-
2
-
-
84880331846
-
The changing epidemiology of HIV in 2013
-
Beyrer C, Abdool Karim Q (2013) The changing epidemiology of HIV in 2013. Curr Opin HIV AIDS 8: 306-310.
-
(2013)
Curr Opin HIV AIDS
, vol.8
, pp. 306-310
-
-
Beyrer, C.1
Abdool Karim, Q.2
-
4
-
-
0037195104
-
Molecular evidence of HIV-1 transmission in a criminal case
-
Metzker ML, Mindell DP, Liu XM, Ptak RG, Gibbs RA, et al. (2002) Molecular evidence of HIV-1 transmission in a criminal case. Proc Natl Acad Sci U S A 99: 14292-14297.
-
(2002)
Proc Natl Acad Sci U S A
, vol.99
, pp. 14292-14297
-
-
Metzker, M.L.1
Mindell, D.P.2
Liu, X.M.3
Ptak, R.G.4
Gibbs, R.A.5
-
5
-
-
0028346264
-
Support for dental HIV transmission
-
Hillis DM, Huelsenbeck JP (1994) Support for dental HIV transmission. Nature 369: 24-25.
-
(1994)
Nature
, vol.369
, pp. 24-25
-
-
Hillis, D.M.1
Huelsenbeck, J.P.2
-
6
-
-
0031958110
-
Molecular evidence for nosocomial transmission of human immunodeficiency virus from a surgeon to one of his patients
-
Blanchard A, Ferris S, Chamaret S, Guetard D, Montagnier L (1998) Molecular evidence for nosocomial transmission of human immunodeficiency virus from a surgeon to one of his patients. J Virol 72: 4537-4540.
-
(1998)
J Virol
, vol.72
, pp. 4537-4540
-
-
Blanchard, A.1
Ferris, S.2
Chamaret, S.3
Guetard, D.4
Montagnier, L.5
-
7
-
-
0034048273
-
Phylogenetic analyses indicate an atypical nurse-to-patient transmission of human immunodeficiency virus type 1
-
Goujon CP, Schneider VM, Grofti J, Montigny J, Jeantils V, et al. (2000) Phylogenetic analyses indicate an atypical nurse-to-patient transmission of human immunodeficiency virus type 1. J Virol 74: 2525-2532.
-
(2000)
J Virol
, vol.74
, pp. 2525-2532
-
-
Goujon, C.P.1
Schneider, V.M.2
Grofti, J.3
Montigny, J.4
Jeantils, V.5
-
8
-
-
0026777199
-
Molecular epidemiology of HIV transmission in a dental practice
-
Ou CY, Ciesielski CA, Myers G, Bandea CI, Luo CC, et al. (1992) Molecular epidemiology of HIV transmission in a dental practice. Science 256: 1165-1171.
-
(1992)
Science
, vol.256
, pp. 1165-1171
-
-
Ou, C.Y.1
Ciesielski, C.A.2
Myers, G.3
Bandea, C.I.4
Luo, C.C.5
-
9
-
-
0028604415
-
Lack of HIV transmission in the practice of a dentist with AIDS
-
Jaffe HW, McCurdy JM, Kalish ML, Liberti T, Metellus G, et al. (1994) Lack of HIV transmission in the practice of a dentist with AIDS. Ann Intern Med 121: 855-859.
-
(1994)
Ann Intern Med
, vol.121
, pp. 855-859
-
-
Jaffe, H.W.1
McCurdy, J.M.2
Kalish, M.L.3
Liberti, T.4
Metellus, G.5
-
10
-
-
0027175227
-
Molecular investigation of human immunodeficiency virus (HIV) infection in a patient of an HIV-infected surgeon
-
Holmes EC, Zhang LQ, Simmonds P, Rogers AS, Brown AJ (1993) Molecular investigation of human immunodeficiency virus (HIV) infection in a patient of an HIV-infected surgeon. J Infect Dis 167: 1411-1414.
-
(1993)
J Infect Dis
, vol.167
, pp. 1411-1414
-
-
Holmes, E.C.1
Zhang, L.Q.2
Simmonds, P.3
Rogers, A.S.4
Brown, A.J.5
-
11
-
-
0029130259
-
Sequence distances between env genes of HIV-1 from individuals infected from the same source: Implications for the investigation of possible transmission events
-
Arnold C, Balfe P, Clewley JP (1995) Sequence distances between env genes of HIV-1 from individuals infected from the same source: implications for the investigation of possible transmission events. Virology 211: 198-203.
-
(1995)
Virology
, vol.211
, pp. 198-203
-
-
Arnold, C.1
Balfe, P.2
Clewley, J.P.3
-
12
-
-
79952302074
-
Viral linkage in HIV-1 seroconverters and their partners in an HIV-1 prevention clinical trial
-
Campbell MS, Mullins JI, Hughes JP, Celum C, Wong KG, et al. (2011) Viral linkage in HIV-1 seroconverters and their partners in an HIV-1 prevention clinical trial. PLoS One 6: e16986.
-
(2011)
PLoS One
, vol.6
-
-
Campbell, M.S.1
Mullins, J.I.2
Hughes, J.P.3
Celum, C.4
Wong, K.G.5
-
13
-
-
81055124999
-
Analysis of genetic linkage of HIV from couples enrolled in the HIV Prevention Trials Network 052 trial
-
Eshleman SH, Hudelson SE, Redd AD, Wang L, Debes R, et al. (2011) Analysis of genetic linkage of HIV from couples enrolled in the HIV Prevention Trials Network 052 trial. J Infect Dis 204: 1918-1926.
-
(2011)
J Infect Dis
, vol.204
, pp. 1918-1926
-
-
Eshleman, S.H.1
Hudelson, S.E.2
Redd, A.D.3
Wang, L.4
Debes, R.5
-
14
-
-
57349137641
-
Transmission networks of drug resistance acquired in primary/early stage HIV infection
-
Brenner BG, Roger M, Moisi DD, Oliveira M, Hardy I, et al. (2008) Transmission networks of drug resistance acquired in primary/early stage HIV infection. AIDS 22: 2509-2515.
-
(2008)
AIDS
, vol.22
, pp. 2509-2515
-
-
Brenner, B.G.1
Roger, M.2
Moisi, D.D.3
Oliveira, M.4
Hardy, I.5
-
15
-
-
33947375214
-
High rates of forward transmission events after acute/early HIV-1 infection
-
Brenner BG, Roger M, Routy JP, Moisi D, Ntemgwa M, et al. (2007) High rates of forward transmission events after acute/early HIV-1 infection. J Infect Dis 195: 951-959.
-
(2007)
J Infect Dis
, vol.195
, pp. 951-959
-
-
Brenner, B.G.1
Roger, M.2
Routy, J.P.3
Moisi, D.4
Ntemgwa, M.5
-
16
-
-
80052409994
-
Transmission Clustering Drives the Onward Spread of the HIV Epidemic Among Men Who Have Sex With Men in Quebec
-
Brenner BG, Roger M, Stephens D, Moisi D, Hardy I, et al. (2011) Transmission Clustering Drives the Onward Spread of the HIV Epidemic Among Men Who Have Sex With Men in Quebec. J Infect Dis 204: 1115-1119.
-
(2011)
J Infect Dis
, vol.204
, pp. 1115-1119
-
-
Brenner, B.G.1
Roger, M.2
Stephens, D.3
Moisi, D.4
Hardy, I.5
-
17
-
-
77953027429
-
Explosive HIV-1 subtype B′ epidemics in Asia driven by geographic and risk group founder events
-
Li Y, Uenishi R, Hase S, Liao H, Li XJ, et al. (2010) Explosive HIV-1 subtype B′ epidemics in Asia driven by geographic and risk group founder events. Virology 402: 223-227.
-
(2010)
Virology
, vol.402
, pp. 223-227
-
-
Li, Y.1
Uenishi, R.2
Hase, S.3
Liao, H.4
Li, X.J.5
-
18
-
-
77951643501
-
Phylodynamics of HIV-1 circulating recombinant forms 12-BF and 38-BF in Argentina and Uruguay
-
Bello G, Aulicino PC, Ruchansky D, Guimaraes ML, Lopez-Galindez C, et al. (2010) Phylodynamics of HIV-1 circulating recombinant forms 12-BF and 38-BF in Argentina and Uruguay. Retrovirology 7: 22.
-
(2010)
Retrovirology
, vol.7
, pp. 22
-
-
Bello, G.1
Aulicino, P.C.2
Ruchansky, D.3
Guimaraes, M.L.4
Lopez-Galindez, C.5
-
19
-
-
79952527522
-
Phylodynamics of HIV-1 from a phase III AIDS vaccine trial in Bangkok, Thailand
-
Perez-Losada M, Jobes DV, Sinangil F, Crandall KA, Arenas M, et al. (2011) Phylodynamics of HIV-1 from a phase III AIDS vaccine trial in Bangkok, Thailand. PLoS One 6: e16902.
-
(2011)
PLoS One
, vol.6
-
-
Perez-Losada, M.1
Jobes, D.V.2
Sinangil, F.3
Crandall, K.A.4
Arenas, M.5
-
20
-
-
74549175896
-
Phylodynamics of HIV-1 from a phase-III AIDS vaccine trial in North America
-
Perez-Losada M, Jobes DV, Sinangil F, Crandall KA, Posada D, et al. (2010) Phylodynamics of HIV-1 from a phase-III AIDS vaccine trial in North America. Mol Biol Evol 27: 417-425.
-
(2010)
Mol Biol Evol
, vol.27
, pp. 417-425
-
-
Perez-Losada, M.1
Jobes, D.V.2
Sinangil, F.3
Crandall, K.A.4
Posada, D.5
-
21
-
-
79952075443
-
HIV-1 Subtype C Phylodynamics in the Global Epidemic
-
PMCID: PMC3185553
-
Novitsky V, Wang R, Lagakos S, Essex M (2010) HIV-1 Subtype C Phylodynamics in the Global Epidemic. Viruses 2: 33-54. PMCID: PMC3185553.
-
(2010)
Viruses
, vol.2
, pp. 33-54
-
-
Novitsky, V.1
Wang, R.2
Lagakos, S.3
Essex, M.4
-
23
-
-
70349655085
-
Molecular phylodynamics of the heterosexual HIV epidemic in the United Kingdom
-
Hughes GJ, Fearnhill E, Dunn D, Lycett SJ, Rambaut A, et al. (2009) Molecular phylodynamics of the heterosexual HIV epidemic in the United Kingdom. PLoS Pathog 5: e1000590.
-
(2009)
PLoS Pathog
, vol.5
-
-
Hughes, G.J.1
Fearnhill, E.2
Dunn, D.3
Lycett, S.J.4
Rambaut, A.5
-
24
-
-
41549160713
-
Episodic sexual transmission of HIV revealed by molecular phylodynamics
-
Lewis F, Hughes GJ, Rambaut A, Pozniak A, Leigh Brown AJ (2008) Episodic sexual transmission of HIV revealed by molecular phylodynamics. PLoS Med 5: e50.
-
(2008)
PLoS Med
, vol.5
-
-
Lewis, F.1
Hughes, G.J.2
Rambaut, A.3
Pozniak, A.4
Leigh Brown, A.J.5
-
25
-
-
80053427855
-
Transmission network parameters estimated from HIV sequences for a nationwide epidemic
-
Leigh Brown AJ, Lycett SJ, Weinert L, Hughes GJ, Fearnhill E, et al. (2011) Transmission network parameters estimated from HIV sequences for a nationwide epidemic. J Infect Dis 204: 1463-1469.
-
(2011)
J Infect Dis
, vol.204
, pp. 1463-1469
-
-
Leigh Brown, A.J.1
Lycett, S.J.2
Weinert, L.3
Hughes, G.J.4
Fearnhill, E.5
-
26
-
-
77957294810
-
Population dynamics of HIV-1 subtype B in a cohort of men-having-sex-with-men in Rome, Italy
-
Zehender G, Ebranati E, Lai A, Santoro MM, Alteri C, et al. (2010) Population dynamics of HIV-1 subtype B in a cohort of men-having-sex-with-men in Rome, Italy. J Acquir Immune Defic Syndr 55: 156-160.
-
(2010)
J Acquir Immune Defic Syndr
, vol.55
, pp. 156-160
-
-
Zehender, G.1
Ebranati, E.2
Lai, A.3
Santoro, M.M.4
Alteri, C.5
-
27
-
-
79957564900
-
A novel methodology for large-scale phylogeny partition
-
Prosperi MC, Ciccozzi M, Fanti I, Saladini F, Pecorari M, et al. (2011) A novel methodology for large-scale phylogeny partition. Nat Commun 2: 321.
-
(2011)
Nat Commun
, vol.2
, pp. 321
-
-
Prosperi, M.C.1
Ciccozzi, M.2
Fanti, I.3
Saladini, F.4
Pecorari, M.5
-
28
-
-
84876287809
-
Social network-based recruitment successfully reveals HIV-1 transmission networks among high-risk individuals in El Salvador
-
Dennis AM, Murillo W, de Maria Hernandez F, Guardado ME, Nieto AI, et al. (2013) Social network-based recruitment successfully reveals HIV-1 transmission networks among high-risk individuals in El Salvador. J Acquir Immune Defic Syndr 63: 135-141.
-
(2013)
J Acquir Immune Defic Syndr
, vol.63
, pp. 135-141
-
-
Dennis, A.M.1
Murillo, W.2
De Maria Hernandez, F.3
Guardado, M.E.4
Nieto, A.I.5
-
29
-
-
84880367442
-
A Single Early Introduction of HIV-1 Subtype B into Central America Accounts for Most Current Cases
-
Murillo W, Veras N, Prosperi M, de Rivera IL, Paz-Bailey G, et al. (2013) A Single Early Introduction of HIV-1 Subtype B into Central America Accounts for Most Current Cases. J Virol 87: 7463-7470.
-
(2013)
J Virol
, vol.87
, pp. 7463-7470
-
-
Murillo, W.1
Veras, N.2
Prosperi, M.3
De Rivera, I.L.4
Paz-Bailey, G.5
-
30
-
-
84866328903
-
Phylogenetic insights into regional HIV transmission
-
Dennis AM, Hue S, Hurt CB, Napravnik S, Sebastian J, et al. (2012) Phylogenetic insights into regional HIV transmission. AIDS 26: 1813-1822.
-
(2012)
AIDS
, vol.26
, pp. 1813-1822
-
-
Dennis, A.M.1
Hue, S.2
Hurt, C.B.3
Napravnik, S.4
Sebastian, J.5
-
31
-
-
70350347718
-
A HIV-1 heterosexual transmission chain in Guangzhou, China: A molecular epidemiological study
-
Han Z, Leung TW, Zhao J, Wang M, Fan L, et al. (2009) A HIV-1 heterosexual transmission chain in Guangzhou, China: a molecular epidemiological study. Virol J 6: 148.
-
(2009)
Virol J
, vol.6
, pp. 148
-
-
Han, Z.1
Leung, T.W.2
Zhao, J.3
Wang, M.4
Fan, L.5
-
32
-
-
67049171008
-
Molecular epidemiological tracing of HIV-1 outbreaks in Hainan island of southern China
-
Deng W, Fu P, Bao L, Vidal N, He Q, et al. (2009) Molecular epidemiological tracing of HIV-1 outbreaks in Hainan island of southern China. AIDS 23: 977-985.
-
(2009)
AIDS
, vol.23
, pp. 977-985
-
-
Deng, W.1
Fu, P.2
Bao, L.3
Vidal, N.4
He, Q.5
-
33
-
-
65549145836
-
HIV transmission in a state prison system, 1988-2005
-
Jafa K, McElroy P, Fitzpatrick L, Borkowf CB, Macgowan R, et al. (2009) HIV transmission in a state prison system, 1988-2005. PLoS One 4: e5416.
-
(2009)
PLoS One
, vol.4
-
-
Jafa, K.1
McElroy, P.2
Fitzpatrick, L.3
Borkowf, C.B.4
Macgowan, R.5
-
34
-
-
34248562424
-
An outbreak of HIV-1 subtype G among Italian injecting drug users
-
Ciccozzi M, Montieri S, Salemi M, De Oliveira T, Dorrucci M, et al. (2007) An outbreak of HIV-1 subtype G among Italian injecting drug users. AIDS 21: 1213-1215.
-
(2007)
AIDS
, vol.21
, pp. 1213-1215
-
-
Ciccozzi, M.1
Montieri, S.2
Salemi, M.3
De Oliveira, T.4
Dorrucci, M.5
-
35
-
-
79954600726
-
The early phase of an HIV epidemic in a population exposed previously to HCV in the Philippines
-
Telan EF, Samonte GM, Abellanosa-Tac-An IP, Alesna ET, Leano PS, et al. (2011) The early phase of an HIV epidemic in a population exposed previously to HCV in the Philippines. J Med Virol 83: 941-947.
-
(2011)
J Med Virol
, vol.83
, pp. 941-947
-
-
Telan, E.F.1
Samonte, G.M.2
Abellanosa-Tac-An, I.P.3
Alesna, E.T.4
Leano, P.S.5
-
36
-
-
80052774224
-
HIV-1 outbreak among injecting drug users in Greece, 2011: A preliminary report
-
Paraskevis D, Nikolopoulos G, Tsiara C, Paraskeva D, Antoniadou A, et al. (2011) HIV-1 outbreak among injecting drug users in Greece, 2011: a preliminary report. Euro Surveill 16.
-
(2011)
Euro Surveill
, vol.16
-
-
Paraskevis, D.1
Nikolopoulos, G.2
Tsiara, C.3
Paraskeva, D.4
Antoniadou, A.5
-
37
-
-
79957617150
-
Phylogenetic analysis of full-length pol gene from Korean hemophiliacs and plasma donors infected with Korean subclade B of HIV type 1
-
Cho YK, Jung YS, Foley BT (2011) Phylogenetic analysis of full-length pol gene from Korean hemophiliacs and plasma donors infected with Korean subclade B of HIV type 1. AIDS Res Hum Retroviruses 27: 613-621.
-
(2011)
AIDS Res Hum Retroviruses
, vol.27
, pp. 613-621
-
-
Cho, Y.K.1
Jung, Y.S.2
Foley, B.T.3
-
38
-
-
78650045775
-
Dynamics of two separate but linked HIV-1 CRF01-AE outbreaks among injection drug users in Stockholm, Sweden, and Helsinki, Finland
-
Skar H, Axelsson M, Berggren I, Thalme A, Gyllensten K, et al. (2011) Dynamics of two separate but linked HIV-1 CRF01-AE outbreaks among injection drug users in Stockholm, Sweden, and Helsinki, Finland. J Virol 85: 510-518.
-
(2011)
J Virol
, vol.85
, pp. 510-518
-
-
Skar, H.1
Axelsson, M.2
Berggren, I.3
Thalme, A.4
Gyllensten, K.5
-
39
-
-
55249118583
-
Transmission cluster of multiclass highly drug-resistant HIV-1 among 9 men who have sex with men in Seattle/King County, WA, 2005-2007
-
Buskin SE, Ellis GM, Pepper GG, Frenkel LM, Pergam SA, et al. (2008) Transmission cluster of multiclass highly drug-resistant HIV-1 among 9 men who have sex with men in Seattle/King County, WA, 2005-2007. J Acquir Immune Defic Syndr 49: 205-211.
-
(2008)
J Acquir Immune Defic Syndr
, vol.49
, pp. 205-211
-
-
Buskin, S.E.1
Ellis, G.M.2
Pepper, G.G.3
Frenkel, L.M.4
Pergam, S.A.5
-
40
-
-
0031001414
-
Molecular investigation into outbreak of HIV in a Scottish prison
-
Yirrell DL, Robertson P, Goldberg DJ, McMenamin J, Cameron S, et al. (1997) Molecular investigation into outbreak of HIV in a Scottish prison. BMJ 314: 1446-1450.
-
(1997)
BMJ
, vol.314
, pp. 1446-1450
-
-
Yirrell, D.L.1
Robertson, P.2
Goldberg, D.J.3
McMenamin, J.4
Cameron, S.5
-
41
-
-
47749095118
-
Taxon sampling affects inferences of macroevolutionary processes from phylogenetic trees
-
Heath TA, Zwickl DJ, Kim J, Hillis DM (2008) Taxon sampling affects inferences of macroevolutionary processes from phylogenetic trees. Syst Biol 57: 160-166.
-
(2008)
Syst Biol
, vol.57
, pp. 160-166
-
-
Heath, T.A.1
Zwickl, D.J.2
Kim, J.3
Hillis, D.M.4
-
43
-
-
33747099592
-
Breastfeeding plus infant zidovudine prophylaxis for 6 months vs formula feeding plus infant zidovudine for 1 month to reduce mother-to-child HIV transmission in Botswana: A randomized trial: The Mashi Study
-
Thior I, Lockman S, Smeaton LM, Shapiro RL, Wester C, et al. (2006) Breastfeeding plus infant zidovudine prophylaxis for 6 months vs formula feeding plus infant zidovudine for 1 month to reduce mother-to-child HIV transmission in Botswana: a randomized trial: the Mashi Study. JAMA 296: 794-805.
-
(2006)
JAMA
, vol.296
, pp. 794-805
-
-
Thior, I.1
Lockman, S.2
Smeaton, L.M.3
Shapiro, R.L.4
Wester, C.5
-
44
-
-
33745832728
-
Maternal single-dose nevirapine versus placebo as part of an antiretroviral strategy to prevent mother-to-child HIV transmission in Botswana
-
Shapiro RL, Thior I, Gilbert PB, Lockman S, Wester C, et al. (2006) Maternal single-dose nevirapine versus placebo as part of an antiretroviral strategy to prevent mother-to-child HIV transmission in Botswana. AIDS 20: 1281-1288.
-
(2006)
AIDS
, vol.20
, pp. 1281-1288
-
-
Shapiro, R.L.1
Thior, I.2
Gilbert, P.B.3
Lockman, S.4
Wester, C.5
-
45
-
-
57149143564
-
Evolution of proviral gp120 over the first year of HIV-1 subtype C infection
-
NIHMSID # 79286. PMCID: PMC2642736
-
Novitsky V, Lagakos S, Herzig M, Bonney C, Kebaabetswe L, et al. (2009) Evolution of proviral gp120 over the first year of HIV-1 subtype C infection. NIHMSID # 79286. Virology 383: 47-59. PMCID: PMC2642736.
-
(2009)
Virology
, vol.383
, pp. 47-59
-
-
Novitsky, V.1
Lagakos, S.2
Herzig, M.3
Bonney, C.4
Kebaabetswe, L.5
-
46
-
-
79951805495
-
Transmission of Single and Multiple Viral Variants in Primary HIV-1 Subtype C Infection
-
PMCID: PMC3048432
-
Novitsky V, Wang R, Margolin L, Baca J, Rossenkhan R, et al. (2011) Transmission of Single and Multiple Viral Variants in Primary HIV-1 Subtype C Infection. PLoS One 6: e16714.PMCID: PMC3048432.
-
(2011)
PLoS One
, vol.6
-
-
Novitsky, V.1
Wang, R.2
Margolin, L.3
Baca, J.4
Rossenkhan, R.5
-
47
-
-
84900179100
-
Intra-host evolutionary rates in HIV-1C env and gag during primary infection
-
Novitsky V, Wang R, Rossenkhan R, Moyo S, Essex M (2013) Intra-host evolutionary rates in HIV-1C env and gag during primary infection. Infect Genet Evol 19: 361-368.
-
(2013)
Infect Genet Evol
, vol.19
, pp. 361-368
-
-
Novitsky, V.1
Wang, R.2
Rossenkhan, R.3
Moyo, S.4
Essex, M.5
-
48
-
-
0027690383
-
Genetic relationships determined by a DNA heteroduplex mobility assay: Analysis of HIV-1 env genes
-
Delwart EL, Shpaer EG, McCutchan FE, Louwagie J, Grez M, et al. (1993) Genetic relationships determined by a DNA heteroduplex mobility assay: Analysis of HIV-1 env genes. Science 262: 1257-1261.
-
(1993)
Science
, vol.262
, pp. 1257-1261
-
-
Delwart, E.L.1
Shpaer, E.G.2
McCutchan, F.E.3
Louwagie, J.4
Grez, M.5
-
49
-
-
0036315006
-
An improved method for post-PCR purification for mtDNA sequence analysis
-
Dugan KA, Lawrence HS, Hares DR, Fisher CL, Budowle B (2002) An improved method for post-PCR purification for mtDNA sequence analysis. J Forensic Sci 47: 811-818.
-
(2002)
J Forensic Sci
, vol.47
, pp. 811-818
-
-
Dugan, K.A.1
Lawrence, H.S.2
Hares, D.R.3
Fisher, C.L.4
Budowle, B.5
-
50
-
-
3042666256
-
MUSCLE: Multiple sequence alignment with high accuracy and high throughput
-
Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
51
-
-
0002051540
-
BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT
-
Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 41: 95-98.
-
(1999)
Nucl Acids Symp Ser
, vol.41
, pp. 95-98
-
-
Hall, T.A.1
-
52
-
-
36448991500
-
Clustal W and Clustal X version 2.0
-
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947-2948.
-
(2007)
Bioinformatics
, vol.23
, pp. 2947-2948
-
-
Larkin, M.A.1
Blackshields, G.2
Brown, N.P.3
Chenna, R.4
McGettigan, P.A.5
-
54
-
-
67649327176
-
FastTree: Computing large minimum evolution trees with profiles instead of a distance matrix
-
Price MN, Dehal PS, Arkin AP (2009) FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol 26: 1641-1650.
-
(2009)
Mol Biol Evol
, vol.26
, pp. 1641-1650
-
-
Price, M.N.1
Dehal, P.S.2
Arkin, A.P.3
-
55
-
-
77949718257
-
FastTree 2-approximately maximumlikelihood trees for large alignments
-
Price MN, Dehal PS, Arkin AP (2010) FastTree 2-approximately maximumlikelihood trees for large alignments. PLoS One 5: e9490.
-
(2010)
PLoS One
, vol.5
-
-
Price, M.N.1
Dehal, P.S.2
Arkin, A.P.3
-
56
-
-
77950806408
-
New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0
-
Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, et al. (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59: 307-321.
-
(2010)
Syst Biol
, vol.59
, pp. 307-321
-
-
Guindon, S.1
Dufayard, J.F.2
Lefort, V.3
Anisimova, M.4
Hordijk, W.5
-
57
-
-
33750403801
-
RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
-
Stamatakis A (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688- 2690.
-
(2006)
Bioinformatics
, vol.22
, pp. 2688-2690
-
-
Stamatakis, A.1
-
58
-
-
0026660413
-
A simple method for estimating and testing minimum evolution trees
-
Rzhetsky A, Nei M (1992) A simple method for estimating and testing minimum evolution trees. Molecular Biology and Evolution 9: 945-967.
-
(1992)
Molecular Biology and Evolution
, vol.9
, pp. 945-967
-
-
Rzhetsky, A.1
Nei, M.2
-
59
-
-
79957613599
-
MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods
-
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Mol Biol Evol 28: 2731-2739.
-
(2011)
Mol Biol Evol
, vol.28
, pp. 2731-2739
-
-
Tamura, K.1
Peterson, D.2
Peterson, N.3
Stecher, G.4
Nei, M.5
-
60
-
-
3342920601
-
Prospects for inferring very large phylogenies by using the neighbor-joining method
-
Tamura K, Nei M, Kumar S (2004) Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci U S A 101: 11030-11035.
-
(2004)
Proc Natl Acad Sci U S A
, vol.101
, pp. 11030-11035
-
-
Tamura, K.1
Nei, M.2
Kumar, S.3
-
61
-
-
84864489995
-
T-REX: A web server for inferring, validating and visualizing phylogenetic trees and networks
-
Alix B, Boubacar DA, Vladimir M (2012) T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks. Nucleic Acids Res 40: W573-579.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Alix, B.1
Boubacar, D.A.2
Vladimir, M.3
-
62
-
-
77954202497
-
DendroPy: A Python library for phylogenetic computing
-
Sukumaran J, Holder MT (2010) DendroPy: a Python library for phylogenetic computing. Bioinformatics 26: 1569-1571.
-
(2010)
Bioinformatics
, vol.26
, pp. 1569-1571
-
-
Sukumaran, J.1
Holder, M.T.2
-
63
-
-
74549125386
-
SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building
-
Gouy M, Guindon S, Gascuel O (2010) SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol 27: 221-224.
-
(2010)
Mol Biol Evol
, vol.27
, pp. 221-224
-
-
Gouy, M.1
Guindon, S.2
Gascuel, O.3
-
64
-
-
33646167864
-
A simple and robust statistical test for detecting the presence of recombination
-
Bruen TC, Philippe H, Bryant D (2006) A simple and robust statistical test for detecting the presence of recombination. Genetics 172: 2665-2681.
-
(2006)
Genetics
, vol.172
, pp. 2665-2681
-
-
Bruen, T.C.1
Philippe, H.2
Bryant, D.3
-
65
-
-
0031678692
-
SplitsTree: Analyzing and visualizing evolutionary data
-
Huson DH (1998) SplitsTree: analyzing and visualizing evolutionary data. Bioinformatics 14: 68-73.
-
(1998)
Bioinformatics
, vol.14
, pp. 68-73
-
-
Huson, D.H.1
-
66
-
-
30744470609
-
Application of phylogenetic networks in evolutionary studies
-
Huson DH, Bryant D (2006) Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 23: 254-267.
-
(2006)
Mol Biol Evol
, vol.23
, pp. 254-267
-
-
Huson, D.H.1
Bryant, D.2
-
67
-
-
77957243284
-
RDP3: A flexible and fast computer program for analyzing recombination
-
Martin DP, Lemey P, Lott M, Moulton V, Posada D, et al. (2010) RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics 26: 2462-2463.
-
(2010)
Bioinformatics
, vol.26
, pp. 2462-2463
-
-
Martin, D.P.1
Lemey, P.2
Lott, M.3
Moulton, V.4
Posada, D.5
-
68
-
-
0033824415
-
RDP: Detection of recombination amongst aligned sequences
-
Martin D, Rybicki E (2000) RDP: detection of recombination amongst aligned sequences. Bioinformatics 16: 562-563.
-
(2000)
Bioinformatics
, vol.16
, pp. 562-563
-
-
Martin, D.1
Rybicki, E.2
-
69
-
-
0033590220
-
Possible emergence of new geminiviruses by frequent recombination
-
Padidam M, Sawyer S, Fauquet CM (1999) Possible emergence of new geminiviruses by frequent recombination. Virology 265: 218-225.
-
(1999)
Virology
, vol.265
, pp. 218-225
-
-
Padidam, M.1
Sawyer, S.2
Fauquet, C.M.3
-
70
-
-
13144283628
-
A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints
-
Martin DP, Posada D, Crandall KA, Williamson C (2005) A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints. AIDS Res Hum Retroviruses 21: 98-102.
-
(2005)
AIDS Res Hum Retroviruses
, vol.21
, pp. 98-102
-
-
Martin, D.P.1
Posada, D.2
Crandall, K.A.3
Williamson, C.4
-
71
-
-
0026708873
-
Analyzing the mosaic structure of genes
-
Smith MJ (1992) Analyzing the mosaic structure of genes. J Mol Evol 34: 126-129.
-
(1992)
J Mol Evol
, vol.34
, pp. 126-129
-
-
Smith, M.J.1
-
72
-
-
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 U S A 98: 13757-13762.
-
(2001)
Proc Natl Acad Sci U S A
, vol.98
, pp. 13757-13762
-
-
Posada, D.1
Crandall, K.A.2
-
73
-
-
0033753825
-
Sister-scanning: A Monte Carlo procedure for assessing signals in recombinant sequences
-
Gibbs MJ, Armstrong JS, Gibbs AJ (2000) Sister-scanning: a Monte Carlo procedure for assessing signals in recombinant sequences. Bioinformatics 16: 573-582.
-
(2000)
Bioinformatics
, vol.16
, pp. 573-582
-
-
Gibbs, M.J.1
Armstrong, J.S.2
Gibbs, A.J.3
-
74
-
-
34250757252
-
An exact nonparametric method for inferring mosaic structure in sequence triplets
-
Boni MF, Posada D, Feldman MW (2007) An exact nonparametric method for inferring mosaic structure in sequence triplets. Genetics 176: 1035-1047.
-
(2007)
Genetics
, vol.176
, pp. 1035-1047
-
-
Boni, M.F.1
Posada, D.2
Feldman, M.W.3
-
76
-
-
85027958165
-
Extended high viremics: A substantial fraction of individuals maintain high plasma viral RNA levels after acute HIV-1 subtype C infection
-
Novitsky V, Ndung'u T, Wang R, Bussmann H, Chonco F, et al. (2011) Extended high viremics: a substantial fraction of individuals maintain high plasma viral RNA levels after acute HIV-1 subtype C infection. AIDS 25: 1515-1522.
-
(2011)
AIDS
, vol.25
, pp. 1515-1522
-
-
Novitsky, V.1
Ndung'u, T.2
Wang, R.3
Bussmann, H.4
Chonco, F.5
-
77
-
-
0026739607
-
Signature pattern analysis: A method for assessing viral sequence relatedness
-
Korber B, Myers G (1992) Signature pattern analysis: a method for assessing viral sequence relatedness. AIDS Res Hum Retroviruses 8: 1549-1560.
-
(1992)
AIDS Res Hum Retroviruses
, vol.8
, pp. 1549-1560
-
-
Korber, B.1
Myers, G.2
-
78
-
-
79961174964
-
The genetic bottleneck in vertical transmission of subtype C HIV-1 is not driven by selection of especially neutralization-resistant virus from the maternal viral population
-
Russell ES, Kwiek JJ, Keys J, Barton K, Mwapasa V, et al. (2011) The genetic bottleneck in vertical transmission of subtype C HIV-1 is not driven by selection of especially neutralization-resistant virus from the maternal viral population. J Virol 85: 8253-8262.
-
(2011)
J Virol
, vol.85
, pp. 8253-8262
-
-
Russell, E.S.1
Kwiek, J.J.2
Keys, J.3
Barton, K.4
Mwapasa, V.5
-
79
-
-
79960418197
-
Different regions of HIV-1 subtype C env are associated with placental localization and in utero mother-to-child transmission
-
Kumar SB, Handelman SK, Voronkin I, Mwapasa V, Janies D, et al. (2011) Different regions of HIV-1 subtype C env are associated with placental localization and in utero mother-to-child transmission. J Virol 85: 7142-7152.
-
(2011)
J Virol
, vol.85
, pp. 7142-7152
-
-
Kumar, S.B.1
Handelman, S.K.2
Voronkin, I.3
Mwapasa, V.4
Janies, D.5
-
80
-
-
64249109641
-
Viral Load and CD4+ T Cell Dynamics in Primary HIV-1 Subtype C Infection
-
PMCID: PMC2701379
-
Novitsky V, Woldegabriel E, Kebaabetswe L, Rossenkhan R, Mlotshwa B, et al. (2009) Viral Load and CD4+ T Cell Dynamics in Primary HIV-1 Subtype C Infection. J Acquir Immune Defic Syndr 50: 65-76.PMCID: PMC2701379.
-
(2009)
J Acquir Immune Defic Syndr
, vol.50
, pp. 65-76
-
-
Novitsky, V.1
Woldegabriel, E.2
Kebaabetswe, L.3
Rossenkhan, R.4
Mlotshwa, B.5
-
81
-
-
50449111172
-
Identification of primary HIV-1C infection in Botswana
-
NIHMSID # 79283. PMCID: PMC2605733
-
Novitsky V, Woldegabriel E, Wester C, McDonald E, Rossenkhan R, et al. (2008) Identification of primary HIV-1C infection in Botswana. NIHMSID # 79283. AIDS Care 20: 806-811.PMCID: PMC2605733.
-
(2008)
AIDS Care
, vol.20
, pp. 806-811
-
-
Novitsky, V.1
Woldegabriel, E.2
Wester, C.3
McDonald, E.4
Rossenkhan, R.5
-
82
-
-
70349213939
-
Adult combination antiretroviral therapy in sub-Saharan Africa: Lessons from Botswana and future challenges
-
Wester CW, Bussmann H, Koethe J, Moffat C, Vermund S, et al. (2009) Adult combination antiretroviral therapy in sub-Saharan Africa: lessons from Botswana and future challenges. HIV Ther 3: 501-526.
-
(2009)
HIV Ther
, vol.3
, pp. 501-526
-
-
Wester, C.W.1
Bussmann, H.2
Koethe, J.3
Moffat, C.4
Vermund, S.5
-
83
-
-
56749185586
-
Five-year outcomes of initial patients treated in Botswana's National Antiretroviral Treatment Program
-
Bussmann H, Wester CW, Ndwapi N, Grundmann N, Gaolathe T, et al. (2008) Five-year outcomes of initial patients treated in Botswana's National Antiretroviral Treatment Program. AIDS 22: 2303-2311.
-
(2008)
AIDS
, vol.22
, pp. 2303-2311
-
-
Bussmann, H.1
Wester, C.W.2
Ndwapi, N.3
Grundmann, N.4
Gaolathe, T.5
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