-
1
-
-
0027738868
-
Horizontal transfer of ATPase genes - The tree of life becomes a net of life
-
Hilario E, Gogarten JP (1993) Horizontal transfer of ATPase genes - the tree of life becomes a net of life. Biosystems 31:111-119. (Pubitemid 24045859)
-
(1993)
BioSystems
, vol.31
, Issue.2-3
, pp. 111-119
-
-
Hilario, E.1
Gogarten, J.P.2
-
4
-
-
33745760575
-
Ancient horizontal gene transfer can benefit phylogenetic reconstruction
-
DOI 10.1016/j.tig.2006.05.004, PII S0168952506001466
-
Huang J, Gogarten JP (2006) Ancient horizontal gene transfer can benefit phylogenetic reconstruction. Trends Genet 22:361-366. (Pubitemid 44015971)
-
(2006)
Trends in Genetics
, vol.22
, Issue.7
, pp. 361-366
-
-
Huang, J.1
Gogarten, J.P.2
-
5
-
-
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. (Pubitemid 44320397)
-
(2006)
Genome Research
, vol.16
, Issue.9
, pp. 1099-1108
-
-
Zhaxybayeva, O.1
Gogarten, J.P.2
Charlebois, R.L.3
Doolittle, W.F.4
Papke, R.T.5
-
6
-
-
26444543426
-
The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic
-
DOI 10.1093/molbev/msi221
-
Huang J, Xu Y, Gogarten JP (2005) The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic. Mol Biol Evol 22:2142-2146. (Pubitemid 41437795)
-
(2005)
Molecular Biology and Evolution
, vol.22
, Issue.11
, pp. 2142-2146
-
-
Huang, J.1
Xu, Y.2
Gogarten, J.P.3
-
7
-
-
23944437942
-
Opinion: Re-evaluating prokaryotic species
-
Gevers D, et al. (2005) Opinion: Re-evaluating prokaryotic species. Nat Rev Microbiol 3:733-739.
-
(2005)
Nat Rev Microbiol
, vol.3
, pp. 733-739
-
-
Gevers, D.1
-
8
-
-
0029163720
-
The early evolution of cellular life
-
Gogarten JP (1995) The early evolution of cellular life. Trends Ecol Evol 10:147-151.
-
(1995)
Trends Ecol Evol
, vol.10
, pp. 147-151
-
-
Gogarten, J.P.1
-
9
-
-
48249151749
-
Modular networks and cumulative impact of lateral transfer inprokaryote genome evolution
-
Dagan T, Artzy-Randrup Y, Martin W (2008) Modular networks and cumulative impact of lateral transfer inprokaryote genome evolution. Proc Natl Acad Sci USA 105:10039-10044.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 10039-10044
-
-
Dagan, T.1
Artzy-Randrup, Y.2
Martin, W.3
-
10
-
-
1342271382
-
From gene trees to organismal phylogeny in prokaryotes: The case of the gamma-Proteobacteria
-
Lerat E, Daubin V, Moran NA (2003) From gene trees to organismal phylogeny in prokaryotes: The case of the gamma-Proteobacteria. PLoS Biol 1:E19.
-
(2003)
PLoS Biol
, vol.1
-
-
Lerat, E.1
Daubin, V.2
Moran, N.A.3
-
11
-
-
33644700003
-
Toward automatic reconstruction of a highly resolved tree of life
-
Ciccarelli FD, et al. (2006) Toward automatic reconstruction of a highly resolved tree of life. Science 311:1283-1287.
-
(2006)
Science
, vol.311
, pp. 1283-1287
-
-
Ciccarelli, F.D.1
-
13
-
-
68149093715
-
Search for a 'Tree of Life' in the thicket of the phylogenetic forest
-
Puigbò P, Wolf YI, Koonin EV (2009) Search for a 'Tree of Life' in the thicket of the phylogenetic forest. J Biol 8:59.
-
(2009)
J Biol
, vol.8
, pp. 59
-
-
Puigbò, P.1
Wolf, Y.I.2
Koonin, E.V.3
-
14
-
-
56349169406
-
Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria
-
Boussau B, Guéguen L, Gouy M (2008) Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria. BMC Evol Biol 8:272.
-
(2008)
BMC Evol Biol
, vol.8
, pp. 272
-
-
Boussau, B.1
Guéguen, L.2
Gouy, M.3
-
15
-
-
65249126970
-
On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales
-
Zhaxybayeva O, et al. (2009) On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales. Proc Natl Acad Sci USA 106:5865-5870.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 5865-5870
-
-
Zhaxybayeva, O.1
-
16
-
-
36249021315
-
Genome-wide experimental determination of barriers to horizontal gene transfer
-
Sorek R, et al. (2007) Genome-wide experimental determination of barriers to horizontal gene transfer. Science 318:1449-1452.
-
(2007)
Science
, vol.318
, pp. 1449-1452
-
-
Sorek, R.1
-
19
-
-
23944453816
-
Cellular Origin and Life in Extreme Habitats
-
ed Seckbach J (Kluwer, Dordrecht, The Netherlands)
-
Olendzenski L, Zhaxybayeva O, Gogarten JP (2001) Cellular Origin and Life in Extreme Habitats. Vol. 4: Symbiosis, ed Seckbach J (Kluwer, Dordrecht, The Netherlands), pp 67-78.
-
(2001)
Symbiosis
, vol.4
, pp. 67-78
-
-
Olendzenski, L.1
Zhaxybayeva, O.2
Gogarten, J.P.3
-
20
-
-
0034053846
-
Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process
-
Woese CR, Olsen GJ, Ibba M, Söll D (2000) Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process. Microbiol Mol Biol Rev 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
-
21
-
-
2342661195
-
Detection of lateral gene transfer events in the prokaryotic tRNA synthetases by the ratios of evolutionary distances method
-
Farahi K, Pusch GD, Overbeek R, Whitman WB (2004) Detection of lateral gene transfer events in the prokaryotic tRNA synthetases by the ratios of evolutionary distances method. J Mol Evol 58:615-631.
-
(2004)
J Mol Evol
, vol.58
, pp. 615-631
-
-
Farahi, K.1
Pusch, G.D.2
Overbeek, R.3
Whitman, W.B.4
-
22
-
-
4544298806
-
Genome-wide molecular clock and horizontal gene transfer in bacterial evolution
-
Novichkov PS, et al. (2004) Genome-wide molecular clock and horizontal gene transfer in bacterial evolution. J Bacteriol 186:6575-6585.
-
(2004)
J Bacteriol
, vol.186
, pp. 6575-6585
-
-
Novichkov, P.S.1
-
23
-
-
77953743159
-
-
eds Xu Y, Gogarten JP (Imperial College Press, London)
-
Gogarten JP, Zhaxybayeva O (2008) Computational Methods for Understanding Bacterial and Archaeal Genomes, eds Xu Y, Gogarten JP (Imperial College Press, London), pp 137-151.
-
(2008)
Computational Methods for Understanding Bacterial and Archaeal Genomes
, pp. 137-151
-
-
Gogarten, J.P.1
Zhaxybayeva, O.2
-
24
-
-
77649249551
-
An evolutionary analysis of lateral gene transfer in thymidylate synthase enzymes
-
Stern A, et al. (2010) An evolutionary analysis of lateral gene transfer in thymidylate synthase enzymes. Syst Biol 59:212-225.
-
(2010)
Syst Biol
, vol.59
, pp. 212-225
-
-
Stern, A.1
-
25
-
-
23944499633
-
Horizontal gene transfer, genome innovation and evolution
-
Gogarten JP, Townsend JP (2005) Horizontal gene transfer, genome innovation and evolution. Nat Rev Microbiol 3:679-687.
-
(2005)
Nat Rev Microbiol
, vol.3
, pp. 679-687
-
-
Gogarten, J.P.1
Townsend, J.P.2
-
26
-
-
25144518786
-
Genome evolution in bacteria: Order beneath chaos
-
Lawrence JG, Hendrickson H (2005) Genome evolution in bacteria: Order beneath chaos. Curr Opin Microbiol 8:572-578.
-
(2005)
Curr Opin Microbiol
, vol.8
, pp. 572-578
-
-
Lawrence, J.G.1
Hendrickson, H.2
-
28
-
-
0025183708
-
Basic local alignment search tool
-
DOI 10.1006/jmbi.1990.9999
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403-410. (Pubitemid 20364473)
-
(1990)
Journal of Molecular Biology
, vol.215
, Issue.3
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
29
-
-
3042666256
-
MUSCLE: Multiple sequence alignment with high accuracy and high throughput
-
DOI 10.1093/nar/gkh340
-
Edgar RC (2004) MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792-1797. (Pubitemid 38832724)
-
(2004)
Nucleic Acids Research
, vol.32
, Issue.5
, pp. 1792-1797
-
-
Edgar, R.C.1
-
30
-
-
0242578620
-
A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
-
DOI 10.1080/10635150390235520
-
Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52:696-704. (Pubitemid 37365050)
-
(2003)
Systematic Biology
, vol.52
, Issue.5
, pp. 696-704
-
-
Guindon, S.1
Gascuel, O.2
-
31
-
-
0036205377
-
TREE-PUZZLE: Maximum likelihood phylogenetic analysis using quartets and parallel computing
-
Schmidt HA, Strimmer K, Vingron M, von Haeseler A (2002) TREE-PUZZLE: Maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18:502-504. (Pubitemid 34284960)
-
(2002)
Bioinformatics
, vol.18
, Issue.3
, pp. 502-504
-
-
Schmidt, H.A.1
Strimmer, K.2
Vingron, M.3
Von Haeseler, A.4
-
32
-
-
0007507214
-
-
Marine Biological Laboratory, Woods Hole, MA
-
Holder ME, Roger A (1999) PUZZLEBOOT (Marine Biological Laboratory, Woods Hole, MA).
-
(1999)
Puzzleboot
-
-
Holder, M.E.1
Roger, A.2
-
33
-
-
0041386108
-
MrBayes 3: Bayesian phylogenetic inference under mixed models
-
DOI 10.1093/bioinformatics/btg180
-
Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574. (Pubitemid 37038874)
-
(2003)
Bioinformatics
, vol.19
, Issue.12
, pp. 1572-1574
-
-
Ronquist, F.1
Huelsenbeck, J.P.2
-
34
-
-
0030305457
-
R: A language for data analysis and graphics
-
Ihaka R, Gentleman R (1996) R: A language for data analysis and graphics. J Comput Graph Stat 5:299-314.
-
(1996)
J Comput Graph Stat
, vol.5
, pp. 299-314
-
-
Ihaka, R.1
Gentleman, R.2
|