-
1
-
-
72949103741
-
New dimensions of the virus world discovered through metagenomics
-
Kristensen DM, Mushegian AR, Dolja VV, Koonin EV. New dimensions of the virus world discovered through metagenomics. Trends Microbiol. 2010;18(1):11-9.
-
(2010)
Trends Microbiol
, vol.18
, Issue.1
, pp. 11-19
-
-
Kristensen, D.M.1
Mushegian, A.R.2
Dolja, V.V.3
Koonin, E.V.4
-
2
-
-
80053370586
-
Exploring the viral world through metagenomics
-
Rosario K, Breitbart M. Exploring the viral world through metagenomics. Curr Opin Virol. 2011;1(4):289-97.
-
(2011)
Curr Opin Virol
, vol.1
, Issue.4
, pp. 289-297
-
-
Rosario, K.1
Breitbart, M.2
-
3
-
-
84857371051
-
Metagenomics and future perspectives in virus discovery
-
Mokili JL, Rohwer F, Dutilh BE. Metagenomics and future perspectives in virus discovery. Curr Opin Virol. 2012;2(1):63-77.
-
(2012)
Curr Opin Virol
, vol.2
, Issue.1
, pp. 63-77
-
-
Mokili, J.L.1
Rohwer, F.2
Dutilh, B.E.3
-
4
-
-
84859814245
-
A novel virus genome discovered in an extreme environment suggests recombination between unrelated groups of RNA and DNA viruses
-
Diemer GS, Stedman KM. A novel virus genome discovered in an extreme environment suggests recombination between unrelated groups of RNA and DNA viruses. Biol Direct. 2012;7:13.
-
(2012)
Biol Direct
, vol.7
, pp. 13
-
-
Diemer, G.S.1
Stedman, K.M.2
-
5
-
-
84866288241
-
Recombination between RNA viruses and plasmids might have played a central role in the origin and evolution of small DNA viruses
-
Krupovic M. Recombination between RNA viruses and plasmids might have played a central role in the origin and evolution of small DNA viruses. Bioessays. 2012;34(10):867-70.
-
(2012)
Bioessays
, vol.34
, Issue.10
, pp. 867-870
-
-
Krupovic, M.1
-
6
-
-
84928531300
-
Multiple layers of chimerism in a single-stranded DNA virus discovered by deep sequencing
-
in press.
-
Krupovic M, Zhi N, Li J, Hu G, Koonin EV, Wong S, et al. Multiple layers of chimerism in a single-stranded DNA virus discovered by deep sequencing. Genome Biol Evol. 2015, in press.
-
(2015)
Genome Biol Evol
-
-
Krupovic, M.1
Zhi, N.2
Li, J.3
Hu, G.4
Koonin, E.V.5
Wong, S.6
-
7
-
-
84889253615
-
Chimeric viruses blur the borders between the major groups of eukaryotic single-stranded DNA viruses
-
Roux S, Enault F, Bronner G, Vaulot D, Forterre P, Krupovic M. Chimeric viruses blur the borders between the major groups of eukaryotic single-stranded DNA viruses. Nat Commun. 2013;4:2700.
-
(2013)
Nat Commun
, vol.4
, pp. 2700
-
-
Roux, S.1
Enault, F.2
Bronner, G.3
Vaulot, D.4
Forterre, P.5
Krupovic, M.6
-
8
-
-
84905041075
-
A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes
-
Dutilh BE, Cassman N, McNair K, Sanchez SE, Silva GG, Boling L, et al. A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes. Nat Commun. 2014;5:4498.
-
(2014)
Nat Commun
, vol.5
, pp. 4498
-
-
Dutilh, B.E.1
Cassman, N.2
McNair, K.3
Sanchez, S.E.4
Silva, G.G.5
Boling, L.6
-
9
-
-
84858163750
-
Sputnik, a virophage infecting the viral domain of life
-
Desnues C, Boyer M, Raoult D. Sputnik, a virophage infecting the viral domain of life. Adv Virus Res. 2012;82:63-89.
-
(2012)
Adv Virus Res
, vol.82
, pp. 63-89
-
-
Desnues, C.1
Boyer, M.2
Raoult, D.3
-
10
-
-
84868550621
-
Structure of Sputnik, a virophage, at 3.5-A resolution
-
Zhang X, Sun S, Xiang Y, Wong J, Klose T, Raoult D, et al. Structure of Sputnik, a virophage, at 3.5-A resolution. Proc Natl Acad Sci U S A. 2012;109(45):18431-6.
-
(2012)
Proc Natl Acad Sci U S A
, vol.109
, Issue.45
, pp. 18431-18436
-
-
Zhang, X.1
Sun, S.2
Xiang, Y.3
Wong, J.4
Klose, T.5
Raoult, D.6
-
11
-
-
51349125147
-
The virophage as a unique parasite of the giant mimivirus
-
La Scola B, Desnues C, Pagnier I, Robert C, Barrassi L, Fournous G, et al. The virophage as a unique parasite of the giant mimivirus. Nature. 2008;455(7209):100-4.
-
(2008)
Nature
, vol.455
, Issue.7209
, pp. 100-104
-
-
Scola, B.1
Desnues, C.2
Pagnier, I.3
Robert, C.4
Barrassi, L.5
Fournous, G.6
-
12
-
-
79953806385
-
A virophage at the origin of large DNA transposons
-
Fischer MG, Suttle CA. A virophage at the origin of large DNA transposons. Science. 2011;332(6026):231-4.
-
(2011)
Science
, vol.332
, Issue.6026
, pp. 231-234
-
-
Fischer, M.G.1
Suttle, C.A.2
-
13
-
-
84899701948
-
Zamilon, a novel virophage with Mimiviridae host specificity
-
Gaia M, Benamar S, Boughalmi M, Pagnier I, Croce O, Colson P, et al. Zamilon, a novel virophage with Mimiviridae host specificity. PLoS One. 2014;9(4):e94923.
-
(2014)
PLoS One
, vol.9
, Issue.4
, pp. e94923
-
-
Gaia, M.1
Benamar, S.2
Boughalmi, M.3
Pagnier, I.4
Croce, O.5
Colson, P.6
-
14
-
-
79955006806
-
Virophage control of antarctic algal host-virus dynamics
-
Yau S, Lauro FM, DeMaere MZ, Brown MV, Thomas T, Raftery MJ, et al. Virophage control of antarctic algal host-virus dynamics. Proc Natl Acad Sci U S A. 2011;108(15):6163-8.
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, Issue.15
, pp. 6163-6168
-
-
Yau, S.1
Lauro, F.M.2
DeMaere, M.Z.3
Brown, M.V.4
Thomas, T.5
Raftery, M.J.6
-
15
-
-
84875777180
-
Diversity of virophages in metagenomic data sets
-
Zhou J, Zhang W, Yan S, Xiao J, Zhang Y, Li B, et al. Diversity of virophages in metagenomic data sets. J Virol. 2013;87(8):4225-36.
-
(2013)
J Virol
, vol.87
, Issue.8
, pp. 4225-4236
-
-
Zhou, J.1
Zhang, W.2
Yan, S.3
Xiao, J.4
Zhang, Y.5
Li, B.6
-
16
-
-
84920842319
-
Three novel virophage genomes discovered from Yellowstone Lake metagenomes
-
Zhou J, Sun D, Childers A, McDermott TR, Wang Y, Liles MR. Three novel virophage genomes discovered from Yellowstone Lake metagenomes. J Virol. 2015;89(2):1278-85.
-
(2015)
J Virol
, vol.89
, Issue.2
, pp. 1278-1285
-
-
Zhou, J.1
Sun, D.2
Childers, A.3
McDermott, T.R.4
Wang, Y.5
Liles, M.R.6
-
17
-
-
84875689946
-
Mimiviridae: clusters of orthologous genes, reconstruction of gene repertoire evolution and proposed expansion of the giant virus family
-
Yutin N, Colson P, Raoult D, Koonin EV. Mimiviridae: clusters of orthologous genes, reconstruction of gene repertoire evolution and proposed expansion of the giant virus family. Virol J. 2013;10:106.
-
(2013)
Virol J
, vol.10
, pp. 106
-
-
Yutin, N.1
Colson, P.2
Raoult, D.3
Koonin, E.V.4
-
18
-
-
84879516342
-
Genome of Phaeocystis globosa virus PgV-16 T highlights the common ancestry of the largest known DNA viruses infecting eukaryotes
-
Santini S, Jeudy S, Bartoli J, Poirot O, Lescot M, Abergel C, et al. Genome of Phaeocystis globosa virus PgV-16 T highlights the common ancestry of the largest known DNA viruses infecting eukaryotes. Proc Natl Acad Sci U S A. 2013;110(26):10800-5.
-
(2013)
Proc Natl Acad Sci U S A
, vol.110
, Issue.26
, pp. 10800-10805
-
-
Santini, S.1
Jeudy, S.2
Bartoli, J.3
Poirot, O.4
Lescot, M.5
Abergel, C.6
-
19
-
-
84878007916
-
Virophages, polintons, and transpovirons: a complex evolutionary network of diverse selfish genetic elements with different reproduction strategies
-
Yutin N, Raoult D, Koonin EV. Virophages, polintons, and transpovirons: a complex evolutionary network of diverse selfish genetic elements with different reproduction strategies. Virol J. 2013;10:158.
-
(2013)
Virol J
, vol.10
, pp. 158
-
-
Yutin, N.1
Raoult, D.2
Koonin, E.V.3
-
20
-
-
33645227457
-
Self-synthesizing DNA transposons in eukaryotes
-
Kapitonov VV, Jurka J. Self-synthesizing DNA transposons in eukaryotes. Proc Natl Acad Sci U S A. 2006;103(12):4540-5.
-
(2006)
Proc Natl Acad Sci U S A
, vol.103
, Issue.12
, pp. 4540-4545
-
-
Kapitonov, V.V.1
Jurka, J.2
-
21
-
-
37549029474
-
DNA transposons and the evolution of eukaryotic genomes
-
Feschotte C, Pritham EJ. DNA transposons and the evolution of eukaryotic genomes. Annu Rev Genet. 2007;41:331-68.
-
(2007)
Annu Rev Genet
, vol.41
, pp. 331-368
-
-
Feschotte, C.1
Pritham, E.J.2
-
22
-
-
84901235660
-
Conservation of major and minor jelly-roll capsid proteins in Polinton (Maverick) transposons suggests that they are bona fide viruses
-
Krupovic M, Bamford DH, Koonin EV. Conservation of major and minor jelly-roll capsid proteins in Polinton (Maverick) transposons suggests that they are bona fide viruses. Biol Direct. 2014;9:6.
-
(2014)
Biol Direct
, vol.9
, pp. 6
-
-
Krupovic, M.1
Bamford, D.H.2
Koonin, E.V.3
-
23
-
-
84923103071
-
Polintons: a hotbed of eukaryotic virus, transposon and plasmid evolution
-
Krupovic M, Koonin EV. Polintons: a hotbed of eukaryotic virus, transposon and plasmid evolution. Nat Rev Microbiol. 2015;13(2):105-15.
-
(2015)
Nat Rev Microbiol
, vol.13
, Issue.2
, pp. 105-115
-
-
Krupovic, M.1
Koonin, E.V.2
-
24
-
-
84873684861
-
Simultaneous amplicon sequencing to explore co-occurrence patterns of bacterial, archaeal and eukaryotic microorganisms in rumen microbial communities
-
Kittelmann S, Seedorf H, Walters WA, Clemente JC, Knight R, Gordon JI, et al. Simultaneous amplicon sequencing to explore co-occurrence patterns of bacterial, archaeal and eukaryotic microorganisms in rumen microbial communities. PLoS One. 2013;8(2):e47879.
-
(2013)
PLoS One
, vol.8
, Issue.2
, pp. e47879
-
-
Kittelmann, S.1
Seedorf, H.2
Walters, W.A.3
Clemente, J.C.4
Knight, R.5
Gordon, J.I.6
-
25
-
-
84896075409
-
The symbiotic intestinal ciliates and the evolution of their hosts
-
der Staay SY M-v, van der Staay GW, Michalowski T, Jouany JP, Pristas P, Javorsky P, et al. The symbiotic intestinal ciliates and the evolution of their hosts. Eur J Protistol. 2014;50(2):166-73.
-
(2014)
Eur J Protistol
, vol.50
, Issue.2
, pp. 166-173
-
-
Staay S.Y, M.1
Staay, G.W.2
Michalowski, T.3
Jouany, J.P.4
Pristas, P.5
Javorsky, P.6
-
26
-
-
84885961394
-
Networks of evolutionary interactions underlying the polyphyletic origin of ssDNA viruses
-
Krupovic M. Networks of evolutionary interactions underlying the polyphyletic origin of ssDNA viruses. Curr Opin Virol. 2013;3(5):578-86.
-
(2013)
Curr Opin Virol
, vol.3
, Issue.5
, pp. 578-586
-
-
Krupovic, M.1
-
27
-
-
84937511221
-
Origins and evolution of viruses of eukaryotes: the ultimate modularity
-
in press.
-
Koonin EV, Dolja VV, Krupovic M. Origins and evolution of viruses of eukaryotes: the ultimate modularity. Virology 2015, in press.
-
Virology 2015
-
-
Koonin, E.V.1
Dolja, V.V.2
Krupovic, M.3
-
28
-
-
84868146121
-
Provirophages and transpovirons as the diverse mobilome of giant viruses
-
Desnues C, La Scola B, Yutin N, Fournous G, Robert C, Azza S, et al. Provirophages and transpovirons as the diverse mobilome of giant viruses. Proc Natl Acad Sci U S A. 2012;109(44):18078-83.
-
(2012)
Proc Natl Acad Sci U S A
, vol.109
, Issue.44
, pp. 18078-18083
-
-
Desnues, C.1
Scola, B.2
Yutin, N.3
Fournous, G.4
Robert, C.5
Azza, S.6
-
29
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
-
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25(17):3389-402.
-
(1997)
Nucleic Acids Res
, vol.25
, Issue.17
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
-
30
-
-
84903118394
-
Gene identification in prokaryotic genomes, phages, metagenomes, and EST sequences with GeneMarkS suite
-
Unit 1E 7
-
Borodovsky M, Lomsadze A. Gene identification in prokaryotic genomes, phages, metagenomes, and EST sequences with GeneMarkS suite. Curr Protoc Microbiol. 2014;32:Unit 1E 7.
-
(2014)
Curr Protoc Microbiol
, vol.32
-
-
Borodovsky, M.1
Lomsadze, A.2
-
31
-
-
3042666256
-
MUSCLE: multiple sequence alignment with high accuracy and high throughput
-
Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32(5):1792-7.
-
(2004)
Nucleic Acids Res
, vol.32
, Issue.5
, pp. 1792-1797
-
-
Edgar, R.C.1
-
32
-
-
47649125916
-
The deep archaeal roots of eukaryotes
-
Yutin N, Makarova KS, Mekhedov SL, Wolf YI, Koonin EV. The deep archaeal roots of eukaryotes. Mol Biol Evol. 2008;25(8):1619-30.
-
(2008)
Mol Biol Evol
, vol.25
, Issue.8
, pp. 1619-1630
-
-
Yutin, N.1
Makarova, K.S.2
Mekhedov, S.L.3
Wolf, Y.I.4
Koonin, E.V.5
-
33
-
-
77949718257
-
FastTree 2-approximately maximum-likelihood trees for large alignments
-
Price MN, Dehal PS, Arkin AP. FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS One. 2010;5(3), e9490.
-
(2010)
PLoS One
, vol.5
, Issue.3
-
-
Price, M.N.1
Dehal, P.S.2
Arkin, A.P.3
-
34
-
-
79954529507
-
ProtTest 3: fast selection of best-fit models of protein evolution
-
Darriba D, Taboada GL, Doallo R, Posada D. ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics. 2011;27(8):1164-5.
-
(2011)
Bioinformatics
, vol.27
, Issue.8
, pp. 1164-1165
-
-
Darriba, D.1
Taboada, G.L.2
Doallo, R.3
Posada, D.4
-
35
-
-
13444259388
-
TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics
-
Jobb G, von Haeseler A, Strimmer K. TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics. BMC Evol Biol. 2004;4:18.
-
(2004)
BMC Evol Biol
, vol.4
, pp. 18
-
-
Jobb, G.1
Haeseler, A.2
Strimmer, K.3
-
36
-
-
33750831582
-
Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor
-
Kohany O, Gentles AJ, Hankus L, Jurka J. Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor. BMC Bioinformatics. 2006;7:474.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 474
-
-
Kohany, O.1
Gentles, A.J.2
Hankus, L.3
Jurka, J.4
|