-
1
-
-
0034897709
-
Accuracy and power of the likelihood ratio test to detect adaptive molecular evolution
-
Anisimova MJ, Bielawski JP, Yang Z (2001) Accuracy and power of the likelihood ratio test to detect adaptive molecular evolution. Mol Biol Evol 18:1585-1592
-
(2001)
Mol Biol Evol
, vol.18
, pp. 1585-1592
-
-
Anisimova, M.J.1
Bielawski, J.P.2
Yang, Z.3
-
2
-
-
0036272936
-
Accuracy and power of Bayes prediction of amino acid sites under positive selection
-
Anisimova M, Bielawski JP, Yang Z (2002) Accuracy and power of Bayes prediction of amino acid sites under positive selection. Mol Biol Evol 19:950-958
-
(2002)
Mol Biol Evol
, vol.19
, pp. 950-958
-
-
Anisimova, M.1
Bielawski, J.P.2
Yang, Z.3
-
3
-
-
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
-
4
-
-
0033601201
-
Linkage disequilibrium and recombination in hominid mitochondrial DNA
-
Awadalla P, Eyre-Walker A, Smith JM (1999) Linkage disequilibrium and recombination in hominid mitochondrial DNA. Science 286:2524-2525
-
(1999)
Science
, vol.286
, pp. 2524-2525
-
-
Awadalla, P.1
Eyre-Walker, A.2
Smith, J.M.3
-
5
-
-
0037191796
-
Virus evolution: The importance of being erroneous
-
Bonhoeffer S, Sniegowski P (2002) Virus evolution: The importance of being erroneous. Nature 420:367-369
-
(2002)
Nature
, vol.420
, pp. 367-369
-
-
Bonhoeffer, S.1
Sniegowski, P.2
-
6
-
-
0031901637
-
Genotype-specific complementation of hepatitis delta virus RNA replication by hepatitis delta antigen
-
Casey JL, Gerin JL (1998) Genotype-specific complementation of hepatitis delta virus RNA replication by hepatitis delta antigen. J Virol 72:2806-2814
-
(1998)
J Virol
, vol.72
, pp. 2806-2814
-
-
Casey, J.L.1
Gerin, J.L.2
-
7
-
-
0032110130
-
Local helix content and RNA-binding activity of the N-terminal leucine-repeat region of hepatitis delta antigen
-
Cheng JW, Lin IJ, Lou YC, Pai MT, Wu HN (1998) Local helix content and RNA-binding activity of the N-terminal leucine-repeat region of hepatitis delta antigen. J Biomol NMR 12:183-188
-
(1998)
J Biomol NMR
, vol.12
, pp. 183-188
-
-
Cheng, J.W.1
Lin, I.J.2
Lou, Y.C.3
Pai, M.T.4
Wu, H.N.5
-
8
-
-
0029563023
-
A method for estimating the numbers of synonymous and nonsynonymous substitutions per site
-
Comeron JM (1995) A method for estimating the numbers of synonymous and nonsynonymous substitutions per site. J Mol Evol, 41:1152-1159
-
(1995)
J Mol Evol
, vol.41
, pp. 1152-1159
-
-
Comeron, J.M.1
-
9
-
-
0036943052
-
Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle
-
Desper R, Gascuel O (2002) Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle. J Comput Biol 9:687-705
-
(2002)
J Comput Biol
, vol.9
, pp. 687-705
-
-
Desper, R.1
Gascuel, O.2
-
10
-
-
0035157361
-
Evidence for positive selection in the capsid protein-coding region of the foot-and-mouth disease virus (FMDV) subjected to experimental passage regimens
-
Fares MA, Moya A, Escarmis C, Baranowski E, Domingo E, Barrio E (2001) Evidence for positive selection in the capsid protein-coding region of the foot-and-mouth disease virus (FMDV) subjected to experimental passage regimens. Mol Biol Evol 18:10-21
-
(2001)
Mol Biol Evol
, vol.18
, pp. 10-21
-
-
Fares, M.A.1
Moya, A.2
Escarmis, C.3
Baranowski, E.4
Domingo, E.5
Barrio, E.6
-
11
-
-
0035675042
-
Estimating recombination rates from population genetic data
-
Fearnhead P, Donnell P (2001) Estimating recombination rates from population genetic data. Genetics 159:1299-1318
-
(2001)
Genetics
, vol.159
, pp. 1299-1318
-
-
Fearnhead, P.1
Donnell, P.2
-
12
-
-
0035860629
-
Immunization of woodchucks (Marmota monax) with hepatitis delta virus DNA vaccine
-
Fiedler M, Lu M, Siegel F, Whipple J, Roggendorf M (2001) Immunization of woodchucks (Marmota monax) with hepatitis delta virus DNA vaccine. Vaccine 19:4618-4626
-
(2001)
Vaccine
, vol.19
, pp. 4618-4626
-
-
Fiedler, M.1
Lu, M.2
Siegel, F.3
Whipple, J.4
Roggendorf, M.5
-
13
-
-
0030807655
-
BIONJ: An improved version of the NJ algorithm based on a simple model of sequence data
-
Gascuel O (1997) BIONJ: An improved version of the NJ algorithm based on a simple model of sequence data. Mol Biol Evol 14:685-695
-
(1997)
Mol Biol Evol
, vol.14
, pp. 685-695
-
-
Gascuel, O.1
-
14
-
-
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
-
15
-
-
0031041347
-
A likelihood method for the detection of selection and recombination using nucleotide sequences
-
Grassly NC, Holmes EC (1997) A likelihood method for the detection of selection and recombination using nucleotide sequences. Mol Biol Evol 14:239-247
-
(1997)
Mol Biol Evol
, vol.14
, pp. 239-247
-
-
Grassly, N.C.1
Holmes, E.C.2
-
16
-
-
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
-
17
-
-
0027756896
-
A switch between two-, three-, and four-stranded coiled coils in GCN4 leucine zipper mutants
-
Harbury PB, Zhang T, Kim PS, Alber T (1993) A switch between two-, three-, and four-stranded coiled coils in GCN4 leucine zipper mutants. Science 262:1401-1407
-
(1993)
Science
, vol.262
, pp. 1401-1407
-
-
Harbury, P.B.1
Zhang, T.2
Kim, P.S.3
Alber, T.4
-
18
-
-
0022376704
-
Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
-
Hasegawa M, Kishino H, Yano T (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 22:160-174
-
(1985)
J Mol Evol
, vol.22
, pp. 160-174
-
-
Hasegawa, M.1
Kishino, H.2
Yano, T.3
-
19
-
-
0035148533
-
Evidence for positive selection in foot-and-mouth disease virus capsid genes from field isolates
-
Haydon DT, Bastos AD, Samuel AR (2001) Evidence for positive selection in foot-and-mouth disease virus capsid genes from field isolates. Genetics 157:7-15
-
(2001)
Genetics
, vol.157
, pp. 7-15
-
-
Haydon, D.T.1
Bastos, A.D.2
Samuel, A.R.3
-
20
-
-
0036056122
-
Genetic constraints and the adaptive evolution of rabies virus in nature
-
Holmes EC, Woelk CH, Kassis R, Bourhy H (2002) Genetic constraints and the adaptive evolution of rabies virus in nature. Virology 292:247-257
-
(2002)
Virology
, vol.292
, pp. 247-257
-
-
Holmes, E.C.1
Woelk, C.H.2
Kassis, R.3
Bourhy, H.4
-
21
-
-
0035692320
-
Two-locus sampling distributions and their application
-
Hudson RR (2001) Two-locus sampling distributions and their application. Genetics 159:1805-1817
-
(2001)
Genetics
, vol.159
, pp. 1805-1817
-
-
Hudson, R.R.1
-
22
-
-
0029591604
-
Substitution rates in hepatitis delta virus
-
Krushkal J, Li WH (1995) Substitution rates in hepatitis delta virus. J Mol Evol 41:721-726
-
(1995)
J Mol Evol
, vol.41
, pp. 721-726
-
-
Krushkal, J.1
Li, W.H.2
-
23
-
-
0033756316
-
Maximum likelihood estimation of recombination rates from population data
-
Kuhner MK, Yamato J, Felsenstein J (2000) Maximum likelihood estimation of recombination rates from population data. Genetics 156:1393-1401
-
(2000)
Genetics
, vol.156
, pp. 1393-1401
-
-
Kuhner, M.K.1
Yamato, J.2
Felsenstein, J.3
-
25
-
-
0027468751
-
RNA-binding activity of hepatitis delta antigen involves two arginine-rich motifs and is required for hepatitis delta virus RNA replication
-
Lee CZ, Lin JH, Chao M, McKnight K, Lai MM (1993) RNA-binding activity of hepatitis delta antigen involves two arginine-rich motifs and is required for hepatitis delta virus RNA replication. J Virol 67:2221-2227
-
(1993)
J Virol
, vol.67
, pp. 2221-2227
-
-
Lee, C.Z.1
Lin, J.H.2
Chao, M.3
McKnight, K.4
Lai, M.M.5
-
26
-
-
0027403961
-
Unbiased estimation of the rates of synonymous and nonsynonymous substitution
-
Li WH (1993) Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J Mol Evol 36:96-99
-
(1993)
J Mol Evol
, vol.36
, pp. 96-99
-
-
Li, W.H.1
-
27
-
-
0003421005
-
-
Sinauer Associates, Sunderland, MA
-
Li WH (1997) Molecular Evolution. Sinauer Associates, Sunderland, MA
-
(1997)
Molecular Evolution
-
-
Li, W.H.1
-
28
-
-
0036199914
-
A coalescent-based method for detecting and estimating recombination from gene sequences
-
McVeam G, Awadalla P, Fearnhead P (2002) A coalescent-based method for detecting and estimating recombination from gene sequences. Genetics 160:1231-1241
-
(2002)
Genetics
, vol.160
, pp. 1231-1241
-
-
McVeam, G.1
Awadalla, P.2
Fearnhead, P.3
-
29
-
-
0031972161
-
Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene
-
Nielsen R, Yang Z (1998) Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148:929-936
-
(1998)
Genetics
, vol.148
, pp. 929-936
-
-
Nielsen, R.1
Yang, Z.2
-
30
-
-
0031058478
-
Human CD4+ T-cell response to hepatitis delta virus: Identification of multiple epitopes and characterization of T-helper cytokine profiles
-
Nisini RM, Paroli M, Accapezzato D, Bonino F, Rosina F, Santantanio T, Sallusto F, Amoroso A, Houghton M, Barnaba V (1997) Human CD4+ T-cell response to hepatitis delta virus: Identification of multiple epitopes and characterization of T-helper cytokine profiles. J Virol 71:2241-2251
-
(1997)
J Virol
, vol.71
, pp. 2241-2251
-
-
Nisini, R.M.1
Paroli, M.2
Accapezzato, D.3
Bonino, F.4
Rosina, F.5
Santantanio, T.6
Sallusto, F.7
Amoroso, A.8
Houghton, M.9
Barnaba, V.10
-
32
-
-
0346095401
-
Analysis of the evolutionary relationships of HIV-1 and SIV cpz sequences using bayesian inference: Implications for the origin of HIV-1
-
Paraskevis D, Lemey P, Salemi M, Suchard M, Van De PY, Vandamme AM (2003) Analysis of the evolutionary relationships of HIV-1 and SIV cpz sequences using bayesian inference: Implications for the origin of HIV-1. Mol Biol Evol 20:1986-1996
-
(2003)
Mol Biol Evol
, vol.20
, pp. 1986-1996
-
-
Paraskevis, D.1
Lemey, P.2
Salemi, M.3
Suchard, M.4
Van De, P.Y.5
Vandamme, A.M.6
-
33
-
-
0035923699
-
Evaluation of methods for detecting recombination from DNA sequences: Computer simulations
-
Posada D, Crandall KA (2001) Evaluation of methods for detecting recombination from DNA sequences: computer simulations. Proc Natl Acad Sci USA 98:13757-13762
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, pp. 13757-13762
-
-
Posada, D.1
Crandall, K.A.2
-
34
-
-
0036828069
-
Immune-mediated positive selection drives human immunodeficiency virus type 1 molecular variation and predicts disease duration
-
Ross HA, Rodrigo AG (2002) Immune-mediated positive selection drives human immunodeficiency virus type 1 molecular variation and predicts disease duration. J Virol 76:11715-11720
-
(2002)
J Virol
, vol.76
, pp. 11715-11720
-
-
Ross, H.A.1
Rodrigo, A.G.2
-
35
-
-
0028796010
-
Self-association of a synthetic peptide from the N terminus of the hepatitis delta virus protein into an immunoreactive alpha-helical multimer
-
Rozzelle JE, Wang JG, Wagner DS, Erickson BW, Lemon SM (1995) Self-association of a synthetic peptide from the N terminus of the hepatitis delta virus protein into an immunoreactive alpha-helical multimer. Proc Natl Acad Sci USA 92:382-386
-
(1995)
Proc Natl Acad Sci USA
, vol.92
, pp. 382-386
-
-
Rozzelle, J.E.1
Wang, J.G.2
Wagner, D.S.3
Erickson, B.W.4
Lemon, S.M.5
-
36
-
-
0037230001
-
Pervasive adaptive evolution in mammalian fertilization proteins
-
Swanson WJ, Nielsen R, Yang Q (2003) Pervasive adaptive evolution in mammalian fertilization proteins. Mol Biol Evol 20:18-20
-
(2003)
Mol Biol Evol
, vol.20
, pp. 18-20
-
-
Swanson, W.J.1
Nielsen, R.2
Yang, Q.3
-
39
-
-
0026801056
-
Discontinuous, conserved neutralization epitopes overlapping the CD4-binding region of human immunodeficiency virus type 1 gp 120 envelope glycoprotein
-
Thali MC, Furman C, Ho DD, Robinson J, Tilley S, Pinter A, Sodroski J (1992) Discontinuous, conserved neutralization epitopes overlapping the CD4-binding region of human immunodeficiency virus type 1 gp 120 envelope glycoprotein. J Virol 66:5635-5641
-
(1992)
J Virol
, vol.66
, pp. 5635-5641
-
-
Thali, M.C.1
Furman, C.2
Ho, D.D.3
Robinson, J.4
Tilley, S.5
Pinter, A.6
Sodroski, J.7
-
40
-
-
0025236831
-
Immunogenic domains of hepatitis delta virus antigen: Peptide mapping of epitopes recognized by human and woodchuck antibodies
-
Wang JG, Jansen RW, Brown EA, Lemon SM (1990) Immunogenic domains of hepatitis delta virus antigen: Peptide mapping of epitopes recognized by human and woodchuck antibodies. J Virol 64:1108-1116
-
(1990)
J Virol
, vol.64
, pp. 1108-1116
-
-
Wang, J.G.1
Jansen, R.W.2
Brown, E.A.3
Lemon, S.M.4
-
41
-
-
0034897826
-
A novel approach to detecting and measuring recombination: New insights into evolution in viruses, bacteria, and mitochondria
-
Worobey M (2001) A novel approach to detecting and measuring recombination: New insights into evolution in viruses, bacteria, and mitochondria. Mol Biol Evol 18:1425-1434
-
(2001)
Mol Biol Evol
, vol.18
, pp. 1425-1434
-
-
Worobey, M.1
-
42
-
-
0037066845
-
Questioning the evidence for genetic recombination in the 1918 "Spanish flu" virus
-
Worobey M, Rambaut A, Pybus OG, Robertson DL (2002) Questioning the evidence for genetic recombination in the 1918 "Spanish flu" virus. Science 296:211a
-
(2002)
Science
, vol.296
-
-
Worobey, M.1
Rambaut, A.2
Pybus, O.G.3
Robertson, D.L.4
-
43
-
-
0032755757
-
Recombination of hepatitis D virus RNA sequences and its implications
-
Wu JC, Chiang TY, Shiue WK, Wang SY, Sheen IJ, Huang YH, Syu WJ (1999) Recombination of hepatitis D virus RNA sequences and its implications. Mol Biol Evol 16:1622-1632
-
(1999)
Mol Biol Evol
, vol.16
, pp. 1622-1632
-
-
Wu, J.C.1
Chiang, T.Y.2
Shiue, W.K.3
Wang, S.Y.4
Sheen, I.J.5
Huang, Y.H.6
Syu, W.J.7
-
44
-
-
0034848170
-
DAMBE: Data analysis in molecular biology and evolution
-
Xia X, Xie Z (2001) DAMBE: Data analysis in molecular biology and evolution. J Hered 92:371-373
-
(2001)
J Hered
, vol.92
, pp. 371-373
-
-
Xia, X.1
Xie, Z.2
-
45
-
-
0033995286
-
Reevaluation of amino acid variability of the human immunodeficiency virus type 1 gp 120 envelope glycoprotein and prediction of new discontinuous epitopes
-
Yamaguchi-Kabata Y, Gojobori T (2000) Reevaluation of amino acid variability of the human immunodeficiency virus type 1 gp 120 envelope glycoprotein and prediction of new discontinuous epitopes. J Virol 74:4335-4350
-
(2000)
J Virol
, vol.74
, pp. 4335-4350
-
-
Yamaguchi-Kabata, Y.1
Gojobori, T.2
-
46
-
-
0041884768
-
Widespread adaptive evolution in the human immunodeficiency virus type I genome
-
Yang W, Bielawski JP, Yang Z (2003) Widespread adaptive evolution in the human immunodeficiency virus type I genome. J Mol Evol 57:212-221
-
(2003)
J Mol Evol
, vol.57
, pp. 212-221
-
-
Yang, W.1
Bielawski, J.P.2
Yang, Z.3
-
47
-
-
0028064845
-
Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
-
Yang Z (1994) Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods. J Mol Evol 39:306-314
-
(1994)
J Mol Evol
, vol.39
, pp. 306-314
-
-
Yang, Z.1
-
48
-
-
0030683599
-
PAML: A program package for phylogenetic analysis by maximum likelihood
-
Yang Z (1997) PAML: A program package for phylogenetic analysis by maximum likelihood. Cabios 13:555-556
-
(1997)
Cabios
, vol.13
, pp. 555-556
-
-
Yang, Z.1
-
49
-
-
0033692959
-
Maximum likelihood estimation on large phylogenies and analysis of adaptive evolution in human influenza virus
-
Yang Z (2000) Maximum likelihood estimation on large phylogenies and analysis of adaptive evolution in human influenza virus. J Mol Evol 51:423-432
-
(2000)
J Mol Evol
, vol.51
, pp. 423-432
-
-
Yang, Z.1
-
50
-
-
0035221557
-
Maximum likelihood analysis of adaptive evolution in HIV-1 gp120 env gene
-
Yang Z (2001) Maximum likelihood analysis of adaptive evolution in HIV-1 gp120 env gene. Pacif Symp Biocomput pp 226-237
-
(2001)
Pacif Symp Biocomput
, pp. 226-237
-
-
Yang, Z.1
-
51
-
-
0033639150
-
Statistical methods for detecting molecular adaptation
-
Yang Z, Bielawski JP (2000) Statistical methods for detecting molecular adaptation. TREE 15:496-503
-
(2000)
TREE
, vol.15
, pp. 496-503
-
-
Yang, Z.1
Bielawski, J.P.2
-
52
-
-
0034097381
-
Codon-substitution models for heterogeneous selection pressure at amino acid sites
-
Yang Z, Nielsen R, Goldman N, Pedersen A-M (2000) Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155:431-449
-
(2000)
Genetics
, vol.155
, pp. 431-449
-
-
Yang, Z.1
Nielsen, R.2
Goldman, N.3
Pedersen, A.-M.4
-
53
-
-
0032737463
-
Genealogical evidence for positive selection in the nef gene of HIV-1
-
Zanotto PM, Kallas EG, de Souza RF, Holmes EC (1999) Genealogical evidence for positive selection in the nef gene of HIV-1. Genetics 153:1077-1089
-
(1999)
Genetics
, vol.153
, pp. 1077-1089
-
-
Zanotto, P.M.1
Kallas, E.G.2
De Souza, R.F.3
Holmes, E.C.4
-
54
-
-
0032527989
-
Structural basis of the oligomerization of hepatitis delta antigen
-
Zuccola HJ, Rozzelle JE, Lemon SM, Erickson BW, Hogle JM (1998) Structural basis of the oligomerization of hepatitis delta antigen. Structure 6:821-830
-
(1998)
Structure
, vol.6
, pp. 821-830
-
-
Zuccola, H.J.1
Rozzelle, J.E.2
Lemon, S.M.3
Erickson, B.W.4
Hogle, J.M.5
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