-
1
-
-
0001677717
-
Controlling the false discovery rate: A practical and powerful approach to multiple testing
-
Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc B 57:289-300.
-
(1995)
J R Stat Soc B
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
2
-
-
9444282038
-
Evidence for positive epistasis in HIV-1
-
Bonhoeffer S, Chappey C, Parkin NT, Whitcomb JM, Petropoulos CJ. 2004. Evidence for positive epistasis in HIV-1. Science 306:1547-50.
-
(2004)
Science
, vol.306
, pp. 1547-1550
-
-
Bonhoeffer, S.1
Chappey, C.2
Parkin, N.T.3
Whitcomb, J.M.4
Petropoulos, C.J.5
-
3
-
-
0033055004
-
Evolution by small steps and rugged landscapes in the RNA virus phi 6
-
Burch CL, Chao L. 1999. Evolution by small steps and rugged landscapes in the RNA virus phi 6. Genetics 151:921-7.
-
(1999)
Genetics
, vol.151
, pp. 921-927
-
-
Burch, C.L.1
Chao, L.2
-
4
-
-
5444273530
-
Selection pressures in the capsid genes of plant RNA viruses reflect mode of transmission
-
Chare ER, Holmes EC. 2004. Selection pressures in the capsid genes of plant RNA viruses reflect mode of transmission. J Gen Virol 85:3149-57.
-
(2004)
J Gen Virol
, vol.85
, pp. 3149-3157
-
-
Chare, E.R.1
Holmes, E.C.2
-
6
-
-
0031458777
-
Test of synergistic interactions among deleterious mutations in bacteria
-
Elena SF, Lenski RE. 1997. Test of synergistic interactions among deleterious mutations in bacteria. Nature 390:395-8.
-
(1997)
Nature
, vol.390
, pp. 395-398
-
-
Elena, S.F.1
Lenski, R.E.2
-
7
-
-
0030034795
-
A hidden Markov model approach to variation among sites in rate of evolution
-
Felsenstein J, Churchill GA. 1996. A hidden Markov model approach to variation among sites in rate of evolution. Mol Biol Evol 13:93-104.
-
(1996)
Mol Biol Evol
, vol.13
, pp. 93-104
-
-
Felsenstein, J.1
Churchill, G.A.2
-
8
-
-
0036138056
-
Localization of the single-stranded RNA-binding domains of Bluetongue virus nonstructural protein NS2
-
Filmore GC, Lin H, Li JK-K. 2002. Localization of the single-stranded RNA-binding domains of Bluetongue virus nonstructural protein NS2. J Virol 76:499-506.
-
(2002)
J Virol
, vol.76
, pp. 499-506
-
-
Filmore, G.C.1
Lin, H.2
Li, J.K.-K.3
-
9
-
-
10844264563
-
Cofolding organizes alfalfa mosaic virus RNA and coat protein for replication
-
Gougas LM, Filman DJ, Hogle JM, Gehrke L. 2004. Cofolding organizes alfalfa mosaic virus RNA and coat protein for replication. Science 306:2108-11.
-
(2004)
Science
, vol.306
, pp. 2108-2111
-
-
Gougas, L.M.1
Filman, D.J.2
Hogle, J.M.3
Gehrke, L.4
-
10
-
-
0141721420
-
RNA-based phylogenetic methods: Application to mammalian mitochondrial RNA sequences
-
Hudolet C, Gowri-Shankar V, Jow H, Rattray M, Higgs PG. 2003. RNA-based phylogenetic methods: application to mammalian mitochondrial RNA sequences. Mol Phylogenet Evol 28:241-52.
-
(2003)
Mol Phylogenet Evol
, vol.28
, pp. 241-252
-
-
Hudolet, C.1
Gowri-Shankar, V.2
Jow, H.3
Rattray, M.4
Higgs, P.G.5
-
11
-
-
11444249527
-
Mapping the RNA-binding domain on the apple chlorotic leaf spot virus movement protein
-
Isogai M, Yoshikawa N. 2005. Mapping the RNA-binding domain on the apple chlorotic leaf spot virus movement protein. J Gen Virol 86:225-9.
-
(2005)
J Gen Virol
, vol.86
, pp. 225-229
-
-
Isogai, M.1
Yoshikawa, N.2
-
12
-
-
0036147047
-
Rates of molecular evolution in RNA viruses: A quantitative phylogenetic analysis
-
Jenkins GM, Rambaut A, Pybus OG, Holmes EC. 2002. Rates of molecular evolution in RNA viruses: a quantitative phylogenetic analysis. J Mol Evol 54:152-61.
-
(2002)
J Mol Evol
, vol.54
, pp. 152-161
-
-
Jenkins, G.M.1
Rambaut, A.2
Pybus, O.G.3
Holmes, E.C.4
-
13
-
-
0036728808
-
Bayesian phylogenetics using an RNA substitution model applied to early mammalian evolution
-
Jow H, Hudolet C, Rattray M, Higgs PG. 2002. Bayesian phylogenetics using an RNA substitution model applied to early mammalian evolution. Mol Biol Evol 19:1591-601.
-
(2002)
Mol Biol Evol
, vol.19
, pp. 1591-1601
-
-
Jow, H.1
Hudolet, C.2
Rattray, M.3
Higgs, P.G.4
-
14
-
-
0035808775
-
Clustered mutations in HIV-1 gag are consistently required for escape from HLA-B27-restricted cytotoxic T-lymphocyte responses
-
Kelleher AD, Long C, Holmes EC, et al. (18 co-authors). 2001. Clustered mutations in HIV-1 gag are consistently required for escape from HLA-B27-restricted cytotoxic T-lymphocyte responses. J Exp Med 193:375-85.
-
(2001)
J Exp Med
, vol.193
, pp. 375-385
-
-
Kelleher, A.D.1
Long, C.2
Holmes, E.C.3
-
15
-
-
0023737547
-
Deleterious mutations and the evolution of sexual reproduction
-
Kondrashov AS. 1988. Deleterious mutations and the evolution of sexual reproduction. Nature 336:435-40.
-
(1988)
Nature
, vol.336
, pp. 435-440
-
-
Kondrashov, A.S.1
-
16
-
-
13244276706
-
A nucleotide substitution model with nearest-neighbor interactions
-
Lunter G, Hein J. 2004. A nucleotide substitution model with nearest-neighbor interactions. Bioinformatics 20:i216-23.
-
(2004)
Bioinformatics
, vol.20
-
-
Lunter, G.1
Hein, J.2
-
17
-
-
9444245288
-
Epistasis in RNA viruses
-
Michalakis Y, Roze D. 2004. Epistasis in RNA viruses. Science 306:1492-3.
-
(2004)
Science
, vol.306
, pp. 1492-1493
-
-
Michalakis, Y.1
Roze, D.2
-
18
-
-
20044369940
-
Full restoration of viral fitness by multiple compensatory mutations in the nucleoprotein of influenza A virus cytotoxic T-lymphocyte escape mutants
-
Rimmelzwann GF, Berkhoff EG, Nieuwkoop NJ, Smith DJ, Fouchier RA, Osterhaus AD. 2005. Full restoration of viral fitness by multiple compensatory mutations in the nucleoprotein of influenza A virus cytotoxic T-lymphocyte escape mutants. J Gen Virol 86:1801-5.
-
(2005)
J Gen Virol
, vol.86
, pp. 1801-1805
-
-
Rimmelzwann, G.F.1
Berkhoff, E.G.2
Nieuwkoop, N.J.3
Smith, D.J.4
Fouchier, R.A.5
Osterhaus, A.D.6
-
19
-
-
2942565781
-
The distribution of fitness effects caused by single-nucleotide substitutions in an RNA virus
-
Sanjuan R, Moya A, Elena SF. 2004. The distribution of fitness effects caused by single-nucleotide substitutions in an RNA virus. Proc Natl Acad Sci USA 101:8396-401.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 8396-8401
-
-
Sanjuan, R.1
Moya, A.2
Elena, S.F.3
-
20
-
-
1542510106
-
Phylogenetic estimation of context-dependent substitution rates by maximum likelihood
-
Siepel A, Haussler D. 2004. Phylogenetic estimation of context-dependent substitution rates by maximum likelihood. Mol Biol Evol 21:468-88.
-
(2004)
Mol Biol Evol
, vol.21
, pp. 468-488
-
-
Siepel, A.1
Haussler, D.2
-
21
-
-
0033039492
-
Structural constraints on RNA virus evolution
-
Simmonds P, Smith DB. 1999. Structural constraints on RNA virus evolution. J Virol 73:5787-94.
-
(1999)
J Virol
, vol.73
, pp. 5787-5794
-
-
Simmonds, P.1
Smith, D.B.2
-
22
-
-
4344619191
-
Detection of genome-scale ordered RNA structure (GORS) in genomes of positive-stranded RNA viruses: Implications for virus evolution and host persistence
-
Simmonds P, Tuplin A, Evans DJ. 2004. Detection of genome-scale ordered RNA structure (GORS) in genomes of positive-stranded RNA viruses: implications for virus evolution and host persistence. RNA 10:1337-51.
-
(2004)
RNA
, vol.10
, pp. 1337-1351
-
-
Simmonds, P.1
Tuplin, A.2
Evans, D.J.3
-
24
-
-
0000142497
-
Reconstructing ancestral character states under Wagner parsimony
-
Swofford DL, Maddison DR. 1987. Reconstructing ancestral character states under Wagner parsimony. Math Biosci 87:199-229.
-
(1987)
Math Biosci
, vol.87
, pp. 199-229
-
-
Swofford, D.L.1
Maddison, D.R.2
-
25
-
-
0041666589
-
Molecular biology of umbra-viruses: Phantom warriors
-
Taliansky ME, Robinson DJ. 2003. Molecular biology of umbra-viruses: phantom warriors. J Gen Virol 84:1951-60.
-
(2003)
J Gen Virol
, vol.84
, pp. 1951-1960
-
-
Taliansky, M.E.1
Robinson, D.J.2
-
27
-
-
0035031966
-
A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach
-
Whelan S, Goldman N. 2001. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol 18:691-9.
-
(2001)
Mol Biol Evol
, vol.18
, pp. 691-699
-
-
Whelan, S.1
Goldman, N.2
-
28
-
-
1842507188
-
Compensatory mutations cause excess of antagonistic epistasis in RNA secondary structure folding
-
Wilke CO, Lenski RE, Adami C. 2003. Compensatory mutations cause excess of antagonistic epistasis in RNA secondary structure folding. BMC Evol Biol 3:3.
-
(2003)
BMC Evol Biol
, vol.3
, pp. 3
-
-
Wilke, C.O.1
Lenski, R.E.2
Adami, C.3
-
29
-
-
0030683599
-
PAML: A program package for phylogenetic analysis by maximum likelihood
-
Yang ZH. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13:555-6.
-
(1997)
Comput Appl Biosci
, vol.13
, pp. 555-556
-
-
Yang, Z.H.1
-
30
-
-
0031960185
-
Synonymous and nonsynonymous rate variation in nuclear genes of mammals
-
Yang ZH, Nielsen R. 1998. Synonymous and nonsynonymous rate variation in nuclear genes of mammals. J Mol Evol 46:409-18.
-
(1998)
J Mol Evol
, vol.46
, pp. 409-418
-
-
Yang, Z.H.1
Nielsen, R.2
|