-
1
-
-
33645310157
-
Biochemistry: gas with an ancient history
-
Canfield DE, (2006) Biochemistry: gas with an ancient history. Nature 440: 426-427.
-
(2006)
Nature
, vol.440
, pp. 426-427
-
-
Canfield, D.E.1
-
2
-
-
38349105591
-
The rise of atmospheric oxygen
-
Kump LR, (2008) The rise of atmospheric oxygen. Nature 451: 277-278.
-
(2008)
Nature
, vol.451
, pp. 277-278
-
-
Kump, L.R.1
-
4
-
-
0000549919
-
Mitochondrial origins
-
Yang D, Oyaizu Y, Oyaizu H, Olsen GJ, Woese CR, (1985) Mitochondrial origins. Proc Natl Acad Sci U S A 82: 4443-4447.
-
(1985)
Proc Natl Acad Sci U S A
, vol.82
, pp. 4443-4447
-
-
Yang, D.1
Oyaizu, Y.2
Oyaizu, H.3
Olsen, G.J.4
Woese, C.R.5
-
5
-
-
3042840997
-
Computational inference of scenarios for alpha-proteobacterial genome evolution
-
Boussau B, Karlberg EO, Frank AC, Legault BA, Andersson SG, (2004) Computational inference of scenarios for alpha-proteobacterial genome evolution. Proc Natl Acad Sci U S A 101: 9722-9727.
-
(2004)
Proc Natl Acad Sci U S A
, vol.101
, pp. 9722-9727
-
-
Boussau, B.1
Karlberg, E.O.2
Frank, A.C.3
Legault, B.A.4
Andersson, S.G.5
-
6
-
-
0042266921
-
Reconstruction of the proto-mitochondrial metabolism
-
Gabaldon T, Huynen MA, (2003) Reconstruction of the proto-mitochondrial metabolism. Science 301: 609.
-
(2003)
Science
, vol.301
, pp. 609
-
-
Gabaldon, T.1
Huynen, M.A.2
-
7
-
-
0023665552
-
Eukaryotes with no mitochondria
-
Cavalier-Smith T, (1987) Eukaryotes with no mitochondria. Nature 326: 332-333.
-
(1987)
Nature
, vol.326
, pp. 332-333
-
-
Cavalier-Smith, T.1
-
8
-
-
33645456207
-
Eukaryotic evolution, changes and challenges
-
Embley TM, Martin W, (2006) Eukaryotic evolution, changes and challenges. Nature 440: 623-630.
-
(2006)
Nature
, vol.440
, pp. 623-630
-
-
Embley, T.M.1
Martin, W.2
-
9
-
-
2642689666
-
The hydrogen hypothesis for the first eukaryote
-
Martin W, Muller M, (1998) The hydrogen hypothesis for the first eukaryote. Nature 392: 37-41.
-
(1998)
Nature
, vol.392
, pp. 37-41
-
-
Martin, W.1
Muller, M.2
-
10
-
-
0032512051
-
The genome sequence of Rickettsia prowazekii and the origin of mitochondria
-
Andersson SG, Zomorodipour A, Andersson JO, Sicheritz-Ponten T, Alsmark UC, et al. (1998) The genome sequence of Rickettsia prowazekii and the origin of mitochondria. Nature 396: 133-140.
-
(1998)
Nature
, vol.396
, pp. 133-140
-
-
Andersson, S.G.1
Zomorodipour, A.2
Andersson, J.O.3
Sicheritz-Ponten, T.4
Alsmark, U.C.5
-
11
-
-
77955795400
-
Uniting sex and eukaryote origins in an emerging oxygenic world
-
Gross J, Bhattacharya D, (2010) Uniting sex and eukaryote origins in an emerging oxygenic world. Biol Direct 5: 53.
-
(2010)
Biol Direct
, vol.5
, pp. 53
-
-
Gross, J.1
Bhattacharya, D.2
-
12
-
-
0034443285
-
Origin and evolution of the mitochondrial proteome
-
Kurland CG, Andersson SG, (2000) Origin and evolution of the mitochondrial proteome. Microbiol Mol Biol Rev 64: 786-820.
-
(2000)
Microbiol Mol Biol Rev
, vol.64
, pp. 786-820
-
-
Kurland, C.G.1
Andersson, S.G.2
-
13
-
-
4143093598
-
A genome phylogeny for mitochondria among alpha-proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes
-
Esser C, Ahmadinejad N, Wiegand C, Rotte C, Sebastiani F, et al. (2004) A genome phylogeny for mitochondria among alpha-proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes. Mol Biol Evol 21: 1643-1660.
-
(2004)
Mol Biol Evol
, vol.21
, pp. 1643-1660
-
-
Esser, C.1
Ahmadinejad, N.2
Wiegand, C.3
Rotte, C.4
Sebastiani, F.5
-
14
-
-
28944434614
-
Genome phylogenies indicate a meaningful alpha-proteobacterial phylogeny and support a grouping of the mitochondria with the Rickettsiales
-
Fitzpatrick DA, Creevey CJ, McInerney JO, (2006) Genome phylogenies indicate a meaningful alpha-proteobacterial phylogeny and support a grouping of the mitochondria with the Rickettsiales. Mol Biol Evol 23: 74-85.
-
(2006)
Mol Biol Evol
, vol.23
, pp. 74-85
-
-
Fitzpatrick, D.A.1
Creevey, C.J.2
McInerney, J.O.3
-
15
-
-
34347390665
-
A robust species tree for the alphaproteobacteria
-
Williams KP, Sobral BW, Dickerman AW, (2007) A robust species tree for the alphaproteobacteria. J Bacteriol 189: 4578-4586.
-
(2007)
J Bacteriol
, vol.189
, pp. 4578-4586
-
-
Williams, K.P.1
Sobral, B.W.2
Dickerman, A.W.3
-
16
-
-
34848903282
-
Intracellular pathogens go extreme: genome evolution in the Rickettsiales
-
Darby AC, Cho NH, Fuxelius HH, Westberg J, Andersson SG, (2007) Intracellular pathogens go extreme: genome evolution in the Rickettsiales. Trends Genet 23: 511-520.
-
(2007)
Trends Genet
, vol.23
, pp. 511-520
-
-
Darby, A.C.1
Cho, N.H.2
Fuxelius, H.H.3
Westberg, J.4
Andersson, S.G.5
-
17
-
-
0036946865
-
The genus Caedibacter comprises endosymbionts of Paramecium spp. related to the Rickettsiales (Alphaproteobacteria) and to Francisella tularensis (Gammaproteobacteria)
-
Beier CL, Horn M, Michel R, Schweikert M, Gortz HD, et al. (2002) The genus Caedibacter comprises endosymbionts of Paramecium spp. related to the Rickettsiales (Alphaproteobacteria) and to Francisella tularensis (Gammaproteobacteria). Appl Environ Microbiol 68: 6043-6050.
-
(2002)
Appl Environ Microbiol
, vol.68
, pp. 6043-6050
-
-
Beier, C.L.1
Horn, M.2
Michel, R.3
Schweikert, M.4
Gortz, H.D.5
-
18
-
-
23844446418
-
Genome streamlining in a cosmopolitan oceanic bacterium
-
Giovannoni SJ, Tripp HJ, Givan S, Podar M, Vergin KL, et al. (2005) Genome streamlining in a cosmopolitan oceanic bacterium. Science 309: 1242-1245.
-
(2005)
Science
, vol.309
, pp. 1242-1245
-
-
Giovannoni, S.J.1
Tripp, H.J.2
Givan, S.3
Podar, M.4
Vergin, K.L.5
-
19
-
-
33947238287
-
The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific
-
Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, et al. (2007) The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol 5: e77.
-
(2007)
PLoS Biol
, vol.5
-
-
Rusch, D.B.1
Halpern, A.L.2
Sutton, G.3
Heidelberg, K.B.4
Williamson, S.5
-
20
-
-
63849269776
-
Prokaryotic Genomes and Diversity in the Surface Ocean: Interrogating the Global Ocean Sampling Metagenome
-
Biers EJ, Sun S, Howard EC, (2009) Prokaryotic Genomes and Diversity in the Surface Ocean: Interrogating the Global Ocean Sampling Metagenome. Appl Environ Microbiol 75: 2221-2229.
-
(2009)
Appl Environ Microbiol
, vol.75
, pp. 2221-2229
-
-
Biers, E.J.1
Sun, S.2
Howard, E.C.3
-
21
-
-
0031007907
-
An ancestral mitochondrial DNA resembling a eubacterial genome in miniature
-
Lang BF, Burger G, O'Kelly CJ, Cedergren R, Golding GB, et al. (1997) An ancestral mitochondrial DNA resembling a eubacterial genome in miniature. Nature 387: 493-497.
-
(1997)
Nature
, vol.387
, pp. 493-497
-
-
Lang, B.F.1
Burger, G.2
O'Kelly, C.J.3
Cedergren, R.4
Golding, G.B.5
-
22
-
-
0242578620
-
A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
-
Guindon S, Gascuel O, (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52: 696-704.
-
(2003)
Syst Biol
, vol.52
, pp. 696-704
-
-
Guindon, S.1
Gascuel, O.2
-
23
-
-
52149099649
-
Multilocus phylogenetics of a rapid radiation in the genus Thomomys (Rodentia: Geomyidae)
-
Belfiore NM, Liu L, Moritz C, (2008) Multilocus phylogenetics of a rapid radiation in the genus Thomomys (Rodentia: Geomyidae). Syst Biol 57: 294-310.
-
(2008)
Syst Biol
, vol.57
, pp. 294-310
-
-
Belfiore, N.M.1
Liu, L.2
Moritz, C.3
-
24
-
-
3242701529
-
Modeling compositional heterogeneity
-
Foster PG, (2004) Modeling compositional heterogeneity. Syst Biol 53: 485-495.
-
(2004)
Syst Biol
, vol.53
, pp. 485-495
-
-
Foster, P.G.1
-
25
-
-
0033004743
-
Compositional bias may affect both DNA-based and protein-based phylogenetic reconstructions
-
Foster PG, Hickey DA, (1999) Compositional bias may affect both DNA-based and protein-based phylogenetic reconstructions. J Mol Evol 48: 284-290.
-
(1999)
J Mol Evol
, vol.48
, pp. 284-290
-
-
Foster, P.G.1
Hickey, D.A.2
-
26
-
-
0028790653
-
Inferring phylogenies from DNA sequences of unequal base compositions
-
Galtier N, Gouy M, (1995) Inferring phylogenies from DNA sequences of unequal base compositions. Proc Natl Acad Sci U S A 92: 11317-11321.
-
(1995)
Proc Natl Acad Sci U S A
, vol.92
, pp. 11317-11321
-
-
Galtier, N.1
Gouy, M.2
-
27
-
-
33847302458
-
Inconsistency of phylogenetic estimates from concatenated data under coalescence
-
Kubatko LS, Degnan JH, (2007) Inconsistency of phylogenetic estimates from concatenated data under coalescence. Syst Biol 56: 17-24.
-
(2007)
Syst Biol
, vol.56
, pp. 17-24
-
-
Kubatko, L.S.1
Degnan, J.H.2
-
28
-
-
0028181246
-
Reconstructing evolutionary trees from DNA and protein sequences: paralinear distances
-
Lake JA, (1994) Reconstructing evolutionary trees from DNA and protein sequences: paralinear distances. Proc Natl Acad Sci U S A 91: 1455-1459.
-
(1994)
Proc Natl Acad Sci U S A
, vol.91
, pp. 1455-1459
-
-
Lake, J.A.1
-
29
-
-
34248159030
-
Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model
-
Lartillot N, Brinkmann H, Philippe H, (2007) Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model. BMC Evol Biol 7 (Suppl 1): S4.
-
(2007)
BMC Evol Biol
, vol.7
, Issue.SUPPL. 1
-
-
Lartillot, N.1
Brinkmann, H.2
Philippe, H.3
-
30
-
-
2442691520
-
A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process
-
Lartillot N, Philippe H, (2004) A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Mol Biol Evol 21: 1095-1109.
-
(2004)
Mol Biol Evol
, vol.21
, pp. 1095-1109
-
-
Lartillot, N.1
Philippe, H.2
-
31
-
-
0026681831
-
Substitutional bias confounds inference of cyanelle origins from sequence data
-
Lockhart PJ, Howe CJ, Bryant DA, Beanland TJ, Larkum AW, (1992) Substitutional bias confounds inference of cyanelle origins from sequence data. J Mol Evol 34: 153-162.
-
(1992)
J Mol Evol
, vol.34
, pp. 153-162
-
-
Lockhart, P.J.1
Howe, C.J.2
Bryant, D.A.3
Beanland, T.J.4
Larkum, A.W.5
-
32
-
-
0028361182
-
Recovering evolutionary trees under a more realistic model of sequence evolution
-
Lockhart PJ, Steel MA, Hendy MD, Penny D, (1994) Recovering evolutionary trees under a more realistic model of sequence evolution. Mol Biol Evol 11: 605-612.
-
(1994)
Mol Biol Evol
, vol.11
, pp. 605-612
-
-
Lockhart, P.J.1
Steel, M.A.2
Hendy, M.D.3
Penny, D.4
-
33
-
-
0033844505
-
The evolution of base composition and phylogenetic inference
-
Mooers AO, Holmes EC, (2000) The evolution of base composition and phylogenetic inference. Trends Ecol Evol 15: 365-369.
-
(2000)
Trends Ecol Evol
, vol.15
, pp. 365-369
-
-
Mooers, A.O.1
Holmes, E.C.2
-
34
-
-
0028961933
-
On the use of nucleic acid sequences to infer early branchings in the tree of life
-
Yang Z, Roberts D, (1995) On the use of nucleic acid sequences to infer early branchings in the tree of life. Mol Biol Evol 12: 451-458.
-
(1995)
Mol Biol Evol
, vol.12
, pp. 451-458
-
-
Yang, Z.1
Roberts, D.2
-
35
-
-
34547775666
-
Improvements of high-throughput culturing yielded novel SAR11 strains and other abundant marine bacteria from the Oregon coast and the Bermuda Atlantic Time Series study site
-
Stingl U, Tripp HJ, Giovannoni SJ, (2007) Improvements of high-throughput culturing yielded novel SAR11 strains and other abundant marine bacteria from the Oregon coast and the Bermuda Atlantic Time Series study site. ISME J 1: 361-371.
-
(2007)
ISME J
, vol.1
, pp. 361-371
-
-
Stingl, U.1
Tripp, H.J.2
Giovannoni, S.J.3
-
36
-
-
70349638531
-
New insights into the diversity of marine picoeukaryotes
-
Not F, del Campo J, Balague V, de Vargas C, Massana R, (2009) New insights into the diversity of marine picoeukaryotes. PLoS One 4: e7143.
-
(2009)
PLoS One
, vol.4
-
-
Not, F.1
del Campo, J.2
Balague, V.3
de Vargas, C.4
Massana, R.5
-
37
-
-
72949101201
-
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
-
Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, et al. (2009) A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 462: 1056-1060.
-
(2009)
Nature
, vol.462
, pp. 1056-1060
-
-
Wu, D.1
Hugenholtz, P.2
Mavromatis, K.3
Pukall, R.4
Dalin, E.5
-
38
-
-
80052836854
-
Independent genome reduction and phylogenetic reclassification of the oceanic SAR11 clade
-
in press
-
Viklund J, Ettema TJ, Andersson SG, (2011) Independent genome reduction and phylogenetic reclassification of the oceanic SAR11 clade. Mol Biol Evol in press.
-
(2011)
Mol Biol Evol
-
-
Viklund, J.1
Ettema, T.J.2
Andersson, S.G.3
-
39
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ, (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
-
(1990)
J Mol Biol
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
40
-
-
33846086800
-
STRING 7-recent developments in the integration and prediction of protein interactions
-
von Mering C, Jensen LJ, Kuhn M, Chaffron S, Doerks T, et al. (2007) STRING 7-recent developments in the integration and prediction of protein interactions. Nucleic Acids Res 35: D358-362.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
von Mering, C.1
Jensen, L.J.2
Kuhn, M.3
Chaffron, S.4
Doerks, T.5
-
41
-
-
33947215475
-
CAMERA: a community resource for metagenomics
-
Seshadri R, Kravitz SA, Smarr L, Gilna P, Frazier M, (2007) CAMERA: a community resource for metagenomics. PLoS Biol 5: e75.
-
(2007)
PLoS Biol
, vol.5
-
-
Seshadri, R.1
Kravitz, S.A.2
Smarr, L.3
Gilna, P.4
Frazier, M.5
-
42
-
-
0026499429
-
Conservation evaluation and phylogenetic diversity
-
Faith DP, (1992) Conservation evaluation and phylogenetic diversity. Biol Conserv 61: 1-10.
-
(1992)
Biol Conserv
, vol.61
, pp. 1-10
-
-
Faith, D.P.1
-
43
-
-
25144472531
-
Phylogenetic diversity and the greedy algorithm
-
Steel M, (2005) Phylogenetic diversity and the greedy algorithm. Syst Biol 54: 527-529.
-
(2005)
Syst Biol
, vol.54
, pp. 527-529
-
-
Steel, M.1
-
44
-
-
80052869485
-
MrTwig - Phylogenetic diversity in trees and areas
-
Pre-release version ed
-
Wallberg A, (2007) MrTwig- Phylogenetic diversity in trees and areas. Pre-release version ed.
-
(2007)
-
-
Wallberg, A.1
-
45
-
-
33747818327
-
Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment
-
Lassmann T, Sonnhammer EL, (2006) Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment. Nucleic Acids Res 34: W596-599.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Lassmann, T.1
Sonnhammer, E.L.2
-
46
-
-
34547489084
-
Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments
-
Talavera G, Castresana J, (2007) Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol 56: 564-577.
-
(2007)
Syst Biol
, vol.56
, pp. 564-577
-
-
Talavera, G.1
Castresana, J.2
-
47
-
-
0031678692
-
SplitsTree: analyzing and visualizing evolutionary data
-
Huson DH, (1998) SplitsTree: analyzing and visualizing evolutionary data. Bioinformatics 14: 68-73.
-
(1998)
Bioinformatics
, vol.14
, pp. 68-73
-
-
Huson, D.H.1
-
48
-
-
30744470609
-
Application of phylogenetic networks in evolutionary studies
-
Huson DH, Bryant D, (2006) Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 23: 254-267.
-
(2006)
Mol Biol Evol
, vol.23
, pp. 254-267
-
-
Huson, D.H.1
Bryant, D.2
|