-
1
-
-
0018734713
-
Arms races between and within species
-
doi:10.1098/rspb.1979.0081)
-
Dawkins R, Krebs JR. 1979 Arms races between and within species. Proc. R. Soc. Lond. B 205, 489-511.(doi:10.1098/rspb.1979.0081)
-
(1979)
Proc. R. Soc. Lond. B
, vol.205
, pp. 489-511
-
-
Dawkins, R.1
Krebs, J.R.2
-
2
-
-
14544281087
-
Positive selection of primate TRIM5a identifies a critical species-specific retroviral restriction domain
-
doi:10.1073/pnas.0409853102)
-
Sawyer SL, Wu LI, Emerman M, Malik HS. 2005 Positive selection of primate TRIM5a identifies a critical species-specific retroviral restriction domain. Proc. Natl Acad. Sci. USA 102, 2832-2837.(doi:10.1073/pnas.0409853102)
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 2832-2837
-
-
Sawyer, S.L.1
Wu, L.I.2
Emerman, M.3
Malik, H.S.4
-
3
-
-
70350208780
-
The evolutionary conundrum of pathogen mimicry
-
doi:10.1038/nrmicro2222)
-
Elde NC, Malik HS. 2009 The evolutionary conundrum of pathogen mimicry. Nat. Rev. Microbiol. 7, 787-797.(doi:10.1038/nrmicro2222)
-
(2009)
Nat. Rev. Microbiol
, vol.7
, pp. 787-797
-
-
Elde, N.C.1
Malik, H.S.2
-
4
-
-
79957868276
-
Two-stepping through time: Mammals and viruses
-
doi:10.1016/j.tim.2011.03.006)
-
Meyerson NR, Sawyer SL. 2011 Two-stepping through time: mammals and viruses. Trends Microbiol. 19, 286-294.(doi:10.1016/j.tim.2011.03.006)
-
(2011)
Trends Microbiol
, vol.19
, pp. 286-294
-
-
Meyerson, N.R.1
Sawyer, S.L.2
-
5
-
-
34250738281
-
A call to arms: Coevolution of animal viruses and host innate immune responses
-
doi:10.1016/j.tig.2007.04.004)
-
Marques JT, Carthew RW. 2007 A call to arms: coevolution of animal viruses and host innate immune responses. Trends Genet. 23, 359-364.(doi:10.1016/j.tig.2007.04.004)
-
(2007)
Trends Genet
, vol.23
, pp. 359-364
-
-
Marques, J.T.1
Carthew, R.W.2
-
6
-
-
58249090017
-
The evolution of RNAi as a defence against viruses and transposable elements
-
doi:10.1098/rstb. 2008.0168)
-
Obbard D, Gordon K, Buck A, Jiggins F. 2009. The evolution of RNAi as a defence against viruses and transposable elements. Phil. Trans. R. Soc. B 364, 99-115.(doi:10.1098/rstb. 2008.0168)
-
(2009)
Phil. Trans. R. Soc. B
, vol.364
, pp. 99-115
-
-
Obbard, D.1
Gordon, K.2
Buck, A.3
Jiggins, F.4
-
7
-
-
34547587566
-
Antiviral immunity directed by small RNAs
-
doi:10. 1016/j.cell.2007.07.039)
-
Ding S-W, Voinnet O. 2007 Antiviral immunity directed by small RNAs. Cell 130, 413-426. (doi:10. 1016/j.cell.2007.07.039)
-
(2007)
Cell
, vol.130
, pp. 413-426
-
-
Ding, S.-W.1
Voinnet, O.2
-
8
-
-
84863675121
-
Diversity of animal small RNA pathways and their biological utility. Wiley Interdiscip
-
doi:10.1002/ wrna.113)
-
Okamura K. 2011 Diversity of animal small RNA pathways and their biological utility. Wiley Interdiscip. Rev. RNA. 3, 351-368.(doi:10.1002/ wrna.113)
-
(2011)
Rev. RNA
, vol.3
, pp. 351-368
-
-
Okamura, K.1
-
9
-
-
33745951984
-
On the origin and functions of RNA-mediated silencing: From protists to man
-
doi:10.1007/ s00294-006-0078-x)
-
Cerutti H, Casas-Mollano JA. 2006 On the origin and functions of RNA-mediated silencing: from protists to man. Curr. Genet. 50, 81-99.(doi:10.1007/ s00294-006-0078-x)
-
(2006)
Curr. Genet
, vol.50
, pp. 81-99
-
-
Cerutti, H.1
Casas-Mollano, J.A.2
-
10
-
-
0031056933
-
Plants combat infection by gene silencing
-
doi:10.1038/385781a0)
-
Covey SN, Al-Kaff NS, Lángara A, Turner DS. 1997 Plants combat infection by gene silencing. Nature 385, 781-782.(doi:10.1038/385781a0)
-
(1997)
Nature
, vol.385
, pp. 781-782
-
-
Covey, S.N.1
Al-Kaff, N.S.2
Lángara, A.3
Turner, D.S.4
-
11
-
-
0037123630
-
Induction and suppression of RNA silencing by an animal virus
-
doi:10.1126/science.1070948)
-
Li H. 2002 Induction and suppression of RNA silencing by an animal virus. Science 296, 1319-1321.(doi:10.1126/science.1070948)
-
(2002)
Science
, vol.296
, pp. 1319-1321
-
-
Li, H.1
-
12
-
-
10344257532
-
From the cover: RNA interference acts as a natural antiviral response to O'nyong-nyong virus (Alphavirus; Togaviridae) infection of Anopheles gambiae
-
doi:10.1073/pnas.0406983101)
-
Keene KM. 2004 From the cover: RNA interference acts as a natural antiviral response to O'nyong-nyong virus (Alphavirus; Togaviridae) infection of Anopheles gambiae. Proc. Natl Acad. Sci. USA 101, 17240-17245. (doi:10.1073/pnas.0406983101)
-
(2004)
Proc. Natl Acad. Sci. USA
, vol.101
, pp. 17240-17245
-
-
Keene, K.M.1
-
13
-
-
79851477108
-
Natural and experimental infection of Caenorhabditis nematodes by novel viruses related to nodaviruses
-
doi:10.1371/journal.pbio.1000586)
-
Felix MA et al. 2011 Natural and experimental infection of Caenorhabditis nematodes by novel viruses related to nodaviruses. PLoS Biol. 9, e1000586.(doi:10.1371/journal.pbio.1000586)
-
(2011)
PLoS Biol
, vol.9
-
-
Felix, M.A.1
-
14
-
-
34547922042
-
Evidence that RNA silencing functions as an antiviral defense mechanism in fungi
-
doi:10.1073/pnas.0702500104)
-
Segers GC, Zhang X, Deng F, Sun Q, Nuss DL. 2007 Evidence that RNA silencing functions as an antiviral defense mechanism in fungi. Proc. Natl Acad. Sci. USA 104, 12902-12906.(doi:10.1073/pnas.0702500104)
-
(2007)
Proc. Natl Acad. Sci. USA
, vol.104
, pp. 12902-12906
-
-
Segers, G.C.1
Zhang, X.2
Deng, F.3
Sun, Q.4
Nuss, D.L.5
-
15
-
-
79959334012
-
Argonaute proteins
-
doi:10.1016/j.cub.2011. 05.020)
-
Cenik ES, Zamore PD. 2011 Argonaute proteins. Curr. Biol. 21, R446-R449.(doi:10.1016/j.cub.2011. 05.020)
-
(2011)
Curr. Biol
, vol.21
-
-
Cenik, E.S.1
Zamore, P.D.2
-
16
-
-
35348996554
-
Specialization and evolution of endogenous small RNA pathways
-
doi:10.1038/nrg2179)
-
Chapman EJ, Carrington JC. 2007 Specialization and evolution of endogenous small RNA pathways. Nat. Rev. Genet. 8, 884-896. (doi:10.1038/nrg2179)
-
(2007)
Nat Rev. Genet
, vol.8
, pp. 884-896
-
-
Chapman, E.J.1
Carrington, J.C.2
-
17
-
-
66149098226
-
Cell-to-cell spread of the RNA interference response suppresses Semliki Forest virus (SFV) infection of mosquito cell cultures and cannot be antagonized by SFV
-
doi:10.1128/JVI.02440-08)
-
Attarzadeh-Yazdi G et al. 2009 Cell-to-cell spread of the RNA interference response suppresses Semliki Forest virus (SFV) infection of mosquito cell cultures and cannot be antagonized by SFV. J. Virol. 83, 5735-5748. (doi:10.1128/JVI.02440-08)
-
(2009)
J. Virol
, vol.83
, pp. 5735-5748
-
-
Attarzadeh-Yazdi, G.1
-
18
-
-
33750361188
-
Virus counterdefense: Diverse strategies for evading the RNA-silencing immunity
-
doi:10.1146/ annurev.micro.60.080805.142205)
-
Li F, Ding S-W. 2006 Virus counterdefense: diverse strategies for evading the RNA-silencing immunity. Annu. Rev. Microbiol. 60, 503-531. (doi:10.1146/ annurev.micro.60.080805.142205)
-
(2006)
Annu Rev. Microbiol
, vol.60
, pp. 503-531
-
-
Li, F.1
Ding, S.-W.2
-
19
-
-
8144226266
-
Three distinct suppressors of RNA silencing encoded by a 20-kb viral RNA genome
-
doi:10.1073/pnas.0404940101)
-
Lu R, Folimonov A, Shintaku M, Li WX, Falk BW, Dawson WO, Ding SW. 2004 Three distinct suppressors of RNA silencing encoded by a 20-kb viral RNA genome. Proc. Natl Acad. Sci. USA 101, 15742-15747. (doi:10.1073/pnas.0404940101)
-
(2004)
Proc. Natl Acad. Sci. USA
, vol.101
, pp. 15742-15747
-
-
Lu, R.1
Folimonov, A.2
Shintaku, M.3
Li, W.X.4
Falk, B.W.5
Dawson, W.O.6
Ding, S.W.7
-
20
-
-
33847637711
-
Recombination and gene duplication in the evolutionary diversification of P1 proteins in the family Potyviridae
-
doi:10.1099/vir.0.82402-0)
-
Valli A, Lopez-Moya JJ, Garcia JA. 2007 Recombination and gene duplication in the evolutionary diversification of P1 proteins in the family Potyviridae. J. Gen. Virol. 88, 1016-1028. (doi:10.1099/vir.0.82402-0)
-
(2007)
J. Gen. Virol
, vol.88
, pp. 1016-1028
-
-
Valli, A.1
Lopez-Moya, J.J.2
Garcia, J.A.3
-
21
-
-
33746821799
-
Identification of an RNA-silencing suppressor in the genome of Grapevine virus A
-
doi:10.1099/vir.0. 81893-0)
-
Zhou ZS. 2006 Identification of an RNA-silencing suppressor in the genome of Grapevine virus A. J. Gen. Virol. 87, 2387-2395. (doi:10.1099/vir.0. 81893-0)
-
(2006)
J. Gen. Virol
, vol.87
, pp. 2387-2395
-
-
Zhou, Z.S.1
-
22
-
-
63749087829
-
Characterization and subcellular localization of an RNA silencing suppressor encoded by Rice stripe tenuivirus
-
doi:10.1016/j. virol.2009.01.045)
-
Xiong R, Wu J, Zhou Y, Zhou X. 2009 Characterization and subcellular localization of an RNA silencing suppressor encoded by Rice stripe tenuivirus. Virology 387, 29-40. (doi:10.1016/j. virol.2009.01.045)
-
(2009)
Virology
, vol.387
, pp. 29-40
-
-
Xiong, R.1
Wu, J.2
Zhou, Y.3
Zhou, X.4
-
23
-
-
0037227813
-
Negative-strand tospoviruses and tenuiviruses carry a gene for a suppressor of gene silencing at analogous genomic positions
-
doi:10.1128/JVI.77.2.1329-1336.2003)
-
Bucher E, Sijen T, de Haan P, Goldbach R, Prins M. 2003 Negative-strand tospoviruses and tenuiviruses carry a gene for a suppressor of gene silencing at analogous genomic positions. J. Virol. 77, 1329-1336. (doi:10.1128/JVI.77.2.1329-1336.2003)
-
(2003)
J. Virol
, vol.77
, pp. 1329-1336
-
-
Bucher, E.1
Sijen, T.2
de Haan, P.3
Goldbach, R.4
Prins, M.5
-
24
-
-
33745516843
-
Small RNA binding is a common strategy to suppress RNA silencing by several viral suppressors
-
doi:10.1038/sj.emboj.7601164)
-
Lakatos L et al. 2006 Small RNA binding is a common strategy to suppress RNA silencing by several viral suppressors. EMBO J. 25, 2768-2780. (doi:10.1038/sj.emboj.7601164)
-
(2006)
EMBO J
, vol.25
, pp. 2768-2780
-
-
Lakatos, L.1
-
25
-
-
33845391778
-
Cucumber mosaic virus-encoded 2b suppressor inhibits Arabidopsis Argonaute1 cleavage activity to counter plant defense
-
doi:10.1101/gad.1495506)
-
Zhang X, Yuan YR, Pei Y, Lin SS, Tuschl T, Patel DJ, Chua NH. 2006 Cucumber mosaic virus-encoded 2b suppressor inhibits Arabidopsis Argonaute1 cleavage activity to counter plant defense. Genes Dev. 20, 3255-3268. (doi:10.1101/gad.1495506)
-
(2006)
Genes Dev
, vol.20
, pp. 3255-3268
-
-
Zhang, X.1
Yuan, Y.R.2
Pei, Y.3
Lin, S.S.4
Tuschl, T.5
Patel, D.J.6
Chua, N.H.7
-
26
-
-
34548474870
-
The Polerovirus silencing suppressor P0 targets ARGONAUTE proteins for degradation
-
doi:10. 1016/j.cub.2007.08.039)
-
Baumberger N, Tsai C-H, Lie M, Havecker E, Baulcombe David C. 2007 The Polerovirus silencing suppressor P0 targets ARGONAUTE proteins for degradation. Curr. Biol. 17, 1609-1614. (doi:10. 1016/j.cub.2007.08.039)
-
(2007)
Curr. Biol
, vol.17
, pp. 1609-1614
-
-
Baumberger, N.1
Tsai, C.-H.2
Lie, M.3
Havecker, E.4
Baulcombe David, C.5
-
27
-
-
0141789662
-
Tomato mosaic virus replication protein suppresses virus-targeted posttranscriptional gene silencing
-
doi:10.1128/JVI.77.20.11016- 11026.2003)
-
Kubota K, Tsuda S, Tamai A, Meshi T. 2003 Tomato mosaic virus replication protein suppresses virus-targeted posttranscriptional gene silencing. J. Virol. 77, 11016-11026. (doi:10.1128/JVI.77.20.11016- 11026.2003)
-
(2003)
J. Virol
, vol.77
, pp. 11016-11026
-
-
Kubota, K.1
Tsuda, S.2
Tamai, A.3
Meshi, T.4
-
28
-
-
41949139714
-
Tobacco rattle virus 16-kilodalton protein encodes a suppressor of RNA silencing that allows transient viral entry in meristems
-
doi:10.1128/JVI.02438-07)
-
Martin-Hernandez AM, Baulcombe DC. 2008 Tobacco rattle virus 16-kilodalton protein encodes a suppressor of RNA silencing that allows transient viral entry in meristems. J. Virol. 82, 4064-4071. (doi:10.1128/JVI.02438-07)
-
(2008)
J. Virol
, vol.82
, pp. 4064-4071
-
-
Martin-Hernandez, A.M.1
Baulcombe, D.C.2
-
29
-
-
0037967527
-
The capacity of transgenic tobacco to send a systemic RNA silencing signal depends on the nature of the inducing transgene locus
-
doi:10.1046/j.1365-313X.2003.01785.x)
-
Mallory AC, Mlotshwa S, Bowman LH, Vance VB. 2003 The capacity of transgenic tobacco to send a systemic RNA silencing signal depends on the nature of the inducing transgene locus. Plant J. 35, 82-92. (doi:10.1046/j.1365-313X.2003.01785.x)
-
(2003)
Plant J
, vol.35
, pp. 82-92
-
-
Mallory, A.C.1
Mlotshwa, S.2
Bowman, L.H.3
Vance, V.B.4
-
30
-
-
33644838714
-
Cell-to-cell movement of Potato Potexvirus X is dependent on suppression of RNA silencing
-
doi:10.1111/j.1365-313X.2005.02539.x)
-
Bayne EH, Rakitina DV, Morozov SY, Baulcombe DC. 2005. Cell-to-cell movement of Potato Potexvirus X is dependent on suppression of RNA silencing. Plant J. 44, 471-482.(doi:10.1111/j.1365-313X.2005.02539.x)
-
(2005)
Plant J
, vol.44
, pp. 471-482
-
-
Bayne, E.H.1
Rakitina, D.V.2
Morozov, S.Y.3
Baulcombe, D.C.4
-
31
-
-
77955255337
-
The silencing suppressor P25 of Potato virus X interacts with Argonaute1 and mediates its degradation through the proteasome pathway
-
doi:10.1111/j.1364- 3703.2010.00634.x)
-
Chiu MH, Chen IH, Baulcombe DC, Tsai CH. 2010 The silencing suppressor P25 of Potato virus X interacts with Argonaute1 and mediates its degradation through the proteasome pathway. Mol. Plant Pathol. 11, 641-649. (doi:10.1111/j.1364- 3703.2010.00634.x)
-
(2010)
Mol. Plant Pathol
, vol.11
, pp. 641-649
-
-
Chiu, M.H.1
Chen, I.H.2
Baulcombe, D.C.3
Tsai, C.H.4
-
32
-
-
75749102212
-
The rice yellow mottle virus P1 protein exhibits dual functions to suppress and activate gene silencing
-
doi:10.1111/j.1365-313X. 2009.04062.x)
-
Lacombe S, Bangratz M, Vignols F, Brugidou C. 2010 The rice yellow mottle virus P1 protein exhibits dual functions to suppress and activate gene silencing. Plant J. 61, 371-382. (doi:10.1111/j.1365-313X. 2009.04062.x)
-
(2010)
Plant J
, vol.61
, pp. 371-382
-
-
Lacombe, S.1
Bangratz, M.2
Vignols, F.3
Brugidou, C.4
-
33
-
-
33644996948
-
Natural selection drives extremely rapid evolution in antiviral RNAi genes
-
doi:10.1016/j.cub.2006.01.065)
-
Obbard DJ, Jiggins FM, Halligan DL, Little TJ. 2006 Natural selection drives extremely rapid evolution in antiviral RNAi genes. Curr. Biol. 16, 580-585. (doi:10.1016/j.cub.2006.01.065)
-
(2006)
Curr. Biol
, vol.16
, pp. 580-585
-
-
Obbard, D.J.1
Jiggins, F.M.2
Halligan, D.L.3
Little, T.J.4
-
34
-
-
73449137909
-
Quantifying adaptive evolution in the Drosophila immune system
-
doi:10. 1371/journal.pgen.1000698)
-
Obbard D, Welch J, Kim K, Jiggins F. 2009 Quantifying adaptive evolution in the Drosophila immune system. PLoS Genet. 5, e1000698. (doi:10. 1371/journal.pgen.1000698)
-
(2009)
PLoS Genet
, vol.5
-
-
Obbard, D.1
Welch, J.2
Kim, K.3
Jiggins, F.4
-
35
-
-
78751560974
-
Recurrent adaptation in RNA interference genes across the Drosophila phylogeny
-
doi:10.1093/molbev/msq284)
-
Kolaczkowski B, Hupalo DN, Kern AD. 2011 Recurrent adaptation in RNA interference genes across the Drosophila phylogeny. Mol. Biol. Evol. 28, 1033-1042. (doi:10.1093/molbev/msq284)
-
(2011)
Mol. Biol. Evol
, vol.28
, pp. 1033-1042
-
-
Kolaczkowski, B.1
Hupalo, D.N.2
Kern, A.D.3
-
36
-
-
78751488038
-
Recent and recurrent selective sweeps of the antiviral RNAi gene Argonaute-2 in three species of Drosophila
-
doi:10. 1093/molbev/msq280)
-
Obbard DJ, Jiggins FM, Bradshaw NJ, Little TJ. 2011 Recent and recurrent selective sweeps of the antiviral RNAi gene Argonaute-2 in three species of Drosophila. Mol. Biol. Evol. 28,1043-1056. (doi:10. 1093/molbev/msq280)
-
(2011)
Mol. Biol. Evol
, vol.28
, pp. 1043-1056
-
-
Obbard, D.J.1
Jiggins, F.M.2
Bradshaw, N.J.3
Little, T.J.4
-
37
-
-
26944443659
-
Suppressors of RNA silencing encoded by plant viruses and their role in viral infections
-
doi:10. 1016/j.febslet.2005.08.041)
-
Qu F, Morris T. 2005 Suppressors of RNA silencing encoded by plant viruses and their role in viral infections. FEBS Lett. 579, 5958-5964. (doi:10. 1016/j.febslet.2005.08.041)
-
(2005)
FEBS Lett
, vol.579
, pp. 5958-5964
-
-
Qu, F.1
Morris, T.2
-
38
-
-
15844406550
-
HyPhy: Hypothesis testing using phylogenies
-
doi:10.1093/ bioinformatics/bti079)
-
Kosakovsky Pond SL, Frost SDW, Muse SV. 2005 HyPhy: hypothesis testing using phylogenies. Bioinformatics 21, 676-679. (doi:10.1093/ bioinformatics/bti079)
-
(2005)
Bioinformatics
, vol.21
, pp. 676-679
-
-
Kosakovsky Pond, S.L.1
Frost, S.D.W.2
Muse, S.V.3
-
39
-
-
34547803197
-
PAML 4: Phylogenetic analysis by maximum likelihood
-
doi:10.1093/molbev/msm088)
-
Yang Z. 2007 PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586-1591. (doi:10.1093/molbev/msm088)
-
(2007)
Mol. Biol. Evol
, vol.24
, pp. 1586-1591
-
-
Yang, Z.1
-
40
-
-
17744396121
-
Not so different after all: A comparison of methods for detecting amino acid sites under selection
-
doi:10.1093/molbev/msi105)
-
Kosakovsky Pond SL. 2005 Not so different after all: a comparison of methods for detecting amino acid sites under selection. Mol. Biol. Evol. 22, 1208-1222. (doi:10.1093/molbev/msi105)
-
(2005)
Mol. Biol. Evol
, vol.22
, pp. 1208-1222
-
-
Kosakovsky Pond, S.L.1
-
41
-
-
0032538794
-
Viral pathogenicity determinants are suppressors of transgene silencing in Nicotiana benthamiana
-
doi:10. 1093/emboj/17.22.6739)
-
Brigneti G. 1998 Viral pathogenicity determinants are suppressors of transgene silencing in Nicotiana benthamiana. EMBO J. 17, 6739-6746. (doi:10. 1093/emboj/17.22.6739)
-
(1998)
EMBO J
, vol.17
, pp. 6739-6746
-
-
Brigneti, G.1
-
42
-
-
0034849552
-
A cucumber mosaic virus (CMV) RNA 1 transgene mediates suppression of the homologous viral RNA 1 constitutively and prevents CMV entry into the phloem
-
doi:10.1128/JVI.75.19.9114-9120.2001)
-
Canto T, Palukaitis P. 2001 A cucumber mosaic virus (CMV) RNA 1 transgene mediates suppression of the homologous viral RNA 1 constitutively and prevents CMV entry into the phloem. J. Virol. 75, 9114-9120. (doi:10.1128/JVI.75.19.9114-9120.2001)
-
(2001)
J. Virol
, vol.75
, pp. 9114-9120
-
-
Canto, T.1
Palukaitis, P.2
-
43
-
-
58549112576
-
The P0 gene of sugarcane yellow leaf virus encodes an RNA silencing suppressor with unique activities
-
doi:10.1016/j.virol.2008.10.034)
-
Mangwende T, Wang M-L, Borth W, Hu J, Moore PH, Mirkov TE, Albert HH. 2009 The P0 gene of sugarcane yellow leaf virus encodes an RNA silencing suppressor with unique activities. Virology 384, 38-50. (doi:10.1016/j.virol.2008.10.034)
-
(2009)
Virology
, vol.384
, pp. 38-50
-
-
Mangwende, T.1
Wang, M.-L.2
Borth, W.3
Hu, J.4
Moore, P.H.5
Mirkov, T.E.6
Albert, H.H.7
-
44
-
-
0037320231
-
P1/HC-Pro, a viral suppressor of RNA silencing, interferes with Arabidopsis development and miRNA function
-
doi:10. 1016/S1534-5807(03) 00025-X)
-
Kasschau KD, Xie Z, Allen E, Llave C, Chapman EJ, Krizan KA, Carrington JC. 2003 P1/HC-Pro, a viral suppressor of RNA silencing, interferes with Arabidopsis development and miRNA function. Dev. Cell 4, 205-217. (doi:10. 1016/S1534-5807(03) 00025-X)
-
(2003)
Dev. Cell
, vol.4
, pp. 205-217
-
-
Kasschau, K.D.1
Xie, Z.2
Allen, E.3
Llave, C.4
Chapman, E.J.5
Krizan, K.A.6
Carrington, J.C.7
-
45
-
-
33144478111
-
MicroRNA-guided processing impairs Plum Pox virus replication, but the virus readily evolves to escape this silencing mechanism
-
doi:10.1128/ JVI.80.5.2429-2436.2006)
-
Simon-Mateo C, Garcia JA. 2006 MicroRNA-guided processing impairs Plum Pox virus replication, but the virus readily evolves to escape this silencing mechanism. J. Virol. 80, 2429-2436. (doi:10.1128/ JVI.80.5.2429-2436.2006)
-
(2006)
J. Virol
, vol.80
, pp. 2429-2436
-
-
Simon-Mateo, C.1
Garcia, J.A.2
-
46
-
-
33749488925
-
RNA silencing suppression by a second copy of the P1 serine protease of Cucumber vein yellowing ipomovirus, a member of the family Potyviridae that lacks the cysteine protease HCPro
-
doi:10.1128/JVI.00985-06)
-
Valli A, Martin-Hernandez AM, Lopez-Moya JJ, Garcia JA. 2005. RNA silencing suppression by a second copy of the P1 serine protease of Cucumber vein yellowing ipomovirus, a member of the family Potyviridae that lacks the cysteine protease HCPro. J. Virol. 80,10055-10063. (doi:10.1128/JVI.00985-06)
-
(2005)
J. Virol
, vol.80
, pp. 10055-10063
-
-
Valli, A.1
Martin-Hernandez, A.M.2
Lopez-Moya, J.J.3
Garcia, J.A.4
-
47
-
-
36448991500
-
Clustal W and Clustal X version 2.0
-
doi:10. 1093/bioinformatics/btm404)
-
Larkin MA et al. 2007 Clustal W and Clustal X version 2.0. Bioinformatics 23, 2947-2948. (doi:10. 1093/bioinformatics/btm404)
-
(2007)
Bioinformatics
, vol.23
, pp. 2947-2948
-
-
Larkin, M.A.1
-
48
-
-
0042208362
-
Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites
-
Anisimova M, Nielsen R, Yang Z. 2003 Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. Genetics 164, 1229-1236.
-
(2003)
Genetics
, vol.164
, pp. 1229-1236
-
-
Anisimova, M.1
Nielsen, R.2
Yang, Z.3
-
49
-
-
33748770095
-
Automated phylogenetic detection of recombination using a genetic algorithm
-
doi:10. 1093/molbev/msl051)
-
Kosakovsky Pond SL, Posada D, Gravenor MB, Woelk CH, Frost SD. 2006 Automated phylogenetic detection of recombination using a genetic algorithm. Mol. Biol. Evol. 23,1891-1901. (doi:10. 1093/molbev/msl051)
-
(2006)
Mol. Biol Evol
, vol.23
, pp. 1891-1901
-
-
Kosakovsky Pond, S.L.1
Posada, D.2
Gravenor, M.B.3
Woelk, C.H.4
Frost, S.D.5
-
50
-
-
0041386108
-
MrBayes 3: Bayesian phylogenetic inference under mixed models
-
doi:10. 1093/bioinformatics/btg180)
-
Ronquist F, Huelsenbeck JP. 2003 MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572-1574. (doi:10. 1093/bioinformatics/btg180)
-
(2003)
Bioinformatics
, vol.19
, pp. 1572-1574
-
-
Ronquist, F.1
Huelsenbeck, J.P.2
-
51
-
-
77249173222
-
Evolutionary fingerprinting of genes
-
doi:10.1093/ molbev/msp260)
-
Kosakovsky Pond SL, Scheffler K, Gravenor MB, Poon AFY, Frost SDW. 2009 Evolutionary fingerprinting of genes. Mol. Biol. Evol. 27, 520-536. (doi:10.1093/ molbev/msp260)
-
(2009)
Mol. Biol. Evol
, vol.27
, pp. 520-536
-
-
Kosakovsky Pond, S.L.1
Scheffler, K.2
Gravenor, M.B.3
Poon, A.F.Y.4
Frost, S.D.W.5
-
52
-
-
84864605220
-
Detecting individual srtes subject to episodic diversifying selection
-
doi:10.1371/journal.pgen.1002764)
-
Murrell B, Wertheim JO, Moola S, Weighill T, Scheffler K, Kosakovsky Pond SL. 2012 Detecting individual srtes subject to episodic diversifying selection. PLoS Genet. 8, e1002764. (doi:10.1371/journal.pgen.1002764)
-
(2012)
PLoS Genet
, vol.8
-
-
Murrell, B.1
Wertheim, J.O.2
Moola, S.3
Weighill, T.4
Scheffler, K.5
Kosakovsky Pond, S.L.6
-
53
-
-
0028168856
-
A codon-based model of nucleotide substitution for protein-coding DNA sequences
-
Goldman N, Yang Z. 1994 A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol. Biol. Evol. 11, 725-736.
-
(1994)
Mol. Biol. Evol
, vol.11
, pp. 725-736
-
-
Goldman, N.1
Yang, Z.2
-
54
-
-
33749066127
-
An empirical examination of the standard errors of maximum likelihood phylogenetic parameters under the molecular clock via bootstrapping
-
Schrago CG. 2006 An empirical examination of the standard errors of maximum likelihood phylogenetic parameters under the molecular clock via bootstrapping. Gen. Mol. Res. 5, 233-241.
-
(2006)
Gen. Mol. Res
, vol.5
, pp. 233-241
-
-
Schrago, C.G.1
-
55
-
-
16344378246
-
Bayes empirical Bayes inference of amino acid sites under positive selection
-
doi:10.1093/molbev/msi097)
-
Yang Z. 2005 Bayes empirical Bayes inference of amino acid sites under positive selection. Mol. Biol. Evol. 22,1107-1118. (doi:10.1093/molbev/msi097)
-
(2005)
Mol. Biol. Evol
, vol.22
, pp. 1107-1118
-
-
Yang, Z.1
-
56
-
-
27844569825
-
Site-to-site variation of synonymous substitution rates
-
doi:10.1093/molbev/msi232
-
Kosakovsky Pond S, Muse SV. 2005 Site-to-site variation of synonymous substitution rates. Mol. Biol. Evol. 22, 2375-2385.(doi:10.1093/molbev/msi232)
-
(2005)
Mol. Biol. Evol
, vol.22
, pp. 2375-2385
-
-
Kosakovsky Pond, S.1
Muse, S.V.2
-
57
-
-
77957233168
-
Datamonkey 2010: A suite of phylogenetic analysis tools for evolutionary biology
-
doi:10.1093/ bioinformatics/btq429)
-
Delport W, Poon AF, Frost SD, Kosakovsky Pond SL. 2009. Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology. Bioinformatics 26, 2455-2457. (doi:10.1093/ bioinformatics/btq429)
-
(2009)
Bioinformatics
, vol.26
, pp. 2455-2457
-
-
Delport, W.1
Poon, A.F.2
Frost, S.D.3
Kosakovsky Pond, S.L.4
-
58
-
-
0348186338
-
-
Cambridge, UK: Cambridge University Press
-
Davison AC. 2003 Statistical models. Cambridge, UK: Cambridge University Press.
-
(2003)
Statistical Models
-
-
Davison, A.C.1
-
59
-
-
84879363825
-
-
ASReml user guide release 2.0. Hemel Hempstead, UK: VSN International
-
Gilmour AR, Gogel BJ, Cullis BR, Thompson R. 2006 ASReml user guide release 2.0. Hemel Hempstead, UK: VSN International.
-
(2006)
-
-
Gilmour, A.R.1
Gogel, B.J.2
Cullis, B.R.3
Thompson, R.4
-
60
-
-
8544225780
-
Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites
-
doi:10.1534/genetics.104.031153)
-
Wong WSW, Yang Z, Goldman N, Nielsen R. 2004 Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites. Genetics 168, 1041-1051. (doi:10.1534/genetics.104.031153)
-
(2004)
Genetics
, vol.168
, pp. 1041-1051
-
-
Wong, W.S.W.1
Yang, Z.2
Goldman, N.3
Nielsen, R.4
-
61
-
-
0003465579
-
-
Version: 20th August 1996
-
Brunt AA, Crabtree K, Dallwitz MJ, Gibbs AJ, Watson L, Zurcher EJ. (eds) 1996 Plant viruses online: descriptions and lists from the VIDE database. Version: 20th August 1996. See http://biology.anu.edu.au/Groups/MES/vide/.
-
(1996)
Plant Viruses Online: Descriptions and Lists From the VIDE Database
-
-
Brunt, A.A.1
Crabtree, K.2
Dallwitz, M.J.3
Gibbs, A.J.4
Watson, L.5
Zurcher, E.J.6
-
62
-
-
0037186564
-
Adaptive protein evolution in Drosophila
-
doi:10.1038/4151022a)
-
Smith NG, Eyre-Walker A. 2002 Adaptive protein evolution in Drosophila. Nature 415, 1022-1024. (doi:10.1038/4151022a)
-
(2002)
Nature
, vol.415
, pp. 1022-1024
-
-
Smith, N.G.1
Eyre-Walker, A.2
-
63
-
-
58549090139
-
The impact of natural selection on the genome: Emerging patterns in Drosophila and Arabidopsis
-
doi:10.1146/annurev.ecolsys. 39.110707.173342)
-
Wright SI, Andolfatto P. 2008 The impact of natural selection on the genome: emerging patterns in Drosophila and Arabidopsis. Annu. Rev. Ecol. Evol. Syst. 39, 193-213. (doi:10.1146/annurev.ecolsys. 39.110707.173342)
-
(2008)
Annu. Rev. Ecol. Evol. Syst
, vol.39
, pp. 193-213
-
-
Wright, S.I.1
Andolfatto, P.2
-
64
-
-
80052153094
-
The genomic rate of molecular adaptation of the human influenza A virus
-
doi:10.1093/molbev/msr044)
-
Bhatt S, Holmes EC, Pybus OG. 2011 The genomic rate of molecular adaptation of the human influenza A virus. Mol. Biol. Evol. 28, 2443-2451. (doi:10.1093/molbev/msr044)
-
(2011)
Mol. Biol Evol
, vol.28
, pp. 2443-2451
-
-
Bhatt, S.1
Holmes, E.C.2
Pybus, O.G.3
-
65
-
-
33750297873
-
HIV evolutionary dynamics within and among hosts
-
Lemey P, Rambaut A, Pybus OG. 2006 HIV evolutionary dynamics within and among hosts. AIDS Rev. 8, 125-140.
-
(2006)
AIDS Rev
, vol.8
, pp. 125-140
-
-
Lemey, P.1
Rambaut, A.2
Pybus, O.G.3
-
66
-
-
40749085180
-
Pacing a small cage: Mutation and RNA viruses
-
doi:10.1016/j.tree. 2007.11.010)
-
Belshaw R, Gardner A, RarnbaUt A, Pybus OG. 2008 Pacing a small cage: mutation and RNA viruses. Trends Ecol. Evol. 23,188-193. (doi:10.1016/j.tree. 2007.11.010)
-
(2008)
Trends Ecol Evol
, vol.23
, pp. 188-193
-
-
Belshaw, R.1
Gardner, A.2
Rarnbaut, A.3
Pybus, O.G.4
-
67
-
-
34547471449
-
Recent LTR retrotransposon insertion contrasts with waves of non-LTR insertion since speciation in Drosophila melanogaster
-
(doi:10.1073/pnas.0702552104)
-
Bergman CM, Bensasson D. 2007 Recent LTR retrotransposon insertion contrasts with waves of non-LTR insertion since speciation in Drosophila melanogaster. Proc. Natl Acad. Sci. USA 104, 10340-11345. (doi:10.1073/pnas.0702552104)
-
(2007)
Proc. Natl Acad. Sci. USA
, vol.104
, pp. 10340-11345
-
-
Bergman, C.M.1
Bensasson, D.2
-
68
-
-
79955468851
-
The Arabidopsis lyrata genome sequence and the basis of rapid genome size change
-
doi:10.1038/ng.807)
-
Hu TT et al. 2011 The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nat. Genet. 43, 476. (doi:10.1038/ng.807)
-
(2011)
Nat. Genet
, vol.43
, pp. 476
-
-
Hu, T.T.1
|