-
1
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. 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
-
-
0242276676
-
Lateral gene transfer and the origins of prokaryotic groups
-
Boucher, Y., Douady, C.J., Papke, R.T., Walsh, D.A., Boudreau, M.E., Nesbø, C.L., Case, R.J., and Doolittle, W.F. 2003. Lateral gene transfer and the origins of prokaryotic groups. Annu. Rev. Genet. 37: 283-328.
-
(2003)
Annu. Rev. Genet.
, vol.37
, pp. 283-328
-
-
Boucher, Y.1
Douady, C.J.2
Papke, R.T.3
Walsh, D.A.4
Boudreau, M.E.5
Nesbø, C.L.6
Case, R.J.7
Doolittle, W.F.8
-
3
-
-
0036137155
-
Eubacterial phylogeny based on translational apparatus proteins
-
Brochier, C., Bapteste, E., Moreira, D., and Philippe, H. 2002. Eubacterial phylogeny based on translational apparatus proteins. Trends Genet. 18: 1-5.
-
(2002)
Trends Genet.
, vol.18
, pp. 1-5
-
-
Brochier, C.1
Bapteste, E.2
Moreira, D.3
Philippe, H.4
-
4
-
-
0034942865
-
Universal trees based on large combined protein sequence data sets
-
Brown, J.R., Douady, C.J., Italia, M.J., Marshall, W.E., and Stanhope, M.J. 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
-
5
-
-
0642333696
-
Characterization of species-specific genes using a flexible, web-based querying system
-
Charlebois, R,L., Clarke, G.D.P., Beiko, R.G., and St. Jean, A. 2003. Characterization of species-specific genes using a flexible, web-based querying system. FEMS Microbiol. Lett. 225: 213-220.
-
(2003)
FEMS Microbiol. Lett.
, vol.225
, pp. 213-220
-
-
Charlebois, R.L.1
Clarke, G.D.P.2
Beiko, R.G.3
St. Jean, A.4
-
6
-
-
10944251626
-
Genome phylogenies
-
(eds. R.P. Hirt and D.S. Horne) CRC Press, Boca Raton, FL
-
Charlebois, R.L., Beiko, R.G., and Ragan, M.A. 2004. Genome phylogenies. In Organelles, genomes and eukaryote phylogeny: An evolutionary synthesis in the age of genomics (eds. R.P. Hirt and D.S. Horne), pp. 189-206. CRC Press, Boca Raton, FL.
-
(2004)
Organelles, Genomes and Eukaryote Phylogeny: an Evolutionary Synthesis in the Age of Genomics
, pp. 189-206
-
-
Charlebois, R.L.1
Beiko, R.G.2
Ragan, M.A.3
-
7
-
-
0036210883
-
Inferring genome trees using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on normalized BLASTP scores
-
Clarke, G.D.P., Beiko, R.G., Ragan, M.A., and Charlebois, R.L. 2002. Inferring genome trees using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on normalized BLASTP scores. J. Bacteriol. 184: 2072-2080.
-
(2002)
J. Bacteriol.
, vol.184
, pp. 2072-2080
-
-
Clarke, G.D.P.1
Beiko, R.G.2
Ragan, M.A.3
Charlebois, R.L.4
-
8
-
-
0036061865
-
A phylogenomic approach to bacterial phylogeny: Evidence of a core of genes sharing a common history
-
Daubin, V., Gouy, M., and Perrière, G. 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
Perrière, G.3
-
9
-
-
0042027842
-
Phylogenetics and the cohesion of bacterial genomes
-
Daubin, V., Moran, N.A., and Ochman, H. 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
-
11
-
-
0037352585
-
The genetic core of the universal ancestor
-
Harris, J.K., Kelley, S.T., Spiegelman, G.B., and Pace, N.R. 2003. The genetic core of the universal ancestor. Genome Res. 13: 407-412.
-
(2003)
Genome Res.
, vol.13
, pp. 407-412
-
-
Harris, J.K.1
Kelley, S.T.2
Spiegelman, G.B.3
Pace, N.R.4
-
12
-
-
0033582265
-
Substrate recognition by class I lysyl-tRNA synthetases: A molecular basis for gene displacement
-
Ibba, M., Losey, H.C., Kawarabayasi, Y., Kikuchi, H., Bunjun, S., and Söll, D. 1999. Substrate recognition by class I lysyl-tRNA synthetases: A molecular basis for gene displacement. Proc. Natl. Acad. Sci. 96: 418-423.
-
(1999)
Proc. Natl. Acad. Sci.
, vol.96
, pp. 418-423
-
-
Ibba, M.1
Losey, H.C.2
Kawarabayasi, Y.3
Kikuchi, H.4
Bunjun, S.5
Söll, D.6
-
13
-
-
0036595304
-
Horizontal gene transfer in microbial genome evolution
-
Jain, R., Rivera, M.C., Moore, J.E., and Lake, J.A. 2002. Horizontal gene transfer in microbial genome evolution. Theor. Popul. Biol. 61: 489-495.
-
(2002)
Theor. Popul. Biol.
, vol.61
, pp. 489-495
-
-
Jain, R.1
Rivera, M.C.2
Moore, J.E.3
Lake, J.A.4
-
14
-
-
1542272747
-
Comparative genomics, minimal gene-sets and the last universal common ancestor
-
Koonin, E.V. 2003. Comparative genomics, minimal gene-sets and the last universal common ancestor. Nat. Rev. Microbiol. 1: 127-136.
-
(2003)
Nat. Rev. Microbiol.
, vol.1
, pp. 127-136
-
-
Koonin, E.V.1
-
15
-
-
0030249023
-
Non-orthologous gene displacement
-
Koonin, E.V., Mushegian, A.R., and Bork, P. 1996. Non-orthologous gene displacement. Trends Genet. 12: 334-336.
-
(1996)
Trends Genet.
, vol.12
, pp. 334-336
-
-
Koonin, E.V.1
Mushegian, A.R.2
Bork, P.3
-
16
-
-
0038486918
-
The balance of driving forces during genome evolution in prokaryotes
-
Kunin, V. and Ouzounis, C.A. 2003. The balance of driving forces during genome evolution in prokaryotes. Genome Res. 13: 1589-1594.
-
(2003)
Genome Res.
, vol.13
, pp. 1589-1594
-
-
Kunin, V.1
Ouzounis, C.A.2
-
17
-
-
0142124263
-
Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution
-
Krylov, D.M., Wolf, Y.I., Rogozin, I.B., and Koonin, E.V. 2003. Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution. Genome Res. 13: 2229-2235.
-
(2003)
Genome Res.
, vol.13
, pp. 2229-2235
-
-
Krylov, D.M.1
Wolf, Y.I.2
Rogozin, I.B.3
Koonin, E.V.4
-
18
-
-
0033605625
-
Mix and match in the tree of life
-
Lake, J.A., Jain, R., and Rivera, M.C. 1999. Mix and match in the tree of life. Science 283: 2027-2028.
-
(1999)
Science
, vol.283
, pp. 2027-2028
-
-
Lake, J.A.1
Jain, R.2
Rivera, M.C.3
-
19
-
-
0037115872
-
Comparative analysis of ribosomal proteins in complete genomes: An example of reductive evolution at the domain scale
-
Lecompte, O., Ripp, R., Thierry, J.C., Moras, D., and Poch, O. 2002. Comparative analysis of ribosomal proteins in complete genomes: An example of reductive evolution at the domain scale. Nucleic Acids Res. 30: 5382-5390.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 5382-5390
-
-
Lecompte, O.1
Ripp, R.2
Thierry, J.C.3
Moras, D.4
Poch, O.5
-
20
-
-
1342271382
-
From gene trees to organismal phylogeny in prokaryotes: The case of the γ-Proteobacteria
-
Lerat, E., Daubin, V., and Moran, N.A. 2003. From gene trees to organismal phylogeny in prokaryotes: The case of the γ-Proteobacteria. PLoS Biol. 1: E19.
-
(2003)
PLoS Biol.
, vol.1
-
-
Lerat, E.1
Daubin, V.2
Moran, N.A.3
-
21
-
-
0043011009
-
Comparative genomics of archaea: How much have we learned in six years, and what's next?
-
Makarova, K.S. and Koonin, E.V. 2003. Comparative genomics of archaea: How much have we learned in six years, and what's next? Genome Biol. 4: 115.
-
(2003)
Genome Biol.
, vol.4
, pp. 115
-
-
Makarova, K.S.1
Koonin, E.V.2
-
22
-
-
0032766490
-
Comparative genomics of the Archaea (Euryarchaeota): Evolution of conserved protein families, the stable core, and the variable shell
-
Makarova, K.S., Aravind, L., Galperin, M.Y., Grishin, N.V., Tatusov, R.L., Wolf, Y.I., and Koonin, E.V. 1999. Comparative genomics of the Archaea (Euryarchaeota): Evolution of conserved protein families, the stable core, and the variable shell. Genome Res. 9: 608-628.
-
(1999)
Genome Res.
, vol.9
, pp. 608-628
-
-
Makarova, K.S.1
Aravind, L.2
Galperin, M.Y.3
Grishin, N.V.4
Tatusov, R.L.5
Wolf, Y.I.6
Koonin, E.V.7
-
23
-
-
0036098562
-
Archaeal phylogeny based on ribosomal proteins
-
Matte-Tailliez, O., Brochier, C., Forterre, P., and Phillippe, H. 2002. Archaeal phylogeny based on ribosomal proteins. Mol. Biol. Evol. 19: 631-639.
-
(2002)
Mol. Biol. Evol.
, vol.19
, pp. 631-639
-
-
Matte-Tailliez, O.1
Brochier, C.2
Forterre, P.3
Phillippe, H.4
-
24
-
-
2942622384
-
Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes
-
Mirkin, B.G., Fenner, T.I., Galperin, M.Y., and Koonin, E.V. 2003. Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes. BMC Evol. Biol. 3: 2.
-
(2003)
BMC Evol. Biol.
, vol.3
, pp. 2
-
-
Mirkin, B.G.1
Fenner, T.I.2
Galperin, M.Y.3
Koonin, E.V.4
-
25
-
-
0029789824
-
A minimal gene set for cellular life derived by comparison of complete bacterial genomes
-
Mushegian, A.R. and Koonin, E.V. 1996. A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proc. Natl. Acad. Sci. 93: 10268-10273.
-
(1996)
Proc. Natl. Acad. Sci.
, vol.93
, pp. 10268-10273
-
-
Mushegian, A.R.1
Koonin, E.V.2
-
26
-
-
0034831587
-
Defining the core of nontransferable prokaryotic genes: The euryarchaeal core
-
Nesbø, C.L., Boucher, Y., and Doolittle, W.F. 2001. Defining the core of nontransferable prokaryotic genes: The euryarchaeal core. J. Mol. Evol. 53: 340-350.
-
(2001)
J. Mol. Evol.
, vol.53
, pp. 340-350
-
-
Nesbø, C.L.1
Boucher, Y.2
Doolittle, W.F.3
-
27
-
-
0035989433
-
Distributional profiles of homologous open reading frames among bacterial phyla: Implications for vertical and lateral transmission
-
Ragan, M.A. and Charlebois, R.L. 2002. Distributional profiles of homologous open reading frames among bacterial phyla: Implications for vertical and lateral transmission. Int. J. Syst. Evol. Microbiol. 52: 777-787.
-
(2002)
Int. J. Syst. Evol. Microbiol.
, vol.52
, pp. 777-787
-
-
Ragan, M.A.1
Charlebois, R.L.2
-
28
-
-
0036143446
-
Genomes in flux: The evolution of archaeal and proteobacterial gene content
-
Snel, B., Bork, P., and Huynen, M.A. 2002. Genomes in flux: The evolution of archaeal and proteobacterial gene content. Genome Res. 12: 17-25.
-
(2002)
Genome Res.
, vol.12
, pp. 17-25
-
-
Snel, B.1
Bork, P.2
Huynen, M.A.3
-
29
-
-
0030660581
-
A genomic perspective on protein families
-
Tatusov, R.L., Koonin, E.V., and Lipman, D.J. 1997. A genomic perspective on protein families. Science 278: 631-637.
-
(1997)
Science
, vol.278
, pp. 631-637
-
-
Tatusov, R.L.1
Koonin, E.V.2
Lipman, D.J.3
-
30
-
-
0033043696
-
Is there a phylogenetic signal in prokaryote proteins?
-
Teichmann, S.A. and Mitchison, G. 1999. Is there a phylogenetic signal in prokaryote proteins? J. Mol. Evol. 49: 98-107.
-
(1999)
J. Mol. Evol.
, vol.49
, pp. 98-107
-
-
Teichmann, S.A.1
Mitchison, G.2
-
31
-
-
0242300069
-
The genome of Nanoarchaeum equitans: Insights into early archaeal evolution and derived parasitism
-
Waters, E., Hohn, M.J., Ahel, I., Graham, D.E., Adams, M.D., Barnstead, M., Beeson, K.Y., Bibbs, L., Bolanos, R., Keller, M., et al. 2003. The genome of Nanoarchaeum equitans: Insights into early archaeal evolution and derived parasitism. Proc. Natl. Acad. Sci. 100: 12984-12988.
-
(2003)
Proc. Natl. Acad. Sci.
, vol.100
, pp. 12984-12988
-
-
Waters, E.1
Hohn, M.J.2
Ahel, I.3
Graham, D.E.4
Adams, M.D.5
Barnstead, M.6
Beeson, K.Y.7
Bibbs, L.8
Bolanos, R.9
Keller, M.10
-
32
-
-
0032499698
-
The universal ancestor
-
Woese, C. 1998. The universal ancestor. Proc. Natl. Acad. Sci. 95: 6854-6859.
-
(1998)
Proc. Natl. Acad. Sci.
, vol.95
, pp. 6854-6859
-
-
Woese, C.1
-
33
-
-
0023184331
-
Bacterial evolution
-
Woese, C.R. 1987. Bacterial evolution. Microbiol. Rev. 51: 221-271.
-
(1987)
Microbiol. Rev.
, vol.51
, pp. 221-271
-
-
Woese, C.R.1
-
34
-
-
0034682457
-
Interpreting the universal phylogenetic tree
-
Woese, C.R. 2000. Interpreting the universal phylogenetic tree. Proc. Natl. Acad. Sci. 97: 8392-8396.
-
(2000)
Proc. Natl. Acad. Sci.
, vol.97
, pp. 8392-8396
-
-
Woese, C.R.1
-
35
-
-
0037173066
-
On the evolution of cells
-
Woese, C.R. 2002. On the evolution of cells. Proc. Natl. Acad. Sci. 99: 8742-8747.
-
(2002)
Proc. Natl. Acad. Sci.
, vol.99
, pp. 8742-8747
-
-
Woese, C.R.1
-
36
-
-
0037436116
-
Genomics. Tinker, tailor: Can Venter stitch together a genome from scratch?
-
Zimmer, C. 2003. Genomics. Tinker, tailor: Can Venter stitch together a genome from scratch? Science 299: 1006-1007.
-
(2003)
Science
, vol.299
, pp. 1006-1007
-
-
Zimmer, C.1
|