-
1
-
-
0013776758
-
Molecules as documents of evolutionary history
-
10.1016/0022-5193(65)90083-4, 5876245
-
Zuckerkandl E, Pauling L. Molecules as documents of evolutionary history. Journal of Theoretical Biology 1965, 8(2):357-66. 10.1016/0022-5193(65)90083-4, 5876245.
-
(1965)
Journal of Theoretical Biology
, vol.8
, Issue.2
, pp. 357-366
-
-
Zuckerkandl, E.1
Pauling, L.2
-
2
-
-
0025300402
-
Towards a natural system of organisms - proposal for the domains archaea, bacteria, and eucarya
-
10.1073/pnas.87.12.4576, 54159, 2112744
-
Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms - proposal for the domains archaea, bacteria, and eucarya. Proceedings of the National Academy of Sciences of the United States of America 1990, 87(12):4576-4579. 10.1073/pnas.87.12.4576, 54159, 2112744.
-
(1990)
Proceedings of the National Academy of Sciences of the United States of America
, vol.87
, Issue.12
, pp. 4576-4579
-
-
Woese, C.R.1
Kandler, O.2
Wheelis, M.L.3
-
3
-
-
72949101201
-
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
-
10.1038/nature08656, 3073058, 20033048
-
Wu DY, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, Hooper SD, Pati A, Lykidis A, Spring S, Anderson IJ, D'haeseleer P, Zemla A, Singer M, Lapidus A, Nolan M, Copeland A, Han C, Chen F, Cheng JF, Lucas S, Kerfeld C, Lang E, Gronow S, Chain P, Bruce D, Rubin EM, Kyrpides NC, Klenk HP, Eisen JA. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 2009, 462(7276):1056-1060. 10.1038/nature08656, 3073058, 20033048.
-
(2009)
Nature
, vol.462
, Issue.7276
, pp. 1056-1060
-
-
Wu, D.Y.1
Hugenholtz, P.2
Mavromatis, K.3
Pukall, R.4
Dalin, E.5
Ivanova, N.N.6
Kunin, V.7
Goodwin, L.8
Wu, M.9
Tindall, B.J.10
Hooper, S.D.11
Pati, A.12
Lykidis, A.13
Spring, S.14
Anderson, I.J.15
D'haeseleer, P.16
Zemla, A.17
Singer, M.18
Lapidus, A.19
Nolan, M.20
Copeland, A.21
Han, C.22
Chen, F.23
Cheng, J.F.24
Lucas, S.25
Kerfeld, C.26
Lang, E.27
Gronow, S.28
Chain, P.29
Bruce, D.30
Rubin, E.M.31
Kyrpides, N.C.32
Klenk, H.P.33
Eisen, J.A.34
more..
-
4
-
-
48249151749
-
Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution
-
10.1073/pnas.0800679105, 2474566, 18632554
-
Dagan T, Artzy-Randrup Y, Martin W. Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution. Proceedings of the National Academy of Sciences of the United States of America 2008, 105(29):10039-10044. 10.1073/pnas.0800679105, 2474566, 18632554.
-
(2008)
Proceedings of the National Academy of Sciences of the United States of America
, vol.105
, Issue.29
, pp. 10039-10044
-
-
Dagan, T.1
Artzy-Randrup, Y.2
Martin, W.3
-
5
-
-
0033603539
-
Phylogenetic classification and the universal tree
-
10.1126/science.284.5423.2124, 10381871
-
Doolittle WF. Phylogenetic classification and the universal tree. Science 1999, 284(5423):2124-2128. 10.1126/science.284.5423.2124, 10381871.
-
(1999)
Science
, vol.284
, Issue.5423
, pp. 2124-2128
-
-
Doolittle, W.F.1
-
6
-
-
0027738868
-
Horizontal transfer of ATPase genes - the tree of life becomes a net of life
-
10.1016/0303-2647(93)90038-E, 8155843
-
Hilario E, Gogarten J. Horizontal transfer of ATPase genes - the tree of life becomes a net of life. BioSystems 1993, 31(2-3):111-119. 10.1016/0303-2647(93)90038-E, 8155843.
-
(1993)
BioSystems
, vol.31
, Issue.2-3
, pp. 111-119
-
-
Hilario, E.1
Gogarten, J.2
-
7
-
-
13244259056
-
Diversity and evolutionary history of plastids and their hosts
-
10.3732/ajb.91.10.1481, 21652304
-
Keeling PJ. Diversity and evolutionary history of plastids and their hosts. American Journal of Botany 2004, 91(10):1481-1493. 10.3732/ajb.91.10.1481, 21652304.
-
(2004)
American Journal of Botany
, vol.91
, Issue.10
, pp. 1481-1493
-
-
Keeling, P.J.1
-
8
-
-
23944499633
-
Horizontal gene transfer, genome innovation and evolution
-
10.1038/nrmicro1204, 16138096
-
Gogarten J, Townsend J. Horizontal gene transfer, genome innovation and evolution. Nature Reviews Microbiology 2005, 3(9):679-687. 10.1038/nrmicro1204, 16138096.
-
(2005)
Nature Reviews Microbiology
, vol.3
, Issue.9
, pp. 679-687
-
-
Gogarten, J.1
Townsend, J.2
-
9
-
-
0034682335
-
Lateral gene transfer and the nature of bacterial innovation
-
10.1038/35012500, 10830951
-
Ochman H, Lawrence J, Grolsman E. Lateral gene transfer and the nature of bacterial innovation. Nature 2000, 405(6784):299-304. 10.1038/35012500, 10830951.
-
(2000)
Nature
, vol.405
, Issue.6784
, pp. 299-304
-
-
Ochman, H.1
Lawrence, J.2
Grolsman, E.3
-
10
-
-
26444506791
-
Highways of gene sharing in prokaryotes
-
10.1073/pnas.0504068102, 1242295, 16176988
-
Beiko R, Harlow T, Ragan M. Highways of gene sharing in prokaryotes. Proceedings of the National Academy of Sciences of the United States of America 2005, 102(40):14332-14337. 10.1073/pnas.0504068102, 1242295, 16176988.
-
(2005)
Proceedings of the National Academy of Sciences of the United States of America
, vol.102
, Issue.40
, pp. 14332-14337
-
-
Beiko, R.1
Harlow, T.2
Ragan, M.3
-
11
-
-
70349979453
-
Phylogeny of prokaryotes: does it exist and why should we care?
-
10.1016/j.resmic.2009.07.006, 19631737
-
Gribaldo S, Brochier C. Phylogeny of prokaryotes: does it exist and why should we care?. Research In Microbiology 2009, 160(7):513-521. 10.1016/j.resmic.2009.07.006, 19631737.
-
(2009)
Research In Microbiology
, vol.160
, Issue.7
, pp. 513-521
-
-
Gribaldo, S.1
Brochier, C.2
-
12
-
-
77954075974
-
Save the tree of life or get lost in the woods
-
Valas RE, Bourne PE. Save the tree of life or get lost in the woods. Biology Direct 2010, 5.
-
(2010)
Biology Direct
, vol.5
-
-
Valas, R.E.1
Bourne, P.E.2
-
13
-
-
33644700003
-
Toward automatic reconstruction of a highly resolved tree of life
-
10.1126/science.1123061, 16513982
-
Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P. Toward automatic reconstruction of a highly resolved tree of life. Science 2006, 311(5765):1283-1287. 10.1126/science.1123061, 16513982.
-
(2006)
Science
, vol.311
, Issue.5765
, pp. 1283-1287
-
-
Ciccarelli, F.D.1
Doerks, T.2
von Mering, C.3
Creevey, C.J.4
Snel, B.5
Bork, P.6
-
14
-
-
18244402898
-
Decoding the genomic tree of life
-
10.1073/pnas.0501996102, 1131872, 15851667
-
Simonson AB, Servin JA, Skophammer RG, Herbold CW, Rivera MC, Lake JA. Decoding the genomic tree of life. Proceedings of the National Academy of Sciences of the United States of America 2005, 102:6608-6613. 10.1073/pnas.0501996102, 1131872, 15851667.
-
(2005)
Proceedings of the National Academy of Sciences of the United States of America
, vol.102
, pp. 6608-6613
-
-
Simonson, A.B.1
Servin, J.A.2
Skophammer, R.G.3
Herbold, C.W.4
Rivera, M.C.5
Lake, J.A.6
-
15
-
-
0020710588
-
Dietary-intake, energy-metabolism, and excretory losses of adult male germfree Wistar rats
-
Wostmann BS, Larkin C, Moriarty A, Brucknerkardoss E. Dietary-intake, energy-metabolism, and excretory losses of adult male germfree Wistar rats. Laboratory Animal Science 1983, 33:46-50.
-
(1983)
Laboratory Animal Science
, vol.33
, pp. 46-50
-
-
Wostmann, B.S.1
Larkin, C.2
Moriarty, A.3
Brucknerkardoss, E.4
-
16
-
-
33846349924
-
Rooting the tree of life by transition analyses
-
Cavalier-Smith T. Rooting the tree of life by transition analyses. Biology Direct 2006, 1.
-
(2006)
Biology Direct
, vol.1
-
-
Cavalier-Smith, T.1
-
17
-
-
17744394753
-
Phylogenomics and the reconstruction of the tree of life
-
Delsuc F, Brinkmann H, Philippe H. Phylogenomics and the reconstruction of the tree of life. Nature Reviews Genetics 2005, 6(5):361-375.
-
(2005)
Nature Reviews Genetics
, vol.6
, Issue.5
, pp. 361-375
-
-
Delsuc, F.1
Brinkmann, H.2
Philippe, H.3
-
18
-
-
2942600199
-
The evolution of supertrees
-
10.1016/j.tree.2004.03.015, 21939080
-
Bininda-Emonds ORP. The evolution of supertrees. Trends In Ecology & Evolution 2004, 19(6):315-322. 10.1016/j.tree.2004.03.015, 21939080.
-
(2004)
Trends In Ecology & Evolution
, vol.19
, Issue.6
, pp. 315-322
-
-
Bininda-Emonds, O.R.P.1
-
19
-
-
77954993696
-
Rooting the ribosomal tree of life
-
10.1093/molbev/msq057, 20194428
-
Fournier GP, Gogarten JP. Rooting the ribosomal tree of life. Molecular Biology and Evolution 2010, 27(8):1792-1801. 10.1093/molbev/msq057, 20194428.
-
(2010)
Molecular Biology and Evolution
, vol.27
, Issue.8
, pp. 1792-1801
-
-
Fournier, G.P.1
Gogarten, J.P.2
-
20
-
-
34447284787
-
Properties of supertree methods in the consensus setting
-
10.1080/10635150701245370, 17464887
-
Wilkinson M, Cotton JA, Lapointe FJ, Pisani D. Properties of supertree methods in the consensus setting. Systematic Biology 2007, 56(2):330-337. 10.1080/10635150701245370, 17464887.
-
(2007)
Systematic Biology
, vol.56
, Issue.2
, pp. 330-337
-
-
Wilkinson, M.1
Cotton, J.A.2
Lapointe, F.J.3
Pisani, D.4
-
23
-
-
0029163720
-
The early evolution of cellular life
-
10.1016/S0169-5347(00)89024-2, 21939080
-
Gogarten JP. The early evolution of cellular life. Trends In Ecology & Evolution 1995, 10(4):147-151. 10.1016/S0169-5347(00)89024-2, 21939080.
-
(1995)
Trends In Ecology & Evolution
, vol.10
, Issue.4
, pp. 147-151
-
-
Gogarten, J.P.1
-
24
-
-
68149085959
-
Trees in the web of life
-
10.1186/jbiol160, 2737374, 19664165
-
Swithers KS, Gogarten JP, Fournier GP. Trees in the web of life. Journal of Biology 2009, 8(6):54. 10.1186/jbiol160, 2737374, 19664165.
-
(2009)
Journal of Biology
, vol.8
, Issue.6
, pp. 54
-
-
Swithers, K.S.1
Gogarten, J.P.2
Fournier, G.P.3
-
25
-
-
36249021315
-
Genome-wide experimental determination of barriers to horizontal gene transfer
-
10.1126/science.1147112, 17947550
-
Sorek R, Zhu YW, Creevey CJ, Francino MP, Bork P, Rubin EM. Genome-wide experimental determination of barriers to horizontal gene transfer. Science 2007, 318:1449-1452. 10.1126/science.1147112, 17947550.
-
(2007)
Science
, vol.318
, pp. 1449-1452
-
-
Sorek, R.1
Zhu, Y.W.2
Creevey, C.J.3
Francino, M.P.4
Bork, P.5
Rubin, E.M.6
-
26
-
-
29944434209
-
Ancient gene duplications and the root(s) of the tree of life
-
10.1007/s00709-005-0135-1, 16389494
-
Zhaxybayeva O, Lapierre P, Gogarten JP. Ancient gene duplications and the root(s) of the tree of life. Protoplasma 2005, 227:53-64. 10.1007/s00709-005-0135-1, 16389494.
-
(2005)
Protoplasma
, vol.227
, pp. 53-64
-
-
Zhaxybayeva, O.1
Lapierre, P.2
Gogarten, J.P.3
-
27
-
-
77958506738
-
Genome Networks Root the Tree of Life between Prokaryotic Domains
-
10.1093/gbe/evq025, 2997548, 20624742
-
Dagan T, Roettger M, Bryant D, Martin W. Genome Networks Root the Tree of Life between Prokaryotic Domains. Genome Biology and Evolution 2010, 2:379-392. 10.1093/gbe/evq025, 2997548, 20624742.
-
(2010)
Genome Biology and Evolution
, vol.2
, pp. 379-392
-
-
Dagan, T.1
Roettger, M.2
Bryant, D.3
Martin, W.4
-
28
-
-
79952201675
-
The tree and net components of prokaryote evolution
-
10.1093/gbe/evq062, 2997564, 20889655
-
Puigbo P, Wolf YI, Koonin EV. The tree and net components of prokaryote evolution. Genome Biol Evol 2010, 2:745-56. 10.1093/gbe/evq062, 2997564, 20889655.
-
(2010)
Genome Biol Evol
, vol.2
, pp. 745-756
-
-
Puigbo, P.1
Wolf, Y.I.2
Koonin, E.V.3
-
29
-
-
0032830481
-
Evolution of aminoacyl-tRNA synthetases - analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events
-
Wolf YI, Aravind L, Grishin NV, Koonin EV. Evolution of aminoacyl-tRNA synthetases - analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. Genome Research 1999, 9(8):689-710.
-
(1999)
Genome Research
, vol.9
, Issue.8
, pp. 689-710
-
-
Wolf, Y.I.1
Aravind, L.2
Grishin, N.V.3
Koonin, E.V.4
-
30
-
-
38649114368
-
Evolution of acetoclastic methanogenesis in Methanosarcina via horizontal gene transfer from cellulolytic Clostridia
-
10.1128/JB.01382-07, 2223567, 18055595
-
Fournier G, Gogarten J. Evolution of acetoclastic methanogenesis in Methanosarcina via horizontal gene transfer from cellulolytic Clostridia. Journal of Bacteriology 2008, 190(3):1124-1127. 10.1128/JB.01382-07, 2223567, 18055595.
-
(2008)
Journal of Bacteriology
, vol.190
, Issue.3
, pp. 1124-1127
-
-
Fournier, G.1
Gogarten, J.2
-
31
-
-
20444468864
-
Contribution of horizontal gene transfer to the evolution of Saccharomyces cerevisiae
-
10.1128/EC.4.6.1102-1115.2005, 1151995, 15947202
-
Hall C, Brachat S, Dietrich FS. Contribution of horizontal gene transfer to the evolution of Saccharomyces cerevisiae. Eukaryotic Cell 2005, 4(6):1102-1115. 10.1128/EC.4.6.1102-1115.2005, 1151995, 15947202.
-
(2005)
Eukaryotic Cell
, vol.4
, Issue.6
, pp. 1102-1115
-
-
Hall, C.1
Brachat, S.2
Dietrich, F.S.3
-
32
-
-
47349124015
-
Evidence of recent interkingdom horizontal gene transfer between bacteria and Candida parapsilosis
-
Fitzpatrick DA, Logue ME, Butler G. Evidence of recent interkingdom horizontal gene transfer between bacteria and Candida parapsilosis. BMC Evolutionary Biology 2008, 8.
-
(2008)
BMC Evolutionary Biology
, vol.8
-
-
Fitzpatrick, D.A.1
Logue, M.E.2
Butler, G.3
-
33
-
-
0033995545
-
Horizontal gene transfer of glycosyl hydrolases of the rumen fungi
-
Garcia-Vallve S, Romeu A, Palau J. Horizontal gene transfer of glycosyl hydrolases of the rumen fungi. Molecular Biology and Evolution 2000, 17(3):352-361.
-
(2000)
Molecular Biology and Evolution
, vol.17
, Issue.3
, pp. 352-361
-
-
Garcia-Vallve, S.1
Romeu, A.2
Palau, J.3
-
34
-
-
84887212800
-
Ancient Horizontal Gene Transfer from Bacteria Enhances Biosynthetic Capabilities of Fungi
-
Schmitt I, Lumbsch HT. Ancient Horizontal Gene Transfer from Bacteria Enhances Biosynthetic Capabilities of Fungi. PLoS One 2009, 4(2).
-
(2009)
PLoS One
, vol.4
, Issue.2
-
-
Schmitt, I.1
Lumbsch, H.T.2
-
35
-
-
72449164089
-
Acquisition of prokaryotic genes by fungal genomes
-
10.1016/j.tig.2009.11.007, 19969385
-
Marcet-Houben M, Gabaldon T. Acquisition of prokaryotic genes by fungal genomes. Trends In Genetics 2010, 26:5-8. 10.1016/j.tig.2009.11.007, 19969385.
-
(2010)
Trends In Genetics
, vol.26
, pp. 5-8
-
-
Marcet-Houben, M.1
Gabaldon, T.2
-
37
-
-
79953094250
-
Genome sequence of the stramenopile Blastocystis, a human anaerobic parasite
-
10.1186/gb-2011-12-3-r29, 3129679, 21439036
-
Denoeud F, Roussel M, Noel B, Wawrzyniak I, Da Silva C, Diogon M, Viscogliosi E, Brochier-Armanet C, Couloux A, Poulain J, Segurens B, Anthouard V, Texier C, Blot N, Poirier P, Ng GC, Tan K, Artiguenave F, Jaillon O, Aury JM, Delbac F, Wincker P, Vivares C, El Alaoui H. Genome sequence of the stramenopile Blastocystis, a human anaerobic parasite. Genome Biology 2011, 12(3):R29. 10.1186/gb-2011-12-3-r29, 3129679, 21439036.
-
(2011)
Genome Biology
, vol.12
, Issue.3
-
-
Denoeud, F.1
Roussel, M.2
Noel, B.3
Wawrzyniak, I.4
Da Silva, C.5
Diogon, M.6
Viscogliosi, E.7
Brochier-Armanet, C.8
Couloux, A.9
Poulain, J.10
Segurens, B.11
Anthouard, V.12
Texier, C.13
Blot, N.14
Poirier, P.15
Ng, G.C.16
Tan, K.17
Artiguenave, F.18
Jaillon, O.19
Aury, J.M.20
Delbac, F.21
Wincker, P.22
Vivares, C.23
El Alaoui, H.24
more..
-
38
-
-
56249098614
-
The Phaeodactylum genome reveals the evolutionary history of diatom genomes
-
10.1038/nature07410, 18923393
-
Bowler C, Allen AE, Badger JH, Grimwood J, Jabbari K, Kuo A, Maheswari U, Martens C, Maumus F, Otillar RP, Rayko E, Salamov A, Vandepoele K, Beszteri B, Gruber A, Heijde M, Katinka M, Mock T, Valentin K, Verret F, Berges JA, Brownlee C, Cadoret JP, Chiovitti A, Choi CJ, Coesel S, De Martino A, Detter JC, Durkin C, Falciatore A, Fournet J, Haruta M, Huysman MJJ, Jenkins BD, Jiroutova K, Jorgensen RE, Joubert Y, Kaplan A, Kroger N, Kroth PG, La Roche J, Lindquist E, Lommer M, Martin-Jezequel V, Lopez PJ, Lucas S, Mangogna M, McGinnis K, Medlin LK, Montsant A, Oudot-Le Secq MP, Napoli C, Obornik M, Parker MS, Petit JL, Porcel BM, Poulsen N, Robison M, Rychlewski L, Rynearson TA, Schmutz J, Shapiro H, Siaut M, Stanley M, Sussman MR, Taylor AR, Vardi A, von Dassow P, Vyverman W, Willis A, Wyrwicz LS, Rokhsar DS, Weissenbach J, Armbrust EV, Green BR, Van De Peer Y, Grigoriev IV. The Phaeodactylum genome reveals the evolutionary history of diatom genomes. Nature 2008, 456(7219):239-244. 10.1038/nature07410, 18923393.
-
(2008)
Nature
, vol.456
, Issue.7219
, pp. 239-244
-
-
Bowler, C.1
Allen, A.E.2
Badger, J.H.3
Grimwood, J.4
Jabbari, K.5
Kuo, A.6
Maheswari, U.7
Martens, C.8
Maumus, F.9
Otillar, R.P.10
Rayko, E.11
Salamov, A.12
Vandepoele, K.13
Beszteri, B.14
Gruber, A.15
Heijde, M.16
Katinka, M.17
Mock, T.18
Valentin, K.19
Verret, F.20
Berges, J.A.21
Brownlee, C.22
Cadoret, J.P.23
Chiovitti, A.24
Choi, C.J.25
Coesel, S.26
De Martino, A.27
Detter, J.C.28
Durkin, C.29
Falciatore, A.30
Fournet, J.31
Haruta, M.32
Huysman, M.J.J.33
Jenkins, B.D.34
Jiroutova, K.35
Jorgensen, R.E.36
Joubert, Y.37
Kaplan, A.38
Kroger, N.39
Kroth, P.G.40
La Roche, J.41
Lindquist, E.42
Lommer, M.43
Martin-Jezequel, V.44
Lopez, P.J.45
Lucas, S.46
Mangogna, M.47
McGinnis, K.48
Medlin, L.K.49
Montsant, A.50
Oudot-Le Secq, M.P.51
Napoli, C.52
Obornik, M.53
Parker, M.S.54
Petit, J.L.55
Porcel, B.M.56
Poulsen, N.57
Robison, M.58
Rychlewski, L.59
Rynearson, T.A.60
Schmutz, J.61
Shapiro, H.62
Siaut, M.63
Stanley, M.64
Sussman, M.R.65
Taylor, A.R.66
Vardi, A.67
von Dassow, P.68
Vyverman, W.69
Willis, A.70
Wyrwicz, L.S.71
Rokhsar, D.S.72
Weissenbach, J.73
Armbrust, E.V.74
Green, B.R.75
Van De Peer, Y.76
Grigoriev, I.V.77
more..
-
39
-
-
45849089569
-
Massive horizontal gene transfer in bdelloid rotifers
-
10.1126/science.1156407, 18511688
-
Gladyshev EA, Meselson M, Arkhipova IR. Massive horizontal gene transfer in bdelloid rotifers. Science 2008, 320(5880):1210-1213. 10.1126/science.1156407, 18511688.
-
(2008)
Science
, vol.320
, Issue.5880
, pp. 1210-1213
-
-
Gladyshev, E.A.1
Meselson, M.2
Arkhipova, I.R.3
-
40
-
-
52249104410
-
Horizontal gene transfer and the evolution of cnidarian stinging cells
-
10.1016/j.cub.2008.07.031, 18812079
-
Denker E, Bapteste E, Le Guyader H, Manuel M, Rabet N. Horizontal gene transfer and the evolution of cnidarian stinging cells. Current Biology 2008, 18(18):R858-R859. 10.1016/j.cub.2008.07.031, 18812079.
-
(2008)
Current Biology
, vol.18
, Issue.18
-
-
Denker, E.1
Bapteste, E.2
Le Guyader, H.3
Manuel, M.4
Rabet, N.5
-
41
-
-
33745289074
-
Poly-gamma-glutamate in bacteria
-
10.1111/j.1365-2958.2006.05179.x, 16689787
-
Candela T, Fouet A. Poly-gamma-glutamate in bacteria. Molecular Microbiology 2006, 60(5):1091-1098. 10.1111/j.1365-2958.2006.05179.x, 16689787.
-
(2006)
Molecular Microbiology
, vol.60
, Issue.5
, pp. 1091-1098
-
-
Candela, T.1
Fouet, A.2
-
42
-
-
78651268231
-
Horizontal gene transfer of microbial cellulases into nematode genomes is associated with functional assimilation and gene turnover
-
10.1186/1471-2148-11-31, 3041686, 21272359
-
Mayer W, Schuster L, Bartelmes G, Dieterich C, Sommer R. Horizontal gene transfer of microbial cellulases into nematode genomes is associated with functional assimilation and gene turnover. BMC Evolutionary Biology 2011, 11:31. 10.1186/1471-2148-11-31, 3041686, 21272359.
-
(2011)
BMC Evolutionary Biology
, vol.11
, pp. 31
-
-
Mayer, W.1
Schuster, L.2
Bartelmes, G.3
Dieterich, C.4
Sommer, R.5
-
43
-
-
49449094166
-
Nematology: terra incognita no more
-
10.1038/nbt0808-882, 18688240
-
McCarter JP. Nematology: terra incognita no more. Nature Biotechnology 2008, 26(8):882-884. 10.1038/nbt0808-882, 18688240.
-
(2008)
Nature Biotechnology
, vol.26
, Issue.8
, pp. 882-884
-
-
McCarter, J.P.1
-
44
-
-
65549151729
-
Role of horizontal gene transfer in the evolution of plant parasitism among nematodes
-
Mitreva M, Smant G, Heider J. Role of horizontal gene transfer in the evolution of plant parasitism among nematodes. Horizontal Gene Transfer: Genomes in Flux 2009, 517-535.
-
(2009)
Horizontal Gene Transfer: Genomes in Flux
, pp. 517-535
-
-
Mitreva, M.1
Smant, G.2
Heider, J.3
-
45
-
-
65349129373
-
How to become a parasite - lessons from the genomes of nematodes
-
10.1016/j.tig.2009.03.006, 19361881
-
Dieterich C, Sommer RJ. How to become a parasite - lessons from the genomes of nematodes. Trends In Genetics 2009, 25(5):203-209. 10.1016/j.tig.2009.03.006, 19361881.
-
(2009)
Trends In Genetics
, vol.25
, Issue.5
, pp. 203-209
-
-
Dieterich, C.1
Sommer, R.J.2
-
46
-
-
0037195120
-
Genome fragment of Wolbachia endosymbiont transferred to X chromosome of host insect
-
10.1073/pnas.222228199, 137875, 12386340
-
Kondo N, Nikoh N, Ijichi N, Shimada M, Fukatsu T. Genome fragment of Wolbachia endosymbiont transferred to X chromosome of host insect. Proceedings of the National Academy of Sciences of the United States of America 2002, 99(22):14280-14285. 10.1073/pnas.222228199, 137875, 12386340.
-
(2002)
Proceedings of the National Academy of Sciences of the United States of America
, vol.99
, Issue.22
, pp. 14280-14285
-
-
Kondo, N.1
Nikoh, N.2
Ijichi, N.3
Shimada, M.4
Fukatsu, T.5
-
47
-
-
61449155587
-
Horizontal gene transfer between Wolbachia and the mosquito Aedes aegypti
-
Klasson L, Kambris Z, Cook PE, Walker T, Sinkins SP. Horizontal gene transfer between Wolbachia and the mosquito Aedes aegypti. BMC Genomics 2009, 10.
-
(2009)
BMC Genomics
, vol.10
-
-
Klasson, L.1
Kambris, Z.2
Cook, P.E.3
Walker, T.4
Sinkins, S.P.5
-
48
-
-
65249126970
-
On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales
-
10.1073/pnas.0901260106, 2667022, 19307556
-
Zhaxybayeva O, Swithers KS, Lapierre P, Fournier GP, Bickhart DM, Deboy RT, Nelson KE, Nesbo CL, Doolittle WF, Gogarten JP, Noll KM. On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales. Proceedings of the National Academy of Sciences of the United States of America 2009, 106(14):5865-5870. 10.1073/pnas.0901260106, 2667022, 19307556.
-
(2009)
Proceedings of the National Academy of Sciences of the United States of America
, vol.106
, Issue.14
, pp. 5865-5870
-
-
Zhaxybayeva, O.1
Swithers, K.S.2
Lapierre, P.3
Fournier, G.P.4
Bickhart, D.M.5
Deboy, R.T.6
Nelson, K.E.7
Nesbo, C.L.8
Doolittle, W.F.9
Gogarten, J.P.10
Noll, K.M.11
-
49
-
-
14544295684
-
Weighted genome trees: refinements and applications
-
10.1128/JB.187.4.1305-1316.2005, 545607, 15687194
-
Gophna U, Doolittle WF, Charlebois RL. Weighted genome trees: refinements and applications. Journal of Bacteriology 2005, 187(4):1305-1316. 10.1128/JB.187.4.1305-1316.2005, 545607, 15687194.
-
(2005)
Journal of Bacteriology
, vol.187
, Issue.4
, pp. 1305-1316
-
-
Gophna, U.1
Doolittle, W.F.2
Charlebois, R.L.3
-
50
-
-
56349169406
-
Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria
-
Boussau B, Gueguen L, Gouy M. Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria. BMC Evolutionary Biology 2008, 8.
-
(2008)
BMC Evolutionary Biology
, vol.8
-
-
Boussau, B.1
Gueguen, L.2
Gouy, M.3
-
51
-
-
33748743530
-
Insights into extreme thermoacidophily based on genome analysis of Picrophilus torridus and other thermoacidophilic archaea
-
10.1016/j.jbiotec.2006.02.017, 16621083
-
Angelov A, Liebl W. Insights into extreme thermoacidophily based on genome analysis of Picrophilus torridus and other thermoacidophilic archaea. Journal of Biotechnology 2006, 126:3-10. 10.1016/j.jbiotec.2006.02.017, 16621083.
-
(2006)
Journal of Biotechnology
, vol.126
, pp. 3-10
-
-
Angelov, A.1
Liebl, W.2
-
52
-
-
4944233611
-
PhyloGenie: automated phylome generation and analysis
-
10.1093/nar/gkh867, 521674, 15459293
-
Frickey T, Lupas AN. PhyloGenie: automated phylome generation and analysis. Nucleic Acids Research 2004, 32(17):5231-5238. 10.1093/nar/gkh867, 521674, 15459293.
-
(2004)
Nucleic Acids Research
, vol.32
, Issue.17
, pp. 5231-5238
-
-
Frickey, T.1
Lupas, A.N.2
-
53
-
-
2942682647
-
Genome sequence of Picrophilus torridus and its implications for life around pH 0
-
10.1073/pnas.0401356101, 428478, 15184674
-
Futterer O, Angelov A, Liesegang H, Gottschalk G, Schleper C, Schepers B, Dock C, Antranikian G, Liebl W. Genome sequence of Picrophilus torridus and its implications for life around pH 0. Proceedings of the National Academy of Sciences of the United States of America 2004, 101(24):9091-9096. 10.1073/pnas.0401356101, 428478, 15184674.
-
(2004)
Proceedings of the National Academy of Sciences of the United States of America
, vol.101
, Issue.24
, pp. 9091-9096
-
-
Futterer, O.1
Angelov, A.2
Liesegang, H.3
Gottschalk, G.4
Schleper, C.5
Schepers, B.6
Dock, C.7
Antranikian, G.8
Liebl, W.9
-
54
-
-
0035988323
-
The genome of Methanosarcina mazei: Evidence for lateral gene transfer between bacteria and archaea
-
Deppenmeier U, Johann A, Hartsch T, Merkl R, Schmitz R, Martinez-Arias R, Henne A, Wiezer A, Bäumer S, Jacobi C, Brüggemann H, Lienard T, Christmann A, Bameke M, Steckel S, Bhattacharyya A, Lykidis A, Overbeek R, Klenk HP, Gunsalus R, Fritz HJ, Gottschalk G. The genome of Methanosarcina mazei: Evidence for lateral gene transfer between bacteria and archaea. Journal of Molecular Microbiology and Biotechnology 2002, 4(4):453-461.
-
(2002)
Journal of Molecular Microbiology and Biotechnology
, vol.4
, Issue.4
, pp. 453-461
-
-
Deppenmeier, U.1
Johann, A.2
Hartsch, T.3
Merkl, R.4
Schmitz, R.5
Martinez-Arias, R.6
Henne, A.7
Wiezer, A.8
Bäumer, S.9
Jacobi, C.10
Brüggemann, H.11
Lienard, T.12
Christmann, A.13
Bameke, M.14
Steckel, S.15
Bhattacharyya, A.16
Lykidis, A.17
Overbeek, R.18
Klenk, H.P.19
Gunsalus, R.20
Fritz, H.J.21
Gottschalk, G.22
more..
-
55
-
-
36949048082
-
Evolution of eucaryotic cells
-
Goksøyr J. Evolution of eucaryotic cells. Nature 1967, 214:1161.
-
(1967)
Nature
, vol.214
, pp. 1161
-
-
Goksøyr, J.1
-
56
-
-
0027169132
-
Evidence for a chimeric nature of nuclear genomes - eubacterial origin of eukaryotic glyceraldehyde-3-phosphate dehydrogenase genes
-
10.1073/pnas.90.18.8692, 47424, 8378350
-
Martin W, Brinkmann H, Savonna C, Cerff R. Evidence for a chimeric nature of nuclear genomes - eubacterial origin of eukaryotic glyceraldehyde-3-phosphate dehydrogenase genes. Proceedings of the National Academy of Sciences of the United States of America 1993, 90(18):8692-8696. 10.1073/pnas.90.18.8692, 47424, 8378350.
-
(1993)
Proceedings of the National Academy of Sciences of the United States of America
, vol.90
, Issue.18
, pp. 8692-8696
-
-
Martin, W.1
Brinkmann, H.2
Savonna, C.3
Cerff, R.4
-
57
-
-
0035852245
-
Toc, Tic, and chloroplast protein import
-
Jarvis P, Soll M. Toc, Tic, and chloroplast protein import. Biochimica Et Biophysica Acta-molecular Cell Research 2001, 1541(1-2):64-79.
-
(2001)
Biochimica Et Biophysica Acta-molecular Cell Research
, vol.1541
, Issue.1-2
, pp. 64-79
-
-
Jarvis, P.1
Soll, M.2
-
58
-
-
33847790997
-
Pattern pluralism and the Tree of Life hypothesis
-
10.1073/pnas.0610699104, 1892968, 17261804
-
Doolittle WF, Bapteste E. Pattern pluralism and the Tree of Life hypothesis. Proceedings of the National Academy of Sciences of the United States of America 2007, 104(7):2043-2049. 10.1073/pnas.0610699104, 1892968, 17261804.
-
(2007)
Proceedings of the National Academy of Sciences of the United States of America
, vol.104
, Issue.7
, pp. 2043-2049
-
-
Doolittle, W.F.1
Bapteste, E.2
-
59
-
-
33646928341
-
Discordance of species trees with their most likely gene trees
-
Degnan J, Rosenberg N. Discordance of species trees with their most likely gene trees. PLoS Genetics 2006, 2(5):762-768.
-
(2006)
PLoS Genetics
, vol.2
, Issue.5
, pp. 762-768
-
-
Degnan, J.1
Rosenberg, N.2
-
60
-
-
33847656285
-
Detecting and overcoming systematic errors in genome-scale phylogenies
-
10.1080/10635150701397643, 17520503
-
Rodriguez-Ezpeleta N, Brinkmann H, Roure B, Lartillot N, Lang BF, Philippe H. Detecting and overcoming systematic errors in genome-scale phylogenies. Systematic Biology 2007, 56(3):389-399. 10.1080/10635150701397643, 17520503.
-
(2007)
Systematic Biology
, vol.56
, Issue.3
, pp. 389-399
-
-
Rodriguez-Ezpeleta, N.1
Brinkmann, H.2
Roure, B.3
Lartillot, N.4
Lang, B.F.5
Philippe, H.6
-
61
-
-
58149231047
-
The Impact of Reticulate Evolution on Genome Phylogeny
-
10.1080/10635150802559265, 19085328
-
Beiko RG, Doolittle WF, Charlebois RL. The Impact of Reticulate Evolution on Genome Phylogeny. Systematic Biology 2008, 57(6):844-856. 10.1080/10635150802559265, 19085328.
-
(2008)
Systematic Biology
, vol.57
, Issue.6
, pp. 844-856
-
-
Beiko, R.G.1
Doolittle, W.F.2
Charlebois, R.L.3
-
62
-
-
0028790653
-
Inferring phylogenies from DNA-sequences of unequal base compositions
-
10.1073/pnas.92.24.11317, 40623, 7479987
-
Galtier N, Gouy M. Inferring phylogenies from DNA-sequences of unequal base compositions. Proceedings of the National Academy of Sciences of the United States of America 1995, 92(24):11317-11321. 10.1073/pnas.92.24.11317, 40623, 7479987.
-
(1995)
Proceedings of the National Academy of Sciences of the United States of America
, vol.92
, Issue.24
, pp. 11317-11321
-
-
Galtier, N.1
Gouy, M.2
-
63
-
-
7244221755
-
Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous
-
10.1038/nature02917, 15496922
-
Kolaczkowski B, Thornton JW. Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature 2004, 431(7011):980-984. 10.1038/nature02917, 15496922.
-
(2004)
Nature
, vol.431
, Issue.7011
, pp. 980-984
-
-
Kolaczkowski, B.1
Thornton, J.W.2
-
64
-
-
3242701529
-
Modeling compositional heterogeneity
-
10.1080/10635150490445779, 15503675
-
Foster PG. Modeling compositional heterogeneity. Systematic Biology 2004, 53(3):485-495. 10.1080/10635150490445779, 15503675.
-
(2004)
Systematic Biology
, vol.53
, Issue.3
, pp. 485-495
-
-
Foster, P.G.1
-
65
-
-
27744488568
-
Heterotachy and long-branch attraction in phylogenetics
-
Philippe H, Zhou Y, Brinkmann H, Rodrigue N, Delsuc F. Heterotachy and long-branch attraction in phylogenetics. BMC Evolutionary Biology 2005, 5.
-
(2005)
BMC Evolutionary Biology
, vol.5
-
-
Philippe, H.1
Zhou, Y.2
Brinkmann, H.3
Rodrigue, N.4
Delsuc, F.5
-
66
-
-
1542642309
-
Protein evolution with dependence among codons due to tertiary structure
-
10.1093/molbev/msg184, 12885968
-
Robinson DM, Jones DT, Kishino H, Goldman N, Thorne JL. Protein evolution with dependence among codons due to tertiary structure. Molecular Biology and Evolution 2003, 20(10):1692-1704. 10.1093/molbev/msg184, 12885968.
-
(2003)
Molecular Biology and Evolution
, vol.20
, Issue.10
, pp. 1692-1704
-
-
Robinson, D.M.1
Jones, D.T.2
Kishino, H.3
Goldman, N.4
Thorne, J.L.5
-
67
-
-
33646586721
-
A Dirichlet process model for detecting positive selection in protein-coding DNA sequences
-
10.1073/pnas.0508279103, 1458866, 16606848
-
Huelsenbeck JP, Jain S, Frost SWD, Pond SLK. A Dirichlet process model for detecting positive selection in protein-coding DNA sequences. Proceedings of the National Academy of Sciences of the United States of America 2006, 103(16):6263-6268. 10.1073/pnas.0508279103, 1458866, 16606848.
-
(2006)
Proceedings of the National Academy of Sciences of the United States of America
, vol.103
, Issue.16
, pp. 6263-6268
-
-
Huelsenbeck, J.P.1
Jain, S.2
Frost, S.W.D.3
Pond, S.L.K.4
-
68
-
-
67649329427
-
Computational methods for evaluating phylogenetic models of coding sequence evolution with dependence between codons
-
10.1093/molbev/msp078, 19383983
-
Rodrigue N, Kleinman C, Philippe H, Lartillot N. Computational methods for evaluating phylogenetic models of coding sequence evolution with dependence between codons. Molecular Biology and Evolution 2009, 26(7):1663-1676. 10.1093/molbev/msp078, 19383983.
-
(2009)
Molecular Biology and Evolution
, vol.26
, Issue.7
, pp. 1663-1676
-
-
Rodrigue, N.1
Kleinman, C.2
Philippe, H.3
Lartillot, N.4
-
69
-
-
77958119109
-
The impact of rRNA secondary structure consideration in alignment and tree reconstruction: simulated data and a case study on the phylogeny of hexapods
-
10.1093/molbev/msq140, 20530152
-
Letsch HO, Kuck P, Stocsits RR, Misof B. The impact of rRNA secondary structure consideration in alignment and tree reconstruction: simulated data and a case study on the phylogeny of hexapods. Molecular Biology and Evolution 2010, 27(11):2507-2521. 10.1093/molbev/msq140, 20530152.
-
(2010)
Molecular Biology and Evolution
, vol.27
, Issue.11
, pp. 2507-2521
-
-
Letsch, H.O.1
Kuck, P.2
Stocsits, R.R.3
Misof, B.4
-
70
-
-
34248176323
-
Phylogenetic analyses under secondary structure-specific substitution models outperform traditional approaches: case studies with diploblast LSU
-
10.1007/s00239-006-0146-3, 17460808
-
Erpenbeck D, Nichols SA, Voigt O, Dohrmann M, Degnan BM, Hooper JNA, Worheide G. Phylogenetic analyses under secondary structure-specific substitution models outperform traditional approaches: case studies with diploblast LSU. Journal of Molecular Evolution 2007, 64(5):543-557. 10.1007/s00239-006-0146-3, 17460808.
-
(2007)
Journal of Molecular Evolution
, vol.64
, Issue.5
, pp. 543-557
-
-
Erpenbeck, D.1
Nichols, S.A.2
Voigt, O.3
Dohrmann, M.4
Degnan, B.M.5
Hooper, J.N.A.6
Worheide, G.7
-
71
-
-
53249100490
-
Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs
-
Dutheil J, Boussau B. Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs. BMC Evolutionary Biology 2008, 8.
-
(2008)
BMC Evolutionary Biology
, vol.8
-
-
Dutheil, J.1
Boussau, B.2
-
72
-
-
84959798530
-
Cases in which parsimony or compatibility methods will be positively mislead
-
Felsenstein J. Cases in which parsimony or compatibility methods will be positively mislead. Systematic Zoology 1978, 27:401-410.
-
(1978)
Systematic Zoology
, vol.27
, pp. 401-410
-
-
Felsenstein, J.1
-
73
-
-
3042601821
-
Covarion shifts cause a long-branch attraction artifact that unites microsporidia and archaebacteria in EF-1α phylogenies
-
10.1093/molbev/msh130, 15034136
-
Inagaki Y, Susko E, Fast N, Roger A. Covarion shifts cause a long-branch attraction artifact that unites microsporidia and archaebacteria in EF-1α phylogenies. Molecular Biology and Evolution 2004, 21(7):1340-1349. 10.1093/molbev/msh130, 15034136.
-
(2004)
Molecular Biology and Evolution
, vol.21
, Issue.7
, pp. 1340-1349
-
-
Inagaki, Y.1
Susko, E.2
Fast, N.3
Roger, A.4
-
74
-
-
0031938847
-
Origins of microsporidia
-
10.1016/S0966-842X(97)01185-2, 9481819
-
Keeling PJ, McFadden GI. Origins of microsporidia. Trends In Microbiology 1998, 6:19-23. 10.1016/S0966-842X(97)01185-2, 9481819.
-
(1998)
Trends In Microbiology
, vol.6
, pp. 19-23
-
-
Keeling, P.J.1
McFadden, G.I.2
-
75
-
-
0041843801
-
Molecular phylogenies link rates of evolution and speciation
-
10.1126/science.1083202, 12881561
-
Webster A, Payne R, Pagel M. Molecular phylogenies link rates of evolution and speciation. Science 2003, 301(5632):478. 10.1126/science.1083202, 12881561.
-
(2003)
Science
, vol.301
, Issue.5632
, pp. 478
-
-
Webster, A.1
Payne, R.2
Pagel, M.3
-
76
-
-
84871992357
-
NCBI Complete Microbial Genomes
-
NCBI Complete Microbial Genomes. , http://www.ncbi.nlm.nih.gov/genomes/MICROBES/Complete.html
-
-
-
-
77
-
-
77953646161
-
Diversity of 16S rRNA genes within individual prokaryotic genomes
-
10.1128/AEM.02953-09, 2893482, 20418441
-
Pei AY, Oberdorf WE, Nossa CW, Agarwal A, Chokshi P, Gerz EA, Jin ZD, Lee P, Yang LY, Poles M, Brown SM, Sotero S, DeSantis T, Brodie E, Nelson K, Pei ZH. Diversity of 16S rRNA genes within individual prokaryotic genomes. Applied and Environmental Microbiology 2010, 76(12):3886-3897. 10.1128/AEM.02953-09, 2893482, 20418441.
-
(2010)
Applied and Environmental Microbiology
, vol.76
, Issue.12
, pp. 3886-3897
-
-
Pei, A.Y.1
Oberdorf, W.E.2
Nossa, C.W.3
Agarwal, A.4
Chokshi, P.5
Gerz, E.A.6
Jin, Z.D.7
Lee, P.8
Yang, L.Y.9
Poles, M.10
Brown, S.M.11
Sotero, S.12
DeSantis, T.13
Brodie, E.14
Nelson, K.15
Pei, Z.H.16
-
78
-
-
0028028182
-
A place for DNA-DNA reassociation and 16S ribosomal-RNA sequence analysis in the present species definition in bacteriology
-
Stackebrandt E, Goebel BM. A place for DNA-DNA reassociation and 16S ribosomal-RNA sequence analysis in the present species definition in bacteriology. International Journal of Systematic Bacteriology 1994, 44(4):846-849.
-
(1994)
International Journal of Systematic Bacteriology
, vol.44
, Issue.4
, pp. 846-849
-
-
Stackebrandt, E.1
Goebel, B.M.2
-
79
-
-
2942545812
-
Intragenomic heterogeneity and intergenomic recombination among haloarchaeal rRNA genes
-
10.1128/JB.186.12.3980-3990.2004, 419955, 15175312
-
Boucher Y, Douady C, Sharma A, Kamekura M, Doolittle W. Intragenomic heterogeneity and intergenomic recombination among haloarchaeal rRNA genes. Journal of Bacteriology 2004, 186(12):3980-3990. 10.1128/JB.186.12.3980-3990.2004, 419955, 15175312.
-
(2004)
Journal of Bacteriology
, vol.186
, Issue.12
, pp. 3980-3990
-
-
Boucher, Y.1
Douady, C.2
Sharma, A.3
Kamekura, M.4
Doolittle, W.5
-
80
-
-
58149178756
-
Intraspecific polymorphism of 16S rRNA genes in two halophilic archaeal genera, Haloarcula and Halomicrobium
-
10.1007/s00792-008-0194-2, 18836684
-
Cui HL, Zhou PJ, Oren A, Liu SJ. Intraspecific polymorphism of 16S rRNA genes in two halophilic archaeal genera, Haloarcula and Halomicrobium. Extremophiles 2009, 13:31-37. 10.1007/s00792-008-0194-2, 18836684.
-
(2009)
Extremophiles
, vol.13
, pp. 31-37
-
-
Cui, H.L.1
Zhou, P.J.2
Oren, A.3
Liu, S.J.4
-
81
-
-
33846839390
-
Bayesian estimation of concordance among gene trees
-
Ané C, Larget B, Baum D, Smith S, Rokas A. Bayesian estimation of concordance among gene trees. Molecular Biology and Evolution 2007, 24(2):412-426.
-
(2007)
Molecular Biology and Evolution
, vol.24
, Issue.2
, pp. 412-426
-
-
Ané, C.1
Larget, B.2
Baum, D.3
Smith, S.4
Rokas, A.5
-
82
-
-
63549118031
-
STEM: species tree estimation using maximum likelihood for gene trees under coalescence
-
10.1093/bioinformatics/btp079, 19211573
-
Kubatko L, Carstens B, Knowles L. STEM: species tree estimation using maximum likelihood for gene trees under coalescence. Bioinformatics 2009, 25(7):971-973. 10.1093/bioinformatics/btp079, 19211573.
-
(2009)
Bioinformatics
, vol.25
, Issue.7
, pp. 971-973
-
-
Kubatko, L.1
Carstens, B.2
Knowles, L.3
-
83
-
-
75149135738
-
Efficient genome-scale phylogenetic analysis under the duplication-loss and deep coalescence cost models
-
Bansal MS, Burleigh JG, Eulenstein O. Efficient genome-scale phylogenetic analysis under the duplication-loss and deep coalescence cost models. BMC Bioinformatics 2010, 11.
-
(2010)
BMC Bioinformatics
, vol.11
-
-
Bansal, M.S.1
Burleigh, J.G.2
Eulenstein, O.3
-
84
-
-
33645568886
-
Phylogenetic identification of lateral genetic transfer events
-
Beiko RG, Hamilton N. Phylogenetic identification of lateral genetic transfer events. BMC Evolutionary Biology 2006, 6.
-
(2006)
BMC Evolutionary Biology
, vol.6
-
-
Beiko, R.G.1
Hamilton, N.2
-
85
-
-
78650987950
-
Rapid evolutionary innovation during an Archean genetic expansion
-
10.1038/nature09649, 21170026
-
Lawrence AD, Alm EJ. Rapid evolutionary innovation during an Archean genetic expansion. Nature 2011, 469:93-96. 10.1038/nature09649, 21170026.
-
(2011)
Nature
, vol.469
, pp. 93-96
-
-
Lawrence, A.D.1
Alm, E.J.2
-
86
-
-
68149093715
-
Search for a 'Tree of Life' in the thicket of the phylogenetic forest
-
10.1186/jbiol159, 2737373, 19594957
-
Puigbo P, Wolf YI, Koonin EV. Search for a 'Tree of Life' in the thicket of the phylogenetic forest. Journal of Biology 2009, 8(6):59. 10.1186/jbiol159, 2737373, 19594957.
-
(2009)
Journal of Biology
, vol.8
, Issue.6
, pp. 59
-
-
Puigbo, P.1
Wolf, Y.I.2
Koonin, E.V.3
-
87
-
-
77955266548
-
Clanistics: a multi-level perspective for harvesting unrooted gene trees
-
10.1016/j.tim.2010.03.009, 20605718
-
Lapointe FJ, Lopez P, Boucher Y, Koenig J, Bapteste E. Clanistics: a multi-level perspective for harvesting unrooted gene trees. Trends In Microbiology 2010, 18(8):341-347. 10.1016/j.tim.2010.03.009, 20605718.
-
(2010)
Trends In Microbiology
, vol.18
, Issue.8
, pp. 341-347
-
-
Lapointe, F.J.1
Lopez, P.2
Boucher, Y.3
Koenig, J.4
Bapteste, E.5
-
88
-
-
79952835117
-
Harvesting Evolutionary Signals in a Forest of Prokaryotic Gene Trees
-
10.1093/molbev/msq323, 21172835
-
Schliep K, Lopez P, Lapointe FJ, Bapteste E. Harvesting Evolutionary Signals in a Forest of Prokaryotic Gene Trees. Molecular Biology and Evolution 2011, 28(4):1393-1405. 10.1093/molbev/msq323, 21172835.
-
(2011)
Molecular Biology and Evolution
, vol.28
, Issue.4
, pp. 1393-1405
-
-
Schliep, K.1
Lopez, P.2
Lapointe, F.J.3
Bapteste, E.4
-
89
-
-
65549147805
-
Microbial co-habitation and lateral gene transfer: what transposases can tell us
-
Hooper SD, Mavromatis K, Kyrpides NC. Microbial co-habitation and lateral gene transfer: what transposases can tell us. Genome Biology 2009, 10(4).
-
(2009)
Genome Biology
, vol.10
, Issue.4
-
-
Hooper, S.D.1
Mavromatis, K.2
Kyrpides, N.C.3
-
90
-
-
77953776263
-
Biased gene transfer mimics patterns created through shared ancestry
-
10.1073/pnas.1001418107, 2890805, 20495090
-
Andam CP, Williams D, Gogarten JP. Biased gene transfer mimics patterns created through shared ancestry. Proceedings of the National Academy of Sciences of the United States of America 2010, 107(23):10679-10684. 10.1073/pnas.1001418107, 2890805, 20495090.
-
(2010)
Proceedings of the National Academy of Sciences of the United States of America
, vol.107
, Issue.23
, pp. 10679-10684
-
-
Andam, C.P.1
Williams, D.2
Gogarten, J.P.3
-
91
-
-
79953315166
-
Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes
-
10.1101/gr.115592.110, 3065707, 21270172
-
Popa O, Hazkani-Covo E, Landan G, Martin W, Dagan T. Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes. Genome Research 2011, 21(4):599-609. 10.1101/gr.115592.110, 3065707, 21270172.
-
(2011)
Genome Research
, vol.21
, Issue.4
, pp. 599-609
-
-
Popa, O.1
Hazkani-Covo, E.2
Landan, G.3
Martin, W.4
Dagan, T.5
-
92
-
-
24944473090
-
Evolutionary and diagnostic implications of intragenomic heterogeneity in the 16S rRNA gene in Aeromonas strains
-
10.1128/JB.187.18.6561-6564.2005, 1236645, 16159790
-
Morandi A, Zhaxybayeva O, Gogarten JP, Graf J. Evolutionary and diagnostic implications of intragenomic heterogeneity in the 16S rRNA gene in Aeromonas strains. Journal of Bacteriology 2005, 187(18):6561-6564. 10.1128/JB.187.18.6561-6564.2005, 1236645, 16159790.
-
(2005)
Journal of Bacteriology
, vol.187
, Issue.18
, pp. 6561-6564
-
-
Morandi, A.1
Zhaxybayeva, O.2
Gogarten, J.P.3
Graf, J.4
-
93
-
-
79951935646
-
Complex Evolutionary History of the Aeromonas veronii Group Revealed by Host Interaction and DNA Sequence Data
-
Silver AC, Williams D, Faucher J, Horneman AJ, Gogarten JP, Graf J. Complex Evolutionary History of the Aeromonas veronii Group Revealed by Host Interaction and DNA Sequence Data. PLoS One 2011, 6(2).
-
(2011)
PLoS One
, vol.6
, Issue.2
-
-
Silver, A.C.1
Williams, D.2
Faucher, J.3
Horneman, A.J.4
Gogarten, J.P.5
Graf, J.6
-
94
-
-
0036137155
-
Eubacterial phylogeny based on translational apparatus proteins
-
10.1016/S0168-9525(01)02522-7, 11750686
-
Brochier C, Bapteste E, Moreira D, Philippe H. Eubacterial phylogeny based on translational apparatus proteins. Trends In Genetics 2002, 18:1-5. 10.1016/S0168-9525(01)02522-7, 11750686.
-
(2002)
Trends In Genetics
, vol.18
, pp. 1-5
-
-
Brochier, C.1
Bapteste, E.2
Moreira, D.3
Philippe, H.4
-
95
-
-
78650356229
-
On the shape and fabric of human history
-
Gray RD, Bryant D, Greenhill SJ. On the shape and fabric of human history. Philosophical Transactions of the Royal Society B: Biological Sciences 2010, 365(1559):3923-3933., http://rstb.royalsocietypublishing.org/content/365/1559/3923.abstract
-
(2010)
Philosophical Transactions of the Royal Society B: Biological Sciences
, vol.365
, Issue.1559
, pp. 3923-3933
-
-
Gray, R.D.1
Bryant, D.2
Greenhill, S.J.3
-
96
-
-
80053572930
-
-
Humana press, chap. Philosophy and evolution: minding the gap between Evolutionary Patterns and Tree-like Patterns
-
Bapteste B, Burian. Evolutionary Genomics: Statistical and Computational Methods 2011, Humana press, chap. Philosophy and evolution: minding the gap between Evolutionary Patterns and Tree-like Patterns.
-
(2011)
Evolutionary Genomics: Statistical and Computational Methods
-
-
Bapteste, B.1
Burian2
-
97
-
-
79551492021
-
Manipulation of cellular syntheses and the nature of viruses: The virocell concept
-
Forterre P. Manipulation of cellular syntheses and the nature of viruses: The virocell concept. Comptes Rendus Chimie 2011, 14(4):392-399., http://www.sciencedirect.com/science/article/pii/S1631074810001724
-
(2011)
Comptes Rendus Chimie
, vol.14
, Issue.4
, pp. 392-399
-
-
Forterre, P.1
-
98
-
-
77956011404
-
On the need for integrative phylogenomics, and some steps toward its creation
-
Bapteste E, Burian R. On the need for integrative phylogenomics, and some steps toward its creation. Biology and Philosophy 2010, 25(4):711-736., http://dx.doi.org/10.1007/s10539-010-9218-2
-
(2010)
Biology and Philosophy
, vol.25
, Issue.4
, pp. 711-736
-
-
Bapteste, E.1
Burian, R.2
-
99
-
-
76249102181
-
Network analyses structure genetic diversity in independent genetic worlds
-
Halary S, Leigh J, Cheaib B, Lopez P, Bapteste E. Network analyses structure genetic diversity in independent genetic worlds. Proceedings of the National Academy of Sciences 2010, 107:127-132., http://www.pnas.org/content/107/1/127.abstract
-
(2010)
Proceedings of the National Academy of Sciences
, vol.107
, pp. 127-132
-
-
Halary, S.1
Leigh, J.2
Cheaib, B.3
Lopez, P.4
Bapteste, E.5
-
100
-
-
79960313230
-
Lateral genetic transfer and the construction of genetic exchange communities
-
10.1111/j.1574-6976.2010.00261.x, 21223321
-
Skippington E, Ragan MA. Lateral genetic transfer and the construction of genetic exchange communities. FEMS Microbiology Reviews 2011, 35(5):707-735. 10.1111/j.1574-6976.2010.00261.x, 21223321., http://dx.doi.org/10.1111/j.1574-6976.2010.00261.x
-
(2011)
FEMS Microbiology Reviews
, vol.35
, Issue.5
, pp. 707-735
-
-
Skippington, E.1
Ragan, M.A.2
-
102
-
-
65549102123
-
Detection and quantitative assessment of horizontal gene transfer
-
10.1007/978-1-60327-853-9_11, 19271186
-
Zhaxybayeva O. Detection and quantitative assessment of horizontal gene transfer. Methods in Molecular Biology 2009, 532:195-213. 10.1007/978-1-60327-853-9_11, 19271186.
-
(2009)
Methods in Molecular Biology
, vol.532
, pp. 195-213
-
-
Zhaxybayeva, O.1
-
103
-
-
59249089471
-
Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths
-
Touchon M, Hoede C, Tenaillon O, Barbe V, Baeriswyl S, Bidet P, Bingen E, Bonacorsi S, Bouchier C, Bouvet O, Calteau A, Chiapello H, Clermont O, Cruveiller S, Danchin A, Diard M, Dossat C, El Karoui M, Frapy E, Garry L, Ghigo J, Gilles A, Johnson J, Le Bouguénec C, Lescat M, Mangenot S, Martinez-Jéhanne V, Matic I, Nassif X, Oztas S, Petit M, Pichon C, Rouy Z, Ruf C, Schneider D, Tourret J, Vacherie B, Vallenet D, Médigue C, Rocha E, Denamur E. Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genetics 2009, 5., http://www.scopus.com/scopus/inward/record.url?eid=2-s2.0-59249089471&partnerID=40
-
(2009)
PLoS Genetics
, vol.5
-
-
Touchon, M.1
Hoede, C.2
Tenaillon, O.3
Barbe, V.4
Baeriswyl, S.5
Bidet, P.6
Bingen, E.7
Bonacorsi, S.8
Bouchier, C.9
Bouvet, O.10
Calteau, A.11
Chiapello, H.12
Clermont, O.13
Cruveiller, S.14
Danchin, A.15
Diard, M.16
Dossat, C.17
El Karoui, M.18
Frapy, E.19
Garry, L.20
Ghigo, J.21
Gilles, A.22
Johnson, J.23
Le Bouguénec, C.24
Lescat, M.25
Mangenot, S.26
Martinez-Jéhanne, V.27
Matic, I.28
Nassif, X.29
Oztas, S.30
Petit, M.31
Pichon, C.32
Rouy, Z.33
Ruf, C.34
Schneider, D.35
Tourret, J.36
Vacherie, B.37
Vallenet, D.38
Médigue, C.39
Rocha, E.40
Denamur, E.41
more..
-
104
-
-
66449130374
-
Revisiting the concept of lineage in prokaryotes: a phylogenetic perspective
-
10.1002/bies.200800216, 19319912
-
Boucher Y, Bapteste E. Revisiting the concept of lineage in prokaryotes: a phylogenetic perspective. Bioessays 2009, 31(5):526-536. 10.1002/bies.200800216, 19319912., http://dx.doi.org/10.1002/bies.200800216
-
(2009)
Bioessays
, vol.31
, Issue.5
, pp. 526-536
-
-
Boucher, Y.1
Bapteste, E.2
-
105
-
-
9144225618
-
Bootstrap, Bayesian probability and maximum likelihood mapping: exploring new tools for comparative genome analyses
-
Zhaxybayeva O, Gogarten JP. Bootstrap, Bayesian probability and maximum likelihood mapping: exploring new tools for comparative genome analyses. BMC Genomics 2002, 3.
-
(2002)
BMC Genomics
, vol.3
-
-
Zhaxybayeva, O.1
Gogarten, J.P.2
-
106
-
-
1942422301
-
Genome mosaicism and organismal lineages
-
10.1016/j.tig.2004.03.009, 15109780
-
Zhaxybayeva O, Lapierre P, Gogarten JP. Genome mosaicism and organismal lineages. Trends In Genetics 2004, 20(5):254-260. 10.1016/j.tig.2004.03.009, 15109780.
-
(2004)
Trends In Genetics
, vol.20
, Issue.5
, pp. 254-260
-
-
Zhaxybayeva, O.1
Lapierre, P.2
Gogarten, J.P.3
-
108
-
-
33748277982
-
Phylogenetic analyses of cyanobacterial genomes: Quantification of horizontal gene transfer events
-
10.1101/gr.5322306, 1557764, 16899658
-
Zhaxybayeva O, Gogarten J, Charlebois R, Doolittle W, Papke R. Phylogenetic analyses of cyanobacterial genomes: Quantification of horizontal gene transfer events. Genome Research 2006, 16(9):1099-1108. 10.1101/gr.5322306, 1557764, 16899658.
-
(2006)
Genome Research
, vol.16
, Issue.9
, pp. 1099-1108
-
-
Zhaxybayeva, O.1
Gogarten, J.2
Charlebois, R.3
Doolittle, W.4
Papke, R.5
-
109
-
-
0023184331
-
Bacterial Evolution
-
373105, 2439888
-
Woese CR. Bacterial Evolution. Microbiological Reviews 1987, 51(2):221-271. 373105, 2439888.
-
(1987)
Microbiological Reviews
, vol.51
, Issue.2
, pp. 221-271
-
-
Woese, C.R.1
-
110
-
-
43049101618
-
Lateral gene transfer challenges principles of microbial systematics
-
10.1016/j.tim.2008.02.005, 18420414
-
Bapteste E, Boucher Y. Lateral gene transfer challenges principles of microbial systematics. Trends In Microbiology 2008, 16(5):200-207. 10.1016/j.tim.2008.02.005, 18420414.
-
(2008)
Trends In Microbiology
, vol.16
, Issue.5
, pp. 200-207
-
-
Bapteste, E.1
Boucher, Y.2
-
111
-
-
0026947857
-
Evolution and Isoforms of V-ATPase Subunits
-
Gogarten JP, Starke T, Kibak H, Fishmann J, Taiz L. Evolution and Isoforms of V-ATPase Subunits. Journal of Experimental Biology 1992, 172:137-147.
-
(1992)
Journal of Experimental Biology
, vol.172
, pp. 137-147
-
-
Gogarten, J.P.1
Starke, T.2
Kibak, H.3
Fishmann, J.4
Taiz, L.5
-
112
-
-
79959655385
-
Telling the Whole Story in a 10,000-Genome World
-
10.1186/1745-6150-6-34, 3158115, 21714939
-
Beiko R. Telling the Whole Story in a 10,000-Genome World. Biology Direct 2011, 6:34. 10.1186/1745-6150-6-34, 3158115, 21714939., http://www.biology-direct.com/content/6/1/34
-
(2011)
Biology Direct
, vol.6
, pp. 34
-
-
Beiko, R.1
-
113
-
-
34547803197
-
PAML 4: Phylogenetic analysis by maximum likelihood
-
10.1093/molbev/msm088, 17483113
-
Yang Z. PAML 4: Phylogenetic analysis by maximum likelihood. Molecular Biology and Evolution 2007, 24(8):1586-1591. 10.1093/molbev/msm088, 17483113.
-
(2007)
Molecular Biology and Evolution
, vol.24
, Issue.8
, pp. 1586-1591
-
-
Yang, Z.1
-
114
-
-
36448991500
-
Clustal W and Clustal X version 2.0
-
10.1093/bioinformatics/btm404, 17846036
-
Larkin M, Blackshields G, Brown N, Chenna R, McGettigan P, McWilliam H, Valentin F, Wallace I, Wilm A, Lopez R, Thompson J, Gibson T, Higgins D. Clustal W and Clustal X version 2.0. Bioinformatics 2007, 23(21):2947-2948. 10.1093/bioinformatics/btm404, 17846036.
-
(2007)
Bioinformatics
, vol.23
, Issue.21
, pp. 2947-2948
-
-
Larkin, M.1
Blackshields, G.2
Brown, N.3
Chenna, R.4
McGettigan, P.5
McWilliam, H.6
Valentin, F.7
Wallace, I.8
Wilm, A.9
Lopez, R.10
Thompson, J.11
Gibson, T.12
Higgins, D.13
-
115
-
-
77950806408
-
New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0
-
10.1093/sysbio/syq010, 20525638
-
Guindon S, Dufayard J, Lefort V, Anisimova M, Hordijk W, O G. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Systematic Biology 2010, 59:307-21. 10.1093/sysbio/syq010, 20525638.
-
(2010)
Systematic Biology
, vol.59
, pp. 307-321
-
-
Guindon, S.1
Dufayard, J.2
Lefort, V.3
Anisimova, M.4
Hordijk, W.5
O, G.6
-
116
-
-
9144255640
-
An improved probability mapping approach to assess genome mosaicism
-
Zhaxybayeva O, Gogarten JP. An improved probability mapping approach to assess genome mosaicism. BMC Genomics 2003, 4.
-
(2003)
BMC Genomics
, vol.4
-
-
Zhaxybayeva, O.1
Gogarten, J.P.2
-
117
-
-
80053568596
-
Quartet suite v1.0 (supertrees by quartets)
-
Piaggio-Talice R. Quartet suite v1.0 (supertrees by quartets). 2004, http://genome.cs.iastate.edu/CBL/download/
-
(2004)
-
-
Piaggio-Talice, R.1
|