-
1
-
-
4944263648
-
A robust measure of HIV-1 population turnover within chronically infected individuals
-
ACHAZ, G., S. PALMER, M. KEARNEY, F. MALDARELLI, J. W. MELLORS et al., 2004 A robust measure of HIV-1 population turnover within chronically infected individuals. Mol. Biol. Evol. 21: 1902-1912.
-
(2004)
Mol. Biol. Evol.
, vol.21
, pp. 1902-1912
-
-
Achaz, G.1
Palmer, S.2
Kearney, M.3
Maldarelli, F.4
Mellors, J.W.5
-
2
-
-
33845864966
-
Robustness-epistasis link shapes the fitness landscape of a randomly drifting protein
-
BERSHTEIN, S., M. SEGAL, R. BEKERMAN, N. TOKURIKI and D. S. TAWFIK, 2006 Robustness-epistasis link shapes the fitness landscape of a randomly drifting protein. Nature 444: 929-932.
-
(2006)
Nature
, vol.444
, pp. 929-932
-
-
Bershtein, S.1
Segal, M.2
Bekerman, R.3
Tokuriki, N.4
Tawfik, D.S.5
-
3
-
-
0029849837
-
Covariability of V3 loop amino acids
-
BICKEL, P. J., P. C. COSMAN, R. A. OLSHEN, P. C. SPECTOR, A. G. RODRIGO et al., 1996 Covariability of V3 loop amino acids. AIDS Res. Hum. Retroviruses 12: 1401-1411.
-
(1996)
AIDS Res. Hum. Retroviruses
, vol.12
, pp. 1401-1411
-
-
Bickel, P.J.1
Cosman, P.C.2
Olshen, R.A.3
Spector, P.C.4
Rodrigo, A.G.5
-
4
-
-
9444282038
-
Evidence for positive epistasis in HIV-1
-
BONHOEFFER, S., C. CHAPPEY, N. T. PARKIN, J. M. WHITCOMB and C. J. PETROPOULOS, 2004 Evidence for positive epistasis in HIV-1. Science 306: 1547-1550.
-
(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
-
5
-
-
0034632830
-
Evolvability of an RNA virus is determined by its mutational neighbourhood
-
BURCH, C. L., and L. CHAO, 2000 Evolvability of an RNA virus is determined by its mutational neighbourhood. Nature 406: 625-628.
-
(2000)
Nature
, vol.406
, pp. 625-628
-
-
Burch, C.L.1
Chao, L.2
-
6
-
-
3142755598
-
Epistasis and its relationship to canalization in the RNA virus f6
-
DOI 10.1534/genetics.103.021196
-
BURCH, C. L., and L. CHAO, 2004 Epistasis and its relationship to canalization in the RNA virus f6. Genetics 167: 559-567. (Pubitemid 38931847)
-
(2004)
Genetics
, vol.167
, Issue.2
, pp. 559-567
-
-
Burch, C.L.1
Chao, L.2
-
7
-
-
34247214426
-
Structural basis for coreceptor selectivity by the HIV type 1 V3 loop
-
CARDOZO, T., T. KIMURA, S. PHILPOTT, B. WEISER, H. BURGER et al., 2007 Structural basis for coreceptor selectivity by the HIV type 1 V3 loop. AIDS Res. Hum. Retroviruses 23: 415-426.
-
(2007)
AIDS Res. Hum. Retroviruses
, vol.23
, pp. 415-426
-
-
Cardozo, T.1
Kimura, T.2
Philpott, S.3
Weiser, B.4
Burger, H.5
-
8
-
-
0030913366
-
Quantification of latent tissue reservoirs and total body viral load in HIV-1 infection
-
CHUN, T. W., L. CARRUTH, D. FINZI, X. SHEN, J. A. DIGIUSEPPE et al., 1997 Quantification of latent tissue reservoirs and total body viral load in HIV-1 infection. Nature 387: 183-188.
-
(1997)
Nature
, vol.387
, pp. 183-188
-
-
Chun, T.W.1
Carruth, L.2
Finzi, D.3
Shen, X.4
Digiuseppe, J.A.5
-
9
-
-
56449100427
-
Evolution of CCR5 use before and during coreceptor switching
-
COETZER, M., R. NEDELLEC, J. SALKOWITZ, S. MCLAUGHLIN, Y. LIU et al., 2008 Evolution of CCR5 use before and during coreceptor switching. J. Virol. 82: 11758-11766.
-
(2008)
J. Virol.
, vol.82
, pp. 11758-11766
-
-
Coetzer, M.1
Nedellec, R.2
Salkowitz, J.3
Mclaughlin, S.4
Liu, Y.5
-
10
-
-
0002436375
-
Molecular biology of HIV
-
edited by K. A. CRANDALL. The John Hopkins University Press, Baltimore
-
COFFIN, J. M., 1999 Molecular biology of HIV, pp. 3-40 in The Evolution of HIV, edited by K. A. CRANDALL. The John Hopkins University Press, Baltimore.
-
(1999)
The Evolution of HIV
, pp. 3-40
-
-
Coffin, J.M.1
-
11
-
-
0036333648
-
The crown and stem of the V3 loop play distinct roles in human immunodeficiency virus type 1 envelope glycoprotein interactions with the CCR5 coreceptor
-
CORMIER, E. G., and T. DRAGIC, 2002 The crown and stem of the V3 loop play distinct roles in human immunodeficiency virus type 1 envelope glycoprotein interactions with the CCR5 coreceptor. J. Virol. 76: 8953-8957.
-
(2002)
J. Virol.
, vol.76
, pp. 8953-8957
-
-
Cormier, E.G.1
Dragic, T.2
-
12
-
-
33751310799
-
Site-specific amino acid frequency, fitness and the mutational landscape model of adaptation in human immunodeficiency virus type 1
-
DA SILVA, J., 2006 Site-specific amino acid frequency, fitness and the mutational landscape model of adaptation in human immunodeficiency virus type 1. Genetics 174: 1689-1694.
-
(2006)
Genetics
, vol.174
, pp. 1689-1694
-
-
Da Silva, J.1
-
13
-
-
66149185556
-
Compensatory mutations are repeatable and clustered within proteins
-
DAVIS, B. H., A. F. Y. POON and M. C. WHITLOCK, 2009 Compensatory mutations are repeatable and clustered within proteins. Proc. R. Soc. B. Biol. Sci. 276: 1823-1827.
-
(2009)
Proc. R. Soc. B. Biol. Sci.
, vol.276
, pp. 1823-1827
-
-
Davis, B.H.1
Poon, A.F.Y.2
Whitlock, M.C.3
-
14
-
-
0026702003
-
Minimal requirements for the human immunodeficiency virus type 1 V3 domain to support the syncytium-inducing phenotype: Analysis by single amino acid substitution
-
DE JONG, J. J., A. DE RONDE, W. KEULEN, M. TERSMETTE and J. GOUDSMIT, 1992 Minimal requirements for the human immunodeficiency virus type 1 V3 domain to support the syncytium-inducing phenotype: analysis by single amino acid substitution. J. Virol. 66: 6777-6780.
-
(1992)
J. Virol.
, vol.66
, pp. 6777-6780
-
-
De Jong, J.J.1
De Ronde, A.2
Keulen, W.3
Tersmette, M.4
Goudsmit, J.5
-
15
-
-
33846277942
-
The evolution of sex: Empirical insights into the roles of epistasis and drift
-
DE VISSER, J. A. G. M., and S. F. ELENA, 2007 The evolution of sex: empirical insights into the roles of epistasis and drift. Nat. Rev. Genet. 8: 139-149.
-
(2007)
Nat. Rev. Genet.
, vol.8
, pp. 139-149
-
-
De Visser, J.A.G.M.1
Elena, S.F.2
-
16
-
-
68549127130
-
Exploring the effect of sex on empirical fitness landscapes
-
DE VISSER, J. A. G. M., S. Ä. PARK and J. KRUG, 2009 Exploring the effect of sex on empirical fitness landscapes. Am. Nat. 174: S15-S30.
-
(2009)
Am. Nat.
, vol.174
-
-
De Visser, J.A.G.M.1
Park, S.Ä.2
Krug, J.3
-
17
-
-
34547769282
-
Mutational reversions during adaptive protein evolution
-
DEPRISTO, M. A., D. L. HARTL and D. M. WEINREICH, 2007 Mutational reversions during adaptive protein evolution. Mol. Biol. Evol. 24: 1608-1610.
-
(2007)
Mol. Biol. Evol.
, vol.24
, pp. 1608-1610
-
-
Depristo, M.A.1
Hartl, D.L.2
Weinreich, D.M.3
-
18
-
-
23944490117
-
Missense meanderings in sequence space: A biophysical view of protein evolution
-
DEPRISTO, M. A., D. M. WEINREICH and D. L. HARTL, 2005 Missense meanderings in sequence space: a biophysical view of protein evolution. Nat. Rev. Genet. 6: 678-687.
-
(2005)
Nat. Rev. Genet.
, vol.6
, pp. 678-687
-
-
Depristo, M.A.1
Weinreich, D.M.2
Hartl, D.L.3
-
19
-
-
0031028817
-
HIV-1 tropism and co-receptor use
-
DITTMAR, M. T., A. MCKNIGHT, G. SIMMONS, P. R. CLAPHAM, R. A. WEISS et al., 1997 HIV-1 tropism and co-receptor use. Nature 385: 495-496.
-
(1997)
Nature
, vol.385
, pp. 495-496
-
-
Dittmar, M.T.1
Mcknight, A.2
Simmons, G.3
Clapham, P.R.4
Weiss, R.A.5
-
20
-
-
0032582016
-
Use of GPR1, GPR15, and STRL33 as coreceptors by diverse human immunodeficiency virus type 1 and simian immunodeficiency virus envelope proteins
-
EDINGER, A. L., T. L. HOFFMAN, M. SHARRON, B. LEE, B. O'DOWD et al., 1998 Use of GPR1, GPR15, and STRL33 as coreceptors by diverse human immunodeficiency virus type 1 and simian immunodeficiency virus envelope proteins. Virology 249: 367-378.
-
(1998)
Virology
, vol.249
, pp. 367-378
-
-
Edinger, A.L.1
Hoffman, T.L.2
Sharron, M.3
Lee, B.4
O'Dowd, B.5
-
21
-
-
0008058496
-
Sex and the evolution of recombination
-
edited by R. E. MICHOD and B. R. LEVIN. Sinauer Associates, Sunderland
-
FELSENSTEIN, J., 1988 Sex and the evolution of recombination, pp. 74-86 in The Evolution of Sex, edited by R. E. MICHOD and B. R. LEVIN. Sinauer Associates, Sunderland.
-
(1988)
The Evolution of Sex
, pp. 74-86
-
-
Felsenstein, J.1
-
23
-
-
0026606727
-
Phenotype-associated sequence variation in the third variable domain of the human immunodeficiency virus type 1 gp120 molecule
-
FOUCHIER, R. A., M. GROENINK, N. A. KOOTSTRA, M. TERSMETTE, H. G. HUISMAN et al., 1992 Phenotype-associated sequence variation in the third variable domain of the human immunodeficiency virus type 1 gp120 molecule. J. Virol. 66: 3183-3187.
-
(1992)
J. Virol.
, vol.66
, pp. 3183-3187
-
-
Fouchier, R.A.1
Groenink, M.2
Kootstra, N.A.3
Tersmette, M.4
Huisman, H.G.5
-
24
-
-
0001359641
-
Molecular evolution over the mutational landscape
-
GILLESPIE, J. H., 1984 Molecular evolution over the mutational landscape. Evolution 38: 1116-1129.
-
(1984)
Evolution
, vol.38
, pp. 1116-1129
-
-
Gillespie, J.H.1
-
25
-
-
0009787448
-
The variance of the product of k random variables
-
GOODMAN, L. A., 1962 The variance of the product of k random variables. J. Am. Statist. Assoc. 57: 54-60.
-
(1962)
J. Am. Statist. Assoc.
, vol.57
, pp. 54-60
-
-
Goodman, L.A.1
-
26
-
-
34247262093
-
Changes in the V3 region of gp120 contribute to unusually broad coreceptor usage of an HIV-1 isolate from a CCR5 Δ32 heterozygote
-
GORRY, P. R., R. L. DUNFEE, M. E. MEFFORD, K. KUNSTMAN, T. MORGAN et al., 2007 Changes in the V3 region of gp120 contribute to unusually broad coreceptor usage of an HIV-1 isolate from a CCR5 Δ32 heterozygote. Virology 362: 163-178.
-
(2007)
Virology
, vol.362
, pp. 163-178
-
-
Gorry, P.R.1
Dunfee, R.L.2
Mefford, M.E.3
Kunstman, K.4
Morgan, T.5
-
27
-
-
34848868199
-
Structures of the CCR5 N terminus and of a tyrosine-sulfated antibody with HIV-1 gp120 and CD4
-
HUANG, C.-C., S. N. LAM, P. ACHARYA, M. TANG, S.-H. XIANG et al., 2007 Structures of the CCR5 N terminus and of a tyrosine-sulfated antibody with HIV-1 gp120 and CD4. Science 317: 1930-1934.
-
(2007)
Science
, vol.317
, pp. 1930-1934
-
-
Huang, C.-C.1
Lam, S.N.2
Acharya, P.3
Tang, M.4
Xiang, S.-H.5
-
28
-
-
27744597054
-
Structure of a V3-containing HIV-1 gp120 core
-
HUANG, C.-C., M. TANG, M.-Y. ZHANG, S. MAJEED, E. MONTABANA et al., 2005 Structure of a V3-containing HIV-1 gp120 core. Science 310: 1025-1028.
-
(2005)
Science
, vol.310
, pp. 1025-1028
-
-
Huang, C.-C.1
Tang, M.2
Zhang, M.-Y.3
Majeed, S.4
Montabana, E.5
-
29
-
-
0032883082
-
Analysis of the critical domain in the V3 loop of human immunodeficiency virus type 1 gp120 involved in CCR5 utilization
-
HUNG, C. S., N. VANDER HEYDEN and L. RATNER, 1999 Analysis of the critical domain in the V3 loop of human immunodeficiency virus type 1 gp120 involved in CCR5 utilization. J. Virol. 73: 8216-8226.
-
(1999)
J. Virol.
, vol.73
, pp. 8216-8226
-
-
Hung, C.S.1
Vander Heyden, N.2
Ratner, L.3
-
30
-
-
0025783669
-
Identification of the envelope V3 loop as the primary determinant of cell tropism in HIV-1
-
HWANG, S. S., T. J. BOYLE, H. K. LYERLY and B. R. CULLEN, 1991 Identification of the envelope V3 loop as the primary determinant of cell tropism in HIV-1. Science 253: 71-74.
-
(1991)
Science
, vol.253
, pp. 71-74
-
-
Hwang, S.S.1
Boyle, T.J.2
Lyerly, H.K.3
Cullen, B.R.4
-
31
-
-
34047143174
-
Epistatic buffering of fitness loss in yeast double deletion strains
-
JASNOS, L., and R. KORONA, 2007 Epistatic buffering of fitness loss in yeast double deletion strains. Nat. Genet. 39: 550-554.
-
(2007)
Nat. Genet.
, vol.39
, pp. 550-554
-
-
Jasnos, L.1
Korona, R.2
-
32
-
-
0037062939
-
Multiply infected spleen cells in HIV patients
-
DOI 10.1038/418144a
-
JUNG, A., R. MAIER, J. P. VARTANIAN, G. BOCHAROV, V. JUNG et al., 2002 Multiply infected spleen cells in HIV patients. Nature 418: 144. (Pubitemid 34773761)
-
(2002)
Nature
, vol.418
, Issue.6894
, pp. 144
-
-
Jung, A.1
Maier, R.2
Vartanian, J.-P.3
Bocharov, G.4
Jung, V.5
Fischer, U.6
Meese, E.7
Wain-Hobson, S.8
Meyerhans, A.9
-
33
-
-
0001189920
-
A model of a genetic system which leads to closer linkage by natural selection
-
KIMURA, M., 1956 A model of a genetic system which leads to closer linkage by natural selection. Evolution 10: 278-287.
-
(1956)
Evolution
, vol.10
, pp. 278-287
-
-
Kimura, M.1
-
34
-
-
0027486081
-
Classification of hypotheses on the advantage of amphimixis
-
KONDRASHOV, A. S., 1993 Classification of hypotheses on the advantage of amphimixis. J. Hered. 84: 372-387.
-
(1993)
J. Hered.
, vol.84
, pp. 372-387
-
-
Kondrashov, A.S.1
-
35
-
-
0027297096
-
Covariation of mutations in the V3 loop of human immunodeficiency virus type 1 envelope protein: An information theoretic analysis
-
KORBER, B. T., R. M. FARBER, D. H. WOLPERT and A. S. LAPEDES, 1993 Covariation of mutations in the V3 loop of human immunodeficiency virus type 1 envelope protein: an information theoretic analysis. Proc. Natl. Acad. Sci. USA 90: 7176-7180.
-
(1993)
Proc. Natl. Acad. Sci. USA
, vol.90
, pp. 7176-7180
-
-
Korber, B.T.1
Farber, R.M.2
Wolpert, D.H.3
Lapedes, A.S.4
-
36
-
-
33751021082
-
Stochastic or deterministic: What is the effective population size of HIV-1?
-
KOUYOS, R. D., C. L. ALTHAUS and S. BONHOEFFER, 2006 Stochastic or deterministic: What is the effective population size of HIV-1? Trends Microbiol. 14: 507-511.
-
(2006)
Trends Microbiol.
, vol.14
, pp. 507-511
-
-
Kouyos, R.D.1
Althaus, C.L.2
Bonhoeffer, S.3
-
37
-
-
34248364854
-
Epistasis between deleterious mutations and the evolution of recombination
-
KOUYOS, R. D., O. K. SILANDER and S. BONHOEFFER, 2007 Epistasis between deleterious mutations and the evolution of recombination. Trends Ecol. Evol. 22: 308-315.
-
(2007)
Trends Ecol. Evol.
, vol.22
, pp. 308-315
-
-
Kouyos, R.D.1
Silander, O.K.2
Bonhoeffer, S.3
-
38
-
-
70350116536
-
-
Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM
-
KUIKEN, C., T. LEITNER, B. FOLEY, B. HAHN, P. MARX et al. (Editors), 2009 HIV Sequence Compendium 2009. Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM.
-
(2009)
HIV Sequence Compendium 2009
-
-
Kuiken, C.1
Leitner, T.2
Foley, B.3
Hahn, B.4
Marx, P.5
-
39
-
-
0004732896
-
Analysis of HIV-1 env gene sequences reveals evidence for a low effective number in the viral population
-
LEIGH BROWN, A. J., 1997 Analysis of HIV-1 env gene sequences reveals evidence for a low effective number in the viral population. Proc. Natl. Acad. Sci. USA 94: 1862-1865.
-
(1997)
Proc. Natl. Acad. Sci. USA
, vol.94
, pp. 1862-1865
-
-
Leigh Brown, A.J.1
-
40
-
-
1642447695
-
Dynamics of HIV-1 recombination in its natural target cells
-
LEVY, D. N., G. M. ALDROVANDI, O. KUTSCH and G. M. SHAW, 2004 Dynamics of HIV-1 recombination in its natural target cells. Proc. Natl. Acad. Sci. USA 101: 4204-4209.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 4204-4209
-
-
Levy, D.N.1
Aldrovandi, G.M.2
Kutsch, O.3
Shaw, G.M.4
-
41
-
-
0000951097
-
The evolutionary dynamics of complex polymorphisms
-
LEWONTIN, R. C., and K.-I. KOJIMA, 1960 The evolutionary dynamics of complex polymorphisms. Evolution 14: 458-472.
-
(1960)
Evolution
, vol.14
, pp. 458-472
-
-
Lewontin, R.C.1
Kojima, K.-I.2
-
42
-
-
27144538817
-
The biochemical architecture of an ancient adaptive landscape
-
LUNZER, M., S. P. MILLER, R. FELSHEIM and A. M. DEAN, 2005 The biochemical architecture of an ancient adaptive landscape. Science 310: 499-501.
-
(2005)
Science
, vol.310
, pp. 499-501
-
-
Lunzer, M.1
Miller, S.P.2
Felsheim, R.3
Dean, A.M.4
-
43
-
-
2942665668
-
Adaptation to the deleterious effects of antimicrobial drug resistance mutations by compensatory evolution
-
MAISNIER-PATIN, S., and D. I. ANDERSSON, 2004 Adaptation to the deleterious effects of antimicrobial drug resistance mutations by compensatory evolution. Res. Microbiol. 155: 360-369.
-
(2004)
Res. Microbiol.
, vol.155
, pp. 360-369
-
-
Maisnier-Patin, S.1
Andersson, D.I.2
-
44
-
-
28444484984
-
Genomic buffering mitigates the effects of deleterious mutations in bacteria
-
MAISNIER-PATIN, S., J. R. ROTH, A. FREDRIKSSON, T. NYSTROM, O. G. BERG et al., 2005 Genomic buffering mitigates the effects of deleterious mutations in bacteria. Nat. Genet. 37: 1376.
-
(2005)
Nat. Genet.
, vol.37
, pp. 1376
-
-
Maisnier-Patin, S.1
Roth, J.R.2
Fredriksson, A.3
Nystrom, T.4
Berg, O.G.5
-
45
-
-
0033863985
-
Retracing the evolutionary pathways of human immunodeficiency virus type 1 resistance to protease inhibitors: Virus fitness in the absence and in the presence of drug
-
MAMMANO, F., V. TROUPLIN, V. ZENNOU and F. CLAVEL, 2000 Retracing the evolutionary pathways of human immunodeficiency virus type 1 resistance to protease inhibitors: virus fitness in the absence and in the presence of drug. J. Virol. 74: 8524-8531.
-
(2000)
J. Virol.
, vol.74
, pp. 8524-8531
-
-
Mammano, F.1
Trouplin, V.2
Zennou, V.3
Clavel, F.4
-
46
-
-
0032804864
-
Increased fitness of drug resistant HIV-1 protease as a result of acquisition of compensatory mutations during suboptimal therapy
-
NIJHUIS, M., R. SCHUURMAN, D. D. JONG, J. ERICKSON, E. GUSTCHINA et al., 1999 Increased fitness of drug resistant HIV-1 protease as a result of acquisition of compensatory mutations during suboptimal therapy. AIDS 13: 2349-2359.
-
(1999)
AIDS
, vol.13
, pp. 2349-2359
-
-
Nijhuis, M.1
Schuurman, R.2
Jong, D.D.3
Erickson, J.4
Gustchina, E.5
-
47
-
-
0034974149
-
N-Linked glycosylation sites adjacent to and within the V1/V2 and the V3 loops of dualtropic human immunodeficiency virus type 1 isolate DH12 gp120 affect coreceptor usage and cellular tropism
-
OGERT, R. A., M. K. LEE, W. ROSS, A. BUCKLER-WHITE, M. A. MARTIN et al., 2001 N-Linked glycosylation sites adjacent to and within the V1/V2 and the V3 loops of dualtropic human immunodeficiency virus type 1 isolate DH12 gp120 affect coreceptor usage and cellular tropism. J. Virol. 75: 5998-6006.
-
(2001)
J. Virol.
, vol.75
, pp. 5998-6006
-
-
Ogert, R.A.1
Lee, M.K.2
Ross, W.3
Buckler-White, A.4
Martin, M.A.5
-
48
-
-
34548040966
-
Crystal structure of an ancient protein: Evolution by conformational epistasis
-
ORTLUND, E. A., J. T. BRIDGHAM, M. R. REDINBO and J. W. THORNTON, 2007 Crystal structure of an ancient protein: evolution by conformational epistasis. Science 317: 1544-1548.
-
(2007)
Science
, vol.317
, pp. 1544-1548
-
-
Ortlund, E.A.1
Bridgham, J.T.2
Redinbo, M.R.3
Thornton, J.W.4
-
49
-
-
34547105271
-
Conserved changes in envelope function during human immunodeficiency virus type 1 coreceptor switching
-
PASTORE, C., R. NEDELLEC, A. RAMOS, O. HARTLEY, J. L. MIAMIDIAN et al., 2007 Conserved changes in envelope function during human immunodeficiency virus type 1 coreceptor switching. J. Virol. 81: 8165-8179.
-
(2007)
J. Virol.
, vol.81
, pp. 8165-8179
-
-
Pastore, C.1
Nedellec, R.2
Ramos, A.3
Hartley, O.4
Miamidian, J.L.5
-
50
-
-
30344443665
-
Human immunodeficiency virus type 1 coreceptor switching: V1/V2 gain-of-fitness mutations compensate for V3 loss-of-fitness mutations
-
PASTORE, C., R. NEDELLEC, A. RAMOS, S. PONTOW, L. RATNER et al., 2006 Human immunodeficiency virus type 1 coreceptor switching: V1/V2 gain-of-fitness mutations compensate for V3 loss-of-fitness mutations. J. Virol. 80: 750-758.
-
(2006)
J. Virol.
, vol.80
, pp. 750-758
-
-
Pastore, C.1
Nedellec, R.2
Ramos, A.3
Pontow, S.4
Ratner, L.5
-
51
-
-
3142679567
-
Intrinsic obstacles to human immunodeficiency virus type 1 coreceptor switching
-
PASTORE, C., A. RAMOS and D. E. MOSIER, 2004 Intrinsic obstacles to human immunodeficiency virus type 1 coreceptor switching. J. Virol. 78: 7565-7574.
-
(2004)
J. Virol.
, vol.78
, pp. 7565-7574
-
-
Pastore, C.1
Ramos, A.2
Mosier, D.E.3
-
52
-
-
34347332282
-
Variable epistatic effects between mutations at host recognition sites in φX174 bacteriophage
-
PEPIN, K. M., and H. A. WICHMAN, 2007 Variable epistatic effects between mutations at host recognition sites in φX174 bacteriophage. Evolution 61: 1710-1724.
-
(2007)
Evolution
, vol.61
, pp. 1710-1724
-
-
Pepin, K.M.1
Wichman, H.A.2
-
53
-
-
0002854090
-
Beyond the average: The evolutionary importance of gene interactions and variability of epistatic effects
-
edited by J. B. WOLF, E. D. BRODIE and M. J. WADE. Oxford University Press, Oxford
-
PHILLIPS, P. C., S. P. OTTO and M. C. WHITLOCK, 2000 Beyond the average: the evolutionary importance of gene interactions and variability of epistatic effects, pp. 20-38 in Epistasis and the Evolutionary Process, edited by J. B. WOLF, E. D. BRODIE and M. J. WADE. Oxford University Press, Oxford.
-
(2000)
Epistasis and the Evolutionary Process
, pp. 20-38
-
-
Phillips, P.C.1
Otto, S.P.2
Whitlock, M.C.3
-
54
-
-
0037651593
-
HIV-1 coreceptor usage, transmission, and disease progression
-
PHILPOTT, S. M., 2003 HIV-1 coreceptor usage, transmission, and disease progression. Curr. HIV Res. 1: 217-227.
-
(2003)
Curr. HIV Res.
, vol.1
, pp. 217-227
-
-
Philpott, S.M.1
-
55
-
-
15244356599
-
Kinetic factors control efficiencies of cell entry, efficacies of entry inhibitors, and mechanisms of adaptation of human immunodeficiency virus
-
PLATT, E. J., J. P. DURNIN and D. KABAT, 2005 Kinetic factors control efficiencies of cell entry, efficacies of entry inhibitors, and mechanisms of adaptation of human immunodeficiency virus. J. Virol. 79: 4347-4356.
-
(2005)
J. Virol.
, vol.79
, pp. 4347-4356
-
-
Platt, E.J.1
Durnin, J.P.2
Kabat, D.3
-
56
-
-
0035918220
-
N-linked glycosylation of the HIV Type-1 gp120 envelope glycoprotein as a major determinant of CCR5 and CXCR4 coreceptor utilization
-
POLLAKIS, G., S. KANG, A. KLIPHUIS, M. I. CHALABY, J. GOUDSMIT et al., 2001 N-linked glycosylation of the HIV Type-1 gp120 envelope glycoprotein as a major determinant of CCR5 and CXCR4 coreceptor utilization. J. Biol. Chem. 276: 13433-13441.
-
(2001)
J. Biol. Chem.
, vol.276
, pp. 13433-13441
-
-
Pollakis, G.1
Kang, S.2
Kliphuis, A.3
Chalaby, M.I.4
Goudsmit, J.5
-
57
-
-
21044438202
-
The rate of compensatory mutation in the DNA bacteriophage ΦX174
-
POON, A., and L. CHAO, 2005 The rate of compensatory mutation in the DNA bacteriophage ΦX174. Genetics 170: 989-999.
-
(2005)
Genetics
, vol.170
, pp. 989-999
-
-
Poon, A.1
Chao, L.2
-
58
-
-
21044440015
-
The coupon collector and the suppressor mutation: Estimating the number of compensatory mutations by maximum likelihood
-
POON, A., B. H. DAVIS and L. CHAO, 2005 The coupon collector and the suppressor mutation: Estimating the number of compensatory mutations by maximum likelihood. Genetics 170: 1323-1332.
-
(2005)
Genetics
, vol.170
, pp. 1323-1332
-
-
Poon, A.1
Davis, B.H.2
Chao, L.3
-
59
-
-
33751310355
-
Functional origins of fitness effect-sizes of compensatory mutations in the DNA bacteriophage φX174
-
POON, A. F., and L. CHAO, 2006 Functional origins of fitness effect-sizes of compensatory mutations in the DNA bacteriophage φX174. Evolution 60: 2032-2043.
-
(2006)
Evolution
, vol.60
, pp. 2032-2043
-
-
Poon, A.F.1
Chao, L.2
-
60
-
-
36948998606
-
An evolutionary-network model reveals stratified interactions in the V3 loop of the HIV-1 envelope
-
POON, A. F., F. I. LEWIS, S. L. POND and S. D. FROST, 2007 An evolutionary-network model reveals stratified interactions in the V3 loop of the HIV-1 envelope. PLoS Comput. Biol. 3: e231.
-
(2007)
PLoS Comput. Biol.
, vol.3
-
-
Poon, A.F.1
Lewis, F.I.2
Pond, S.L.3
Frost, S.D.4
-
61
-
-
0037389643
-
Rapid evolution of the neutralizing antibody response to HIV type 1 infection
-
RICHMAN, D. D., T. WRIN, S. J. LITTLE and C. J. PETROPOULOS, 2003 Rapid evolution of the neutralizing antibody response to HIV type 1 infection. Proc. Natl. Acad. Sci. USA 100: 4144-4149.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 4144-4149
-
-
Richman, D.D.1
Wrin, T.2
Little, S.J.3
Petropoulos, C.J.4
-
62
-
-
33748996485
-
Molecular switch for alternative conformations of the HIV-1 V3 region: Implications for phenotype conversion
-
ROSEN, O., M. SHARON, S. R. QUADT-AKABAYOV and J. ANGLISTER, 2006 Molecular switch for alternative conformations of the HIV-1 V3 region: implications for phenotype conversion. Proc. Natl. Acad. Sci. USA 103: 13950-13955.
-
(2006)
Proc. Natl. Acad. Sci. USA
, vol.103
, pp. 13950-13955
-
-
Rosen, O.1
Sharon, M.2
Quadt-Akabayov, S.R.3
Anglister, J.4
-
63
-
-
0032824180
-
Linkage disequilibrium test implies a large effective population number for HIV in vivo
-
ROUZINE, I. M., and J. M. COFFIN, 1999 Linkage disequilibrium test implies a large effective population number for HIV in vivo. Proc. Natl. Acad. Sci. USA 96: 10758-10763.
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, pp. 10758-10763
-
-
Rouzine, I.M.1
Coffin, J.M.2
-
64
-
-
23344432889
-
Epistasis and the adaptability of an RNA virus
-
SANJUAN, R., J. M. CUEVAS, A. MOYA and S. F. ELENA, 2005 Epistasis and the adaptability of an RNA virus. Genetics 170: 1001-1008.
-
(2005)
Genetics
, vol.170
, pp. 1001-1008
-
-
Sanjuan, R.1
Cuevas, J.M.2
Moya, A.3
Elena, S.F.4
-
65
-
-
33749242962
-
Epistasis correlates to genomic complexity
-
SANJUAN, R., and S. F. ELENA, 2006 Epistasis correlates to genomic complexity. Proc. Natl. Acad. Sci. USA 103: 14402-14405.
-
(2006)
Proc. Natl. Acad. Sci. USA
, vol.103
, pp. 14402-14405
-
-
Sanjuan, R.1
Elena, S.F.2
-
66
-
-
7444221704
-
The contribution of epistasis to the architecture of fitness in an RNA virus
-
SANJUAN, R., A. MOYA and S. F. ELENA, 2004 The contribution of epistasis to the architecture of fitness in an RNA virus. Proc. Natl. Acad. Sci. USA 101: 15376-15379.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 15376-15379
-
-
Sanjuan, R.1
Moya, A.2
Elena, S.F.3
-
67
-
-
0036234481
-
Estimation of effective population size of HIV-1 within a host: A pseudomaximum-likelihood approach
-
SEO, T. K., J. L. THORNE, M. HASEGAWA and H. KISHINO, 2002 Estimation of effective population size of HIV-1 within a host: a pseudomaximum-likelihood approach. Genetics 160: 1283-1293.
-
(2002)
Genetics
, vol.160
, pp. 1283-1293
-
-
Seo, T.K.1
Thorne, J.L.2
Hasegawa, M.3
Kishino, H.4
-
68
-
-
33748170576
-
A phylogenetic method for detecting positive epistasis in gene sequences and its application to RNA virus evolution
-
SHAPIRO, B., A. RAMBAUT, O. G. PYBUS and E. C. HOLMES, 2006 A phylogenetic method for detecting positive epistasis in gene sequences and its application to RNA virus evolution. Mol. Biol. Evol. 23: 1724-1730.
-
(2006)
Mol. Biol. Evol.
, vol.23
, pp. 1724-1730
-
-
Shapiro, B.1
Rambaut, A.2
Pybus, O.G.3
Holmes, E.C.4
-
69
-
-
1942421715
-
Influence of random genetic drift on human immunodeficiency virus type 1 env evolution during chronic infection
-
SHRINER, D., R. SHANKARAPPA, M. A. JENSEN, D. C. NICKLE, J. E. MITTLER et al., 2004 Influence of random genetic drift on human immunodeficiency virus type 1 env evolution during chronic infection. Genetics 166: 1155-1164.
-
(2004)
Genetics
, vol.166
, pp. 1155-1164
-
-
Shriner, D.1
Shankarappa, R.2
Jensen, M.A.3
Nickle, D.C.4
Mittler, J.E.5
-
70
-
-
0033542116
-
Establishment of a new system for determination of coreceptor usages of HIV based on the human glioma NP-2 cell line
-
SODA, Y., N. SHIMIZU, A. JINNO, H.-Y. LIU, K. KANBE et al., 1999 Establishment of a new system for determination of coreceptor usages of HIV based on the human glioma NP-2 cell line. Biochem. Biophys. Res. Commun. 258: 313-321.
-
(1999)
Biochem. Biophys. Res. Commun.
, vol.258
, pp. 313-321
-
-
Soda, Y.1
Shimizu, N.2
Jinno, A.3
Liu, H.-Y.4
Kanbe, K.5
-
72
-
-
0013799795
-
Genetics of natural populations. XXXVI. Epistatic interactions of the components of the genetic load in Drosophila pseudoobscura
-
SPASSKY, B., T. DOBZHANSKY and W. W. ANDERSON, 1965 Genetics of natural populations. XXXVI. Epistatic interactions of the components of the genetic load in Drosophila pseudoobscura. Genetics 52: 653-664.
-
(1965)
Genetics
, vol.52
, pp. 653-664
-
-
Spassky, B.1
Dobzhansky, T.2
Anderson, W.W.3
-
73
-
-
0030810706
-
Selective employment of chemokine receptors as human immunodeficiency virus type 1 coreceptors determined by individual amino acids within the envelope V3 loop
-
SPECK, R. F., K. WEHRLY, E. J. PLATT, R. E. ATCHISON, I. F. CHARO et al., 1997 Selective employment of chemokine receptors as human immunodeficiency virus type 1 coreceptors determined by individual amino acids within the envelope V3 loop. J. Virol. 71: 7136-7139.
-
(1997)
J. Virol.
, vol.71
, pp. 7136-7139
-
-
Speck, R.F.1
Wehrly, K.2
Platt, E.J.3
Atchison, R.E.4
Charo, I.F.5
-
74
-
-
0014472490
-
The influence of epistasis on homozygous viability depression in Drosophila melanogaster
-
TEMIN, R. G., H. U. MEYER, P. S. DAWSON and J. F. CROW, 1969 The influence of epistasis on homozygous viability depression in Drosophila melanogaster. Genetics 61: 497-519.
-
(1969)
Genetics
, vol.61
, pp. 497-519
-
-
Temin, R.G.1
Meyer, H.U.2
Dawson, P.S.3
Crow, J.F.4
-
75
-
-
0037456827
-
Antibody neutralization and escape by HIV-1
-
WEI, X., J. M. DECKER, S. WANG, H. HUI, J. C. KAPPES et al., 2003 Antibody neutralization and escape by HIV-1. Nature 422: 307-312.
-
(2003)
Nature
, vol.422
, pp. 307-312
-
-
Wei, X.1
Decker, J.M.2
Wang, S.3
Hui, H.4
Kappes, J.C.5
-
76
-
-
21044446722
-
Rapid evolutionary escape by large populations from local fitness peaks is likely in nature
-
WEINREICH, D. M., and L. CHAO, 2005 Rapid evolutionary escape by large populations from local fitness peaks is likely in nature. Evolution 59: 1175-1182.
-
(2005)
Evolution
, vol.59
, pp. 1175-1182
-
-
Weinreich, D.M.1
Chao, L.2
-
77
-
-
33645666942
-
Darwinian evolution can follow only very few mutational paths to fitter proteins
-
WEINREICH, D. M., N. F. DELANEY, M. A. DEPRISTO and D. L. HARTL, 2006 Darwinian evolution can follow only very few mutational paths to fitter proteins. Science 312: 111-114.
-
(2006)
Science
, vol.312
, pp. 111-114
-
-
Weinreich, D.M.1
Delaney, N.F.2
Depristo, M.A.3
Hartl, D.L.4
-
78
-
-
21044435697
-
Sign epistasis and genetic constraint on evolutionary trajectories
-
WEINREICH, D. M., R. A. WATSON and L. CHAO, 2005 Sign epistasis and genetic constraint on evolutionary trajectories. Evolution 59: 1165-1174.
-
(2005)
Evolution
, vol.59
, pp. 1165-1174
-
-
Weinreich, D.M.1
Watson, R.A.2
Chao, L.3
-
79
-
-
0028996002
-
Multiple fitness peaks and epistasis
-
WHITLOCK, M. C., P. C. PHILLIPS, F. B. MOORE and S. J. TONSOR, 1995 Multiple fitness peaks and epistasis. Ann. Rev. Ecol. Systematics 26: 601-629.
-
(1995)
Ann. Rev. Ecol. Systematics
, vol.26
, pp. 601-629
-
-
Whitlock, M.C.1
Phillips, P.C.2
Moore, F.B.3
Tonsor, S.J.4
-
80
-
-
0000907353
-
The roles of mutation, inbreeding, crossbreeding and selection in evolution
-
edited by D. F. JONES. Brooklyn Botanic Garden, Menasha, WI
-
WRIGHT, S., 1932 The roles of mutation, inbreeding, crossbreeding and selection in evolution, pp. 356-366 in The Sixth International Congress of Genetics, edited by D. F. JONES. Brooklyn Botanic Garden, Menasha, WI.
-
(1932)
The Sixth International Congress of Genetics
, pp. 356-366
-
-
Wright, S.1
-
81
-
-
0032546844
-
The HIV-1 envelope glycoproteins: Fusogens, antigens, and immunogens
-
WYATT, R., and J. SODROSKI, 1998 The HIV-1 envelope glycoproteins: fusogens, antigens, and immunogens. Science 280: 1884-1888.
-
(1998)
Science
, vol.280
, pp. 1884-1888
-
-
Wyatt, R.1
Sodroski, J.2
-
82
-
-
1542615646
-
Identifying epitopes of HIV-1 that induce protective antibodies
-
ZOLLA-PAZNER, S., 2004 Identifying epitopes of HIV-1 that induce protective antibodies. Nat. Rev. Immunol. 4: 199-210.
-
(2004)
Nat. Rev. Immunol.
, vol.4
, pp. 199-210
-
-
Zolla-Pazner, S.1
|