-
1
-
-
33645456207
-
Eukaryotic evolution, changes and challenges
-
Embley, T. M. & Martin, W. Eukaryotic evolution, changes and challenges. Nature 440, 623-630 (2006).
-
(2006)
Nature
, vol.440
, pp. 623-630
-
-
Embley, T.M.1
Martin, W.2
-
2
-
-
84905513696
-
The dispersed archaeal eukaryome and the complex archaeal ancestor of eukaryotes
-
Koonin, E. V. & Yutin, N. The dispersed archaeal eukaryome and the complex archaeal ancestor of eukaryotes. Cold Spring Harb. Perspect. Biol. 6, a016188 (2014).
-
(2014)
Cold Spring Harb. Perspect. Biol.
, vol.6
, pp. a016188
-
-
Koonin, E.V.1
Yutin, N.2
-
3
-
-
84880916121
-
Molecular paleontology and complexity in the last eukaryotic common ancestor
-
Koumandou, V. L. et al. Molecular paleontology and complexity in the last eukaryotic common ancestor. Crit. Rev. Biochem. Mol. Biol. 48, 373-396 (2013).
-
(2013)
Crit. Rev. Biochem. Mol. Biol.
, vol.48
, pp. 373-396
-
-
Koumandou, V.L.1
-
4
-
-
0001271789
-
Phylogenetic structure of the prokaryotic domain: The primary kingdoms
-
Woese, C. R. & Fox, G. E. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc. Natl Acad. Sci. USA 74, 5088-5090 (1977).
-
(1977)
Proc. Natl Acad. Sci. USA
, vol.74
, pp. 5088-5090
-
-
Woese, C.R.1
Fox, G.E.2
-
5
-
-
0025300402
-
Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya
-
Woese, C. R., Kandler, O. & Wheelis, M. L. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc. Natl Acad. Sci. USA 87, 4576-4579 (1990).
-
(1990)
Proc. Natl Acad. Sci. USA
, vol.87
, pp. 4576-4579
-
-
Woese, C.R.1
Kandler, O.2
Wheelis, M.L.3
-
6
-
-
0039985557
-
Archaebacterial DNA-dependent RNA polymerases testify to the evolution of the eukaryotic nuclear genome
-
Pühler, G. et al. Archaebacterial DNA-dependent RNA polymerases testify to the evolution of the eukaryotic nuclear genome. Proc. Natl Acad. Sci. USA 86, 4569-4573 (1989).
-
(1989)
Proc. Natl Acad. Sci. USA
, vol.86
, pp. 4569-4573
-
-
Pühler, G.1
-
7
-
-
16044367245
-
Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii
-
Bult, C. J. et al. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 273, 1058-1073 (1996).
-
(1996)
Science
, vol.273
, pp. 1058-1073
-
-
Bult, C.J.1
-
8
-
-
0032568587
-
Genomic evidence for two functionally distinct gene classes
-
Rivera, M. C., Jain, R., Moore, J. E. & Lake, J. A. Genomic evidence for two functionally distinct gene classes. Proc. Natl Acad. Sci. USA 95, 6239-6244 (1998).
-
(1998)
Proc. Natl Acad. Sci. USA
, vol.95
, pp. 6239-6244
-
-
Rivera, M.C.1
Jain, R.2
Moore, J.E.3
Lake, J.A.4
-
9
-
-
84901203656
-
The hybrid nature of the Eukaryota and a consilient view of life on Earth
-
McInerney, J. O., O'Connell, M. J. & Pisani, D. The hybrid nature of the Eukaryota and a consilient view of life on Earth. Nature Rev. Microbiol. 12, 449-455 (2014).
-
(2014)
Nature Rev. Microbiol.
, vol.12
, pp. 449-455
-
-
McInerney, J.O.1
O'Connell, M.J.2
Pisani, D.3
-
10
-
-
77957134043
-
The origin of eukaryotes and their relationship with the Archaea: Are we at a phylogenomic impasse?
-
Gribaldo, S., Poole, A. M., Daubin, V., Forterre, P. & Brochier-Armanet, C. The origin of eukaryotes and their relationship with the Archaea: are we at a phylogenomic impasse? Nature Rev. Microbiol. 8, 743-752 (2010).
-
(2010)
Nature Rev. Microbiol.
, vol.8
, pp. 743-752
-
-
Gribaldo, S.1
Poole, A.M.2
Daubin, V.3
Forterre, P.4
Brochier-Armanet, C.5
-
11
-
-
47649125916
-
The deep archaeal roots of eukaryotes
-
Yutin, N., Makarova, K. S., Mekhedov, S. L., Wolf, Y. I. & Koonin, E. V. The deep archaeal roots of eukaryotes. Mol. Biol. Evol. 25, 1619-1630 (2008).
-
(2008)
Mol. Biol. Evol.
, vol.25
, pp. 1619-1630
-
-
Yutin, N.1
Makarova, K.S.2
Mekhedov, S.L.3
Wolf, Y.I.4
Koonin, E.V.5
-
12
-
-
84897859298
-
Phylogenomic test of the hypotheses for the evolutionary origin of eukaryotes
-
Rochette, N. C., Brochier-Armanet, C. & Gouy, M. Phylogenomic test of the hypotheses for the evolutionary origin of eukaryotes. Mol. Biol. Evol. 31, 832-845 (2014).
-
(2014)
Mol. Biol. Evol.
, vol.31
, pp. 832-845
-
-
Rochette, N.C.1
Brochier-Armanet, C.2
Gouy, M.3
-
13
-
-
84862562185
-
An evolutionary network of genes present in the eukaryote common ancestor polls genomes on eukaryotic and mitochondrial origin
-
Thiergart, T., Landan, G., Schenk, M., Dagan, T. & Martin, W. F. An evolutionary network of genes present in the eukaryote common ancestor polls genomes on eukaryotic and mitochondrial origin. Genome Biol. Evol. 4, 466-485 (2012).
-
(2012)
Genome Biol. Evol.
, vol.4
, pp. 466-485
-
-
Thiergart, T.1
Landan, G.2
Schenk, M.3
Dagan, T.4
Martin, W.F.5
-
14
-
-
0021229429
-
A new ribosome structure
-
Henderson, E. et al. A new ribosome structure. Science 225, 510-512 (1984).
-
(1984)
Science
, vol.225
, pp. 510-512
-
-
Henderson, E.1
-
15
-
-
77955039174
-
The origin and early evolution of eukaryotes in the light of phylogenomics
-
Koonin, E. V. The origin and early evolution of eukaryotes in the light of phylogenomics. Genome Biol. 11, 209 (2010).
-
(2010)
Genome Biol.
, vol.11
, pp. 209
-
-
Koonin, E.V.1
-
16
-
-
0024285855
-
Origin of the eukaryotic nucleus determined by rate-invariant analysis of rRNA sequences
-
Lake, J. A. Origin of the eukaryotic nucleus determined by rate-invariant analysis of rRNA sequences. Nature 331, 184-186 (1988).
-
(1988)
Nature
, vol.331
, pp. 184-186
-
-
Lake, J.A.1
-
17
-
-
84890355580
-
An archaeal origin of eukaryotes supports only two primary domains of life
-
Williams, T. A., Foster, P. G., Cox, C. J. & Embley, T. M. An archaeal origin of eukaryotes supports only two primary domains of life. Nature 504, 231-236 (2013).
-
(2013)
Nature
, vol.504
, pp. 231-236
-
-
Williams, T.A.1
Foster, P.G.2
Cox, C.J.3
Embley, T.M.4
-
18
-
-
58149512792
-
The archaebacterial origin of eukaryotes
-
Cox, C. J., Foster, P. G., Hirt, R. P., Harris, S. R. & Embley, T. M. The archaebacterial origin of eukaryotes. Proc. Natl Acad. Sci. USA 105, 20356-20361 (2008).
-
(2008)
Proc. Natl Acad. Sci. USA
, vol.105
, pp. 20356-20361
-
-
Cox, C.J.1
Foster, P.G.2
Hirt, R.P.3
Harris, S.R.4
Embley, T.M.5
-
19
-
-
67651039738
-
The primary divisions of life: A phylogenomic approach employing composition-heterogeneous methods
-
Foster, P. G., Cox, C. J. & Embley, T. M. The primary divisions of life: a phylogenomic approach employing composition-heterogeneous methods. Phil. Trans. R. Soc. Lond. B 364, 2197-2207 (2009).
-
(2009)
Phil. Trans. R. Soc. Lond. B
, vol.364
, pp. 2197-2207
-
-
Foster, P.G.1
Cox, C.J.2
Embley, T.M.3
-
20
-
-
84903388029
-
The archaeal legacy of eukaryotes: A phylogenomic perspective
-
Guy, L., Saw, J. H. & Ettema, T. J. The archaeal legacy of eukaryotes: a phylogenomic perspective. Cold Spring Harb. Perspect. Biol. 6, a016022 (2014).
-
(2014)
Cold Spring Harb. Perspect. Biol.
, vol.6
, pp. a016022
-
-
Guy, L.1
Saw, J.H.2
Ettema, T.J.3
-
21
-
-
84880261576
-
The effects of model choice and mitigating bias on the ribosomal tree of life
-
Lasek-Nesselquist, E. & Gogarten, J. P. The effects of model choice and mitigating bias on the ribosomal tree of life. Mol. Phylogenet. Evol. 69, 17-38 (2013).
-
(2013)
Mol. Phylogenet. Evol.
, vol.69
, pp. 17-38
-
-
Lasek-Nesselquist, E.1
Gogarten, J.P.2
-
22
-
-
84869133972
-
A congruent phylogenomic signal places eukaryotes within the Archaea
-
Williams, T. A., Foster, P. G., Nye, T. M., Cox, C. J. & Embley, T. M. A congruent phylogenomic signal places eukaryotes within the Archaea. Proc. R. Soc. Lond. B 279, 4870-4879 (2012).
-
(2012)
Proc. R. Soc. Lond. B
, vol.279
, pp. 4870-4879
-
-
Williams, T.A.1
Foster, P.G.2
Nye, T.M.3
Cox, C.J.4
Embley, T.M.5
-
23
-
-
82355180998
-
The archaeal 'TACK' superphylum and the origin of eukaryotes
-
Guy, L. & Ettema, T. J. The archaeal 'TACK' superphylum and the origin of eukaryotes. Trends Microbiol. 19, 580-587 (2011).
-
(2011)
Trends Microbiol.
, vol.19
, pp. 580-587
-
-
Guy, L.1
Ettema, T.J.2
-
24
-
-
0037022287
-
The origin of the eukaryotic cell: A genomic investigation
-
Hartman, H. & Fedorov, A. The origin of the eukaryotic cell: a genomic investigation. Proc. Natl Acad. Sci. USA 99, 1420-1425 (2002).
-
(2002)
Proc. Natl Acad. Sci. USA
, vol.99
, pp. 1420-1425
-
-
Hartman, H.1
Fedorov, A.2
-
25
-
-
79955706693
-
An actin-based cytoskeleton in archaea
-
Ettema, T. J., Lindås, A.-C. & Bernander, R. An actin-based cytoskeleton in archaea. Mol. Microbiol. 80, 1052-1061 (2011).
-
(2011)
Mol. Microbiol.
, vol.80
, pp. 1052-1061
-
-
Ettema, T.J.1
Lindås, A.-C.2
Bernander, R.3
-
26
-
-
84858968457
-
Archaeal origin of tubulin
-
Yutin, N. & Koonin, E. V. Archaeal origin of tubulin. Biol. Direct 7, 10 (2012).
-
(2012)
Biol. Direct
, vol.7
, pp. 10
-
-
Yutin, N.1
Koonin, E.V.2
-
27
-
-
57749087001
-
A unique cell division machinery in the Archaea
-
Lindås, A.-C., Karlsson, E. A., Lindgren, M. T., Ettema, T. J. & Bernander, R. A unique cell division machinery in the Archaea. Proc. Natl Acad. Sci. USA 105, 18942-18946 (2008).
-
(2008)
Proc. Natl Acad. Sci. USA
, vol.105
, pp. 18942-18946
-
-
Lindås, A.-C.1
Karlsson, E.A.2
Lindgren, M.T.3
Ettema, T.J.4
Bernander, R.5
-
28
-
-
84873164495
-
From archaeon to eukaryote: The evolutionary dark ages of the eukaryotic cell
-
Martijn, J. & Ettema, T. J. From archaeon to eukaryote: the evolutionary dark ages of the eukaryotic cell. Biochem. Soc. Trans. 41, 451-457 (2013).
-
(2013)
Biochem. Soc. Trans.
, vol.41
, pp. 451-457
-
-
Martijn, J.1
Ettema, T.J.2
-
29
-
-
78650051812
-
Discovery of a black smoker vent field and vent fauna at the Arctic Mid-Ocean Ridge
-
Pedersen, R. B. et al. Discovery of a black smoker vent field and vent fauna at the Arctic Mid-Ocean Ridge. Nat. Commun. 1, 126 (2010).
-
(2010)
Nat. Commun.
, vol.1
, pp. 126
-
-
Pedersen, R.B.1
-
30
-
-
84867638141
-
Correlating microbial community profiles with geochemical data in highly stratified sediments from the Arctic Mid-Ocean Ridge
-
Jørgensen, S. L. et al. Correlating microbial community profiles with geochemical data in highly stratified sediments from the Arctic Mid-Ocean Ridge. Proc. Natl Acad. Sci. USA 109, E2846-E2855 (2012).
-
(2012)
Proc. Natl Acad. Sci. USA
, vol.109
, pp. E2846-E2855
-
-
Jørgensen, S.L.1
-
31
-
-
84885399253
-
Quantitative and phylogenetic study of the Deep Sea Archaeal Group in sediments of the Arctic mid-ocean spreading ridge
-
Jørgensen, S. L., Thorseth, I. H., Pedersen, R. B., Baumberger, T. & Schleper, C. Quantitative and phylogenetic study of the Deep Sea Archaeal Group in sediments of the Arctic mid-ocean spreading ridge. Front. Microbiol. 4, 299 (2013).
-
(2013)
Front. Microbiol.
, vol.4
, pp. 299
-
-
Jørgensen, S.L.1
Thorseth, I.H.2
Pedersen, R.B.3
Baumberger, T.4
Schleper, C.5
-
32
-
-
2142857748
-
Microbial communities associated with geological horizons in coastal subseafloor sediments from the Sea of Okhotsk
-
Inagaki, F. et al. Microbial communities associated with geological horizons in coastal subseafloor sediments from the Sea of Okhotsk. Appl. Environ. Microbiol. 69, 7224-7235 (2003).
-
(2003)
Appl. Environ. Microbiol.
, vol.69
, pp. 7224-7235
-
-
Inagaki, F.1
-
33
-
-
0032868072
-
Population structure and phylogenetic characterization of marine benthic Archaea in deep-sea sediments
-
Vetriani, C., Jannasch, H. W., MacGregor, B. J., Stahl, D. A. & Reysenbach, A. L. Population structure and phylogenetic characterization of marine benthic Archaea in deep-sea sediments. Appl. Environ. Microbiol. 65, 4375-4384 (1999).
-
(1999)
Appl. Environ. Microbiol.
, vol.65
, pp. 4375-4384
-
-
Vetriani, C.1
Jannasch, H.W.2
MacGregor, B.J.3
Stahl, D.A.4
Reysenbach, A.L.5
-
34
-
-
61249234512
-
The function of Loki in Snorri Sturluson's Edda
-
Von Schnurbein, S. The function of Loki in Snorri Sturluson's Edda. Hist. Relig. 40, 109-124 (2000).
-
(2000)
Hist. Relig.
, vol.40
, pp. 109-124
-
-
Von Schnurbein, S.1
-
35
-
-
84926123404
-
Pangenome evidence for extensive interdomain horizontal transfer affecting lineage core and shell genes in uncultured planktonic thaumarchaeota and euryarchaeota
-
Deschamps, P., Zivanovic, Y., Moreira, D., Rodriguez-Valera, F. & Lopez-Garcia, P. Pangenome evidence for extensive interdomain horizontal transfer affecting lineage core and shell genes in uncultured planktonic thaumarchaeota and euryarchaeota. Genome Biol. Evol. 6, 1549-1563 (2014).
-
(2014)
Genome Biol. Evol.
, vol.6
, pp. 1549-1563
-
-
Deschamps, P.1
Zivanovic, Y.2
Moreira, D.3
Rodriguez-Valera, F.4
Lopez-Garcia, P.5
-
36
-
-
84922775800
-
Origins of major archaeal clades correspond to gene acquisitions from bacteria
-
Nelson-Sathi, S. et al. Origins of major archaeal clades correspond to gene acquisitions from bacteria. Nature 517, 77-80 (2015).
-
(2015)
Nature
, vol.517
, pp. 77-80
-
-
Nelson-Sathi, S.1
-
37
-
-
62349137215
-
The origins of phagocytosis and eukaryogenesis
-
Yutin, N., Wolf, M. Y., Wolf, Y. I. & Koonin, E. V. The origins of phagocytosis and eukaryogenesis. Biol. Direct 4, 9 (2009).
-
(2009)
Biol. Direct
, vol.4
, pp. 9
-
-
Yutin, N.1
Wolf, M.Y.2
Wolf, Y.I.3
Koonin, E.V.4
-
38
-
-
84897929470
-
High frequency of phylogenetically diverse reductive dehalogenase-homologous genes in deep subseafloor sedimentary metagenomes
-
Kawai, M. et al. High frequency of phylogenetically diverse reductive dehalogenase-homologous genes in deep subseafloor sedimentary metagenomes. Front. Microbiol. 5, 80 (2014).
-
(2014)
Front. Microbiol.
, vol.5
, pp. 80
-
-
Kawai, M.1
-
39
-
-
70849098888
-
Actin, a central player in cell shape and movement
-
Pollard, T. D. & Cooper, J. A. Actin, a central player in cell shape and movement. Science 326, 1208-1212 (2009).
-
(2009)
Science
, vol.326
, pp. 1208-1212
-
-
Pollard, T.D.1
Cooper, J.A.2
-
40
-
-
84868624185
-
An archaeal origin for the actin cytoskeleton: Implications for eukaryogenesis
-
Bernander, R., Lind, A. E. & Ettema, T. J. An archaeal origin for the actin cytoskeleton: Implications for eukaryogenesis. Commun. Integr. Biol. 4, 664-667 (2011).
-
(2011)
Commun. Integr. Biol.
, vol.4
, pp. 664-667
-
-
Bernander, R.1
Lind, A.E.2
Ettema, T.J.3
-
41
-
-
0037459075
-
Cellular motility driven by assembly and disassembly of actin filaments
-
Pollard, T. D. & Borisy, G. G. Cellular motility driven by assembly and disassembly of actin filaments. Cell 112, 453-465 (2003).
-
(2003)
Cell
, vol.112
, pp. 453-465
-
-
Pollard, T.D.1
Borisy, G.G.2
-
42
-
-
0035135929
-
Small GTP-binding proteins
-
Takai, Y., Sasaki, T. & Matozaki, T. Small GTP-binding proteins. Physiol. Rev. 81, 153-208 (2001).
-
(2001)
Physiol. Rev.
, vol.81
, pp. 153-208
-
-
Takai, Y.1
Sasaki, T.2
Matozaki, T.3
-
43
-
-
77955015657
-
A bacterial Ras-like small GTP-binding protein and its cognate GAP establish a dynamic spatial polarity axis to control directed motility
-
Zhang, Y., Franco, M., Ducret, A. & Mignot, T. A bacterial Ras-like small GTP-binding protein and its cognate GAP establish a dynamic spatial polarity axis to control directed motility. PLoS Biol. 8, e1000430 (2010).
-
(2010)
PLoS Biol.
, vol.8
, pp. e1000430
-
-
Zhang, Y.1
Franco, M.2
Ducret, A.3
Mignot, T.4
-
45
-
-
61349170303
-
First and last ancestors: Reconstructing evolution of the endomembrane system with ESCRTs, vesicle coat proteins, and nuclear pore complexes
-
Field, M. C. & Dacks, J. B. First and last ancestors: reconstructing evolution of the endomembrane system with ESCRTs, vesicle coat proteins, and nuclear pore complexes. Curr. Opin. Cell Biol. 21, 4-13 (2009).
-
(2009)
Curr. Opin. Cell Biol.
, vol.21
, pp. 4-13
-
-
Field, M.C.1
Dacks, J.B.2
-
46
-
-
47149100894
-
Evolution of the multivesicular body ESCRT machinery; retention across the eukaryotic lineage
-
Leung, K. F., Dacks, J. B. & Field, M. C. Evolution of the multivesicular body ESCRT machinery; retention across the eukaryotic lineage. Traffic 9, 1698-1716 (2008).
-
(2008)
Traffic
, vol.9
, pp. 1698-1716
-
-
Leung, K.F.1
Dacks, J.B.2
Field, M.C.3
-
47
-
-
33646116786
-
Structural and functional organization of the ESCRT-I trafficking complex
-
Kostelansky, M. S. et al. Structural and functional organization of the ESCRT-I trafficking complex. Cell 125, 113-126 (2006).
-
(2006)
Cell
, vol.125
, pp. 113-126
-
-
Kostelansky, M.S.1
-
48
-
-
63649086486
-
The ESCRT machinery in endosomal sorting of ubiquitylated membrane proteins
-
Raiborg, C. & Stenmark, H. The ESCRT machinery in endosomal sorting of ubiquitylated membrane proteins. Nature 458, 445-452 (2009).
-
(2009)
Nature
, vol.458
, pp. 445-452
-
-
Raiborg, C.1
Stenmark, H.2
-
49
-
-
79955598535
-
Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group
-
Nunoura, T. et al. Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group. Nucleic Acids Res. 39, 3204-3223 (2011).
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. 3204-3223
-
-
Nunoura, T.1
-
50
-
-
84919371822
-
Eukaryotic origins: How and when was the mitochondrion acquired?
-
Poole, A. M. & Gribaldo, S. Eukaryotic origins: how and when was the mitochondrion acquired? Cold Spring Harb. Perspect. Biol. 6, a015990 (2014).
-
(2014)
Cold Spring Harb. Perspect. Biol.
, vol.6
, pp. a015990
-
-
Poole, A.M.1
Gribaldo, S.2
-
51
-
-
84867638141
-
Correlating microbial community profiles with geochemical data in highly stratified sediments from the Arctic Mid-Ocean Ridge
-
Jorgensen, S. L. et al. Correlating microbial community profiles with geochemical data in highly stratified sediments from the Arctic Mid-Ocean Ridge. Proc. Natl Acad. Sci. USA 109, E2846-E2855 (2012).
-
(2012)
Proc. Natl Acad. Sci. USA
, vol.109
, pp. E2846-E2855
-
-
Jorgensen, S.L.1
-
52
-
-
84885399253
-
Quantitative and phylogenetic study of the deep sea archaeal group in sediments of the Arctic Mid-Ocean spreading ridge
-
Jorgensen, S. L., Thorseth, I. H., Pedersen, R. B., Baumberger, T. & Schleper, C. Quantitative and phylogenetic study of the deep sea archaeal group in sediments of the Arctic Mid-Ocean spreading ridge. Front. Microbiol. 4, 299 (2013).
-
(2013)
Front. Microbiol.
, vol.4
, pp. 299
-
-
Jorgensen, S.L.1
Thorseth, I.H.2
Pedersen, R.B.3
Baumberger, T.4
Schleper, C.5
-
53
-
-
0031912606
-
Novel division level bacterial diversity in a Yellowstone hot spring
-
Hugenholtz, P., Pitulle, C., Hershberger, K. L. & Pace, N. R. Novel division level bacterial diversity in a Yellowstone hot spring. J. Bacteriol. 180, 366-376 (1998).
-
(1998)
J. Bacteriol.
, vol.180
, pp. 366-376
-
-
Hugenholtz, P.1
Pitulle, C.2
Hershberger, K.L.3
Pace, N.R.4
-
54
-
-
84905049901
-
Trimmomatic: A flexible trimmer for Illumina sequence data
-
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114-2120 (2014).
-
(2014)
Bioinformatics
, vol.30
, pp. 2114-2120
-
-
Bolger, A.M.1
Lohse, M.2
Usadel, B.3
-
55
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul, S. F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402 (1997).
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
-
56
-
-
84884904719
-
UPARSE: Highly accurate OTU sequences from microbial amplicon reads
-
Edgar, R. C. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nature Methods 10, 996-998 (2013).
-
(2013)
Nature Methods
, vol.10
, pp. 996-998
-
-
Edgar, R.C.1
-
57
-
-
79961181125
-
UCHIME improves sensitivity and speed of chimera detection
-
Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C. & Knight, R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27, 2194-2200 (2011).
-
(2011)
Bioinformatics
, vol.27
, pp. 2194-2200
-
-
Edgar, R.C.1
Haas, B.J.2
Clemente, J.C.3
Quince, C.4
Knight, R.5
-
58
-
-
72949107142
-
Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities
-
Schloss, P. D. et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75, 7537-7541 (2009).
-
(2009)
Appl. Environ. Microbiol.
, vol.75
, pp. 7537-7541
-
-
Schloss, P.D.1
-
59
-
-
84873739311
-
The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools
-
Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590-D596 (2013).
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D590-D596
-
-
Quast, C.1
-
60
-
-
84867649459
-
Archaea in organic-lean and organic-rich marine subsurface sediments: An environmental gradient reflected in distinct phylogenetic lineages
-
Durbin, A. M. & Teske, A. Archaea in organic-lean and organic-rich marine subsurface sediments: an environmental gradient reflected in distinct phylogenetic lineages. Front. Microbiol. 3, 168 (2012).
-
(2012)
Front. Microbiol.
, vol.3
, pp. 168
-
-
Durbin, A.M.1
Teske, A.2
-
61
-
-
84875619226
-
MAFFT multiple sequence alignment software version 7: Improvements in performance and usability
-
Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772-780 (2013).
-
(2013)
Mol. Biol. Evol.
, vol.30
, pp. 772-780
-
-
Katoh, K.1
Standley, D.M.2
-
62
-
-
67650757433
-
trimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses
-
Capella-Gutiérrez, S., Silla-Martinez, J. M. & Gabaldon, T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972-1973 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 1972-1973
-
-
Capella-Gutiérrez, S.1
Silla-Martinez, J.M.2
Gabaldon, T.3
-
63
-
-
84899553363
-
RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies
-
Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312-1313 (2014).
-
(2014)
Bioinformatics
, vol.30
, pp. 1312-1313
-
-
Stamatakis, A.1
-
64
-
-
79960004119
-
Interactive Tree Of Life v2: Online annotation and display of phylogenetic trees made easy
-
Letunic, I. & Bork, P. Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Res. 39, W475-W478 (2011).
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. W475-W478
-
-
Letunic, I.1
Bork, P.2
-
65
-
-
84864134721
-
SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes
-
Pruesse, E., Peplies, J. & Glockner, F. O. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 28, 1823-1829 (2012).
-
(2012)
Bioinformatics
, vol.28
, pp. 1823-1829
-
-
Pruesse, E.1
Peplies, J.2
Glockner, F.O.3
-
66
-
-
74549125386
-
SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building
-
Gouy, M., Guindon, S. & Gascuel, O. SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol. Biol. Evol. 27, 221-224 (2010).
-
(2010)
Mol. Biol. Evol.
, vol.27
, pp. 221-224
-
-
Gouy, M.1
Guindon, S.2
Gascuel, O.3
-
67
-
-
77957244650
-
Search and clustering orders of magnitude faster than BLAST
-
Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460-2461 (2010).
-
(2010)
Bioinformatics
, vol.26
, pp. 2460-2461
-
-
Edgar, R.C.1
-
68
-
-
77954209892
-
The Newick utilities: High-throughput phylogenetic tree processing in the UNIX shell
-
Junier, T. & Zdobnov, E. M. The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell. Bioinformatics 26, 1669-1670 (2010).
-
(2010)
Bioinformatics
, vol.26
, pp. 1669-1670
-
-
Junier, T.1
Zdobnov, E.M.2
-
69
-
-
84860771820
-
SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing
-
Bankevich, A. et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455-477 (2012).
-
(2012)
J. Comput. Biol.
, vol.19
, pp. 455-477
-
-
Bankevich, A.1
-
70
-
-
77952299957
-
Prodigal: Prokaryotic gene recognition and translation initiation site identification
-
Hyatt, D. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11, 119 (2010).
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 119
-
-
Hyatt, D.1
-
71
-
-
34250665888
-
RNAmmer: Consistent and rapid annotation of ribosomal RNA genes
-
Lagesen, K. et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35, 3100-3108 (2007).
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. 3100-3108
-
-
Lagesen, K.1
-
72
-
-
0030854739
-
tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence
-
Lowe, T. M. & Eddy, S. R. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25, 955-964 (1997).
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 955-964
-
-
Lowe, T.M.1
Eddy, S.R.2
-
73
-
-
33845244847
-
SPLITS: A new program for predicting split and intron-containing tRNA genes at the genome level
-
Sugahara, J. et al. SPLITS: a new program for predicting split and intron-containing tRNA genes at the genome level. In Silico Biol. 6, 411-418 (2006).
-
(2006)
In Silico Biol.
, vol.6
, pp. 411-418
-
-
Sugahara, J.1
-
74
-
-
84870950237
-
Updated clusters of orthologous genes for Archaea: A complex ancestor of the Archaea and the by ways of horizontal gene transfer
-
Wolf, Y. I., Makarova, K. S., Yutin, N. & Koonin, E. V. Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the by ways of horizontal gene transfer. Biol. Direct 7, 46 (2012).
-
(2012)
Biol. Direct
, vol.7
, pp. 46
-
-
Wolf, Y.I.1
Makarova, K.S.2
Yutin, N.3
Koonin, E.V.4
-
75
-
-
77954198131
-
A low-polynomial algorithm for assembling clusters of orthologous groups from intergenomic symmetric best matches
-
Kristensen, D. M. et al. A low-polynomial algorithm for assembling clusters of orthologous groups from intergenomic symmetric best matches. Bioinformatics 26, 1481-1487 (2010).
-
(2010)
Bioinformatics
, vol.26
, pp. 1481-1487
-
-
Kristensen, D.M.1
-
76
-
-
84881629698
-
PhyloBayes MPI: Phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment
-
Lartillot, N., Rodrigue, N., Stubbs, D. & Richer, J. PhyloBayes MPI: phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment. Syst. Biol. 62, 611-615 (2013).
-
(2013)
Syst. Biol.
, vol.62
, pp. 611-615
-
-
Lartillot, N.1
Rodrigue, N.2
Stubbs, D.3
Richer, J.4
-
77
-
-
77954202497
-
DendroPy: A Python library for phylogenetic computing
-
Sukumaran, J. & Holder, M. T. DendroPy: a Python library for phylogenetic computing. Bioinformatics 26, 1569-1571 (2010).
-
(2010)
Bioinformatics
, vol.26
, pp. 1569-1571
-
-
Sukumaran, J.1
Holder, M.T.2
-
78
-
-
84855864414
-
Independent genome reduction and phylogenetic reclassification of the oceanic SAR11 clade
-
Viklund, J., Ettema, T. J. & Andersson, S. G. Independent genome reduction and phylogenetic reclassification of the oceanic SAR11 clade. Mol. Biol. Evol. 29, 599-615 (2012).
-
(2012)
Mol. Biol. Evol.
, vol.29
, pp. 599-615
-
-
Viklund, J.1
Ettema, T.J.2
Andersson, S.G.3
-
79
-
-
84903388029
-
The Archaeal Legacy of Eukaryotes: A Phylogenomic Perspective
-
Guy, L., Saw, J. H. & Ettema, T. J. The Archaeal Legacy of Eukaryotes: A Phylogenomic Perspective. Cold Spring Harb. Perspect. Biol. 6, a016022 (2014).
-
(2014)
Cold Spring Harb. Perspect. Biol.
, vol.6
, pp. a016022
-
-
Guy, L.1
Saw, J.H.2
Ettema, T.J.3
-
80
-
-
0036623258
-
An approximately unbiased test of phylogenetic tree selection
-
Shimodaira, H. An approximately unbiased test of phylogenetic tree selection. Syst. Biol. 51, 492-508 (2002).
-
(2002)
Syst. Biol.
, vol.51
, pp. 492-508
-
-
Shimodaira, H.1
-
81
-
-
0036139287
-
CONSEL: For assessing the confidence of phylogenetic tree selection
-
Shimodaira, H. & Hasegawa, M. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17, 1246-1247 (2001).
-
(2001)
Bioinformatics
, vol.17
, pp. 1246-1247
-
-
Shimodaira, H.1
Hasegawa, M.2
-
82
-
-
84903397830
-
'Geoarchaeote NAG1' is a deeply rooting lineage of the archaeal order Thermoproteales rather than a new phylum
-
Guy, L., Spang, A., Saw, J. H. & Ettema, T. J. 'Geoarchaeote NAG1' is a deeply rooting lineage of the archaeal order Thermoproteales rather than a new phylum. ISME J. 8, 1353-1357 (2014).
-
(2014)
ISME J.
, vol.8
, pp. 1353-1357
-
-
Guy, L.1
Spang, A.2
Saw, J.H.3
Ettema, T.J.4
-
85
-
-
69549135124
-
Phymm and PhymmBL: Metagenomic phylogenetic classification with interpolated Markov models
-
Brady, A. & Salzberg, S. L. Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models. Nature Methods 6, 673-676 (2009).
-
(2009)
Nature Methods
, vol.6
, pp. 673-676
-
-
Brady, A.1
Salzberg, S.L.2
-
86
-
-
84881138595
-
Insights into the phylogeny and coding potential of microbial dark matter
-
Rinke, C. et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature 499, 431-437 (2013).
-
(2013)
Nature
, vol.499
, pp. 431-437
-
-
Rinke, C.1
-
87
-
-
67649884743
-
Fast and accurate short read alignment with Burrows-Wheeler transform
-
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
88
-
-
84901417347
-
Prokka: Rapid prokaryotic genome annotation
-
Seemann, T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30, 2068-2069 (2014).
-
(2014)
Bioinformatics
, vol.30
, pp. 2068-2069
-
-
Seemann, T.1
-
89
-
-
33847702910
-
MEGAN analysis of metagenomic data
-
Huson, D. H., Auch, A. F., Qi, J. & Schuster, S. C. MEGAN analysis of metagenomic data. Genome Res. 17, 377-386 (2007).
-
(2007)
Genome Res.
, vol.17
, pp. 377-386
-
-
Huson, D.H.1
Auch, A.F.2
Qi, J.3
Schuster, S.C.4
-
90
-
-
0034800374
-
InterProScan-an integration platform for the signature-recognition methods in InterPro
-
Zdobnov, E. M. & Apweiler, R. InterProScan-an integration platform for the signature-recognition methods in InterPro. Bioinformatics 17, 847-848 (2001).
-
(2001)
Bioinformatics
, vol.17
, pp. 847-848
-
-
Zdobnov, E.M.1
Apweiler, R.2
-
91
-
-
31644444476
-
MaGe: A microbial genome annotation system supported by synteny results
-
Vallenet, D. et al. MaGe: a microbial genome annotation system supported by synteny results. Nucleic Acids Res. 34, 53-65 (2006).
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 53-65
-
-
Vallenet, D.1
-
92
-
-
63849246525
-
Protein structure prediction on the Web: A case study using the Phyre server
-
Kelley, L. A. & Sternberg, M. J. Protein structure prediction on the Web: a case study using the Phyre server. Nature Protocols 4, 363-371 (2009).
-
(2009)
Nature Protocols
, vol.4
, pp. 363-371
-
-
Kelley, L.A.1
Sternberg, M.J.2
-
93
-
-
84861219308
-
Phylogenomics of prokaryotic ribosomal proteins
-
Yutin, N., Puigbo, P., Koonin, E. V. & Wolf, Y. I. Phylogenomics of prokaryotic ribosomal proteins. PLoS ONE 7, e36972 (2012).
-
(2012)
PLoS ONE
, vol.7
, pp. e36972
-
-
Yutin, N.1
Puigbo, P.2
Koonin, E.V.3
Wolf, Y.I.4
-
94
-
-
84891757311
-
eggNOG v4.0: Nested orthology inference across 3686 organisms
-
Powell, S. et al. eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Res. 42, D231-D239 (2014).
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D231-D239
-
-
Powell, S.1
-
95
-
-
84897929470
-
High frequency of phylogenetically diverse reductive dehalogenase-homologous genes in deep subseafloor sedimentary metagenomes
-
Kawai, M. et al. High frequency of phylogenetically diverse reductive dehalogenase-homologous genes in deep subseafloor sedimentary metagenomes. Front. Microbiol. 5, 80 (2014).
-
(2014)
Front. Microbiol.
, vol.5
, pp. 80
-
-
Kawai, M.1
-
96
-
-
84897672150
-
Hot-alkaline DNA extraction method for deep-subseafloor archaeal communities
-
Morono, Y., Terada, T., Hoshino, T. & Inagaki, F. Hot-alkaline DNA extraction method for deep-subseafloor archaeal communities. Appl. Environ. Microbiol. 80, 1985-1994 (2014).
-
(2014)
Appl. Environ. Microbiol.
, vol.80
, pp. 1985-1994
-
-
Morono, Y.1
Terada, T.2
Hoshino, T.3
Inagaki, F.4
-
97
-
-
77957130448
-
Evolution of diverse cell division and vesicle formation systems in Archaea
-
Makarova, K. S., Yutin, N., Bell, S. D. & Koonin, E. V. Evolution of diverse cell division and vesicle formation systems in Archaea. Nature Rev. Microbiol. 8, 731-741 (2010).
-
(2010)
Nature Rev. Microbiol.
, vol.8
, pp. 731-741
-
-
Makarova, K.S.1
Yutin, N.2
Bell, S.D.3
Koonin, E.V.4
-
98
-
-
23144458473
-
InterProScan: Protein domains identifier
-
Quevillon, E. et al. InterProScan: protein domains identifier. Nucleic Acids Res. 33, W116-W120 (2005).
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. W116-W120
-
-
Quevillon, E.1
-
99
-
-
34249282745
-
Homologs of eukaryotic Ras superfamily proteins in prokaryotes and their novel phylogenetic correlation with their eukaryotic analogs
-
Dong, J. H., Wen, J. F. & Tian, H. F. Homologs of eukaryotic Ras superfamily proteins in prokaryotes and their novel phylogenetic correlation with their eukaryotic analogs. Gene 396, 116-124 (2007).
-
(2007)
Gene
, vol.396
, pp. 116-124
-
-
Dong, J.H.1
Wen, J.F.2
Tian, H.F.3
-
100
-
-
79955706693
-
An actin-based cytoskeleton in archaea
-
Ettema, T. J., Lindas, A. C. & Bernander, R. An actin-based cytoskeleton in archaea. Mol. Microbiol. 80, 1052-1061 (2011).
-
(2011)
Mol. Microbiol.
, vol.80
, pp. 1052-1061
-
-
Ettema, T.J.1
Lindas, A.C.2
Bernander, R.3
-
101
-
-
62349137215
-
The origins of phagocytosis and eukaryogenesis
-
Yutin, N., Wolf, M. Y., Wolf, Y. I. & Koonin, E. V. The origins of phagocytosis and eukaryogenesis. Biol. Direct 4, 9 (2009).
-
(2009)
Biol. Direct
, vol.4
, pp. 9
-
-
Yutin, N.1
Wolf, M.Y.2
Wolf, Y.I.3
Koonin, E.V.4
-
102
-
-
0036629334
-
Molecular evolution of the actin family
-
Goodson, H. V. & Hawse, W. F. Molecular evolution of the actin family. J. Cell Sci. 115, 2619-2622 (2002).
-
(2002)
J. Cell Sci.
, vol.115
, pp. 2619-2622
-
-
Goodson, H.V.1
Hawse, W.F.2
-
103
-
-
72949101201
-
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
-
Wu, D. et al. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 462, 1056-1060 (2009).
-
(2009)
Nature
, vol.462
, pp. 1056-1060
-
-
Wu, D.1
-
104
-
-
77956519355
-
genoPlotR: Comparative gene and genome visualization in R
-
Guy, L., Roat Kultima, J. & Andersson, S. G. E. genoPlotR: comparative gene and genome visualization in R. Bioinformatics 26, 2334-2335 (2010).
-
(2010)
Bioinformatics
, vol.26
, pp. 2334-2335
-
-
Guy, L.1
Roat Kultima, J.2
Andersson, S.G.E.3
|