-
1
-
-
0033603539
-
Phylogenetic classification and the universal tree
-
(doi:10.1126/science.284.5423.2124)
-
Doolittle WF. 1999 Phylogenetic classification and the universal tree. Science 284, 2124-2128. (doi:10.1126/science.284.5423.2124)
-
(1999)
Science
, vol.284
, pp. 2124-2128
-
-
Doolittle, W.F.1
-
2
-
-
0034682335
-
Lateral gene transfer and the nature of bacterial innovation
-
(doi:10.1038/35012500)
-
Ochman H, Lawrence JG, Groisman EA. 2000 Lateral gene transfer and the nature of bacterial innovation. Nature 405, 299-304. (doi:10.1038/35012500)
-
(2000)
Nature
, vol.405
, pp. 299-304
-
-
Ochman, H.1
Lawrence, J.G.2
Groisman, E.A.3
-
3
-
-
0242371471
-
Horizontal gene transfer accelerates genome innovation and evolution
-
(doi:10.1093/molbev/msg154)
-
Jain R, Rivera MC, Moore JE, Lake JA. 2003 Horizontal gene transfer accelerates genome innovation and evolution. Mol. Biol. Evol. 20, 1598-1602. (doi:10.1093/molbev/msg154)
-
(2003)
Mol. Biol. Evol.
, vol.20
, pp. 1598-1602
-
-
Jain, R.1
Rivera, M.C.2
Moore, J.E.3
Lake, J.A.4
-
4
-
-
79953778881
-
Lateral gene transfer
-
(doi:10.1016/j. cub.2011.01.045)
-
Zhaxybayeva O, Doolittle WF. 2011 Lateral gene transfer. Curr. Biol. 21, R242 - R246. (doi:10.1016/j. cub.2011.01.045)
-
(2011)
Curr. Biol.
, vol.21
-
-
Zhaxybayeva, O.1
Doolittle, W.F.2
-
5
-
-
79960313230
-
Lateral genetic transfer and the construction of genetic exchange communities
-
(doi:10.1111/j.1574-6976.2010. 00261.x)
-
Skippington E, Ragan MA. 2011 Lateral genetic transfer and the construction of genetic exchange communities. FEMS Microbiol. Rev. 35, 707-735. (doi:10.1111/j.1574-6976.2010. 00261.x)
-
(2011)
FEMS Microbiol. Rev.
, vol.35
, pp. 707-735
-
-
Skippington, E.1
Ragan, M.A.2
-
6
-
-
0036898759
-
Prokaryotic evolution in light of gene transfer
-
(doi:10.1093/oxfordjournals.molbev.a004046)
-
Gogarten JP, Doolittle WF, Lawrence JG. 2002 Prokaryotic evolution in light of gene transfer. Mol. Biol. Evol. 19, 2226-2238. (doi:10.1093/ oxfordjournals.molbev.a004046)
-
(2002)
Mol. Biol. Evol.
, vol.19
, pp. 2226-2238
-
-
Gogarten, J.P.1
Doolittle, W.F.2
Lawrence, J.G.3
-
7
-
-
79952201675
-
The tree and net components of prokaryote evolution
-
(doi:10.1093/gbe/evq062)
-
Puigbò P, Wolf YI, Koonin EV. 2010 The tree and net components of prokaryote evolution. Genome Biol. Evol. 2, 745-756. (doi:10.1093/gbe/evq062)
-
(2010)
Genome Biol. Evol.
, vol.2
, pp. 745-756
-
-
Puigbò, P.1
Wolf, Y.I.2
Koonin, E.V.3
-
8
-
-
77953776263
-
Biased gene transfer mimics patterns created through shared ancestry
-
(doi:10.1073/pnas.1001418107)
-
Andam CP, Williams D, Gogarten JP. 2010 Biased gene transfer mimics patterns created through shared ancestry. Proc. Natl Acad. Sci. USA 107, 10679-10684. (doi:10.1073/pnas.1001418107)
-
(2010)
Proc. Natl Acad. Sci. USA
, vol.107
, pp. 10679-10684
-
-
Andam, C.P.1
Williams, D.2
Gogarten, J.P.3
-
9
-
-
79959256644
-
Biased gene transfer in microbial evolution
-
(doi:10.1038/nrmicro2593)
-
Andam CP, Gogarten JP. 2011 Biased gene transfer in microbial evolution. Nat. Rev. Microbiol. 9, 543-555. (doi:10.1038/nrmicro2593)
-
(2011)
Nat. Rev. Microbiol.
, vol.9
, pp. 543-555
-
-
Andam, C.P.1
Gogarten, J.P.2
-
10
-
-
33748277982
-
Phylogenetic analyses of cyanobacterial genomes: Quantification of horizontal gene transfer events
-
(doi:10.1101/gr.5322306)
-
Zhaxybayeva O, Gogarten JP, Charlebois RL, Doolittle WF, Papke RT. 2006 Phylogenetic analyses of cyanobacterial genomes: quantification of horizontal gene transfer events. Genome Res. 16, 1099-1108. (doi:10.1101/gr.5322306)
-
(2006)
Genome Res.
, vol.16
, pp. 1099-1108
-
-
Zhaxybayeva, O.1
Gogarten, J.P.2
Charlebois, R.L.3
Doolittle, W.F.4
Papke, R.T.5
-
11
-
-
77149147828
-
Intertwined evolutionary histories of marine Synechococcus and Prochlorococcusmarinus
-
(doi:10.1093/gbe/evp032)
-
Zhaxybayeva O, Doolittle WF, Papke RT, Gogarten JP. 2009 Intertwined evolutionary histories of marine Synechococcus and Prochlorococcusmarinus. Genome Biol. Evol. 1, 325-339. (doi:10.1093/gbe/evp032)
-
(2009)
Genome Biol. Evol.
, vol.1
, pp. 325-339
-
-
Zhaxybayeva, O.1
Doolittle, W.F.2
Papke, R.T.3
Gogarten, J.P.4
-
12
-
-
80053175926
-
Biased gene transfer and its implications for the concept of lineage
-
(doi:10.1186/1745-6150-6-47)
-
Andam CP, Gogarten JP. 2011 Biased gene transfer and its implications for the concept of lineage. Biol. Direct. 6, 47. (doi:10.1186/1745-6150-6-47)
-
(2011)
Biol. Direct.
, vol.6
, pp. 47
-
-
Andam, C.P.1
Gogarten, J.P.2
-
13
-
-
79953315166
-
Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes
-
(doi:10.1101/gr.115592.110)
-
Popa O, Hazkani-Covo E, Landan G, Martin W, Dagan T. 2011 Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes. Genome Res. 21, 599-609. (doi:10.1101/gr.115592.110)
-
(2011)
Genome Res.
, vol.21
, pp. 599-609
-
-
Popa, O.1
Hazkani-Covo, E.2
Landan, G.3
Martin, W.4
Dagan, T.5
-
14
-
-
59249089471
-
Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths
-
(doi:10.1371/journal.pgen.1000344)
-
Touchon M. et al. 2009 Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet. 5, e1000344. (doi:10.1371/journal.pgen.1000344)
-
(2009)
PLoS Genet.
, vol.5
-
-
Touchon, M.1
-
15
-
-
78149470831
-
Comparison of 61 sequenced Escherichia coli genomes
-
(doi:10.1007/s00248-010-9717-3)
-
Lukjancenko O, Wassenaar TM, Ussery DW. 2010 Comparison of 61 sequenced Escherichia coli genomes. Microb. Ecol. 60, 708-720. (doi:10.1007/s00248-010- 9717-3)
-
(2010)
Microb. Ecol.
, vol.60
, pp. 708-720
-
-
Lukjancenko, O.1
Wassenaar, T.M.2
Ussery, D.W.3
-
16
-
-
0026332291
-
Evidence for horizontal gene transfer in Escherichia coli speciation
-
(doi:10.1016/0022-2836(91)90575-Q)
-
Médigue C, Rouxel T, Vigier P, Hénaut A, Danchin A. 1991 Evidence for horizontal gene transfer in Escherichia coli speciation. J. Mol. Biol. 222, 851-856. (doi:10.1016/0022-2836(91)90575-Q)
-
(1991)
J. Mol. Biol.
, vol.222
, pp. 851-856
-
-
Médigue, C.1
Rouxel, T.2
Vigier, P.3
Hénaut, A.4
Danchin, A.5
-
17
-
-
80054976329
-
Within-species lateral genetic transfer and the evolution of transcriptional regulation in Escherichia coli and Shigella
-
(doi:10.1186/1471-2164-12-532)
-
Skippington E, Ragan MA. 2011 Within-species lateral genetic transfer and the evolution of transcriptional regulation in Escherichia coli and Shigella. BMC Genomics 12, 532. (doi:10.1186/1471-2164-12-532)
-
(2011)
BMC Genomics
, vol.12
, pp. 532
-
-
Skippington, E.1
Ragan, M.A.2
-
18
-
-
59149104994
-
Complete genome sequence and comparative analysis of the wild-type commensal Escherichia coli strain SE11 isolated from a healthy adult
-
(doi:10.1093/dnares/dsn026)
-
Oshima K et al. 2008 Complete genome sequence and comparative analysis of the wild-type commensal Escherichia coli strain SE11 isolated from a healthy adult. DNA Res. 15, 375-386. (doi:10.1093/dnares/dsn026)
-
(2008)
DNA Res.
, vol.15
, pp. 375-386
-
-
Oshima, K.1
-
19
-
-
53849104729
-
The pangenome structure of Escherichia coli: Comparative genomic analysis of E. coli commensal and pathogenic isolates
-
(doi:10.1128/JB. 00619-08)
-
Rasko DA. et al. 2008 The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates. J. Bacteriol. 190, 6881-6893. (doi:10.1128/JB. 00619-08)
-
(2008)
J. Bacteriol.
, vol.190
, pp. 6881-6893
-
-
Rasko, D.A.1
-
20
-
-
28544440091
-
Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery
-
(doi:10.1093/nar/gki954)
-
Yang F et al. 2005 Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery. Nucleic Acids Res. 33, 6445-6458. (doi:10.1093/nar/gki954)
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 6445-6458
-
-
Yang, F.1
-
21
-
-
0031004145
-
Evolutionary relationships among pathogenic and nonpathogenic Escherichia coli strains inferred from multilocus enzyme electrophoresis and mdh sequence studies
-
Pupo GM, Karaolis DKR, Lan RT, Reeves PR. 1997 Evolutionary relationships among pathogenic and nonpathogenic Escherichia coli strains inferred from multilocus enzyme electrophoresis and mdh sequence studies. Infect. Immun. 65, 2685-2692.
-
(1997)
Infect. Immun.
, vol.65
, pp. 2685-2692
-
-
Pupo, G.M.1
Karaolis, D.K.R.2
Lan, R.T.3
Reeves, P.R.4
-
22
-
-
0242416999
-
Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T
-
(doi:10.1128/IAI.71.5.2775-2786.2003)
-
Wei J. et al. 2003 Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T. Infect. Immun. 71, 2775-2786. (doi:10.1128/IAI.71.5.2775-2786.2003)
-
(2003)
Infect. Immun.
, vol.71
, pp. 2775-2786
-
-
Wei, J.1
-
23
-
-
18644378721
-
Genome sequence of Shigella flexneri 2a: Insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157
-
(doi:10.1093/nar/gkf566)
-
Jin Q. et al. 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. (doi:10.1093/nar/gkf566)
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 4432-4441
-
-
Jin, Q.1
-
24
-
-
33747383567
-
Complete genome sequence of Shigella flexneri 5b and comparison with Shigella flexneri 2a
-
(doi:10.1186/1471-2164-7-173)
-
Nie H. et al. 2006 Complete genome sequence of Shigella flexneri 5b and comparison with Shigella flexneri 2a. BMC Genomics 7, 173. (doi:10.1186/1471- 2164-7-173)
-
(2006)
BMC Genomics
, vol.7
, pp. 173
-
-
Nie, H.1
-
25
-
-
41249084917
-
Combining metabolic engineering and metabolic evolution to develop nonrecombinant strains of Escherichia coli C that produce succinate and malate
-
(doi:10.1002/bit.21694)
-
Jantama K, Haupt MJ, Svoronos SA, Zhang X, Moore JC, Shanmugam KT, Ingram LO. 2008 Combining metabolic engineering and metabolic evolution to develop nonrecombinant strains of Escherichia coli C that produce succinate and malate. Biotechnol. Bioeng. 99, 1140-1153. (doi:10.1002/bit.21694)
-
(2008)
Biotechnol. Bioeng.
, vol.99
, pp. 1140-1153
-
-
Jantama, K.1
Haupt, M.J.2
Svoronos, S.A.3
Zhang, X.4
Moore, J.C.5
Shanmugam, K.T.6
Ingram, L.O.7
-
26
-
-
15444350252
-
The complete genome sequence of Escherichia coli K-12
-
(doi:10.1126/science.277.5331.1453)
-
Blattner FR. et al. 1997 The complete genome sequence of Escherichia coli K-12. Science 277, 1453-1462. (doi:10.1126/science.277.5331.1453)
-
(1997)
Science
, vol.277
, pp. 1453-1462
-
-
Blattner, F.R.1
-
27
-
-
31544443526
-
Escherichia coli K-12: A cooperatively developed annotation snapshot-2005
-
(doi:10.1093/nar/gkj405)
-
Riley M. et al. 2006 Escherichia coli K-12: a cooperatively developed annotation snapshot-2005. Nucleic Acids Res. 34, 1-9. (doi:10.1093/nar/gkj405)
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 1-9
-
-
Riley, M.1
-
28
-
-
0035945586
-
Genome sequence of enterohaemorrhagic Escherichia coli O157: H7
-
(doi:10.1038/35054089)
-
Perna NT. et al. 2001 Genome sequence of enterohaemorrhagic Escherichia coli O157: H7. Nature 410, 240. (doi:10.1038/35054089)
-
(2001)
Nature
, vol.410
, pp. 240
-
-
Perna, N.T.1
-
29
-
-
0035961748
-
Complete genome sequence of enterohemorrhagic Escherichia coli O157: H7 and genomic comparison with a laboratory strain K-12
-
(doi:10.1093/dnares/8.1.11)
-
Hayashi T. et al. 2001 Complete genome sequence of enterohemorrhagic Escherichia coli O157: H7 and genomic comparison with a laboratory strain K-12. DNA Res. 8, 11-22. (doi:10.1093/dnares/8.1.11)
-
(2001)
DNA Res.
, vol.8
, pp. 11-22
-
-
Hayashi, T.1
-
30
-
-
34247846229
-
The genome sequence of avian pathogenic Escherichia coli strain O1: K1: H7 shares strong similarities with human extraintestinal pathogenic E. coli genomes
-
(doi:10.1128/JB.01726-06)
-
Johnson TJ. et al. 2007 The genome sequence of avian pathogenic Escherichia coli strain O1: K1: H7 shares strong similarities with human extraintestinal pathogenic E. coli genomes. J. Bacteriol. 189, 3228-3236. (doi:10.1128/JB.01726-06)
-
(2007)
J. Bacteriol.
, vol.189
, pp. 3228-3236
-
-
Johnson, T.J.1
-
31
-
-
33645827531
-
Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: A comparative genomics approach
-
(doi:10.1073/pnas.0600938103)
-
Chen SL. et al. 2006 Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: a comparative genomics approach. Proc. Natl Acad. Sci. USA 103, 5977-5982. (doi:10.1073/pnas. 0600938103)
-
(2006)
Proc. Natl Acad. Sci. USA
, vol.103
, pp. 5977-5982
-
-
Chen, S.L.1
-
32
-
-
33748320827
-
Role of pathogenicity Island-associated integrases in the genome plasticity of uropathogenic Escherichia coli strain 536
-
(doi:10.1111/j.1365-2958. 2006.05255.x)
-
Hochhut B, Wilde C, Balling G, Middendorf B, Dobrindt U, Brzuszkiewicz E, Gottschalk G, Carniel E, Hacker J. 2006 Role of pathogenicity island-associated integrases in the genome plasticity of uropathogenic Escherichia coli strain 536. Mol. Microbiol. 61, 584-595. (doi:10.1111/j.1365-2958. 2006.05255.x)
-
(2006)
Mol. Microbiol.
, vol.61
, pp. 584-595
-
-
Hochhut, B.1
Wilde, C.2
Balling, G.3
Middendorf, B.4
Dobrindt, U.5
Brzuszkiewicz, E.6
Gottschalk, G.7
Carniel, E.8
Hacker, J.9
-
33
-
-
33748082663
-
How to become a uropathogen: Comparative genomic analysis of extraintestinal pathogenic Escherichia coli strains
-
(doi:10.1073/pnas.0603038103)
-
Brzuszkiewicz E. et al. 2006 How to become a uropathogen: comparative genomic analysis of extraintestinal pathogenic Escherichia coli strains. Proc. Natl Acad. Sci. USA 103, 12879-12884. (doi:10.1073/pnas.0603038103)
-
(2006)
Proc. Natl Acad. Sci. USA
, vol.103
, pp. 12879-12884
-
-
Brzuszkiewicz, E.1
-
34
-
-
0037168538
-
Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli
-
(doi:10.1073/pnas. 252529799)
-
Welch RA. et al. 2002 Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proc. Natl Acad. Sci. USA 99, 17020-17024. (doi:10.1073/pnas. 252529799)
-
(2002)
Proc. Natl Acad. Sci. USA
, vol.99
, pp. 17020-17024
-
-
Welch, R.A.1
-
35
-
-
58149498183
-
Complete genome sequence and comparative genome analysis of enteropathogenic Escherichia coli O127: H6 strain E2348/69
-
(doi:10.1128/JB.01238-08)
-
Iguchi A. et al. 2009 Complete genome sequence and comparative genome analysis of enteropathogenic Escherichia coli O127: H6 strain E2348/69. J. Bacteriol. 191, 347-354. (doi:10.1128/JB.01238-08)
-
(2009)
J. Bacteriol.
, vol.191
, pp. 347-354
-
-
Iguchi, A.1
-
36
-
-
53849112279
-
Insights into the environmental resistance gene pool from the genome sequence of the multidrug-resistant environmental isolate Escherichia coli SMS-3-5
-
(doi:10.1128/JB. 00661-08)
-
Fricke WF, Wright MS, Lindell AH, Harkins DM, Baker-Austin C, Ravel J, Stepanauskas R. 2008 Insights into the environmental resistance gene pool from the genome sequence of the multidrug-resistant environmental isolate Escherichia coli SMS-3-5. J. Bacteriol. 190, 6779-6794. (doi:10.1128/JB. 00661-08)
-
(2008)
J. Bacteriol.
, vol.190
, pp. 6779-6794
-
-
Fricke, W.F.1
Wright, M.S.2
Lindell, A.H.3
Harkins, D.M.4
Baker-Austin, C.5
Ravel, J.6
Stepanauskas, R.7
-
37
-
-
0035861456
-
Bayesian inference of phylogeny and its impact on evolutionary biology
-
(doi:10.1126/science.1065889)
-
Huelsenbeck JP, Ronquist F, Nielsen R, Bollback JP. 2001 Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294, 2310-2314. (doi:10.1126/science.1065889)
-
(2001)
Science
, vol.294
, pp. 2310-2314
-
-
Huelsenbeck, J.P.1
Ronquist, F.2
Nielsen, R.3
Bollback, J.P.4
-
38
-
-
0026822436
-
Phylogenetic inference based on matrix representation of trees
-
(doi:10.1016/1055-7903(92)90035-F)
-
Ragan MA. 1992 Phylogenetic inference based on matrix representation of trees. Mol. Phylogenet. Evol. 1, 53-58. (doi:10.1016/1055-7903(92)90035-F)
-
(1992)
Mol. Phylogenet. Evol.
, vol.1
, pp. 53-58
-
-
Ragan, M.A.1
-
39
-
-
0025096192
-
Phylogenetic distribution of branched RNA-linked multicopy single-stranded DNA among natural isolates of Escherichia coli
-
Herzer PJ, Inouye S, Inouye M, Whittam TS. 1990 Phylogenetic distribution of branched RNA-linked multicopy single-stranded DNA among natural isolates of Escherichia coli. J. Bacteriol. 172, 6175-6181.
-
(1990)
J. Bacteriol.
, vol.172
, pp. 6175-6181
-
-
Herzer, P.J.1
Inouye, S.2
Inouye, M.3
Whittam, T.S.4
-
40
-
-
78650744807
-
Lateral transfer of genes and gene gragments in prokaryotes
-
(doi:10.1093/gbe/evp044)
-
Chan CX, Beiko RG, Darling AE, Ragan MA. 2009 Lateral transfer of genes and gene gragments in prokaryotes. Genome Biol. Evol. 1, 429-438. (doi:10.1093/gbe/evp044)
-
(2009)
Genome Biol. Evol.
, vol.1
, pp. 429-438
-
-
Chan, C.X.1
Beiko, R.G.2
Darling, A.E.3
Ragan, M.A.4
-
41
-
-
65549114090
-
The interplay of homologous recombination and horizontal gene transfer in bacterial speciation
-
(doi:10.1007/978-1-60327-853-9-3)
-
Lawrence JG, Retchless AC. 2009 The interplay of homologous recombination and horizontal gene transfer in bacterial speciation. Methods Mol. Biol. 532, 29-53. (doi:10.1007/978-1-60327-853-9-3)
-
(2009)
Methods Mol. Biol.
, vol.532
, pp. 29-53
-
-
Lawrence, J.G.1
Retchless, A.C.2
-
42
-
-
26444506791
-
Highways of gene sharing in prokaryotes
-
(doi:10.1073/pnas. 0504068102)
-
Beiko RG, Harlow TJ, Ragan MA. 2005 Highways of gene sharing in prokaryotes. Proc. Natl Acad. Sci. USA 102, 14332-14337. (doi:10.1073/pnas. 0504068102)
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 14332-14337
-
-
Beiko, R.G.1
Harlow, T.J.2
Ragan, M.A.3
-
43
-
-
33645568886
-
Phylogenetic identification of lateral genetic transfer events
-
(doi:10.1186/1471-2148-6-15)
-
Beiko RG, Hamilton N. 2006 Phylogenetic identification of lateral genetic transfer events. BMC Evol. Biol. 6, 15. (doi:10.1186/1471-2148-6-15)
-
(2006)
BMC Evol. Biol.
, vol.6
, pp. 15
-
-
Beiko, R.G.1
Hamilton, N.2
-
44
-
-
0034163439
-
Horizontal gene transfer and the origin of species: Lessons from bacteria
-
(doi:10.1016/S0966-842X(00)01703-0)
-
de la Cruz F, Davies J. 2000 Horizontal gene transfer and the origin of species: lessons from bacteria. Trends Microbiol. 8, 128-133. (doi:10.1016/S0966-842X(00)01703-0)
-
(2000)
Trends Microbiol.
, vol.8
, pp. 128-133
-
-
De La Cruz, F.1
Davies, J.2
-
45
-
-
0742305866
-
Network biology: Understanding the cell's functional organization
-
(doi:10.1038/nrg1272)
-
Barabási AL, Oltvai ZN. 2004 Network biology: understanding the cell's functional organization. Nat. Rev. Genet. 5, 101-113. (doi:10.1038/nrg1272)
-
(2004)
Nat. Rev. Genet.
, vol.5
, pp. 101-113
-
-
Barabási, A.L.1
Oltvai, Z.N.2
-
46
-
-
34247623628
-
Getting connected: Analysis and principles of biological networks
-
(doi:10.1101/gad.1528707)
-
Zhu X, Gerstein M, Snyder M. 2007 Getting connected: analysis and principles of biological networks. Genes Dev. 21, 1010-1024. (doi:10.1101/gad.1528707)
-
(2007)
Genes Dev.
, vol.21
, pp. 1010-1024
-
-
Zhu, X.1
Gerstein, M.2
Snyder, M.3
-
47
-
-
51649120558
-
Assigning Escherichia coli strains to phylogenetic groups: Multi-locus sequence typing versus the PCR triplex method
-
(doi:10.1111/j.1462-2920.2008.01669.x)
-
Gordon DM, Clermont O, Tolley H, Denamur E. 2008 Assigning Escherichia coli strains to phylogenetic groups: multi-locus sequence typing versus the PCR triplex method. Environ. Microbiol. 10, 2484-2496. (doi:10.1111/j.1462-2920. 2008.01669.x)
-
(2008)
Environ. Microbiol.
, vol.10
, pp. 2484-2496
-
-
Gordon, D.M.1
Clermont, O.2
Tolley, H.3
Denamur, E.4
-
48
-
-
0029093804
-
Sex in Escherichia coli does not disrupt the clonal structure of the population: Evidence from random amplified polymorphic DNA and restriction-fragment-length polymorphism
-
(doi:10.1007/BF00160315)
-
Desjardins P, Picard B, Kaltenböck B, Elion J, Denamur E. 1995 Sex in Escherichia coli does not disrupt the clonal structure of the population: evidence from random amplified polymorphic DNA and restriction-fragment-length polymorphism. J. Mol. Evol. 41, 440-448. (doi:10.1007/BF00160315)
-
(1995)
J. Mol. Evol.
, vol.41
, pp. 440-448
-
-
Desjardins, P.1
Picard, B.2
Kaltenböck, B.3
Elion, J.4
Denamur, E.5
-
49
-
-
0032965099
-
The link between phylogeny and virulence in Escherichia coli extraintestinal infection
-
Picard B, Garcia JS, Gouriou S, Duriez P, Brahimi N, Bingen E, Elion J, Denamur E. 1999 The link between phylogeny and virulence in Escherichia coli extraintestinal infection. Infect. Immun. 67, 546-553.
-
(1999)
Infect. Immun.
, vol.67
, pp. 546-553
-
-
Picard, B.1
Garcia, J.S.2
Gouriou, S.3
Duriez, P.4
Brahimi, N.5
Bingen, E.6
Elion, J.7
Denamur, E.8
-
50
-
-
0035170978
-
Phylogenetic distribution of extraintestinal virulence-associated traits in Escherichia coli
-
(doi:10.1086/317656)
-
Johnson JR, Delavari P, Kuskowski M, Stell AL. 2001 Phylogenetic distribution of extraintestinal virulence-associated traits in Escherichia coli. J. Infect. Dis. 183, 78-88. (doi:10.1086/317656)
-
(2001)
J. Infect. Dis.
, vol.183
, pp. 78-88
-
-
Johnson, J.R.1
Delavari, P.2
Kuskowski, M.3
Stell, A.L.4
-
51
-
-
33646492926
-
Extraintestinal isolates of Escherichia coli: Identification and prospects for vaccine development
-
(doi:10.1586/14760584.5.1.45)
-
Russo TA, Johnson JR. 2006 Extraintestinal isolates of Escherichia coli: identification and prospects for vaccine development. Expert Rev. Vaccines 5, 45-54. (doi:10.1586/14760584.5.1.45)
-
(2006)
Expert Rev. Vaccines
, vol.5
, pp. 45-54
-
-
Russo, T.A.1
Johnson, J.R.2
-
52
-
-
84887212360
-
Are protein domains modules of lateral genetic transfer?
-
(doi:10.1371/journal.pone. 0004524)
-
Chan CX, Darling AE, Beiko RG, Ragan MA. 2009 Are protein domains modules of lateral genetic transfer? PLoS ONE 4, e4524. (doi:10.1371/journal.pone. 0004524)
-
(2009)
PLoS ONE
, vol.4
-
-
Chan, C.X.1
Darling, A.E.2
Beiko, R.G.3
Ragan, M.A.4
-
53
-
-
79960408082
-
Lateral transfer of genes and gene fragments in Staphylococcus extends beyond mobile elements
-
(doi:10.1128/JB.01524-10)
-
Chan CX, Beiko RG, Ragan MA. 2011 Lateral transfer of genes and gene fragments in Staphylococcus extends beyond mobile elements. J. Bacteriol. 193, 3964-3977. (doi:10.1128/JB.01524-10)
-
(2011)
J. Bacteriol.
, vol.193
, pp. 3964-3977
-
-
Chan, C.X.1
Beiko, R.G.2
Ragan, M.A.3
-
54
-
-
83055186603
-
Ecology drives a global network of gene exchange connecting the human microbiome
-
(doi:10.1038/nature10571)
-
Smillie CS, Smith MB, Friedman J, Cordero OX, David LA, Alm EJ. 2011 Ecology drives a global network of gene exchange connecting the human microbiome. Nature 480, 241-244. (doi:10.1038/nature10571)
-
(2011)
Nature
, vol.480
, pp. 241-244
-
-
Smillie, C.S.1
Smith, M.B.2
Friedman, J.3
Cordero, O.X.4
David, L.A.5
Alm, E.J.6
-
55
-
-
0033616714
-
Horizontal gene transfer among genomes: The complexity hypothesis
-
(doi:10.1073/pnas.96.7.3801)
-
Jain R, Rivera MC, Lake JA. 1999 Horizontal gene transfer among genomes: the complexity hypothesis. Proc. Natl Acad. Sci. USA 96, 3801-3806. (doi:10.1073/pnas.96.7.3801)
-
(1999)
Proc. Natl Acad. Sci. USA
, vol.96
, pp. 3801-3806
-
-
Jain, R.1
Rivera, M.C.2
Lake, J.A.3
-
56
-
-
23944475626
-
Mechanisms of, and barriers to, horizontal gene transfer between bacteria
-
(doi:10.1038/nrmicro1234)
-
Thomas CM, Nielsen KM. 2005 Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nat. Rev. Microbiol. 3, 711-721. (doi:10.1038/nrmicro1234)
-
(2005)
Nat. Rev. Microbiol.
, vol.3
, pp. 711-721
-
-
Thomas, C.M.1
Nielsen, K.M.2
-
57
-
-
3543051830
-
Mauve: Multiple alignment of conserved genomic sequence with rearrangements
-
(doi:10.1101/gr.2289704)
-
Darling ACE, Mau B, Blattner FR, Perna NT. 2004 Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 14, 1394-1403. (doi:10.1101/gr.2289704)
-
(2004)
Genome Res.
, vol.14
, pp. 1394-1403
-
-
Darling, A.C.E.1
Mau, B.2
Blattner, F.R.3
Perna, N.T.4
-
58
-
-
77956193448
-
Progressivemauve: Multiple genome alignment with gene gain, loss and rearrangement
-
(doi:10.1371/journal.pone.0011147)
-
Darling AE, Mau B, Perna NT. 2010 progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS ONE 5, e11147. (doi:10.1371/journal.pone.0011147)
-
(2010)
PLoS ONE
, vol.5
-
-
Darling, A.E.1
Mau, B.2
Perna, N.T.3
-
59
-
-
14644430471
-
ProbCons: Probabilistic consistency-based multiple sequence alignment
-
(doi:10.1101/gr.2821705)
-
Do CB, Mahabhashyam MS, Brudno M, Batzoglou S. 2005 ProbCons: probabilistic consistency-based multiple sequence alignment. Genome Res. 15, 330-340. (doi:10.1101/gr.2821705)
-
(2005)
Genome Res.
, vol.15
, pp. 330-340
-
-
Do, C.B.1
Mahabhashyam, M.S.2
Brudno, M.3
Batzoglou, S.4
-
60
-
-
0034043778
-
Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis
-
(doi:10.1093/oxfordjournals.molbev.a026334)
-
Castresana J. 2000 Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17, 540-552. (doi:10.1093/oxfordjournals.molbev.a026334)
-
(2000)
Mol. Biol. Evol.
, vol.17
, pp. 540-552
-
-
Castresana, J.1
-
61
-
-
0034849408
-
MRBAYES: Bayesian inference of phylogenetic trees
-
(doi:10.1093/bioinformatics/17.8.7540)
-
Huelsenbeck JP, Ronquist F. 2001 MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17, 754-755. (doi:10.1093/bioinformatics/17. 8.7540)
-
(2001)
Bioinformatics
, vol.17
, pp. 754-755
-
-
Huelsenbeck, J.P.1
Ronquist, F.2
-
62
-
-
68149181434
-
A two-phase strategy for detecting recombination in nucleotide sequences
-
Chan CX, Beiko RG, Ragan MA. 2007 A two-phase strategy for detecting recombination in nucleotide sequences. S. Afr. Comp. J. 38, 20-27.
-
(2007)
S. Afr. Comp. J.
, vol.38
, pp. 20-27
-
-
Chan, C.X.1
Beiko, R.G.2
Ragan, M.A.3
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