-
1
-
-
0036842986
-
Genome sequence of the endocellular obligate symbiont of tsetse flies, Wigglesworthia glossinidia
-
Akman, L., A. Yamashita, H. Watanabe, K. Oshima, T. Shiba, M. Hattori, and S. Aksoy. 2002. Genome sequence of the endocellular obligate symbiont of tsetse flies, Wigglesworthia glossinidia. Nat. Genet. 32:402-407.
-
(2002)
Nat. Genet.
, vol.32
, pp. 402-407
-
-
Akman, L.1
Yamashita, A.2
Watanabe, H.3
Oshima, K.4
Shiba, T.5
Hattori, M.6
Aksoy, S.7
-
2
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul, S. F., T. L. Madden, A. A. Schaffer, J. H. 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.H.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
3
-
-
0035029472
-
Pseudogenes, junk DNA, and the dynamics of Rickettsia genomes
-
Andersson, J. O., and S. G. Andersson. 2001. Pseudogenes, junk DNA, and the dynamics of Rickettsia genomes. Mol. Biol. Evol. 18:829-839.
-
(2001)
Mol. Biol. Evol.
, vol.18
, pp. 829-839
-
-
Andersson, J.O.1
Andersson, S.G.2
-
4
-
-
1842481012
-
Evolutionary stability of DNA uptake signal sequences in the Pasteurellaceae
-
Bakkali, M., T. Y. Chen, H. C. Lee, and R. J. Redfield. 2004. Evolutionary stability of DNA uptake signal sequences in the Pasteurellaceae. Proc. Natl. Acad. Sci. USA 101:4513-4518.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 4513-4518
-
-
Bakkali, M.1
Chen, T.Y.2
Lee, H.C.3
Redfield, R.J.4
-
5
-
-
4444353678
-
Phylogenetic reconstruction and lateral gene transfer
-
Bapteste, E., Y. Boucher, J. Leigh, and W. F. Doolittle. 2004. Phylogenetic reconstruction and lateral gene transfer. Trends Microbiol. 12:406-411.
-
(2004)
Trends Microbiol.
, vol.12
, pp. 406-411
-
-
Bapteste, E.1
Boucher, Y.2
Leigh, J.3
Doolittle, W.F.4
-
6
-
-
0028803018
-
Genetics, physiology, and evolutionary relationships of the genus Buchnera-intracellular symbionts of aphids
-
Baumann, P., L. Baumann, C. Y. Lai, D. Roubakhsh, N. A. Moran, and M. A. Clark. 1995. Genetics, physiology, and evolutionary relationships of the genus Buchnera-intracellular symbionts of aphids. Annu. Rev. Microbiol. 49:55-94.
-
(1995)
Annu. Rev. Microbiol.
, vol.49
, pp. 55-94
-
-
Baumann, P.1
Baumann, L.2
Lai, C.Y.3
Roubakhsh, D.4
Moran, N.A.5
Clark, M.A.6
-
8
-
-
0032770572
-
Gene order breakpoint evidence in animal mitochondrial phylogeny
-
Blanchette, M., T. Kunisawa, and D. Sankoff. 1999. Gene order breakpoint evidence in animal mitochondrial phylogeny. J. Mol. Evol. 49:193-203.
-
(1999)
J. Mol. Evol.
, vol.49
, pp. 193-203
-
-
Blanchette, M.1
Kunisawa, T.2
Sankoff, D.3
-
9
-
-
15444350252
-
The complete genome sequence of Escherichia coli K-12
-
Blattner, F. R., G. Plunkett III, C. A. Bloch et al. (14 co-authors). 1997. The complete genome sequence of Escherichia coli K-12. Science 277:1453-1474.
-
(1997)
Science
, vol.277
, pp. 1453-1474
-
-
Blattner, F.R.1
Plunkett III, G.2
Bloch, C.A.3
-
10
-
-
0242276676
-
Lateral gene transfer and the origins of prokaryotic groups
-
Boucher, Y., C. J. Douady, R. T. Papke, D. A. Walsh, M. E. R. Boudreau, C. L. Nesbo, R. J. Case, and W. F. Doolittle. 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.R.5
Nesbo, C.L.6
Case, R.J.7
Doolittle, W.F.8
-
11
-
-
0036143403
-
Genome-scale evolution: Reconstructing gene orders in the ancestral species
-
Bourque, G., and P. A. Pevzner. 2002. Genome-scale evolution: reconstructing gene orders in the ancestral species. Genome Res. 12:26-36.
-
(2002)
Genome Res.
, vol.12
, pp. 26-36
-
-
Bourque, G.1
Pevzner, P.A.2
-
12
-
-
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
-
13
-
-
0041335630
-
The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000
-
Buell, C. R., V. Joardar, M. Lindeberg et al. (41 co-authors). 2003. The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000. Proc. Natl. Acad. Sci. USA 100:10181-10186.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 10181-10186
-
-
Buell, C.R.1
Joardar, V.2
Lindeberg, M.3
-
14
-
-
0942279509
-
Chromosomal constraints in gram-positive bacteria revealed by artificial inversions
-
Campo, N., M. J. Dias, M. L. Daveran-Mingot, P. Ritzenthaler, and P. Le Bourgeois. 2004. Chromosomal constraints in gram-positive bacteria revealed by artificial inversions. Mol. Microbiol. 51:511-522.
-
(2004)
Mol. Microbiol.
, vol.51
, pp. 511-522
-
-
Campo, N.1
Dias, M.J.2
Daveran-Mingot, M.L.3
Ritzenthaler, P.4
Le Bourgeois, P.5
-
15
-
-
2442667671
-
A phylogenomic study of endosymbiotic bacteria
-
Canback, B., I. Tamas, and S. G. Andersson. 2004. A phylogenomic study of endosymbiotic bacteria. Mol. Biol. Evol. 21:1110-1122.
-
(2004)
Mol. Biol. Evol.
, vol.21
, pp. 1110-1122
-
-
Canback, B.1
Tamas, I.2
Andersson, S.G.3
-
16
-
-
0032425482
-
The diverse and dynamic structure of bacterial genomes
-
Casjens, S. 1998. The diverse and dynamic structure of bacterial genomes. Annu. Rev. Genet. 32:339-377.
-
(1998)
Annu. Rev. Genet.
, vol.32
, pp. 339-377
-
-
Casjens, S.1
-
17
-
-
0034043778
-
Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis
-
Castresana, J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17:540-552.
-
(2000)
Mol. Biol. Evol.
, vol.17
, pp. 540-552
-
-
Castresana, J.1
-
18
-
-
0034996704
-
A putative insect intracellular endosymbiont stem clade, within the Enterobacteriaceae, inferred from phylogenetic analysis based on a heterogeneous model of DNA evolution
-
Charles, H., A. Heddi, and Y. Rahbe. 2001. A putative insect intracellular endosymbiont stem clade, within the Enterobacteriaceae, inferred from phylogenetic analysis based on a heterogeneous model of DNA evolution. C. R. Acad. Sci. III 324:489-494.
-
(2001)
C. R. Acad. Sci. III
, vol.324
, pp. 489-494
-
-
Charles, H.1
Heddi, A.2
Rahbe, Y.3
-
19
-
-
0032731436
-
Sequence evolution in bacterial endosymbionts having extreme base compositions
-
Clark, M. A., N. A. Moran, and P. Baumann. 1999. Sequence evolution in bacterial endosymbionts having extreme base compositions. Mol. Biol. Evol. 16:1586-1598.
-
(1999)
Mol. Biol. Evol.
, vol.16
, pp. 1586-1598
-
-
Clark, M.A.1
Moran, N.A.2
Baumann, P.3
-
20
-
-
0037161811
-
Comparison of the genomes of two Xanthomonas pathogens with differing host specificities
-
da Silva, A. C., J. A. Ferro, F. C. Reinach et al. (62 co-authors). 2002. Comparison of the genomes of two Xanthomonas pathogens with differing host specificities. Nature 417:459-463.
-
(2002)
Nature
, vol.417
, pp. 459-463
-
-
Da Silva, A.C.1
Ferro, J.A.2
Reinach, F.C.3
-
21
-
-
0036061865
-
A phylogenomic approach to bacterial phylogeny: Evidence of a core of genes snaring a common history
-
Daubin, V., M. Gouy, and G. Perriere. 2002. A phylogenomic approach to bacterial phylogeny: evidence of a core of genes snaring 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
-
22
-
-
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
-
23
-
-
0036330894
-
Genome sequence of Yersinia pestis KIM
-
Deng, W., V. Burland, G. Plunkett III et al. (18 co-authors). 2002. Genome sequence of Yersinia pestis KIM. J. Bacteriol. 184:4601-4611.
-
(2002)
J. Bacteriol.
, vol.184
, pp. 4601-4611
-
-
Deng, W.1
Burland, V.2
Plunkett III, G.3
-
24
-
-
0037377818
-
Comparative genomics of Salmonella enterica serovar Typhi strains Ty2 and CT18
-
Deng, W., S. R. Liou, G. Plunkett III, G. F. Mayhew, D. J. Rose, V. Burland, V. Kodoyianni, D. C. Schwartz, and F. R. Blattner. 2003. Comparative genomics of Salmonella enterica serovar Typhi strains Ty2 and CT18. J. Bacteriol. 185:2330-2337.
-
(2003)
J. Bacteriol.
, vol.185
, pp. 2330-2337
-
-
Deng, W.1
Liou, S.R.2
Plunkett III, G.3
Mayhew, G.F.4
Rose, D.J.5
Burland, V.6
Kodoyianni, V.7
Schwartz, D.C.8
Blattner, F.R.9
-
25
-
-
0032697140
-
DNA uptake in bacteria
-
Dubnau, D. 1999. DNA uptake in bacteria. Annu. Rev. Microbiol. 53:217-244.
-
(1999)
Annu. Rev. Microbiol.
, vol.53
, pp. 217-244
-
-
Dubnau, D.1
-
26
-
-
2342492364
-
The consistent phylogenetic signal in genome trees revealed by reducing the impact of noise
-
Dutilh, B. E., M. A. Huynen, W. J. Bruno, and B. Snel. 2004. The consistent phylogenetic signal in genome trees revealed by reducing the impact of noise. J. Mol. Evol. 58:527-539.
-
(2004)
J. Mol. Evol.
, vol.58
, pp. 527-539
-
-
Dutilh, B.E.1
Huynen, M.A.2
Bruno, W.J.3
Snel, B.4
-
27
-
-
0034568798
-
Evidence for symmetric chromosomal inversions around the replication origin in bacteria
-
RESEARCH0011.1-0011.9
-
Eisen, J. A., J. F. Heidelberg, O. White, and S. L. Salzberg. 2000. Evidence for symmetric chromosomal inversions around the replication origin in bacteria. Genom. Biol. 1: RESEARCH0011.1-0011.9.
-
(2000)
Genom. Biol.
, vol.1
-
-
Eisen, J.A.1
Heidelberg, J.F.2
White, O.3
Salzberg, S.L.4
-
28
-
-
0014211361
-
Construction of phylogenetic trees
-
Fitch, W. M., and E. Margoliash. 1967. Construction of phylogenetic trees. Science 155:279-284.
-
(1967)
Science
, vol.155
, pp. 279-284
-
-
Fitch, W.M.1
Margoliash, E.2
-
29
-
-
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
-
30
-
-
0029653518
-
Whole-genome random sequencing and assembly of Haemophilus influenzae Rd
-
Fleischmann, R. D., M. D. Adams, O. White et al. (37 co-authors). 1995. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269:496-512.
-
(1995)
Science
, vol.269
, pp. 496-512
-
-
Fleischmann, R.D.1
Adams, M.D.2
White, O.3
-
31
-
-
0037250391
-
HGT-DB: A database of putative horizontally transferred genes in prokaryotic complete genomes
-
Garcia-Vallve, S., E. Guzman, M. A. Montera, and A. Romeu. 2003. HGT-DB: a database of putative horizontally transferred genes in prokaryotic complete genomes. Nucleic Acids Res. 31:187-189.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 187-189
-
-
Garcia-Vallve, S.1
Guzman, E.2
Montera, M.A.3
Romeu, A.4
-
32
-
-
0033670249
-
Horizontal gene transfer in bacterial and archaeal complete genomes
-
Garcia-Valive, S., A. Romeu, and J. Palau. 2000. Horizontal gene transfer in bacterial and archaeal complete genomes. Genome Res. 10:1719-1725.
-
(2000)
Genome Res.
, vol.10
, pp. 1719-1725
-
-
Garcia-Valive, S.1
Romeu, A.2
Palau, J.3
-
33
-
-
0041422250
-
The genome sequence of Blochmannia floridanus: Comparative analysis of reduced genomes
-
Gil, R., F. J. Silva, E. Zientz, F. Delmotte, F. Gonzalez-Candelas, A. Latorre, C. Rausell, J. Kamerbeek, J. Gadau, B. Holldobler, R. C. H. J. van Ham, R. Gross, and A. Moya. 2003. The genome sequence of Blochmannia floridanus: Comparative analysis of reduced genomes. Proc. Natl. Acad. Sci. USA 100:9388-9393.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 9388-9393
-
-
Gil, R.1
Silva, F.J.2
Zientz, E.3
Delmotte, F.4
Gonzalez-Candelas, F.5
Latorre, A.6
Rausell, C.7
Kamerbeek, J.8
Gadau, J.9
Holldobler, B.10
Van Ham, R.C.H.J.11
Gross, R.12
Moya, A.13
-
34
-
-
6344269329
-
The evolutionary fate of nonfunctional DNA in the bacterial endosymbiont Buchnera aphidicola
-
Gomez-Valero, L., A. Latorre, and F. J. Silva. 2004. The evolutionary fate of nonfunctional DNA in the bacterial endosymbiont Buchnera aphidicola. Mol. Biol. Evol. 21:2172-2181.
-
(2004)
Mol. Biol. Evol.
, vol.21
, pp. 2172-2181
-
-
Gomez-Valero, L.1
Latorre, A.2
Silva, F.J.3
-
35
-
-
0033859839
-
Phylogeny of 33 ribosomal and six other proteins encoded in an ancient gene cluster that is conserved across prokaryotic genomes: Influence of excluding poorly alignable sites from analysis
-
Hansmann, S., and W. Martin. 2000. Phylogeny of 33 ribosomal and six other proteins encoded in an ancient gene cluster that is conserved across prokaryotic genomes: influence of excluding poorly alignable sites from analysis. Int. J. Syst. Evol. Microbiol. 50:1655-1663.
-
(2000)
Int. J. Syst. Evol. Microbiol.
, vol.50
, pp. 1655-1663
-
-
Hansmann, S.1
Martin, W.2
-
36
-
-
0035961748
-
Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12
-
Hayashi, T., K. Makino, M. Ohnishi et al. (19 co-authors). 2001. Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12. DNA Res. 8:11-22.
-
(2001)
DNA Res.
, vol.8
, pp. 11-22
-
-
Hayashi, T.1
Makino, K.2
Ohnishi, M.3
-
37
-
-
17144462135
-
DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae
-
Heidelberg, J. F., J. A. Eisen, W. C. Nelson et al. (23 co-authors). 2000. DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae. Nature 406:477-483.
-
(2000)
Nature
, vol.406
, pp. 477-483
-
-
Heidelberg, J.F.1
Eisen, J.A.2
Nelson, W.C.3
-
38
-
-
0036842611
-
Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis
-
Heidelberg, J. F., I. T. Paulsen, K. E. Nelson et al. (40 co-authors). 2002. Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis. Nat. Biotechnol. 20:1118-1123.
-
(2002)
Nat. Biotechnol.
, vol.20
, pp. 1118-1123
-
-
Heidelberg, J.F.1
Paulsen, I.T.2
Nelson, K.E.3
-
39
-
-
19544370050
-
Non-homogeneous model of sequence evolution indicates independent origins of primary endosymbionts within the Enterobacteriales (gamma-Proteobacteria)
-
Herbeck, J. T., P. H. Degnan, and J. J. Wernegreen. 2004. Non-homogeneous model of sequence evolution indicates independent origins of primary endosymbionts within the Enterobacteriales (gamma-Proteobacteria). Mol. Biol. Evol.
-
(2004)
Mol. Biol. Evol.
-
-
Herbeck, J.T.1
Degnan, P.H.2
Wernegreen, J.J.3
-
40
-
-
19544385458
-
Evaluating genome dynamics: The constraints on rearrangements within bacterial genomes
-
Hughes, D. 2000. Evaluating genome dynamics: the constraints on rearrangements within bacterial genomes. Genom. Biol. 22:520-532.
-
(2000)
Genom. Biol.
, vol.22
, pp. 520-532
-
-
Hughes, D.1
-
41
-
-
3042601821
-
Covarion shifts cause a long-branch attraction artifact that unites microsporidia and archaebacteria in EF-1 alpha phylogenies
-
Inagaki, Y., E. Susko, N. M. Fast, and A. J. Roger. 2004. Covarion shifts cause a long-branch attraction artifact that unites microsporidia and archaebacteria in EF-1 alpha phylogenies. Mol. Biol. Evol. 21:1340-1349.
-
(2004)
Mol. Biol. Evol.
, vol.21
, pp. 1340-1349
-
-
Inagaki, Y.1
Susko, E.2
Fast, N.M.3
Roger, A.J.4
-
42
-
-
0036791017
-
Acceleration of genomic evolution caused by enhanced mutation rate in endocellular symbionts
-
Itoh, T., W. Martin, and M. Nei. 2002. Acceleration of genomic evolution caused by enhanced mutation rate in endocellular symbionts. Proc. Natl. Acad. Sci. USA 99:12944-12948.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 12944-12948
-
-
Itoh, T.1
Martin, W.2
Nei, M.3
-
43
-
-
0033616714
-
Horizontal gene transfer among genomes: The complexity hypothesis
-
Jain, R., M. C. Rivera, and J. A. Lake. 1999. Horizontal gene transfer among genomes: the complexity hypothesis. Proc. Natl. Acad. Sci. USA 96:3801-3806.
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, pp. 3801-3806
-
-
Jain, R.1
Rivera, M.C.2
Lake, J.A.3
-
44
-
-
18644378721
-
Genome sequence of Shigella flexneri 2a: Insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157
-
Jin, Q., Z. Yuan, J. Xu et al. (30 co-authors). 2002. Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157. Nucleic Acids Res. 30:4432-4441.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 4432-4441
-
-
Jin, Q.1
Yuan, Z.2
Xu, J.3
-
45
-
-
0345863935
-
The KEGG resource for deciphering the genome
-
Kanehisa, M., S. Goto, S. Kawashima, Y. Okuno, and M. Hattori. 2004. The KEGG resource for deciphering the genome. Nucleic Acids Res. 32:D277-D280.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Kanehisa, M.1
Goto, S.2
Kawashima, S.3
Okuno, Y.4
Hattori, M.5
-
46
-
-
0141781023
-
Characterization and pathogenic significance of Vibrio vulnificus antigens preferentially expressed in septicemic patients
-
Kim, Y. R., S. E. Lee, C. M. Kim, S. Y. Kim, E. K. Shin, D. H. Shin, S. S. Chung, H. E. Choy, A. Progulske-Fox, J. D. Hillman, M. Handfield, and J. H. Rhee. 2003. Characterization and pathogenic significance of Vibrio vulnificus antigens preferentially expressed in septicemic patients. Infect. Immun. 71:5461-5471.
-
(2003)
Infect. Immun.
, vol.71
, pp. 5461-5471
-
-
Kim, Y.R.1
Lee, S.E.2
Kim, C.M.3
Kim, S.Y.4
Shin, E.K.5
Shin, D.H.6
Chung, S.S.7
Choy, H.E.8
Progulske-Fox, A.9
Hillman, J.D.10
Handfield, M.11
Rhee, J.H.12
-
47
-
-
7244221755
-
Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous
-
Kolaczkowski, B., and J. W. Thornton. 2004. Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature 431:980-984.
-
(2004)
Nature
, vol.431
, pp. 980-984
-
-
Kolaczkowski, B.1
Thornton, J.W.2
-
48
-
-
0031459310
-
Prokaryotic genomes: The emerging paradigm of genome-based microbiology
-
Koonin, E. V., and M. Y. Galperin. 1997. Prokaryotic genomes: the emerging paradigm of genome-based microbiology. Curr. Opin. Genet. Dev. 7:757-763.
-
(1997)
Curr. Opin. Genet. Dev.
, vol.7
, pp. 757-763
-
-
Koonin, E.V.1
Galperin, M.Y.2
-
49
-
-
0036499057
-
SHOT: A web server for the construction of genome phylogenies
-
Korbel, J. O., B. Snel, M. A. Huynen, and P. Bork. 2002. SHOT: a web server for the construction of genome phylogenies. Trends Genet. 18:158-162.
-
(2002)
Trends Genet.
, vol.18
, pp. 158-162
-
-
Korbel, J.O.1
Snel, B.2
Huynen, M.A.3
Bork, P.4
-
50
-
-
0032482924
-
Molecular archaeology of the Escherichia coli genome
-
Lawrence, J. G., and H. Ochman. 1998. Molecular archaeology of the Escherichia coli genome. Proc. Natl. Acad. Sci. USA 95:9413-9417.
-
(1998)
Proc. Natl. Acad. Sci. USA
, vol.95
, pp. 9413-9417
-
-
Lawrence, J.G.1
Ochman, H.2
-
51
-
-
1342271382
-
From gene trees to organismal phylogeny in prokaryotes: The case of the gamma-proteobacteria
-
Lerat, E., V. Daubin, and N. A. Moran. 2003. From gene trees to organismal phylogeny in prokaryotes: the case of the gamma-proteobacteria. PLoS. Biol. 1:101-109.
-
(2003)
PLoS. Biol.
, vol.1
, pp. 101-109
-
-
Lerat, E.1
Daubin, V.2
Moran, N.A.3
-
52
-
-
0037333881
-
Genome sequence of Vibrio parahaemolyticus: A pathogenic mechanism distinct from that of V cholerae
-
Makino, K., K. Oshima, K. Kurokawa et al. (14 co-authors). 2003. Genome sequence of Vibrio parahaemolyticus: a pathogenic mechanism distinct from that of V cholerae. Lancet. 361:743-749.
-
(2003)
Lancet
, vol.361
, pp. 743-749
-
-
Makino, K.1
Oshima, K.2
Kurokawa, K.3
-
53
-
-
0035853112
-
Complete genomic sequence of Pasteurella multocida
-
May, B. J., Q. Zhang, L. L. Li, M. L. Paustian, T. S. Whittam, and V. Kapur. 2001. Complete genomic sequence of Pasteurella multocida, Pm70. Proc. Natl. Acad. Sci. USA 98:3460-3465.
-
(2001)
Pm70. Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 3460-3465
-
-
May, B.J.1
Zhang, Q.2
Li, L.L.3
Paustian, M.L.4
Whittam, T.S.5
Kapur, V.6
-
54
-
-
0035950182
-
Complete genome sequence of Salmonella enterica serovar Typhimurium LT2
-
McClelland, M., K. E. Sanderson, J. Spieth et al. (23 co-authors). 2001. Complete genome sequence of Salmonella enterica serovar Typhimurium LT2. Nature 413:852-856.
-
(2001)
Nature
, vol.413
, pp. 852-856
-
-
McClelland, M.1
Sanderson, K.E.2
Spieth, J.3
-
55
-
-
4944262629
-
Successful lateral transfer requires codon usage compatibility between foreign genes and recipient genomes
-
Medrano-Soto, A., G. Moreno-Hagelsieb, P. Vinuesa, J. A. Christen, and J. Collado-Vides. 2004. Successful lateral transfer requires codon usage compatibility between foreign genes and recipient genomes. Mol. Biol. Evol. 21:1884-1894.
-
(2004)
Mol. Biol. Evol.
, vol.21
, pp. 1884-1894
-
-
Medrano-Soto, A.1
Moreno-Hagelsieb, G.2
Vinuesa, P.3
Christen, J.A.4
Collado-Vides, J.5
-
56
-
-
0029866448
-
Accelerated evolution and Muller's rachet in endosymbiotic bacteria
-
Moran, N. A. 1996. Accelerated evolution and Muller's rachet in endosymbiotic bacteria. Proc. Natl. Acad. Sci. USA 93: 2873-2878.
-
(1996)
Proc. Natl. Acad. Sci. USA
, vol.93
, pp. 2873-2878
-
-
Moran, N.A.1
-
57
-
-
0037040394
-
Microbial minimalism: Genome reduction in bacterial pathogens
-
-. 2002. Microbial minimalism: genome reduction in bacterial pathogens. Cell 108:583-586.
-
(2002)
Cell
, vol.108
, pp. 583-586
-
-
-
58
-
-
0035749612
-
The process of genome shrinkage in the obligate symbiont Buchnera aphidicola
-
RESEARCH0054.01-0054.12
-
Moran, N. A., and A. Mira. 2001. The process of genome shrinkage in the obligate symbiont Buchnera aphidicola. Genom. Biol. 2:RESEARCH0054.01-0054.12.
-
(2001)
Genom. Biol.
, vol.2
-
-
Moran, N.A.1
Mira, A.2
-
59
-
-
0035229986
-
New approaches for reconstructing phylogenies from gene order data
-
Moret, B. M., L. S. Wang, T. Warnow, and S. K. Wyman. 2001. New approaches for reconstructing phylogenies from gene order data. Bioinformatics 17(Suppl. 1):S165-S173.
-
(2001)
Bioinformatics
, vol.17
, Issue.SUPPL. 1
-
-
Moret, B.M.1
Wang, L.S.2
Warnow, T.3
Wyman, S.K.4
-
60
-
-
84957042462
-
Inversion medians outperform breakpoint medians in phylogeny reconstruction from gene-order data
-
WABI 2002, Rome, Italy, September 17-21, 2002, ed. R. Guigó and D. Gusfield. Springer-Verlag
-
Moret, B. M. E., A. C. Siepel, J. Tang, and T. Liu. 2002a. Inversion medians outperform breakpoint medians in phylogeny reconstruction from gene-order data. Pp. 521-536 in Algorithms in bioinformatics. Second International Workshop, WABI 2002, Rome, Italy, September 17-21, 2002, ed. R. Guigó and D. Gusfield. Springer-Verlag.
-
(2002)
Algorithms in Bioinformatics. Second International Workshop
, pp. 521-536
-
-
Moret, B.M.E.1
Siepel, A.C.2
Tang, J.3
Liu, T.4
-
61
-
-
23844520968
-
Steps toward accurate reconstructions of phylogenies from gene-order data
-
Moret, B. M. E., J. J. Tang, L. S. Wang, and T. Warnow. 2002b. Steps toward accurate reconstructions of phylogenies from gene-order data. J. Comput. Syst. Sci. 65:508-525.
-
(2002)
J. Comput. Syst. Sci.
, vol.65
, pp. 508-525
-
-
Moret, B.M.E.1
Tang, J.J.2
Wang, L.S.3
Warnow, T.4
-
62
-
-
0034922289
-
Modeling amino acid replacement
-
Muller, T., and M. Vingron. 2000. Modeling amino acid replacement. J. Comput. Biol. 7:761-776.
-
(2000)
J. Comput. Biol.
, vol.7
, pp. 761-776
-
-
Muller, T.1
Vingron, M.2
-
63
-
-
0032401050
-
Counting on comparative maps
-
Nadeau, J. H., and D. Sankoff. 1998. Counting on comparative maps. Trends Genet. 14:495-501.
-
(1998)
Trends Genet.
, vol.14
, pp. 495-501
-
-
Nadeau, J.H.1
Sankoff, D.2
-
64
-
-
0000791476
-
Lengths of chromosomal segments conserved since divergence of man and mouse
-
Nadeau, J. H., and B. A. Taylor. 1984. Lengths of chromosomal segments conserved since divergence of man and mouse. Proc. Natl. Acad. Sci. USA 81:814-818.
-
(1984)
Proc. Natl. Acad. Sci. USA
, vol.81
, pp. 814-818
-
-
Nadeau, J.H.1
Taylor, B.A.2
-
65
-
-
0030458552
-
Phylogenetic analysis in molecular evolutionary genetics
-
Nei, M. 1996. Phylogenetic analysis in molecular evolutionary genetics. Annu. Rev. Genet. 30:371-403.
-
(1996)
Annu. Rev. Genet.
, vol.30
, pp. 371-403
-
-
Nei, M.1
-
66
-
-
0036933705
-
Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440
-
Nelson, K. E., C. Weinel, I. T. Paulsen et al. (40 co-authors). 2002. Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. Environ. Microbiol. 4:799-808.
-
(2002)
Environ. Microbiol.
, vol.4
, pp. 799-808
-
-
Nelson, K.E.1
Weinel, C.2
Paulsen, I.T.3
-
67
-
-
0034682335
-
Lateral gene transfer and the nature of bacterial innovation
-
Ochman, H., J. G. Lawrence, and E. A. Groisman. 2000. Lateral gene transfer and the nature of bacterial innovation. Nature 405:299-304.
-
(2000)
Nature
, vol.405
, pp. 299-304
-
-
Ochman, H.1
Lawrence, J.G.2
Groisman, E.A.3
-
68
-
-
0036730186
-
A strong effect of AT mutational bias on amino acid usage in Buchnera is mitigated at high-expression genes
-
Palacios, C., and J. J. Wernegreen. 2002. A strong effect of AT mutational bias on amino acid usage in Buchnera is mitigated at high-expression genes. Mol. Biol. Evol. 19:1575-1584.
-
(2002)
Mol. Biol. Evol.
, vol.19
, pp. 1575-1584
-
-
Palacios, C.1
Wernegreen, J.J.2
-
69
-
-
0035950154
-
Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18
-
Parkhill, J., G. Dougan, K. D. James et al. (38 co-authors). 2001a. Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18. Nature 413:848-852.
-
(2001)
Nature
, vol.413
, pp. 848-852
-
-
Parkhill, J.1
Dougan, G.2
James, K.D.3
-
70
-
-
0035807385
-
Genome sequence of Yersinia pestis, the causative agent of plague
-
Parkhill, J., B. W. Wren, N. R. Thomson et al. (33 co-authors). 2001. Genome sequence of Yersinia pestis, the causative agent of plague. Nature 413:523-527.
-
(2001)
Nature
, vol.413
, pp. 523-527
-
-
Parkhill, J.1
Wren, B.W.2
Thomson, N.R.3
-
71
-
-
0035945586
-
Genome sequence of enterohaemorrhagic Escherichia coli O157:H7
-
Perna, N. T., G. Plunkett III, V. Burland et al. (25 co-authors). 2001. Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 409:529-533.
-
(2001)
Nature
, vol.409
, pp. 529-533
-
-
Perna, N.T.1
Plunkett III, G.2
Burland, V.3
-
72
-
-
0347135951
-
Mutational and selective pressures on codon and amino acid usage in Buchnera, endosymbiotic bacteria of aphids
-
Rispe, C., F. Delmotte, R. C. H. J. Van Ham, and A. Moya. 2004. Mutational and selective pressures on codon and amino acid usage in Buchnera, endosymbiotic bacteria of aphids. Genome Res. 14:44-53.
-
(2004)
Genome Res.
, vol.14
, pp. 44-53
-
-
Rispe, C.1
Delmotte, F.2
Van Ham, R.C.H.J.3
Moya, A.4
-
73
-
-
0242365676
-
Genome-scale approaches to resolving incongruence in molecular phylogenies
-
Rokas, A., B. L. Williams, N. King, and S. B. Carroll. 2003. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425:798-804.
-
(2003)
Nature
, vol.425
, pp. 798-804
-
-
Rokas, A.1
Williams, B.L.2
King, N.3
Carroll, S.B.4
-
74
-
-
0023375195
-
The neighbor-joining method: A new method for reconstructing phylogenetic trees
-
Saitou, N., and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
-
(1987)
Mol. Biol. Evol.
, vol.4
, pp. 406-425
-
-
Saitou, N.1
Nei, M.2
-
75
-
-
0033803852
-
Systematic relationships and cospeciation of bacterial endosymbionts and their carpenter ant host species: Proposal of the new taxon Candidatus Blochmannia gen. nov.
-
Sauer, C., E. Stackebrandt, J. Gadau, B. Holldobler, and R. Gross. 2000. Systematic relationships and cospeciation of bacterial endosymbionts and their carpenter ant host species: proposal of the new taxon Candidatus Blochmannia gen. nov. Int. J. Syst. Evol. Microbiol. 50:1877-1886.
-
(2000)
Int. J. Syst. Evol. Microbiol.
, vol.50
, pp. 1877-1886
-
-
Sauer, C.1
Stackebrandt, E.2
Gadau, J.3
Holldobler, B.4
Gross, R.5
-
76
-
-
0036205377
-
TREE-PUZZLE: Maximum likelihood phylogenetic analysis using quartets and parallel computing
-
Schmidt, H. A., K. Strimmer, M. Vingron, and A. von Haeseler. 2002. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18:502-504.
-
(2002)
Bioinformatics
, vol.18
, pp. 502-504
-
-
Schmidt, H.A.1
Strimmer, K.2
Vingron, M.3
Von Haeseler, A.4
-
77
-
-
0034618559
-
Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp APS
-
Shigenobu, S., H. Watanabe, M. Hattori, Y. Sakaki, and H. Ishikawa. 2000. Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp APS. Nature 407:81-86.
-
(2000)
Nature
, vol.407
, pp. 81-86
-
-
Shigenobu, S.1
Watanabe, H.2
Hattori, M.3
Sakaki, Y.4
Ishikawa, H.5
-
78
-
-
0034825117
-
Accumulation of species-specific amino acid replacements that cause loss of particular protein functions in Buchnera, an endocellular bacterial symbiont
-
Shigenobu, S., H. Watanabe, Y. Sakaki, and H. Ishikawa. 2001. Accumulation of species-specific amino acid replacements that cause loss of particular protein functions in Buchnera, an endocellular bacterial symbiont. J. Mol. Evol. 53:377-386.
-
(2001)
J. Mol. Evol.
, vol.53
, pp. 377-386
-
-
Shigenobu, S.1
Watanabe, H.2
Sakaki, Y.3
Ishikawa, H.4
-
80
-
-
0035500843
-
Genome size reduction through multiple events of gene disintegration in Buchnera APS
-
Silva, F. J., A. Latorre, and A. Moya. 2001. Genome size reduction through multiple events of gene disintegration in Buchnera APS. Trends Genet. 17:615-618.
-
(2001)
Trends Genet.
, vol.17
, pp. 615-618
-
-
Silva, F.J.1
Latorre, A.2
Moya, A.3
-
81
-
-
0037384544
-
Why are the genomes of endosymbiotic bacteria so stable?
-
-. 2003. Why are the genomes of endosymbiotic bacteria so stable? Trends Genet. 19:176-180.
-
(2003)
Trends Genet
, vol.19
, pp. 176-180
-
-
-
82
-
-
0034644159
-
The genome sequence of the plant pathogen Xylella fastidiosa. The Xylella fastidiosa Consortium of the Organization for Nucleotide Sequencing and Analysis
-
Simpson, A. J., F. C. Reinach, P. Arruda et al. (113 co-authors). 2000. The genome sequence of the plant pathogen Xylella fastidiosa. The Xylella fastidiosa Consortium of the Organization for Nucleotide Sequencing and Analysis. Nature 406:151-157.
-
(2000)
Nature
, vol.406
, pp. 151-157
-
-
Simpson, A.J.1
Reinach, F.C.2
Arruda, P.3
-
83
-
-
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
-
84
-
-
0034739007
-
Complete genome sequence of Pseudomonas aeruginosa PA01, an opportunistic pathogen
-
Stover, C. K., X. Q. Pham, A. L. Erwin et al. (28 co-authors). 2000. Complete genome sequence of Pseudomonas aeruginosa PA01, an opportunistic pathogen. Nature 406:959-964.
-
(2000)
Nature
, vol.406
, pp. 959-964
-
-
Stover, C.K.1
Pham, X.Q.2
Erwin, A.L.3
-
85
-
-
0029836454
-
Quartet puzzling: A quartet maximum-likelihood method for reconstructing tree topologies
-
Strimmer, K., and A. vonHaeseler. 1996. Quartet puzzling: a quartet maximum-likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13:964-969.
-
(1996)
Mol. Biol. Evol.
, vol.13
, pp. 964-969
-
-
Strimmer, K.1
VonHaeseler, A.2
-
86
-
-
3042545431
-
On inconsistency of the neighbor-joining, least squares, and minimum evolution estimation when substitution processes are incorrectly modeled
-
Susko, E., Y. Inagaki, and A. J. Roger. 2004. On inconsistency of the neighbor-joining, least squares, and minimum evolution estimation when substitution processes are incorrectly modeled. Mol. Biol. Evol. 21:1629-1642.
-
(2004)
Mol. Biol. Evol.
, vol.21
, pp. 1629-1642
-
-
Susko, E.1
Inagaki, Y.2
Roger, A.J.3
-
87
-
-
0035058359
-
Evolution of prokaryotic gene order: Genome rearrangements in closely related species
-
Suyama, M., and P. Bork. 2001. Evolution of prokaryotic gene order: genome rearrangements in closely related species. Trends Genet. 17:10-13.
-
(2001)
Trends Genet.
, vol.17
, pp. 10-13
-
-
Suyama, M.1
Bork, P.2
-
88
-
-
0037189373
-
50 Million years of genomic stasis in endosymbiotic bacteria
-
Tamas, I., L. Klasson, B. Canback, A. K. Naslund, A. S. Eriksson, J. J. Wernegreen, J. P. Sandstrom, N. A. Moran, and S. G. E. Andersson. 2002. 50 Million years of genomic stasis in endosymbiotic bacteria. Science 296:2376-2379.
-
(2002)
Science
, vol.296
, pp. 2376-2379
-
-
Tamas, I.1
Klasson, L.2
Canback, B.3
Naslund, A.K.4
Eriksson, A.S.5
Wernegreen, J.J.6
Sandstrom, J.P.7
Moran, N.A.8
Andersson, S.G.E.9
-
89
-
-
0345225320
-
Scaling up accurate phylogenetic reconstruction from gene-order data
-
Tang, J., and B. M. E. Moret. 2003a. Scaling up accurate phylogenetic reconstruction from gene-order data. Bioinformatics 19(Suppl. 1):i305-i312.
-
(2003)
Bioinformatics
, vol.19
, Issue.SUPPL. 1
-
-
Tang, J.1
Moret, B.M.E.2
-
90
-
-
35248841995
-
Phylogenetic reconstruction from gene-rearrangement data with unequal gene content
-
ed. F. Dehne, J.-R. Sack, and M. Smid. Springer-Verlag
-
-. 2003e. Phylogenetic reconstruction from gene-rearrangement data with unequal gene content. Pp. 37-46 in Algorithms and data structures, ed. F. Dehne, J.-R. Sack, and M. Smid. Springer-Verlag.
-
(2003)
Algorithms and Data Structures
, pp. 37-46
-
-
-
91
-
-
0036211065
-
GRIMM: Genome rearrangements web server
-
Tesler, G. 2002. GRIMM: genome rearrangements web server. Bioinformatics 18:492-493.
-
(2002)
Bioinformatics
, vol.18
, pp. 492-493
-
-
Tesler, G.1
-
92
-
-
0031574072
-
The CLUSTAL_X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools
-
Thompson, J. D., T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins. 1997. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25:4876-4882.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 4876-4882
-
-
Thompson, J.D.1
Gibson, T.J.2
Plewniak, F.3
Jeanmougin, F.4
Higgins, D.G.5
-
93
-
-
0033776631
-
Genome rearrangement by replication-directed translocation
-
Tillier, E. R., and R. A. Collins. 2000. Genome rearrangement by replication-directed translocation. Nat. Genet. 26:195-197.
-
(2000)
Nat. Genet.
, vol.26
, pp. 195-197
-
-
Tillier, E.R.1
Collins, R.A.2
-
94
-
-
0037249403
-
MBGD: Microbial genome database for comparative analysis
-
Uchiyama, I. 2003. MBGD: microbial genome database for comparative analysis. Nucleic Acids Res. 31:58-62.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 58-62
-
-
Uchiyama, I.1
-
96
-
-
0037310805
-
Comparative analyses of the complete genome sequences of Pierce's disease and citrus variegated chlorosis strains of Xylella fastidiosa
-
Van Sluys, M. A., M. C. de Oliveira, C. B. Monteiro-Vitorello et al. (55 co-authors). 2003. Comparative analyses of the complete genome sequences of Pierce's disease and citrus variegated chlorosis strains of Xylella fastidiosa. J. Bacteriol. 185:1018-1026.
-
(2003)
J. Bacteriol.
, vol.185
, pp. 1018-1026
-
-
Van Sluys, M.A.1
De Oliveira, M.C.2
Monteiro-Vitorello, C.B.3
-
97
-
-
0034487561
-
Molecular data support a rapid radiation of aphids in the Cretaceous and multiple origins of host alternation
-
Von Dohlen, C. D., and N. A. Moran. 2000. Molecular data support a rapid radiation of aphids in the Cretaceous and multiple origins of host alternation. Biol. J. Linn. Soc. 71:689-717.
-
(2000)
Biol. J. Linn. Soc.
, vol.71
, pp. 689-717
-
-
Von Dohlen, C.D.1
Moran, N.A.2
-
98
-
-
0242416999
-
Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T
-
Wei, J., M. B. Goldberg, V. Burland et al. (14 co-authors). 2003. Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T. Infect. Immun. 71:2775-2786.
-
(2003)
Infect. Immun.
, vol.71
, pp. 2775-2786
-
-
Wei, J.1
Goldberg, M.B.2
Burland, V.3
-
99
-
-
0037168538
-
Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli
-
Welch, R. A., V. Burland, G. Plunkett III et al. (16 co-authors). 2002. Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proc. Natl. Acad. Sci. USA 99:17020-17024.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 17020-17024
-
-
Welch, R.A.1
Burland, V.2
Plunkett III, G.3
-
100
-
-
0036719929
-
Genome trees and the tree of life
-
Wolf, Y. I., I. B. Rogozin, N. V. Grishin, and E. V. Koonin. 2002. Genome trees and the tree of life. Trends Genet. 18:472-479.
-
(2002)
Trends Genet.
, vol.18
, pp. 472-479
-
-
Wolf, Y.I.1
Rogozin, I.B.2
Grishin, N.V.3
Koonin, E.V.4
|