa
-
Woese C.R., Stackebrandt E., Macke T.J., Fox G.E. A phylogenetic definition of the major eubacterial taxa. System. Appl. Microbiol. 1985, 6:143-151.
-
(1985)
System. Appl. Microbiol.
, vol.6
, pp. 143-151
-
-
Woese, C.R.1
Stackebrandt, E.2
Macke, T.J.3
Fox, G.E.4
-
37
-
-
33847304097
-
Phase transition in sequence unique reconstruction
-
Xia L., Zhou C. Phase transition in sequence unique reconstruction. J. Syst. Sci. Compl. 2007, 20:18-29.
-
(2007)
J. Syst. Sci. Compl.
, vol.20
, pp. 18-29
-
-
Xia, L.1
Zhou, C.2
-
38
-
-
67849101838
-
-
CVTree update: a phylogenetic tree reconstruction tool based on whole genomes. Nucl. Acids Res. 37, Web Server Issue, W174-178, published online April 26,doi:10.1093/nar/gkp278
-
Xu, Z., Hao, B.L., 2009. CVTree update: a phylogenetic tree reconstruction tool based on whole genomes. Nucl. Acids Res. 37, Web Server Issue, W174-178, published online April 26, doi:10.1093/nar/gkp278.
-
(2009)
-
-
Xu, Z.1
Hao, B.L.2
-
39
-
-
52149085893
-
The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains
-
Yarza P., Richter M., Peplies J., Euzeby J., Amann R., Schleifer K.-H., Ludwig W., Glöckner F.O., Rosselló-Móra R. The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst. Appl. Microbiol. 2008, 31:241-250.
-
(2008)
Syst. Appl. Microbiol.
, vol.31
, pp. 241-250
-
-
Yarza, P.1
Richter, M.2
Peplies, J.3
Euzeby, J.4
Amann, R.5
Schleifer, K.-H.6
Ludwig, W.7
Glöckner, F.O.8
Rosselló-Móra, R.9
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