-
1
-
-
0033999304
-
The phytochrome gene family in tomato and the rapid differential evolution of this family in angiosperms
-
Alba R, Kelmenson PM, Cordonnier-Pratt MM, Pratt LH (2000) The phytochrome gene family in tomato and the rapid differential evolution of this family in angiosperms. Mol Biol Evol 17:362-373
-
(2000)
Mol Biol Evol
, vol.17
, pp. 362-373
-
-
Alba, R.1
Kelmenson, P.M.2
Cordonnier-Pratt, M.M.3
Pratt, L.H.4
-
2
-
-
1642379871
-
Selection-driven evolution of emergent dengue virus
-
Bennett SN, Holmes EC, Chirivella M, Rodriguez DM, Beltran M, Vorndam V, Gubler DJ, McMillan WO (2003) Selection-driven evolution of emergent dengue virus. Mol Biol Evol 20:1650-1658
-
(2003)
Mol Biol Evol
, vol.20
, pp. 1650-1658
-
-
Bennett, S.N.1
Holmes, E.C.2
Chirivella, M.3
Rodriguez, D.M.4
Beltran, M.5
Vorndam, V.6
Gubler, D.J.7
McMillan, W.O.8
-
4
-
-
3242731376
-
Influenza as a model system for studying the cross-species transfer and evolution of the SARS coronavirus
-
Bush RM (2004) Influenza as a model system for studying the cross-species transfer and evolution of the SARS coronavirus. Philos Trans R Soc Lond B Biol Sci 359:1067-1073
-
(2004)
Philos Trans R Soc Lond B Biol Sci
, vol.359
, pp. 1067-1073
-
-
Bush, R.M.1
-
5
-
-
0033521173
-
Predicting the evolution of human influenza A
-
Bush RM, Bender CA, Subbarao K, Cox NJ, Fitch WM (1999a) Predicting the evolution of human influenza A. Science 286:1921-1925
-
(1999)
Science
, vol.286
, pp. 1921-1925
-
-
Bush, R.M.1
Bender, C.A.2
Subbarao, K.3
Cox, N.J.4
Fitch, W.M.5
-
6
-
-
0032736987
-
Positive selection on the H3 hemagglutinin gene of human influenza virus A
-
Bush RM, Fitch WM, Bender CA, Cox NJ (1999b) Positive selection on the H3 hemagglutinin gene of human influenza virus A. Mol Biol Evol 16:1457-1465
-
(1999)
Mol Biol Evol
, vol.16
, pp. 1457-1465
-
-
Bush, R.M.1
Fitch, W.M.2
Bender, C.A.3
Cox, N.J.4
-
7
-
-
0034691053
-
Effects of passage history and sampling bias on phylogenetic reconstruction of human influenza a evolution
-
Bush RM, Smith CB, Cox NJ, Fitch WM (2000) Effects of passage history and sampling bias on phylogenetic reconstruction of human influenza A evolution. Proc Natl Acad Sci USA 97:6974-6980
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, pp. 6974-6980
-
-
Bush, R.M.1
Smith, C.B.2
Cox, N.J.3
Fitch, W.M.4
-
8
-
-
0028892512
-
Passage of Japanese encephalitis virus in HeLa cells results in attenuation of virulence in mice
-
Pt 11
-
Cao JX, Ni H, Wills MR, Campbell GA, Sil BK, Ryman KD, Kitchen I, Barrett AD (1995) Passage of Japanese encephalitis virus in HeLa cells results in attenuation of virulence in mice. J Gen Virol 76(Pt 11):2757-2764
-
(1995)
J Gen Virol
, vol.76
, pp. 2757-2764
-
-
Cao, J.X.1
Ni, H.2
Wills, M.R.3
Campbell, G.A.4
Sil, B.K.5
Ryman, K.D.6
Kitchen, I.7
Barrett, A.D.8
-
9
-
-
0000228203
-
A model of evolutionary change in proteins
-
National Biomedical Research Foundation Washington, DC
-
Dayhoff MO, Schwartz RM, Orcutt BC (1978) A model of evolutionary change in proteins. In: Dayhoff MO (ed) Atlas of protein sequence and structure. National Biomedical Research Foundation, Washington, DC, pp 345-352
-
(1978)
Atlas of Protein Sequence and Structure
, pp. 345-352
-
-
Dayhoff, M.O.1
Schwartz, R.M.2
Orcutt, B.C.3
Dayhoff, M.O.4
-
12
-
-
0028127766
-
Nucleotide sequence of wild-type hepatitis a virus GBM in comparison with two cell culture-adapted variants
-
Graff J, Normann A, Feinstone SM, Flehmig B (1994) Nucleotide sequence of wild-type hepatitis A virus GBM in comparison with two cell culture-adapted variants. J Virol 68:548-554
-
(1994)
J Virol
, vol.68
, pp. 548-554
-
-
Graff, J.1
Normann, A.2
Feinstone, S.M.3
Flehmig, B.4
-
13
-
-
0028237824
-
Codominant mixtures of viruses in reference strains of influenza virus due to host cell variation
-
Gubareva LV, Wood JM, Meyer WJ, Katz JM, Robertson JS, Major D, Webster RG (1994) Codominant mixtures of viruses in reference strains of influenza virus due to host cell variation. Virology 199:89-97
-
(1994)
Virology
, vol.199
, pp. 89-97
-
-
Gubareva, L.V.1
Wood, J.M.2
Meyer, W.J.3
Katz, J.M.4
Robertson, J.S.5
Major, D.6
Webster, R.G.7
-
15
-
-
0029134072
-
Egg fluids and cells of the chorioallantoic membrane of embryonated chicken eggs can select different variants of influenza a (H3N2) viruses
-
Hardy CT, Young SA, Webster RG, Naeve CW, Owens RJ (1995) Egg fluids and cells of the chorioallantoic membrane of embryonated chicken eggs can select different variants of influenza A (H3N2) viruses. Virology 211:302-306
-
(1995)
Virology
, vol.211
, pp. 302-306
-
-
Hardy, C.T.1
Young, S.A.2
Webster, R.G.3
Naeve, C.W.4
Owens, R.J.5
-
16
-
-
24944468625
-
Whole-genome analysis of human influenza a virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses
-
Holmes EC, Ghedin E, Miller N, Taylor J, Bao Y, St George K, Grenfell BT, Salzberg SL, Fraser CM, Lipman DJ, Taubenberger JK (2005) Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses. PLoS Biol 3:e300
-
(2005)
PLoS Biol
, vol.3
, pp. 300
-
-
Holmes, E.C.1
Ghedin, E.2
Miller, N.3
Taylor, J.4
Bao, Y.5
St George, K.6
Grenfell, B.T.7
Salzberg, S.L.8
Fraser, C.M.9
Lipman, D.J.10
Taubenberger, J.K.11
-
17
-
-
0034849408
-
MRBAYES: Bayesian inference of phylogenetic trees
-
Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17:754-755
-
(2001)
Bioinformatics
, vol.17
, pp. 754-755
-
-
Huelsenbeck, J.P.1
Ronquist, F.2
-
18
-
-
0034425607
-
Adaptive evolution of the tumour suppressor BRCA1 in humans and chimpanzees. Australian Breast Cancer Family Study
-
Huttley GA, Easteal S, Southey MC, Tesoriero A, Giles GG, McCredie MR, Hopper JL, Venter DJ (2000) Adaptive evolution of the tumour suppressor BRCA1 in humans and chimpanzees. Australian Breast Cancer Family Study. Nat Genet 25:410-413
-
(2000)
Nat Genet
, vol.25
, pp. 410-413
-
-
Huttley, G.A.1
Easteal, S.2
Southey, M.C.3
Tesoriero, A.4
Giles, G.G.5
McCredie, M.R.6
Hopper, J.L.7
Venter, D.J.8
-
19
-
-
0033947283
-
Interspecies transmission and receptor recognition of influenza a viruses
-
Ito T (2000) Interspecies transmission and receptor recognition of influenza A viruses. Microbiol Immunol 44:423-430
-
(2000)
Microbiol Immunol
, vol.44
, pp. 423-430
-
-
Ito, T.1
-
20
-
-
0030981954
-
Differences in sialic acid-galactose linkages in the chicken egg amnion and allantois influence human influenza virus receptor specificity and variant selection
-
Ito T, Suzuki Y, Takada A, Kawamoto A, Otsuki K, Masuda H, Yamada M, Suzuki T, Kida H, Kawaoka Y (1997) Differences in sialic acid-galactose linkages in the chicken egg amnion and allantois influence human influenza virus receptor specificity and variant selection. J Virol 71:3357-3362
-
(1997)
J Virol
, vol.71
, pp. 3357-3362
-
-
Ito, T.1
Suzuki, Y.2
Takada, A.3
Kawamoto, A.4
Otsuki, K.5
Masuda, H.6
Yamada, M.7
Suzuki, T.8
Kida, H.9
Kawaoka, Y.10
-
21
-
-
0030780974
-
Isolation of an avirulent mutant of Sendai virus with two amino acid mutations from a highly virulent field strain through adaptation to LLC-MK2 cells
-
Pt 12
-
Itoh M, Isegawa Y, Hotta H, Homma M (1997) Isolation of an avirulent mutant of Sendai virus with two amino acid mutations from a highly virulent field strain through adaptation to LLC-MK2 cells. J Gen Virol 78(Pt 12):3207-3215
-
(1997)
J Gen Virol
, vol.78
, pp. 3207-3215
-
-
Itoh, M.1
Isegawa, Y.2
Hotta, H.3
Homma, M.4
-
22
-
-
0021277009
-
A new method for calculating evolutionary substitution rates
-
Lanave C, Preparata G, Saccone C, Serio G (1984) A new method for calculating evolutionary substitution rates. J Mol Evol 20:86-93
-
(1984)
J Mol Evol
, vol.20
, pp. 86-93
-
-
Lanave, C.1
Preparata, G.2
Saccone, C.3
Serio, G.4
-
23
-
-
3543007739
-
Predicting antigenic variants of influenza A/H3N2 viruses
-
Lee MS, Chen JS (2004) Predicting antigenic variants of influenza A/H3N2 viruses. Emerg Infect Dis 10:1385-1390
-
(2004)
Emerg Infect Dis
, vol.10
, pp. 1385-1390
-
-
Lee, M.S.1
Chen, J.S.2
-
24
-
-
34447622953
-
The value of a database in surveillance and vaccine selection
-
Elsevier Science Amsterdam
-
Macken C, Lu H, Goodman J, Boykin L (2001) the value of a database in surveillance and vaccine selection. In: Osterhaus ADME, Cox N, Hampson AW (eds) Options for the control of influenza IV. Elsevier Science, Amsterdam, pp 103-106
-
(2001)
Options for the Control of Influenza IV
, pp. 103-106
-
-
MacKen, C.1
Lu, H.2
Goodman, J.3
Boykin, L.4
Adme, O.5
Cox, N.6
Hampson, A.W.7
-
25
-
-
0026428610
-
Adaptive protein evolution at the Adh locus in Drosophila
-
McDonald JH, Kreitman M (1991) Adaptive protein evolution at the Adh locus in Drosophila. Nature 351:652-654
-
(1991)
Nature
, vol.351
, pp. 652-654
-
-
McDonald, J.H.1
Kreitman, M.2
-
27
-
-
0021054646
-
Identification of the binding sites to monoclonal antibodies on A/USSR/90/77 (H1N1) hemagglutinin and their involvement in antigenic drift in H1N1 influenza viruses
-
Nakajima S, Nakajima K, Kendal AP (1983) Identification of the binding sites to monoclonal antibodies on A/USSR/90/77 (H1N1) hemagglutinin and their involvement in antigenic drift in H1N1 influenza viruses. Virology 131:116-127
-
(1983)
Virology
, vol.131
, pp. 116-127
-
-
Nakajima, S.1
Nakajima, K.2
Kendal, A.P.3
-
28
-
-
33847044691
-
The evolution of epidemic influenza
-
Nelson MI, Holmes EC (2007) The evolution of epidemic influenza. Nat Rev Genet 8:196-205
-
(2007)
Nat Rev Genet
, vol.8
, pp. 196-205
-
-
Nelson, M.I.1
Holmes, E.C.2
-
29
-
-
0034804321
-
Mutations as missing data: Inferences on the ages and distributions of nonsynonymous and synonymous mutations
-
Nielsen R (2001) Mutations as missing data: inferences on the ages and distributions of nonsynonymous and synonymous mutations. Genetics 159:401-411
-
(2001)
Genetics
, vol.159
, pp. 401-411
-
-
Nielsen, R.1
-
30
-
-
0036804625
-
Mapping mutations on phylogenies
-
Nielsen R (2002) Mapping mutations on phylogenies. Syst Biol 51:729-739
-
(2002)
Syst Biol
, vol.51
, pp. 729-739
-
-
Nielsen, R.1
-
31
-
-
0036366690
-
Detecting positively selected amino acid sites using posterior predictive P-values
-
Nielsen R, Huelsenbeck JP (2002) Detecting positively selected amino acid sites using posterior predictive P-values. Pacif Symp Biocomput 576-588
-
(2002)
Pacif Symp Biocomput
, pp. 576-588
-
-
Nielsen, R.1
Huelsenbeck, J.P.2
-
32
-
-
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
-
33
-
-
0023093912
-
Sequence analysis of the haemagglutinin of A/Taiwan/1/86, a new variant of human influenza A(H1N1) virus
-
Pt 4
-
Robertson JS (1987) Sequence analysis of the haemagglutinin of A/Taiwan/1/86, a new variant of human influenza A(H1N1) virus. J Gen Virol 68(Pt 4):1205-1208
-
(1987)
J Gen Virol
, vol.68
, pp. 1205-1208
-
-
Robertson, J.S.1
-
34
-
-
0001927825
-
Clinical influenza virus and the embryonated hen's egg
-
Robertson JS (1993) Clinical influenza virus and the embryonated hen's egg. Rev Med Virol 3:97-106
-
(1993)
Rev Med Virol
, vol.3
, pp. 97-106
-
-
Robertson, J.S.1
-
35
-
-
0032612225
-
An overview of host cell selection
-
discussion 73-74
-
Robertson JS (1999) An overview of host cell selection. Dev Biol Stand 98:7-11, discussion 73-74
-
(1999)
Dev Biol Stand
, vol.98
, pp. 7-11
-
-
Robertson, J.S.1
-
36
-
-
0027439344
-
Comparison of 10 influenza a (H1N1 and H3N2) haemagglutinin sequences obtained directly from clinical specimens to those of MDCK cell- and egg-grown viruses
-
Pt 11
-
Rocha EP, Xu X, Hall HE, Allen JR, Regnery HL, Cox NJ (1993) Comparison of 10 influenza A (H1N1 and H3N2) haemagglutinin sequences obtained directly from clinical specimens to those of MDCK cell- and egg-grown viruses. J Gen Virol 74(Pt 11):2513-2518
-
(1993)
J Gen Virol
, vol.74
, pp. 2513-2518
-
-
Rocha, E.P.1
Xu, X.2
Hall, H.E.3
Allen, J.R.4
Regnery, H.L.5
Cox, N.J.6
-
37
-
-
0020595851
-
Single amino acid substitutions in influenza haemagglutinin change receptor binding specificity
-
Rogers GN, Paulson JC, Daniels RS, Skehel JJ, Wilson IA, Wiley DC (1983) Single amino acid substitutions in influenza haemagglutinin change receptor binding specificity. Nature 304:76-78
-
(1983)
Nature
, vol.304
, pp. 76-78
-
-
Rogers, G.N.1
Paulson, J.C.2
Daniels, R.S.3
Skehel, J.J.4
Wilson, I.A.5
Wiley, D.C.6
-
38
-
-
0023375195
-
The neighbor-joining method: A new method for reconstructing phylogenetic trees
-
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425
-
(1987)
Mol Biol Evol
, vol.4
, pp. 406-425
-
-
Saitou, N.1
Nei, M.2
-
39
-
-
0028089320
-
Neutralization sensitivity of human immunodeficiency virus type 1 is determined in part by the cell in which the virus is propagated
-
Sawyer LS, Wrin MT, Crawford-Miksza L, Potts B, Wu Y, Weber PA, Alfonso RD, Hanson CV (1994) Neutralization sensitivity of human immunodeficiency virus type 1 is determined in part by the cell in which the virus is propagated. J Virol 68:1342-1349
-
(1994)
J Virol
, vol.68
, pp. 1342-1349
-
-
Sawyer, L.S.1
Wrin, M.T.2
Crawford-Miksza, L.3
Potts, B.4
Wu, Y.5
Weber, P.A.6
Alfonso, R.D.7
Hanson, C.V.8
-
40
-
-
0033783032
-
Receptor binding and membrane fusion in virus entry: The influenza hemagglutinin
-
Skehel JJ, Wiley DC (2000) Receptor binding and membrane fusion in virus entry: the influenza hemagglutinin. Annu Rev Biochem 69:531-569
-
(2000)
Annu Rev Biochem
, vol.69
, pp. 531-569
-
-
Skehel, J.J.1
Wiley, D.C.2
-
41
-
-
0023666025
-
Adaptive evolution in the stomach lysozymes of foregut fermenters
-
Stewart CB, Schilling JW, Wilson AC (1987) Adaptive evolution in the stomach lysozymes of foregut fermenters. Nature 330:401-404
-
(1987)
Nature
, vol.330
, pp. 401-404
-
-
Stewart, C.B.1
Schilling, J.W.2
Wilson, A.C.3
-
42
-
-
0032849322
-
A method for detecting positive selection at single amino acid sites
-
Suzuki Y, Gojobori T (1999) A method for detecting positive selection at single amino acid sites. Mol Biol Evol 16:1315-1328
-
(1999)
Mol Biol Evol
, vol.16
, pp. 1315-1328
-
-
Suzuki, Y.1
Gojobori, T.2
-
43
-
-
0000142497
-
Reconstructing ancestral character states under Wagner pasimony
-
Swofford D, Maddison DR (1987) Reconstructing ancestral character states under Wagner pasimony. Math Biosci 87:199-229
-
(1987)
Math Biosci
, vol.87
, pp. 199-229
-
-
Swofford, D.1
Maddison, D.R.2
-
44
-
-
0027968068
-
CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-4680
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
45
-
-
0023915219
-
Structure of the influenza virus haemagglutinin complexed with its receptor, sialic acid
-
Weis W, Brown JH, Cusack S, Paulson JC, Skehel JJ, Wiley DC (1988) Structure of the influenza virus haemagglutinin complexed with its receptor, sialic acid. Nature 333:426-431
-
(1988)
Nature
, vol.333
, pp. 426-431
-
-
Weis, W.1
Brown, J.H.2
Cusack, S.3
Paulson, J.C.4
Skehel, J.J.5
Wiley, D.C.6
-
46
-
-
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 18:691-699
-
(2001)
Mol Biol Evol
, vol.18
, pp. 691-699
-
-
Whelan, S.1
Goldman, N.2
-
47
-
-
8544225780
-
Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites
-
Wong WS, 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
-
(2004)
Genetics
, vol.168
, pp. 1041-1051
-
-
Wong, W.S.1
Yang, Z.2
Goldman, N.3
Nielsen, R.4
-
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. Comput Appl Biosci 13:555-556
-
(1997)
Comput Appl Biosci
, vol.13
, pp. 555-556
-
-
Yang, Z.1
-
49
-
-
0033639150
-
Statistical methods for detecting molecular adaptation
-
Yang Z, Bielawski JP (2000) Statistical methods for detecting molecular adaptation. Trends Ecol Evol 15:496-503
-
(2000)
Trends Ecol Evol
, vol.15
, pp. 496-503
-
-
Yang, Z.1
Bielawski, J.P.2
-
50
-
-
0033979433
-
Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models
-
Yang Z, Nielsen R (2000) Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol Biol Evol 17:32-43
-
(2000)
Mol Biol Evol
, vol.17
, pp. 32-43
-
-
Yang, Z.1
Nielsen, R.2
-
51
-
-
0036270185
-
Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages
-
Yang Z, Nielsen R (2002) Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol Biol Evol 19:908-917
-
(2002)
Mol Biol Evol
, vol.19
, pp. 908-917
-
-
Yang, Z.1
Nielsen, R.2
-
52
-
-
0034097381
-
Codon-substitution models for heterogeneous selection pressure at amino acid sites
-
Yang Z, Nielsen R, Goldman N, Pedersen AM (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
-
-
16344378246
-
Bayes empirical bayes inference of amino acid sites under positive selection
-
Yang Z, Wong WS, Nielsen R (2005) Bayes empirical bayes inference of amino acid sites under positive selection. Mol Biol Evol 22:1107-1118
-
(2005)
Mol Biol Evol
, vol.22
, pp. 1107-1118
-
-
Yang, Z.1
Wong, W.S.2
Nielsen, R.3
-
54
-
-
0035025126
-
ATV: Display and manipulation of annotated phylogenetic trees
-
Zmasek CM, Eddy SR (2001) ATV: display and manipulation of annotated phylogenetic trees. Bioinformatics 17:383-384
-
(2001)
Bioinformatics
, vol.17
, pp. 383-384
-
-
Zmasek, C.M.1
Eddy, S.R.2
|