-
1
-
-
64049089430
-
Quantitating the multiplicity of infection with human immunodeficiency virus type 1 subtype C reveals a non-Poisson distribution of transmitted variants
-
doi: 10.1128/JVI.02132-08; pmid: 19193811
-
M. R. Abrahams et al., Quantitating the multiplicity of infection with human immunodeficiency virus type 1 subtype C reveals a non-Poisson distribution of transmitted variants. J. Virol. 83, 3556-3567 (2009). doi: 10.1128/JVI.02132-08; pmid: 19193811
-
(2009)
J. Virol.
, vol.83
, pp. 3556-3567
-
-
Abrahams, M.R.1
-
2
-
-
12144289425
-
Envelope-constrained neutralization-sensitive HIV-1 after heterosexual transmission
-
doi: 10.1126/science.1093137; pmid: 15044802
-
C. A. Derdeyn et al., Envelope-constrained neutralization-sensitive HIV-1 after heterosexual transmission. Science 303, 2019-2022 (2004). doi: 10.1126/science.1093137; pmid: 15044802
-
(2004)
Science
, vol.303
, pp. 2019-2022
-
-
Derdeyn, C.A.1
-
3
-
-
59249096215
-
Inflammatory genital infections mitigate a severe genetic bottleneck in heterosexual transmission of subtype A and C HIV-1
-
doi: 10.1371/journal.ppat.1000274; pmid: 19165325
-
R. E. Haaland et al., Inflammatory genital infections mitigate a severe genetic bottleneck in heterosexual transmission of subtype A and C HIV-1. PLOS Pathog. 5, e1000274 (2009). doi: 10.1371/journal.ppat.1000274; pmid: 19165325
-
(2009)
PLOS Pathog.
, vol.5
-
-
Haaland, R.E.1
-
4
-
-
44649102135
-
Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection
-
doi: 10.1073/pnas.0802203105; pmid: 18490657
-
B. F. Keele et al., Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection. Proc. Natl. Acad. Sci. U.S.A. 105, 7552-7557 (2008). doi: 10.1073/pnas.0802203105; pmid: 18490657
-
(2008)
Proc. Natl. Acad. Sci. U.S.A.
, vol.105
, pp. 7552-7557
-
-
Keele, B.F.1
-
5
-
-
70349273723
-
Human immunodeficiency virus type 1 V1-to-V5 envelope variants from the chronic phase of infection use CCR5 and fuse more efficiently than those from early after infection
-
doi: 10.1128/JVI.00925-09; pmid: 19625411
-
B. Etemad et al., Human immunodeficiency virus type 1 V1-to-V5 envelope variants from the chronic phase of infection use CCR5 and fuse more efficiently than those from early after infection. J. Virol. 83, 9694-9708 (2009). doi: 10.1128/JVI.00925-09; pmid: 19625411
-
(2009)
J. Virol.
, vol.83
, pp. 9694-9708
-
-
Etemad, B.1
-
6
-
-
41949124934
-
Deciphering human immunodeficiency virus type 1 transmission and early envelope diversification by single-genome amplification and sequencing
-
doi: 10.1128/JVI.02660-07; pmid: 18256145
-
J. F. Salazar-Gonzalez et al., Deciphering human immunodeficiency virus type 1 transmission and early envelope diversification by single-genome amplification and sequencing. J. Virol. 82, 3952-3970 (2008). doi: 10.1128/JVI.02660-07; pmid: 18256145
-
(2008)
J. Virol.
, vol.82
, pp. 3952-3970
-
-
Salazar-Gonzalez, J.F.1
-
7
-
-
33745774992
-
Passive sexual transmission of human immunodeficiency virus type 1 variants and adaptation in new hosts
-
doi: 10.1128/JVI.02014-05; pmid: 16809328
-
A. J. Frater et al., Passive sexual transmission of human immunodeficiency virus type 1 variants and adaptation in new hosts. J. Virol. 80, 7226-7234 (2006). doi: 10.1128/JVI.02014-05; pmid: 16809328
-
(2006)
J. Virol.
, vol.80
, pp. 7226-7234
-
-
Frater, A.J.1
-
8
-
-
84876864047
-
HIV transmission
-
doi: 10.1101/cshperspect. a006965; pmid: 23043157
-
G. M. Shaw, E. Hunter, HIV transmission. Cold Spring Harb. Perspect. Med. 2, a006965 (2012). doi: 10.1101/cshperspect. a006965; pmid: 23043157
-
(2012)
Cold Spring Harb. Perspect. Med.
, vol.2
-
-
Shaw, G.M.1
Hunter, E.2
-
9
-
-
1842333851
-
Sexual transmission of HIV
-
doi: 10.1056/NEJM199704103361507; pmid: 9091805
-
R. A. Royce, A. Seña, W. Cates Jr., M. S. Cohen, Sexual transmission of HIV. N. Engl. J. Med. 336, 1072-1078 (1997). doi: 10.1056/NEJM199704103361507; pmid: 9091805
-
(1997)
N. Engl. J. Med.
, vol.336
, pp. 1072-1078
-
-
Royce, R.A.1
Seña, A.2
Cates Jr., W.3
Cohen, M.S.4
-
10
-
-
0033012398
-
Chemokine receptors as HIV-1 coreceptors: Roles in viral entry, tropism, and disease
-
doi: 10.1146/annurev.immunol.17.1.657; pmid: 10358771
-
E. A. Berger, P. M. Murphy, J. M. Farber, Chemokine receptors as HIV-1 coreceptors: Roles in viral entry, tropism, and disease. Annu. Rev. Immunol. 17, 657-700 (1999). doi: 10.1146/annurev.immunol.17.1.657; pmid: 10358771
-
(1999)
Annu. Rev. Immunol.
, vol.17
, pp. 657-700
-
-
Berger, E.A.1
Murphy, P.M.2
Farber, J.M.3
-
11
-
-
79251526530
-
HIV-1 envelope, integrins and co-receptor use in mucosal transmission of HIV
-
doi: 10.1186/1479-5876-9-S1-S2; pmid: 21284901
-
C. Cicala, J. Arthos, A. S. Fauci, HIV-1 envelope, integrins and co-receptor use in mucosal transmission of HIV. J. Transl. Med. 9 (Suppl. 1), S2 (2011). doi: 10.1186/1479-5876-9-S1-S2; pmid: 21284901
-
(2011)
J. Transl. Med.
, vol.9
, Issue.SUPPL. 1
-
-
Cicala, C.1
Arthos, J.2
Fauci, A.S.3
-
12
-
-
84876867850
-
Phenotypic properties of transmitted founder HIV-1
-
doi: 10.1073/pnas.1304288110; pmid: 23542380
-
N. F. Parrish et al., Phenotypic properties of transmitted founder HIV-1. Proc. Natl. Acad. Sci. U.S.A. 110, 6626-6633 (2013). doi: 10.1073/pnas. 1304288110; pmid: 23542380
-
(2013)
Proc. Natl. Acad. Sci. U.S.A.
, vol.110
, pp. 6626-6633
-
-
Parrish, N.F.1
-
13
-
-
80053452761
-
Recurrent signature patterns in HIV-1 B clade envelope glycoproteins associated with either early or chronic infections
-
doi: 10.1371/journal.ppat.1002209; pmid: 21980282
-
S. Gnanakaran et al., Recurrent signature patterns in HIV-1 B clade envelope glycoproteins associated with either early or chronic infections. PLOS Pathog. 7, e1002209 (2011). doi: 10.1371/journal.ppat.1002209; pmid: 21980282
-
(2011)
PLOS Pathog.
, vol.7
-
-
Gnanakaran, S.1
-
14
-
-
61849171106
-
Selection of HIV variants with signature genotypic characteristics during heterosexual transmission
-
doi: 10.1086/596557; pmid: 19143562
-
M. Sagar et al., Selection of HIV variants with signature genotypic characteristics during heterosexual transmission. J. Infect. Dis. 199, 580-589 (2009). doi: 10.1086/596557; pmid: 19143562
-
(2009)
J. Infect. Dis.
, vol.199
, pp. 580-589
-
-
Sagar, M.1
-
15
-
-
32444450252
-
Human immunodeficiency virus type 1 env evolves toward ancestral states upon transmission to a new host
-
doi: 10.1128/JVI.80.4.1637-1644.2006; pmid: 16439520
-
J. T. Herbeck et al., Human immunodeficiency virus type 1 env evolves toward ancestral states upon transmission to a new host. J. Virol. 80, 1637-1644 (2006). doi: 10.1128/JVI.80.4.1637-1644.2006; pmid: 16439520
-
(2006)
J. Virol.
, vol.80
, pp. 1637-1644
-
-
Herbeck, J.T.1
-
16
-
-
0037456827
-
Antibody neutralization and escape by HIV-1
-
doi: 10.1038/nature01470; pmid: 12646921
-
X. Wei et al., Antibody neutralization and escape by HIV-1. Nature 422, 307-312 (2003). doi: 10.1038/nature01470; pmid: 12646921
-
(2003)
Nature
, vol.422
, pp. 307-312
-
-
Wei, X.1
-
17
-
-
84888776867
-
Relative resistance of HIV-1 founder viruses to control by interferon-α
-
doi: 10.1186/1742-4690-10-146; pmid: 24299076
-
A. E. Fenton-May et al., Relative resistance of HIV-1 founder viruses to control by interferon-α. Retrovirology 10, 146 (2013). doi: 10.1186/1742-4690-10-146; pmid: 24299076
-
(2013)
Retrovirology
, vol.10
, pp. 146
-
-
Fenton-May, A.E.1
-
18
-
-
78049495989
-
Early selection in Gag by protective HLA alleles contributes to reduced HIV-1 replication capacity that may be largely compensated for in chronic infection
-
doi: 10.1128/JVI.01086-10; pmid: 20810731
-
M. A. Brockman et al., Early selection in Gag by protective HLA alleles contributes to reduced HIV-1 replication capacity that may be largely compensated for in chronic infection. J. Virol. 84, 11937-11949 (2010). doi: 10.1128/JVI.01086-10; pmid: 20810731
-
(2010)
J. Virol.
, vol.84
, pp. 11937-11949
-
-
Brockman, M.A.1
-
19
-
-
84870786421
-
Role of transmitted Gag CTL polymorphisms in defining replicative capacity and early HIV-1 pathogenesis
-
doi: 10.1371/journal.ppat.1003041; pmid: 23209412
-
J. L. Prince et al., Role of transmitted Gag CTL polymorphisms in defining replicative capacity and early HIV-1 pathogenesis. PLOS Pathog. 8, e1003041 (2012). doi: 10.1371/journal.ppat.1003041; pmid: 23209412
-
(2012)
PLOS Pathog.
, vol.8
-
-
Prince, J.L.1
-
20
-
-
77957194223
-
Gag-protease-mediated replication capacity in HIV-1 subtype C chronic infection: Associations with HLA type and clinical parameters
-
doi: 10.1128/JVI.01084-10; pmid: 20702636
-
J. K. Wright et al., Gag-protease-mediated replication capacity in HIV-1 subtype C chronic infection: Associations with HLA type and clinical parameters. J. Virol. 84, 10820-10831 (2010). doi: 10.1128/JVI.01084-10; pmid: 20702636
-
(2010)
J. Virol.
, vol.84
, pp. 10820-10831
-
-
Wright, J.K.1
-
21
-
-
79952846443
-
Influence of Gag-protease-mediated replication capacity on disease progression in individuals recently infected with HIV-1 subtype C
-
doi: 10.1128/JVI.02520-10; pmid: 21289112
-
J. K. Wright et al., Influence of Gag-protease-mediated replication capacity on disease progression in individuals recently infected with HIV-1 subtype C. J. Virol. 85, 3996-4006 (2011). doi: 10.1128/JVI.02520-10; pmid: 21289112
-
(2011)
J. Virol.
, vol.85
, pp. 3996-4006
-
-
Wright, J.K.1
-
22
-
-
0032525137
-
The SH3 domain-binding surface and an acidic motif in HIV-1 Nef regulate trafficking of class I MHC complexes
-
doi: 10.1093/emboj/17.10.2777; pmid: 9582271
-
M. E. Greenberg, A. J. Iafrate, J. Skowronski, The SH3 domain-binding surface and an acidic motif in HIV-1 Nef regulate trafficking of class I MHC complexes. EMBO J. 17, 2777-2789 (1998). doi: 10.1093/emboj/17.10.2777; pmid: 9582271
-
(1998)
EMBO J.
, vol.17
, pp. 2777-2789
-
-
Greenberg, M.E.1
Iafrate, A.J.2
Skowronski, J.3
-
23
-
-
0033013962
-
Nef-induced CD4 and major histocompatibility complex class I (MHC-I) down-regulation are governed by distinct determinants: N-terminal alpha helix and proline repeat of Nef selectively regulate MHC-I trafficking
-
pmid: 9971776
-
A. Mangasarian, V. Piguet, J. K. Wang, Y. L. Chen, D. Trono, Nef-induced CD4 and major histocompatibility complex class I (MHC-I) down-regulation are governed by distinct determinants: N-terminal alpha helix and proline repeat of Nef selectively regulate MHC-I trafficking. J. Virol. 73, 1964-1973 (1999). pmid: 9971776
-
(1999)
J. Virol.
, vol.73
, pp. 1964-1973
-
-
Mangasarian, A.1
Piguet, V.2
Wang, J.K.3
Chen, Y.L.4
Trono, D.5
-
24
-
-
57149090493
-
Phylogenetic dependency networks: Inferring patterns of CTL escape and codon covariation in HIV-1 Gag
-
doi: 10.1371/journal.pcbi.1000225; pmid: 19023406
-
J. M. Carlson et al., Phylogenetic dependency networks: Inferring patterns of CTL escape and codon covariation in HIV-1 Gag. PLOS Comput. Biol. 4, e1000225 (2008). doi: 10.1371/journal.pcbi.1000225; pmid: 19023406
-
(2008)
PLOS Comput. Biol.
, vol.4
-
-
Carlson, J.M.1
-
25
-
-
62749167015
-
Reduced viral replication capacity of human immunodeficiency virus type 1 subtype C caused by cytotoxic-T-lymphocyte escape mutations in HLA-B57 epitopes of capsid protein
-
doi: 10.1128/JVI.01970-08; pmid: 19109381
-
C. L. Boutwell, C. F. Rowley, M. Essex, Reduced viral replication capacity of human immunodeficiency virus type 1 subtype C caused by cytotoxic-T-lymphocyte escape mutations in HLA-B57 epitopes of capsid protein. J. Virol. 83, 2460-2468 (2009). doi: 10.1128/JVI.01970-08; pmid: 19109381
-
(2009)
J. Virol.
, vol.83
, pp. 2460-2468
-
-
Boutwell, C.L.1
Rowley, C.F.2
Essex, M.3
-
26
-
-
84886598817
-
The hierarchical logistic regression model for multilevel analysis
-
doi: 10.1080/01621459.1985.10478148
-
G. Y. Wong, W. M. Mason, The hierarchical logistic regression model for multilevel analysis. J. Am. Stat. Assoc. 80, 513-524 (1985). doi: 10.1080/01621459.1985.10478148
-
(1985)
J. Am. Stat. Assoc.
, vol.80
, pp. 513-524
-
-
Wong, G.Y.1
Mason, W.M.2
-
27
-
-
0034826484
-
Virologic and immunologic determinants of heterosexual transmission of human immunodeficiency virus type 1 in Africa
-
doi: 10.1089/088922201750290023; pmid: 11461676
-
U. S. Fideli et al., Virologic and immunologic determinants of heterosexual transmission of human immunodeficiency virus type 1 in Africa. AIDS Res. Hum. Retroviruses 17, 901-910 (2001). doi: 10.1089/088922201750290023; pmid: 11461676
-
(2001)
AIDS Res. Hum. Retroviruses
, vol.17
, pp. 901-910
-
-
Fideli, U.S.1
-
28
-
-
0035857959
-
Probability of HIV-1 transmission per coital act in monogamous, heterosexual, HIV-1-discordant couples in Rakai, Uganda
-
doi: 10.1016/S0140-6736(00)04331-2; pmid: 11323041
-
R. H. Gray et al., Probability of HIV-1 transmission per coital act in monogamous, heterosexual, HIV-1-discordant couples in Rakai, Uganda. Lancet 357, 1149-1153 (2001). doi: 10.1016/S0140-6736(00)04331-2; pmid: 11323041
-
(2001)
Lancet
, vol.357
, pp. 1149-1153
-
-
Gray, R.H.1
-
29
-
-
0026562144
-
Comparison of female to male and male to female transmission of HIV in 563 stable couples
-
European Study Group on Heterosexual Transmission of HIV doi: 10.1136/bmj.304.6830.809; pmid: 1392708
-
Comparison of female to male and male to female transmission of HIV in 563 stable couples. European Study Group on Heterosexual Transmission of HIV. BMJ 304, 809-813 (1992). doi: 10.1136/bmj.304.6830.809; pmid: 1392708
-
(1992)
BMJ
, vol.304
, pp. 809-813
-
-
-
30
-
-
1842486661
-
The role of sexually transmitted diseases in HIV transmission
-
doi: 10.1038/nrmicro794; pmid: 15035007
-
S. R. Galvin, M. S. Cohen, The role of sexually transmitted diseases in HIV transmission. Nat. Rev. Microbiol. 2, 33-42 (2004). doi: 10.1038/nrmicro794; pmid: 15035007
-
(2004)
Nat. Rev. Microbiol.
, vol.2
, pp. 33-42
-
-
Galvin, S.R.1
Cohen, M.S.2
-
31
-
-
53149084143
-
Human leukocyte antigen class I genotypes in relation to heterosexual HIV type 1 transmission within discordant couples
-
doi: 10.4049/jimmunol.181.4.2626; pmid: 18684953
-
J. Tang et al., Human leukocyte antigen class I genotypes in relation to heterosexual HIV type 1 transmission within discordant couples. J. Immunol. 181, 2626-2635 (2008). doi: 10.4049/jimmunol.181.4.2626; pmid: 18684953
-
(2008)
J. Immunol.
, vol.181
, pp. 2626-2635
-
-
Tang, J.1
-
32
-
-
77950927522
-
HIV RNA level in early infection is predicted by viral load in the transmission source
-
doi: 10.1097/QAD.0b013e328337b12e; pmid: 20168202
-
F. M. Hecht et al., HIV RNA level in early infection is predicted by viral load in the transmission source. AIDS 24, 941-945 (2010). doi: 10.1097/QAD.0b013e328337b12e; pmid: 20168202
-
(2010)
AIDS
, vol.24
, pp. 941-945
-
-
Hecht, F.M.1
-
33
-
-
77954059111
-
HIV-1 transmitting couples have similar viral load set-points in Rakai, Uganda
-
doi: 10.1371/journal.ppat.1000876; pmid: 20463808
-
T. D. Hollingsworth et al., HIV-1 transmitting couples have similar viral load set-points in Rakai, Uganda. PLOS Pathog. 6, e1000876 (2010). doi: 10.1371/journal.ppat.1000876; pmid: 20463808
-
(2010)
PLOS Pathog.
, vol.6
-
-
Hollingsworth, T.D.1
-
34
-
-
84871983347
-
Cumulative impact of host and viral factors on HIV-1 viral-load control during early infection
-
doi: 10.1128/JVI.02118-12; pmid: 23115285
-
L. Yue et al., Cumulative impact of host and viral factors on HIV-1 viral-load control during early infection. J. Virol. 87, 708-715 (2013). doi: 10.1128/JVI.02118-12; pmid: 23115285
-
(2013)
J. Virol.
, vol.87
, pp. 708-715
-
-
Yue, L.1
-
35
-
-
2942672080
-
Selection, transmission, and reversion of an antigen-processing cytotoxic T-lymphocyte escape mutation in human immunodeficiency virus type 1 infection
-
doi: 10.1128/JVI.78.13.7069-7078.2004; pmid: 15194783
-
T. M. Allen et al., Selection, transmission, and reversion of an antigen-processing cytotoxic T-lymphocyte escape mutation in human immunodeficiency virus type 1 infection. J. Virol. 78, 7069-7078 (2004). doi: 10.1128/JVI.78.13.7069-7078.2004; pmid: 15194783
-
(2004)
J. Virol.
, vol.78
, pp. 7069-7078
-
-
Allen, T.M.1
-
36
-
-
50949117244
-
Marked epitope- and allele-specific differences in rates of mutation in human immunodeficiency type 1 (HIV-1) Gag, Pol, and Nef cytotoxic T-lymphocyte epitopes in acute/early HIV-1 infection
-
doi: 10.1128/JVI.01041-08; pmid: 18614631
-
Z. L. Brumme et al., Marked epitope- and allele-specific differences in rates of mutation in human immunodeficiency type 1 (HIV-1) Gag, Pol, and Nef cytotoxic T-lymphocyte epitopes in acute/early HIV-1 infection. J. Virol. 82, 9216-9227 (2008). doi: 10.1128/JVI.01041-08; pmid: 18614631
-
(2008)
J. Virol.
, vol.82
, pp. 9216-9227
-
-
Brumme, Z.L.1
-
37
-
-
34547138161
-
Compensatory mutation partially restores fitness and delays reversion of escape mutation within the immunodominant HLA-B*5703-restricted Gag epitope in chronic human immunodeficiency virus type 1 infection
-
doi: 10.1128/JVI.00465-07; pmid: 17507468
-
H. Crawford et al., Compensatory mutation partially restores fitness and delays reversion of escape mutation within the immunodominant HLA-B*5703-restricted Gag epitope in chronic human immunodeficiency virus type 1 infection. J. Virol. 81, 8346-8351 (2007). doi: 10.1128/JVI.00465-07; pmid: 17507468
-
(2007)
J. Virol.
, vol.81
, pp. 8346-8351
-
-
Crawford, H.1
-
38
-
-
20244373940
-
Transmission and accumulation of CTL escape variants drive negative associations between HIV polymorphisms and HLA
-
doi: 10.1084/jem.20041455; pmid: 15781581
-
A. Leslie et al., Transmission and accumulation of CTL escape variants drive negative associations between HIV polymorphisms and HLA. J. Exp. Med. 201, 891-902 (2005). doi: 10.1084/jem.20041455; pmid: 15781581
-
(2005)
J. Exp. Med.
, vol.201
, pp. 891-902
-
-
Leslie, A.1
-
39
-
-
33645240933
-
Fitness cost of escape mutations in p24 Gag in association with control of human immunodeficiency virus type 1
-
doi: 10.1128/JVI.80.7.3617-3623.2006; pmid: 16537629
-
J. Martinez-Picado et al., Fitness cost of escape mutations in p24 Gag in association with control of human immunodeficiency virus type 1. J. Virol. 80, 3617-3623 (2006). doi: 10.1128/JVI.80.7.3617-3623.2006; pmid: 16537629
-
(2006)
J. Virol.
, vol.80
, pp. 3617-3623
-
-
Martinez-Picado, J.1
-
40
-
-
42949092720
-
Transmission of HIV-1 CTL escape variants provides HLA-mismatched recipients with a survival advantage
-
doi: 10.1371/journal. ppat.1000033; pmid: 18369479
-
D. R. Chopera et al., Transmission of HIV-1 CTL escape variants provides HLA-mismatched recipients with a survival advantage. PLOS Pathog. 4, e1000033 (2008). doi: 10.1371/journal. ppat.1000033; pmid: 18369479
-
(2008)
PLOS Pathog.
, vol.4
-
-
Chopera, D.R.1
-
41
-
-
43549109265
-
Transmission of HIV-1 Gag immune escape mutations is associated with reduced viral load in linked recipients
-
doi: 10.1084/jem.20072457; pmid: 18426987
-
P. A. Goepfert et al., Transmission of HIV-1 Gag immune escape mutations is associated with reduced viral load in linked recipients. J. Exp. Med. 205, 1009-1017 (2008). doi: 10.1084/jem.20072457; pmid: 18426987
-
(2008)
J. Exp. Med.
, vol.205
, pp. 1009-1017
-
-
Goepfert, P.A.1
-
42
-
-
73949112038
-
7 forms a complex with cell-surface CD4 and defines a T-cell subset that is highly susceptible to infection by HIV-1
-
doi: 10.1073/pnas.0911796106; pmid: 19933330
-
7 forms a complex with cell-surface CD4 and defines a T-cell subset that is highly susceptible to infection by HIV-1. Proc. Natl. Acad. Sci. U.S.A. 106, 20877-20882 (2009). doi: 10.1073/pnas.0911796106; pmid: 19933330
-
(2009)
Proc. Natl. Acad. Sci. U.S.A.
, vol.106
, pp. 20877-20882
-
-
Cicala, C.1
-
43
-
-
84901335748
-
Genotypic and functional impact of HIV-1 adaptation to its host population during the North American epidemic
-
doi: 10.1371/journal.pgen.1004295; pmid: 24762668
-
L. A. Cotton et al., Genotypic and functional impact of HIV-1 adaptation to its host population during the North American epidemic. PLOS Genet. 10, e1004295 (2014). doi: 10.1371/journal.pgen.1004295; pmid: 24762668
-
(2014)
PLOS Genet.
, vol.10
-
-
Cotton, L.A.1
-
44
-
-
66049139947
-
Genetic identity, biological phenotype, and evolutionary pathways of transmitted/founder viruses in acute and early HIV-1 infection
-
doi: 10.1084/jem.20090378; pmid: 19487424
-
J. F. Salazar-Gonzalez et al., Genetic identity, biological phenotype, and evolutionary pathways of transmitted/founder viruses in acute and early HIV-1 infection. J. Exp. Med. 206, 1273-1289 (2009). doi: 10.1084/jem.20090378; pmid: 19487424
-
(2009)
J. Exp. Med.
, vol.206
, pp. 1273-1289
-
-
Salazar-Gonzalez, J.F.1
-
45
-
-
39049087577
-
Promotion of couples' voluntary counselling and testing for HIV through influential networks in two African capital cities
-
doi: 10.1186/1471-2458-7-349; pmid: 18072974
-
S. Allen et al., Promotion of couples' voluntary counselling and testing for HIV through influential networks in two African capital cities. BMC Public Health 7, 349 (2007). doi: 10.1186/1471-2458-7-349; pmid: 18072974
-
(2007)
BMC Public Health
, vol.7
, pp. 349
-
-
Allen, S.1
-
46
-
-
39049161208
-
Enrollment and retention of HIV discordant couples in Lusaka Zambia
-
doi: 10.1097/QAI.0b013e31815d2f3f; pmid: 18030162
-
M. C. Kempf et al. Enrollment and retention of HIV discordant couples in Lusaka Zambia. J. Acquir. Immune Defic. Syndr. 47, 116-125 (2008). doi: 10.1097/QAI.0b013e31815d2f3f; pmid: 18030162
-
(2008)
J. Acquir. Immune Defic. Syndr.
, vol.47
, pp. 116-125
-
-
Kempf, M.C.1
-
47
-
-
0030777546
-
Rapid HIV testing and counseling for voluntary testing centers in Africa
-
pmid: 9376093
-
S. L. McKenna et al., Rapid HIV testing and counseling for voluntary testing centers in Africa. AIDS 11, S103-S110 (1997). pmid: 9376093
-
(1997)
AIDS
, vol.11
-
-
McKenna, S.L.1
-
48
-
-
0036133071
-
Molecular epidemiology of human immunodeficiency virus type 1 transmission in a heterosexual cohort of discordant couples in Zambia
-
doi: 10.1128/JVI.76.1.397-405.2002; pmid: 11739704
-
S. A. Trask et al., Molecular epidemiology of human immunodeficiency virus type 1 transmission in a heterosexual cohort of discordant couples in Zambia. J. Virol. 76, 397-405 (2002). doi: 10.1128/JVI.76.1.397-405.2002; pmid: 11739704
-
(2002)
J. Virol.
, vol.76
, pp. 397-405
-
-
Trask, S.A.1
-
49
-
-
0002075787
-
-
C. L. Kuiken, B. Foley, B. Hahn, B. Korber, F. McCutchan, P. A. Marx, J. W. Mellors, J. I. Mullins, J. Sodroski, S. Wolinsky, Eds. Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM
-
V. Piguet, D. Trono, in Human Retroviruses and AIDS 1999, C. L. Kuiken, B. Foley, B. Hahn, B. Korber, F. McCutchan, P. A. Marx, J. W. Mellors, J. I. Mullins, J. Sodroski, S. Wolinsky, Eds. (Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, 1999), pp. 448-459.
-
(1999)
Human Retroviruses and AIDS 1999
, pp. 448-459
-
-
Piguet, V.1
Trono, D.2
-
50
-
-
84861214061
-
Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection
-
doi: 10.1371/journal.ppat.1002529; pmid: 22412369
-
M. R. Henn et al., Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection. PLOS Pathog. 8, e1002529 (2012). doi: 10.1371/journal.ppat.1002529; pmid: 22412369
-
(2012)
PLOS Pathog.
, vol.8
-
-
Henn, M.R.1
-
51
-
-
84866113768
-
De novo assembly of highly diverse viral populations
-
doi: 10.1186/1471-2164-13-475; pmid: 22974120
-
X. Yang et al., De novo assembly of highly diverse viral populations. BMC Genomics 13, 475 (2012). doi: 10.1186/1471-2164-13-475; pmid: 22974120
-
(2012)
BMC Genomics
, vol.13
, pp. 475
-
-
Yang, X.1
-
52
-
-
80051728345
-
Disparate associations of HLA class I markers with HIV-1 acquisition and control of viremia in an African population
-
doi: 10.1371/journal.pone.0023469; pmid: 21858133
-
W. Song et al., Disparate associations of HLA class I markers with HIV-1 acquisition and control of viremia in an African population. PLOS One 6, e23469 (2011). doi: 10.1371/journal.pone.0023469; pmid: 21858133
-
(2011)
PLOS One
, vol.6
-
-
Song, W.1
-
53
-
-
84875527661
-
Frequent and variable cytotoxic-T-lymphocyte escape-associated fitness costs in the human immunodeficiency virus type 1 subtype B Gag proteins
-
doi: 10.1128/JVI.03233-12; pmid: 23365420
-
C. L. Boutwell et al., Frequent and variable cytotoxic-T-lymphocyte escape-associated fitness costs in the human immunodeficiency virus type 1 subtype B Gag proteins. J. Virol. 87, 3952-3965 (2013). doi: 10.1128/JVI.03233-12; pmid: 23365420
-
(2013)
J. Virol.
, vol.87
, pp. 3952-3965
-
-
Boutwell, C.L.1
-
54
-
-
33749009745
-
N133-278
-
doi: 10.1021/bi060927x; pmid: 16981686
-
N133-278. Biochemistry 45, 11257-11266 (2006). doi: 10.1021/bi060927x; pmid: 16981686
-
(2006)
Biochemistry
, vol.45
, pp. 11257-11266
-
-
Kelly, B.N.1
-
55
-
-
67549109069
-
X-ray structures of the hexameric building block of the HIV capsid
-
doi: 10.1016/j.cell.2009.04.063; pmid: 19523676
-
O. Pornillos et al., X-ray structures of the hexameric building block of the HIV capsid. Cell 137, 1282-1292 (2009). doi: 10.1016/j.cell.2009.04.063; pmid: 19523676
-
(2009)
Cell
, vol.137
, pp. 1282-1292
-
-
Pornillos, O.1
-
56
-
-
77649146257
-
Structure of the unbound form of HIV-1 subtype A protease: Comparison with unbound forms of proteases from other HIV subtypes
-
doi: 10.1107/S0907444909054298; pmid: 20179334
-
A. H. Robbins et al., Structure of the unbound form of HIV-1 subtype A protease: Comparison with unbound forms of proteases from other HIV subtypes. Acta Crystallogr. D Biol. Crystallogr. 66, 233-242 (2010). doi: 10.1107/S0907444909054298; pmid: 20179334
-
(2010)
Acta Crystallogr D Biol. Crystallogr.
, vol.66
, pp. 233-242
-
-
Robbins, A.H.1
-
57
-
-
0030586090
-
Structure of unliganded HIV-1 reverse transcriptase at 2.7 Å resolution: Implications of conformational changes for polymerization and inhibition mechanisms
-
doi: 10.1016/S0969-2126(96)00091-3; pmid: 8805568
-
Y. Hsiou et al., Structure of unliganded HIV-1 reverse transcriptase at 2.7 Å resolution: Implications of conformational changes for polymerization and inhibition mechanisms. Structure 4, 853-860 (1996). doi: 10.1016/S0969-2126(96)00091-3; pmid: 8805568
-
(1996)
Structure
, vol.4
, pp. 853-860
-
-
Hsiou, Y.1
-
58
-
-
0032483022
-
Three new structures of the core domain of HIV-1 integrase: An active site that binds magnesium
-
doi: 10.1073/pnas.95.16.9150; pmid: 9689049
-
Y. Goldgur et al., Three new structures of the core domain of HIV-1 integrase: An active site that binds magnesium. Proc. Natl. Acad. Sci. U.S.A. 95, 9150-9154 (1998). doi: 10.1073/pnas.95.16.9150; pmid: 9689049
-
(1998)
Proc. Natl. Acad. Sci. U.S.A.
, vol.95
, pp. 9150-9154
-
-
Goldgur, Y.1
-
59
-
-
0343494918
-
Crystal structure of the conserved core of HIV-1 Nef complexed with a Src family SH3 domain
-
doi: 10.1016/S0092-8674(00)81276-3; pmid: 8681387
-
C. H. Lee, K. Saksela, U. A. Mirza, B. T. Chait, J. Kuriyan, Crystal structure of the conserved core of HIV-1 Nef complexed with a Src family SH3 domain. Cell 85, 931-942 (1996). doi: 10.1016/S0092-8674(00)81276-3; pmid: 8681387
-
(1996)
Cell
, vol.85
, pp. 931-942
-
-
Lee, C.H.1
Saksela, K.2
Mirza, U.A.3
Chait, B.T.4
Kuriyan, J.5
-
60
-
-
0036291145
-
Predicting changes in the stability of proteins and protein complexes: A study of more than 1000 mutations
-
doi: 10.1016/S0022-2836(02)00442-4; pmid: 12079393
-
R. Guerois, J. E. Nielsen, L. Serrano, Predicting changes in the stability of proteins and protein complexes: A study of more than 1000 mutations. J. Mol. Biol. 320, 369-387 (2002). doi: 10.1016/S0022-2836(02)00442- 4; pmid: 12079393
-
(2002)
J. Mol. Biol.
, vol.320
, pp. 369-387
-
-
Guerois, R.1
Nielsen, J.E.2
Serrano, L.3
-
61
-
-
0036318823
-
Favorable and unfavorable HLA class I alleles and haplotypes in Zambians predominantly infected with clade C human immunodeficiency virus type 1
-
doi: 10.1128/JVI.76.16.8276-8284.2002; pmid: 12134033
-
J. Tang et al., Favorable and unfavorable HLA class I alleles and haplotypes in Zambians predominantly infected with clade C human immunodeficiency virus type 1. J. Virol. 76, 8276-8284 (2002). doi: 10.1128/JVI.76.16.8276-8284.2002; pmid: 12134033
-
(2002)
J. Virol.
, vol.76
, pp. 8276-8284
-
-
Tang, J.1
-
62
-
-
77950806408
-
New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0
-
doi: 10.1093/sysbio/syq010; pmid: 20525638
-
S. Guindon et al., New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0. Syst. Biol. 59, 307-321 (2010). doi: 10.1093/sysbio/syq010; pmid: 20525638
-
(2010)
Syst. Biol.
, vol.59
, pp. 307-321
-
-
Guindon, S.1
-
63
-
-
84861325273
-
Widespread impact of HLA restriction on immune control and escape pathways of HIV-1
-
doi: 10.1128/JVI.06728-11; pmid: 22379086
-
J. M. Carlson et al., Widespread impact of HLA restriction on immune control and escape pathways of HIV-1. J. Virol. 86, 5230-5243 (2012). doi: 10.1128/JVI.06728-11; pmid: 22379086
-
(2012)
J. Virol.
, vol.86
, pp. 5230-5243
-
-
Carlson, J.M.1
-
64
-
-
77956827161
-
Additive contribution of HLA class I alleles in the immune control of HIV-1 infection
-
doi: 10.1128/JVI.00320-10; pmid: 20660184
-
A. Leslie et al., Additive contribution of HLA class I alleles in the immune control of HIV-1 infection. J. Virol. 84, 9879-9888 (2010). doi: 10.1128/JVI.00320-10; pmid: 20660184
-
(2010)
J. Virol.
, vol.84
, pp. 9879-9888
-
-
Leslie, A.1
-
65
-
-
50149117938
-
Central role of reverting mutations in HLA associations with human immunodeficiency virus set point
-
doi: 10.1128/JVI.00580-08; pmid: 18596105
-
P. C. Matthews et al., Central role of reverting mutations in HLA associations with human immunodeficiency virus set point. J. Virol. 82, 8548-8559 (2008). doi: 10.1128/JVI.00580-08; pmid: 18596105
-
(2008)
J. Virol.
, vol.82
, pp. 8548-8559
-
-
Matthews, P.C.1
-
66
-
-
72249117588
-
Prevalence of HIV type-1 drug-associated mutations in pre-therapy patients in the Free State, South Africa
-
doi: 10.3851/IMP1416; pmid: 19918101
-
K. H. Huang et al., Prevalence of HIV type-1 drug-associated mutations in pre-therapy patients in the Free State, South Africa. Antivir. Ther. 14, 975-984 (2009). doi: 10.3851/IMP1416; pmid: 19918101
-
(2009)
Antivir. Ther.
, vol.14
, pp. 975-984
-
-
Huang, K.H.1
-
67
-
-
79956209349
-
HLA-A*7401- mediated control of HIV viremia is independent of its linkage disequilibrium with HLA-B*5703
-
doi: 10.4049/jimmunol.1003711; pmid: 21498667
-
P. C. Matthews et al., HLA-A*7401- mediated control of HIV viremia is independent of its linkage disequilibrium with HLA-B*5703. J. Immunol. 186, 5675-5686 (2011). doi: 10.4049/jimmunol.1003711; pmid: 21498667
-
(2011)
J. Immunol.
, vol.186
, pp. 5675-5686
-
-
Matthews, P.C.1
-
68
-
-
77953725982
-
Antiretroviral regimens in pregnancy and breast-feeding in Botswana
-
doi: 10.1056/NEJMoa0907736; pmid: 20554983
-
R. L. Shapiro et al., Antiretroviral regimens in pregnancy and breast-feeding in Botswana. N. Engl. J. Med. 362, 2282-2294 (2010). doi: 10.1056/NEJMoa0907736; pmid: 20554983
-
(2010)
N. Engl. J. Med.
, vol.362
, pp. 2282-2294
-
-
Shapiro, R.L.1
-
69
-
-
40149089453
-
Statistical resolution of ambiguous HLA typing data
-
doi: 10.1371/journal.pcbi.1000016; pmid: 18392148.
-
J. Listgarten et al., Statistical resolution of ambiguous HLA typing data. PLOS Comput. Biol. 4, e1000016 (2008). doi: 10.1371/journal.pcbi.1000016; pmid: 18392148.
-
(2008)
PLOS Comput. Biol.
, vol.4
-
-
Listgarten, J.1
-
70
-
-
84870659964
-
Correlates of protective cellular immunity revealed by analysis of population-level immune escape pathways in HIV-1
-
doi: 10.1128/JVI.01998-12; pmid: 23055555
-
J. M. Carlson et al., Correlates of protective cellular immunity revealed by analysis of population-level immune escape pathways in HIV-1. J. Virol. 86, 13202-13216 (2012). doi: 10.1128/JVI.01998-12; pmid: 23055555
-
(2012)
J. Virol.
, vol.86
, pp. 13202-13216
-
-
Carlson, J.M.1
-
72
-
-
84904093065
-
-
R Core Team (R Foundation for Statistical Computing, Vienna, Austria, 2013)
-
R Core Team (R Foundation for Statistical Computing, Vienna, Austria, 2013).
-
-
-
-
73
-
-
84988052077
-
Nonparametric standard errors and confidence intervals
-
doi: 10.2307/3314608
-
B. Efron, Nonparametric standard errors and confidence intervals. Can. J. Stat. 9, 139-158 (1981). doi: 10.2307/3314608
-
(1981)
Can. J. Stat.
, vol.9
, pp. 139-158
-
-
Efron, B.1
|