-
1
-
-
0031430556
-
Population thinking and tree thinking in systematics
-
O'Hara RJ: Population thinking and tree thinking in systematics. Zoologica Scripta 1997, 26:323-329.
-
(1997)
Zoologica Scripta
, vol.26
, pp. 323-329
-
-
O'Hara, R.J.1
-
2
-
-
0242354974
-
Horizontal gene transfer and phylogenetics
-
Philippe H, Douady CJ: Horizontal gene transfer and phylogenetics. Curr Opin Microbiol 2003, 6:498-505.
-
(2003)
Curr Opin Microbiol
, vol.6
, pp. 498-505
-
-
Philippe, H.1
Douady, C.J.2
-
3
-
-
4544313053
-
The ring of life provides evidence for a genome fusion origin of eukaryotes
-
Rivera MC, Lake JA: The ring of life provides evidence for a genome fusion origin of eukaryotes. Nature 2004, 431:152-5.
-
(2004)
Nature
, vol.431
, pp. 152-155
-
-
Rivera, M.C.1
Lake, J.A.2
-
4
-
-
0036719929
-
Genome trees and the tree of life
-
Wolf YI, Rogozin IB, Grishin NV, Koonin EV: Genome trees and the tree of life. Trends Genet 2002, 18:472-9.
-
(2002)
Trends Genet
, vol.18
, pp. 472-479
-
-
Wolf, Y.I.1
Rogozin, I.B.2
Grishin, N.V.3
Koonin, E.V.4
-
5
-
-
0037022379
-
The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium, Entamoeba, and Mastigamoeba
-
Bapteste E, Brinkmann H, Lee JA, Moore DV, Sensen CW, Gordon P, Durufle L, Gaasterland T, Lopez P, Muller M, Philippe H: The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium, Entamoeba, and Mastigamoeba. Proc Natl Acad Sci U S A 2002, 99:1414-9.
-
(2002)
Proc Natl Acad Sci U S A
, vol.99
, pp. 1414-1419
-
-
Bapteste, E.1
Brinkmann, H.2
Lee, J.A.3
Moore, D.V.4
Sensen, C.W.5
Gordon, P.6
Durufle, L.7
Gaasterland, T.8
Lopez, P.9
Muller, M.10
Philippe, H.11
-
6
-
-
4544235395
-
Archaeal phylogeny based on proteins of the transcription and translation machineries: Tackling the Methanopyrus kandleri paradox
-
Brochier C, Forterre P, Gribaldo S: Archaeal phylogeny based on proteins of the transcription and translation machineries: tackling the Methanopyrus kandleri paradox. Genome Biol 2004, 5:R17.
-
(2004)
Genome Biol
, vol.5
-
-
Brochier, C.1
Forterre, P.2
Gribaldo, S.3
-
7
-
-
1342271382
-
From Gene Trees to Organismal Phylogeny in Prokaryotes: The Case of the gamma-Proteobacteria
-
Lerat E, Daubin V, Moran NA: From Gene Trees to Organismal Phylogeny in Prokaryotes:The Case of the gamma-Proteobacteria. PLoS Biol 2003, 1:E19.
-
(2003)
PLoS Biol
, vol.1
-
-
Lerat, E.1
Daubin, V.2
Moran, N.A.3
-
8
-
-
16644395866
-
Does a tree-like phylogeny only exist at the tips in the prokaryotes?
-
Creevey CJ, Fitzpatrick DA, Philip GK, Kinsella RJ, O'Connell MJ, Pentony MM, Travers SA, Wilkinson M, McInerney JO: Does a tree-like phylogeny only exist at the tips in the prokaryotes? Proc R Soc Lond B Biol Sci 2004, 271:2551-8.
-
(2004)
Proc R Soc Lond B Biol Sci
, vol.271
, pp. 2551-2558
-
-
Creevey, C.J.1
Fitzpatrick, D.A.2
Philip, G.K.3
Kinsella, R.J.4
O'Connell, M.J.5
Pentony, M.M.6
Travers, S.A.7
Wilkinson, M.8
McInerney, J.O.9
-
9
-
-
0013776758
-
Molecules as documents of evolutionary history
-
Zuckerkandl E, Pauling L: Molecules as documents of evolutionary history. J Theor Biol 1965, 8:357-66.
-
(1965)
J Theor Biol
, vol.8
, pp. 357-366
-
-
Zuckerkandl, E.1
Pauling, L.2
-
10
-
-
0036137155
-
Eubacterial phylogeny based on translational apparatus proteins
-
Brochier C, Bapteste E, Moreira D, Philippe H: Eubacterial phylogeny based on translational apparatus proteins. Trends Genet 2002, 18:1-5.
-
(2002)
Trends Genet
, vol.18
, pp. 1-5
-
-
Brochier, C.1
Bapteste, E.2
Moreira, D.3
Philippe, H.4
-
11
-
-
0036098562
-
Archaeal phylogeny based on ribosomal proteins
-
Matte-Tailliez O, Brochier C, Forterre P, Philippe H: Archaeal phylogeny based on ribosomal proteins. Mol Biol Evol 2002, 5:631-9.
-
(2002)
Mol Biol Evol
, vol.5
, pp. 631-639
-
-
Matte-Tailliez, O.1
Brochier, C.2
Forterre, P.3
Philippe, H.4
-
13
-
-
2442598026
-
Performance of flip supertree construction with a heuristic algorithm
-
Eulenstein O, Chen D, Burleigh JG, Fernandez-Baca D, Sanderson MJ: Performance of flip supertree construction with a heuristic algorithm. Syst Biol 2004, 53:299-308.
-
(2004)
Syst Biol
, vol.53
, pp. 299-308
-
-
Eulenstein, O.1
Chen, D.2
Burleigh, J.G.3
Fernandez-Baca, D.4
Sanderson, M.J.5
-
14
-
-
7244239299
-
Supertree algorithms for ancestral divergence dates and nested taxa
-
Semple C, Daniel P, Hordijk W, Page RD, Steel M: Supertree algorithms for ancestral divergence dates and nested taxa. Bioinformatics 2004, 20:2355-60.
-
(2004)
Bioinformatics
, vol.20
, pp. 2355-2360
-
-
Semple, C.1
Daniel, P.2
Hordijk, W.3
Page, R.D.4
Steel, M.5
-
15
-
-
0031513152
-
The average consensus procedure: Combination of weighted trees containing identical or overlapping sets of taxa
-
Lapointe FJ, Cucumel G: The average consensus procedure: combination of weighted trees containing identical or overlapping sets of taxa. Syst Biol 1997, 46:306-312.
-
(1997)
Syst Biol
, vol.46
, pp. 306-312
-
-
Lapointe, F.J.1
Cucumel, G.2
-
16
-
-
0034350430
-
Simple but fundamental limitations on supertree and consensus tree methods
-
Steel M, Dress AWM, Bocker S: Simple but fundamental limitations on supertree and consensus tree methods. Syst Biol 2000, 49:363-368.
-
(2000)
Syst Biol
, vol.49
, pp. 363-368
-
-
Steel, M.1
Dress, A.W.M.2
Bocker, S.3
-
18
-
-
0034602344
-
A kingdom-level phylogeny of eukaryotes based on combined protein data
-
Baldauf SL, Roger AJ, Wenk-Siefert I, Doolittle WF: A kingdom-level phylogeny of eukaryotes based on combined protein data. Science 2000, 290:972-7.
-
(2000)
Science
, vol.290
, pp. 972-977
-
-
Baldauf, S.L.1
Roger, A.J.2
Wenk-Siefert, I.3
Doolittle, W.F.4
-
19
-
-
0036210883
-
Inferring genome trees by using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores
-
Clarke GD, Beiko RG, Ragan MA, Charlebois RL: Inferring genome trees by using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores. J Bacteriol 2002, 184:2072-80.
-
(2002)
J Bacteriol
, vol.184
, pp. 2072-2080
-
-
Clarke, G.D.1
Beiko, R.G.2
Ragan, M.A.3
Charlebois, R.L.4
-
20
-
-
14544295684
-
Weighted genome trees: Refinements and applications
-
Gophna U, Doolittle WF, Charlebois RL: Weighted genome trees: refinements and applications. J Bacteriol 2005, 187:1305-16.
-
(2005)
J Bacteriol
, vol.187
, pp. 1305-1316
-
-
Gophna, U.1
Doolittle, W.F.2
Charlebois, R.L.3
-
21
-
-
0038054297
-
The role played by viruses in the evolution of their hosts: A view based on informational protein phylogenies
-
Filee J, Forterre P, Laurent J: The role played by viruses in the evolution of their hosts: a view based on informational protein phylogenies. Res Microbiol 2003, 154:237-43.
-
(2003)
Res Microbiol
, vol.154
, pp. 237-243
-
-
Filee, J.1
Forterre, P.2
Laurent, J.3
-
22
-
-
0036145420
-
Reconciling the many faces of lateral gene transfer
-
Lawrence JG, Ochman H: Reconciling the many faces of lateral gene transfer. Trends Microbiol 2002, 10:1-4.
-
(2002)
Trends Microbiol
, vol.10
, pp. 1-4
-
-
Lawrence, J.G.1
Ochman, H.2
-
24
-
-
0033609333
-
Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima
-
Nelson KE, Clayton RA, Gill SR, Gwinn ML, Dodson RJ, Haft DH, Hickey EK, Peterson JD, Nelson WC, Ketchum KA, McDonald L, Utterback TR, Malek JA, Linher KD, Garrett MM, Stewart AM, Cotton MD, Pratt MS, Phillips CA, Richardson D, Heidelberg J, Sutton GG, Fleischmann RD, Eisen JA, White O, Salzberg SL, Smith HO, Venter JC, Fraser CM: Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima. Nature 1999, 399:323-9.
-
(1999)
Nature
, vol.399
, pp. 323-329
-
-
Nelson, K.E.1
Clayton, R.A.2
Gill, S.R.3
Gwinn, M.L.4
Dodson, R.J.5
Haft, D.H.6
Hickey, E.K.7
Peterson, J.D.8
Nelson, W.C.9
Ketchum, K.A.10
McDonald, L.11
Utterback, T.R.12
Malek, J.A.13
Linher, K.D.14
Garrett, M.M.15
Stewart, A.M.16
Cotton, M.D.17
Pratt, M.S.18
Phillips, C.A.19
Richardson, D.20
Heidelberg, J.21
Sutton, G.G.22
Fleischmann, R.D.23
Eisen, J.A.24
White, O.25
Salzberg, S.L.26
Smith, H.O.27
Venter, J.C.28
Fraser, C.M.29
more..
-
25
-
-
0033670249
-
Horizontal gene transfer in bacterial and archaeal complete genomes
-
Garcia-Vallve S, Romeu A, Palau J: Horizontal gene transfer in bacterial and archaeal complete genomes. Genome Res 2000, 10:1719-25.
-
(2000)
Genome Res
, vol.10
, pp. 1719-1725
-
-
Garcia-Vallve, S.1
Romeu, A.2
Palau, J.3
-
26
-
-
0034780910
-
Horizontal gene transfer in prokaryotes: Quantification and classification
-
Koonin EV, Makarova KS, Aravind L: Horizontal gene transfer in prokaryotes: quantification and classification. Annu Rev Microbiol 2001, 55:709-42.
-
(2001)
Annu Rev Microbiol
, vol.55
, pp. 709-742
-
-
Koonin, E.V.1
Makarova, K.S.2
Aravind, L.3
-
27
-
-
0242276676
-
Lateral gene transfer and the origins of prokaryotic groups
-
Boucher Y, Douady CJ, Papke RT, Walsh DA, Boudreau ME, Nesbo CL, Case RJ, Doolittle WF: Lateral gene transfer and the origins of prokaryotic groups. Annu Rev Genet 2003, 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
Nesbo, C.L.6
Case, R.J.7
Doolittle, W.F.8
-
28
-
-
10344246580
-
Gene Transfers from Nanoarchaeota to an Ancestor of Diplomonads and Parabasalids
-
Andersson JO, Sarchfield SW, Roger AJ: Gene Transfers from Nanoarchaeota to an Ancestor of Diplomonads and Parabasalids. Mol Biol Evol 2005, 22(1):85-90.
-
(2005)
Mol Biol Evol
, vol.22
, Issue.1
, pp. 85-90
-
-
Andersson, J.O.1
Sarchfield, S.W.2
Roger, A.J.3
-
29
-
-
2942620629
-
Evolution of glutamate dehydrogenase genes: Evidence for lateral gene transfer within and between prokaryotes and eukaryotes
-
Andersson JO, Roger AJ: Evolution of glutamate dehydrogenase genes: evidence for lateral gene transfer within and between prokaryotes and eukaryotes. BMC Evol Biol 2003, 3:14.
-
(2003)
BMC Evol Biol
, vol.3
, pp. 14
-
-
Andersson, J.O.1
Roger, A.J.2
-
30
-
-
0031678692
-
SplitsTree: Analyzing and visualizing evolutionary data
-
Huson DH: SplitsTree: analyzing and visualizing evolutionary data. Bioinformatics 1998, 14:68-73.
-
(1998)
Bioinformatics
, vol.14
, pp. 68-73
-
-
Huson, D.H.1
-
31
-
-
0034894308
-
T-REX: Reconstructing and visualizing phylogenetic trees and reticulation networks
-
Makarenkov V: T-REX: reconstructing and visualizing phylogenetic trees and reticulation networks. Bioinformatics 2001, 17:664-8.
-
(2001)
Bioinformatics
, vol.17
, pp. 664-668
-
-
Makarenkov, V.1
-
32
-
-
4444353678
-
Phylogenetic reconstruction and lateral gene transfer
-
Bapteste E, Boucher Y, Leigh J, Doolittle WF: Phylogenetic reconstruction and lateral gene transfer. Trends Microbiol 2004, 12:406-11.
-
(2004)
Trends Microbiol
, vol.12
, pp. 406-411
-
-
Bapteste, E.1
Boucher, Y.2
Leigh, J.3
Doolittle, W.F.4
-
33
-
-
0036137155
-
Bacterial phylogeny based on translational apparatus proteins
-
Brochier C, Bapteste E, Moreira D, Philippe H: Bacterial phylogeny based on translational apparatus proteins. Trends Genet 2002, 1:1-5.
-
(2002)
Trends Genet
, vol.1
, pp. 1-5
-
-
Brochier, C.1
Bapteste, E.2
Moreira, D.3
Philippe, H.4
-
35
-
-
0033536012
-
Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays
-
Alon U, Barkai N, Notterman DA, Gish K, Ybarra S, Mack D, Levine AJ: Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc Natl Acad Sci U S A 1999, 96:6745-6750.
-
(1999)
Proc Natl Acad Sci U S A
, vol.96
, pp. 6745-6750
-
-
Alon, U.1
Barkai, N.2
Notterman, D.A.3
Gish, K.4
Ybarra, S.5
Mack, D.6
Levine, A.J.7
-
36
-
-
0034710876
-
Coupled two-way clustering analysis of gene microarray data
-
Getz G, Levine E, Domany E: Coupled two-way clustering analysis of gene microarray data. Proc Natl Acad Sci U S A 2000, 97:12079-84.
-
(2000)
Proc Natl Acad Sci U S A
, vol.97
, pp. 12079-12084
-
-
Getz, G.1
Levine, E.2
Domany, E.3
-
37
-
-
21644457840
-
-
ed. Schlosser, G. a. G. P. W.
-
Somogyi R, Fuhrman S, Anderson G, Madill C, Greller LD, Chang B: Modularity in Development and Evolution. (ed. Schlosser, G. a. G. P. W.) 2004:202-221.
-
(2004)
Modularity in Development and Evolution
, pp. 202-221
-
-
Somogyi, R.1
Fuhrman, S.2
Anderson, G.3
Madill, C.4
Greller, L.D.5
Chang, B.6
-
38
-
-
0036143446
-
Genomes in flux: The evolution of archaeal and proteobacterial gene content
-
Snel B, Bork P, Huynen MA: Genomes in flux: the evolution of archaeal and proteobacterial gene content. Genome Res 2002, 12:17-25.
-
(2002)
Genome Res
, vol.12
, pp. 17-25
-
-
Snel, B.1
Bork, P.2
Huynen, M.A.3
-
39
-
-
0038486918
-
The balance of driving forces during genome evolution in prokaryotes
-
Kunin V, Ouzounis CA: The balance of driving forces during genome evolution in prokaryotes. Genome Res 2003, 13:1589-94.
-
(2003)
Genome Res
, vol.13
, pp. 1589-1594
-
-
Kunin, V.1
Ouzounis, C.A.2
-
40
-
-
0034831587
-
Defining the core of nontransferable prokaryotic genes: The euryarchaeal core
-
Nesbo CL, Boucher Y, Doolittle WF: Defining the core of nontransferable prokaryotic genes: the euryarchaeal core. J Mol Evol 2001, 53:340-50.
-
(2001)
J Mol Evol
, vol.53
, pp. 340-350
-
-
Nesbo, C.L.1
Boucher, Y.2
Doolittle, W.F.3
-
41
-
-
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 BG, Fenner TI, Galperin MY, Koonin EV: 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 2003, 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
-
43
-
-
0027494836
-
MUST, a computer package of Management Utilities for Sequences and Trees
-
Philippe H: MUST, a computer package of Management Utilities for Sequences and Trees. Nucleic Acids Res 1993, 21:5264-72.
-
(1993)
Nucleic Acids Res
, vol.21
, pp. 5264-5272
-
-
Philippe, H.1
-
44
-
-
0036139287
-
CONSEL: For assessing the confidence of phylogenetic tree selection
-
Shimodaira H, Hasegawa M: CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 2001, 17:1246-7.
-
(2001)
Bioinformatics
, vol.17
, pp. 1246-1247
-
-
Shimodaira, H.1
Hasegawa, M.2
-
45
-
-
0036623258
-
An approximately unbiased test of phylogenetic tree selection
-
Shimodaira H: An approximately unbiased test of phylogenetic tree selection. Syst Biol 2002, 51:492-508.
-
(2002)
Syst Biol
, vol.51
, pp. 492-508
-
-
Shimodaira, H.1
-
46
-
-
18944369385
-
Deduction of probable events of lateral gene transfer through comparison of phylogenetic trees by recursive consolidation and rearrangement
-
MacLeod D, Charlebois RL, Doolittle WF, Bapteste E: Deduction of probable events of lateral gene transfer through comparison of phylogenetic trees by recursive consolidation and rearrangement. BMC Evol Biol 2005, 27(5(1)):.
-
(2005)
BMC Evol Biol
, vol.27
, Issue.1-5
-
-
MacLeod, D.1
Charlebois, R.L.2
Doolittle, W.F.3
Bapteste, E.4
|