-
1
-
-
19944428265
-
Multiple, linked human immunodeficiency virus type 1 drug resistance mutations in treatment-experienced patients are missed by standard genotype analysis
-
Palmer, S.; Kearney, M.; Maldarelli, F.; Halvas, E.K.; Bixby, C.J.; Bazmi, H.; Rock, D.; Falloon, J.; Davey, R.T., Jr.; Dewar, R.L.; et al. Multiple, linked human immunodeficiency virus type 1 drug resistance mutations in treatment-experienced patients are missed by standard genotype analysis. J. Clin. Microbiol. 2005, 43, 406-413.
-
(2005)
J. Clin. Microbiol
, vol.43
, pp. 406-413
-
-
Palmer, S.1
Kearney, M.2
Maldarelli, F.3
Halvas, E.K.4
Bixby, C.J.5
Bazmi, H.6
Rock, D.7
Falloon, J.8
Davey, R.T.9
Dewar, R.L.10
-
2
-
-
0033037358
-
Worldwide evaluation of DNA sequencing approaches for identification of drug resistance mutations in the human immunodeficiency virus type 1 reverse transcriptase
-
Schuurman, R.; Demeter, L.; Reichelderfer, P.; Tijnagel, J.; de Groot, T.; Boucher, C. Worldwide evaluation of DNA sequencing approaches for identification of drug resistance mutations in the human immunodeficiency virus type 1 reverse transcriptase. J. Clin. Microbiol. 1999, 37, 2291-2296.
-
(1999)
J. Clin. Microbiol
, vol.37
, pp. 2291-2296
-
-
Schuurman, R.1
Demeter, L.2
Reichelderfer, P.3
Tijnagel, J.4
de Groot, T.5
Boucher, C.6
-
3
-
-
33746191676
-
Blinded, multicenter comparison of methods to detect a drug-resistant mutant of human immunodeficiency virus type 1 at low frequency
-
Halvas, E.K.; Aldrovandi, G.M.; Balfe, P.; Beck, I.A.; Boltz, V.F.; Coffin, J.M.; Frenkel, L.M.; Hazelwood, J.D.; Johnson, V.A.; Kearney, M.; et al. Blinded, multicenter comparison of methods to detect a drug-resistant mutant of human immunodeficiency virus type 1 at low frequency. J. Clin. Microbiol. 2006, 44, 2612-2614.
-
(2006)
J. Clin. Microbiol
, vol.44
, pp. 2612-2614
-
-
Halvas, E.K.1
Aldrovandi, G.M.2
Balfe, P.3
Beck, I.A.4
Boltz, V.F.5
Coffin, J.M.6
Frenkel, L.M.7
Hazelwood, J.D.8
Johnson, V.A.9
Kearney, M.10
-
4
-
-
0036210739
-
Underestimation of HIV type 1 drug resistance mutations: Results from the ENVA-2 genotyping proficiency program
-
Schuurman, R.; Brambilla, D.; de Groot, T.; Huang, D.; Land, S.; Bremer, J.; Benders, I.; Boucher, C.A.B.; ENVAWorking Group. Underestimation of HIV type 1 drug resistance mutations: Results from the ENVA-2 genotyping proficiency program. AIDS Res. Hum. Retroviruses 2002, 18, 243-248.
-
(2002)
AIDS Res. Hum. Retroviruses
, vol.18
, pp. 243-248
-
-
Schuurman, R.1
Brambilla, D.2
de Groot, T.3
Huang, D.4
Land, S.5
Bremer, J.6
Benders, I.7
Boucher, C.A.B.8
-
5
-
-
34147118573
-
No response to first-line tenofovir+lamivudine+efavirenz despite optimization according to baseline resistance testing: Impact of resistant minority variants on efficacy of low genetic barrier drugs
-
Van Laethem, K.; de Munter, P.; Schrooten, Y.; Verbesselt, R.; van Ranst, M.; van Wijngaerden, E.; Vandamme, A.M. No response to first-line tenofovir+lamivudine+efavirenz despite optimization according to baseline resistance testing: Impact of resistant minority variants on efficacy of low genetic barrier drugs. J. Clin. Virol. 2007, 39, 43-47.
-
(2007)
J. Clin. Virol
, vol.39
, pp. 43-47
-
-
Van Laethem, K.1
de Munter, P.2
Schrooten, Y.3
Verbesselt, R.4
van Ranst, M.5
van Wijngaerden, E.6
Vandamme, A.M.7
-
6
-
-
77954192930
-
Low-frequency HIV-1 drug resistance mutations can be clinically significant but must be interpreted with caution
-
Johnson, J.A.; Geretti, A.M. Low-frequency HIV-1 drug resistance mutations can be clinically significant but must be interpreted with caution. J. Antimicrob. Chemother. 2010, 65, 1322-1326.
-
(2010)
J. Antimicrob. Chemother
, vol.65
, pp. 1322-1326
-
-
Johnson, J.A.1
Geretti, A.M.2
-
7
-
-
48749086685
-
Minority HIV-1 drug resistance mutations are present in antiretroviral treatment-naïve populations and associate with reduced treatment efficacy
-
Johnson, J.A.; Li, J.F.; Wei, X.; Lipscomb, J.; Irlbeck, D.; Craig, C.; Smith, A.; Bennett, D.E.; Monsour, M.; Sandstrom, P.; et al. Minority HIV-1 drug resistance mutations are present in antiretroviral treatment-naïve populations and associate with reduced treatment efficacy. PLoS Med. 2008, 5, doi:10.1371/journal. pmed.0050158.
-
(2008)
PLoS Med
, vol.5
-
-
Johnson, J.A.1
Li, J.F.2
Wei, X.3
Lipscomb, J.4
Irlbeck, D.5
Craig, C.6
Smith, A.7
Bennett, D.E.8
Monsour, M.9
Sandstrom, P.10
-
8
-
-
79959598119
-
Minor HIV-1 variants with the K103N resistance mutation during intermittent efavirenz-containing antiretroviral therapy and virological failure
-
Delobel, P.; Saliou, A.; Nicot, F.; Dubois, M.; Trancart, S.; Tangre, P.; Aboulker, J.P.; Taburet, A.M.; Molina, J.M.; Massip, P.; et al. Minor HIV-1 variants with the K103N resistance mutation during intermittent efavirenz-containing antiretroviral therapy and virological failure. PLoS ONE 2011, 6, doi:10.1371/journal. pone.0021655.
-
(2011)
PLoS ONE
, vol.6
-
-
Delobel, P.1
Saliou, A.2
Nicot, F.3
Dubois, M.4
Trancart, S.5
Tangre, P.6
Aboulker, J.P.7
Taburet, A.M.8
Molina, J.M.9
Massip, P.10
-
9
-
-
61849172898
-
Low-abundance drug-resistant viral variants in chronically HIV-infected, antiretroviral treatment-naive patients significantly impact treatment outcomes
-
Simen, B.B.; Simons, J.F.; Hullsiek, K.H.; Novak, R.M.; Macarthur, R.D.; Baxter, J.D.; Huang, C.; Lubeski, C.; Turenchalk, G.S.; Braverman, M.S.; et al. Low-abundance drug-resistant viral variants in chronically HIV-infected, antiretroviral treatment-naive patients significantly impact treatment outcomes. J. Infect. Dis. 2009, 199, 693-701.
-
(2009)
J. Infect. Dis
, vol.199
, pp. 693-701
-
-
Simen, B.B.1
Simons, J.F.2
Hullsiek, K.H.3
Novak, R.M.4
Macarthur, R.D.5
Baxter, J.D.6
Huang, C.7
Lubeski, C.8
Turenchalk, G.S.9
Braverman, M.S.10
-
10
-
-
85042812250
-
-
Antiviral Therapy: London, UK
-
Lataillade, M.; Chiarella, J.; Yang, R.; Schnittman, S.; Wirtz, V.; Mancini, M.; Uy, J.; Seekins, D.; Krystal, M.; McGrath, D.; et al. Prevalence and Clinical Significance of Transmitted Drug-Resistant (TDR) HIV Mutations by Ultra-Deep Sequencing (UDS) in HIV-Infected ARV-Naive Subjects in CASTLE Study; Antiviral Therapy: London, UK, 2009; Volume 14, p. A44.
-
(2009)
Prevalence and Clinical Significance of Transmitted Drug-Resistant (TDR) HIV Mutations by Ultra-Deep Sequencing (UDS) in HIV-Infected ARV-Naive Subjects in CASTLE Study
, vol.14
-
-
Lataillade, M.1
Chiarella, J.2
Yang, R.3
Schnittman, S.4
Wirtz, V.5
Mancini, M.6
Uy, J.7
Seekins, D.8
Krystal, M.9
McGrath, D.10
-
11
-
-
83455246850
-
Prevalence and impact of minority variant drug resistance mutations in primary HIV-1 infection
-
Stekler, J.D.; Ellis, G.M.; Carlsson, J.; Eilers, B.; Holte, S.; Maenza, J.; Stevens, C.E.; Collier, A.C.; Frenkel, L.M. Prevalence and impact of minority variant drug resistance mutations in primary HIV-1 infection. PLoS ONE 2011, 6, doi:10.1371/journal.pone.0028952.
-
(2011)
PLoS ONE
, vol.6
-
-
Stekler, J.D.1
Ellis, G.M.2
Carlsson, J.3
Eilers, B.4
Holte, S.5
Maenza, J.6
Stevens, C.E.7
Collier, A.C.8
Frenkel, L.M.9
-
12
-
-
49849095346
-
ANRS CO3 Aquitaine Cohort. Transmission of HIV-1 minority-resistant variants and response to first-line antiretroviral therapy
-
Peuchant, O.; Thiébaut, R.; Capdepont, S.; Lavignolle-Aurillac, V.; Neau, D.; Morlat, P.; Dabis, F.; Fleury, H.; Masquelier, B.; ANRS CO3 Aquitaine Cohort. Transmission of HIV-1 minority-resistant variants and response to first-line antiretroviral therapy. AIDS 2008, 22, 1417-1423.
-
(2008)
AIDS
, vol.22
, pp. 1417-1423
-
-
Peuchant, O.1
Thiébaut, R.2
Capdepont, S.3
Lavignolle-Aurillac, V.4
Neau, D.5
Morlat, P.6
Dabis, F.7
Fleury, H.8
Masquelier, B.9
-
13
-
-
84928171874
-
Low-frequency drug-resistant HIV-1 and risk of virological failure to first-line NNRTI-based ART: A multicohort European case-control study using centralized ultrasensitive 454 pyrosequencing
-
Cozzi-Lepri, A.; Noguera-Julian, M.; di Giallonardo, F.; Schuurman, R.; Däumer, M.; Aitken, S.; Ceccherini-Silberstein, F.; D'Arminio Monforte, A.; Geretti, A.M.; Booth, C.L.; et al. Low-frequency drug-resistant HIV-1 and risk of virological failure to first-line NNRTI-based ART: A multicohort European case-control study using centralized ultrasensitive 454 pyrosequencing. J. Antimicrob. Chemother. 2015, 70, 930-940.
-
(2015)
J. Antimicrob. Chemother
, vol.70
, pp. 930-940
-
-
Cozzi-Lepri, A.1
Noguera-Julian, M.2
di Giallonardo, F.3
Schuurman, R.4
Däumer, M.5
Aitken, S.6
Ceccherini-Silberstein, F.7
D'Arminio Monforte, A.8
Geretti, A.M.9
Booth, C.L.10
-
14
-
-
79955477986
-
Effect of transmitted drug resistance on virological and immunological response to initial combination antiretroviral therapy for HIV (EuroCoord-CHAIN joint project): A European multicohort study
-
Wittkop, L.; Günthard, H.F.; de Wolf, F.; Dunn, D.; Cozzi-Lepri, A.; de Luca, A.; Kücherer, C.; Obel, N.; von Wyl, V.; Masquelier, B.; et al. Effect of transmitted drug resistance on virological and immunological response to initial combination antiretroviral therapy for HIV (EuroCoord-CHAIN joint project): A European multicohort study. Lancet Infect. Dis. 2011, 11, 363-371.
-
(2011)
Lancet Infect. Dis
, vol.11
, pp. 363-371
-
-
Wittkop, L.1
Günthard, H.F.2
de Wolf, F.3
Dunn, D.4
Cozzi-Lepri, A.5
de Luca, A.6
Kücherer, C.7
Obel, N.8
von Wyl, V.9
Masquelier, B.10
-
15
-
-
0037043652
-
Antiretroviral-drug resistance among patients recently infected with HIV
-
Little, S.J.; Holte, S.; Routy, J.P.; Daar, E.S.; Markowitz, M.; Collier, A.C.; Koup, R.A.; Mellors, J.W.; Connick, E.; Conway, B.; et al. Antiretroviral-drug resistance among patients recently infected with HIV. N. Engl. J. Med. 2002, 347, 385-394.
-
(2002)
N. Engl. J. Med
, vol.347
, pp. 385-394
-
-
Little, S.J.1
Holte, S.2
Routy, J.P.3
Daar, E.S.4
Markowitz, M.5
Collier, A.C.6
Koup, R.A.7
Mellors, J.W.8
Connick, E.9
Conway, B.10
-
16
-
-
34447554516
-
Prevalence and determinants of transmitted antiretroviral drug resistance in HIV-1 infection
-
Booth, C.L.; Geretti, A.M. Prevalence and determinants of transmitted antiretroviral drug resistance in HIV-1 infection. J. Antimicrob. Chemother. 2007, 59, 1047-1056.
-
(2007)
J. Antimicrob. Chemother
, vol.59
, pp. 1047-1056
-
-
Booth, C.L.1
Geretti, A.M.2
-
17
-
-
34249314428
-
Minor-drug-resistant HIV populations and treatment failure
-
Gao, F.; Dongning, W. Minor-drug-resistant HIV populations and treatment failure. Future Virol. 2007, 2, 293-302.
-
(2007)
Future Virol
, vol.2
, pp. 293-302
-
-
Gao, F.1
Dongning, W.2
-
18
-
-
70349911886
-
New developments in HIV drug resistance
-
Cane, P.A. New developments in HIV drug resistance. J. Antimicrob. Chemother. 2009, 64, i37-i40.
-
(2009)
J. Antimicrob. Chemother
, vol.64
, pp. i37-i40
-
-
Cane, P.A.1
-
19
-
-
78049524598
-
Whole-genome characterization of human and simian immunodeficiency virus intrahost diversity by ultradeep pyrosequencing
-
Bimber, B.N.; Dudley, D.M.; Lauck, M.; Becker, E.A.; Chin, E.N.; Lank, S.M.; Grunenwald, H.L.; Caruccio, N.C.; Maffitt, M.; Wilson, N.A.; et al. Whole-genome characterization of human and simian immunodeficiency virus intrahost diversity by ultradeep pyrosequencing. J. Virol. 2010, 84, 12087-12092.
-
(2010)
J. Virol
, vol.84
, pp. 12087-12092
-
-
Bimber, B.N.1
Dudley, D.M.2
Lauck, M.3
Becker, E.A.4
Chin, E.N.5
Lank, S.M.6
Grunenwald, H.L.7
Caruccio, N.C.8
Maffitt, M.9
Wilson, N.A.10
-
20
-
-
78149456704
-
Development of a low bias method for characterizing viral populations using next generation sequencing technology
-
Willerth, S.M.; Pedro, H.A.M.; Pachter, L.; Humeau, L.M.; Arkin, A.P.; Schaffer, D.V. Development of a low bias method for characterizing viral populations using next generation sequencing technology. PLoS ONE 2010, 5, doi:10.1371/journal.pone.0013564.
-
(2010)
PLoS ONE
, vol.5
-
-
Willerth, S.M.1
Pedro, H.A.M.2
Pachter, L.3
Humeau, L.M.4
Arkin, A.P.5
Schaffer, D.V.6
-
21
-
-
84869203987
-
Universal amplification, next-generation sequencing, and assembly of HIV-1 genomes
-
Gall, A.; Ferns, B.; Morris, C.;Watson, S.; Cotten, M.; Robinson, M.; Berry, N.; Pillay, D.; Kellam, P. Universal amplification, next-generation sequencing, and assembly of HIV-1 genomes. J. Clin. Microbiol. 2012, 50, 3838-3844.
-
(2012)
J. Clin. Microbiol
, vol.50
, pp. 3838-3844
-
-
Gall, A.1
Ferns, B.2
Morris, C.3
Watson, S.4
Cotten, M.5
Robinson, M.6
Berry, N.7
Pillay, D.8
Kellam, P.9
-
22
-
-
84861214061
-
Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection
-
Henn, M.R.; Boutwell, C.L.; Charlebois, P.; Lennon, N.J.; Power, K.A.; Macalalad, A.R.; Berlin, A.M.; Malboeuf, C.M.; Ryan, E.M.; Gnerre, S.; et al. Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection. PLoS Pathog. 2012, 8, doi:10.1371/journal.ppat.1002529.
-
(2012)
PLoS Pathog
, vol.8
-
-
Henn, M.R.1
Boutwell, C.L.2
Charlebois, P.3
Lennon, N.J.4
Power, K.A.5
Macalalad, A.R.6
Berlin, A.M.7
Malboeuf, C.M.8
Ryan, E.M.9
Gnerre, S.10
-
23
-
-
84896944940
-
Sensitive deep-sequencing-based HIV-1 genotyping assay to simultaneously determine susceptibility to protease, reverse transcriptase, integrase, and maturation inhibitors, as well as HIV-1 coreceptor tropism
-
Gibson, R.M.; Meyer, A.M.; Winner, D.; Archer, J.; Feyertag, F.; Ruiz-Mateos, E.; Leal, M.; Robertson, D.L.; Schmotzer, C.L.; Quiñones-Mateu, M.E. Sensitive deep-sequencing-based HIV-1 genotyping assay to simultaneously determine susceptibility to protease, reverse transcriptase, integrase, and maturation inhibitors, as well as HIV-1 coreceptor tropism. Antimicrob. Agents Chemother. 2014, 58, 2167-2185.
-
(2014)
Antimicrob. Agents Chemother
, vol.58
, pp. 2167-2185
-
-
Gibson, R.M.1
Meyer, A.M.2
Winner, D.3
Archer, J.4
Feyertag, F.5
Ruiz-Mateos, E.6
Leal, M.7
Robertson, D.L.8
Schmotzer, C.L.9
Quiñones-Mateu, M.E.10
-
24
-
-
84907842569
-
A near-full length genotypic assay for HCV1b
-
Cuypers, L.; Snoeck, J.; Vrancken, B.; Kerremans, L.; Vuagniaux, G.; Verbeeck, J.; Nevens, F.; Camacho, R.J.; Vandamme, A.M.; van Dooren, S. A near-full length genotypic assay for HCV1b. J. Virol. Methods 2014, 209, 126-135.
-
(2014)
J. Virol. Methods
, vol.209
, pp. 126-135
-
-
Cuypers, L.1
Snoeck, J.2
Vrancken, B.3
Kerremans, L.4
Vuagniaux, G.5
Verbeeck, J.6
Nevens, F.7
Camacho, R.J.8
Vandamme, A.M.9
van Dooren, S.10
-
25
-
-
84878837128
-
A modified RNA-Seq approach for whole genome sequencing of RNA viruses from faecal and blood samples
-
Batty, E.M.; Wong, T.H.N.; Trebes, A.; Argoud, K.; Attar, M.; Buck, D.; Ip, C.L.C.; Golubchik, T.; Cule, M.; Bowden, R.; et al. A modified RNA-Seq approach for whole genome sequencing of RNA viruses from faecal and blood samples. PLoS ONE 2013, 8, doi:10.1371/journal.pone.0066129.
-
(2013)
PLoS ONE
, vol.8
-
-
Batty, E.M.1
Wong, T.H.N.2
Trebes, A.3
Argoud, K.4
Attar, M.5
Buck, D.6
Ip, C.L.C.7
Golubchik, T.8
Cule, M.9
Bowden, R.10
-
26
-
-
84867398590
-
Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification
-
Malboeuf, C.M.; Yang, X.; Charlebois, P.; Qu, J.; Berlin, A.M.; Casali, M.; Pesko, K.N.; Boutwell, C.L.; DeVincenzo, J.P.; Ebel, G.D.; et al. Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification. Nucleic Acids Res. 2013, 41, doi:10.1093/nar/gks794.
-
(2013)
Nucleic Acids Res
, vol.41
-
-
Malboeuf, C.M.1
Yang, X.2
Charlebois, P.3
Qu, J.4
Berlin, A.M.5
Casali, M.6
Pesko, K.N.7
Boutwell, C.L.8
DeVincenzo, J.P.9
Ebel, G.D.10
-
27
-
-
77956667520
-
Covering all bases in HIV research: Unveiling a hidden world of viral evolution
-
Vrancken, B.; Lequime, S.; Theys, K.; Lemey, P. Covering all bases in HIV research: Unveiling a hidden world of viral evolution. AIDS Rev. 2010, 12, 89-102.
-
(2010)
AIDS Rev
, vol.12
, pp. 89-102
-
-
Vrancken, B.1
Lequime, S.2
Theys, K.3
Lemey, P.4
-
28
-
-
34547829263
-
DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations
-
Hoffmann, C.; Minkah, N.; Leipzig, J.; Wang, G.; Arens, M.Q.; Tebas, P.; Bushman, F.D. DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations. Nucleic Acids Res. 2007, 35, doi:10.1093/nar/gkm435.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Hoffmann, C.1
Minkah, N.2
Leipzig, J.3
Wang, G.4
Arens, M.Q.5
Tebas, P.6
Bushman, F.D.7
-
29
-
-
0028999769
-
In situ isolation of mRNA from individual plant cells: Creation of cell-specific cDNA libraries
-
Karrer, E.E.; Lincoln, J.E.; Hogenhout, S.; Bennett, A.B.; Bostock, R.M.; Martineau, B.; Lucas, W.J.; Gilchrist, D.G.; Alexander, D. In situ isolation of mRNA from individual plant cells: Creation of cell-specific cDNA libraries. Proc. Natl. Acad. Sci. USA 1995, 92, 3814-3818.
-
(1995)
Proc. Natl. Acad. Sci. USA
, vol.92
, pp. 3814-3818
-
-
Karrer, E.E.1
Lincoln, J.E.2
Hogenhout, S.3
Bennett, A.B.4
Bostock, R.M.5
Martineau, B.6
Lucas, W.J.7
Gilchrist, D.G.8
Alexander, D.9
-
30
-
-
0031711754
-
Bias in template-to-product ratios in multitemplate PCR
-
Polz, M.F.; Cavanaugh, C.M. Bias in template-to-product ratios in multitemplate PCR. Appl. Environ. Microbiol. 1998, 64, 3724-3730.
-
(1998)
Appl. Environ. Microbiol
, vol.64
, pp. 3724-3730
-
-
Polz, M.F.1
Cavanaugh, C.M.2
-
31
-
-
79955751104
-
High-throughput HIV sequencing: Evolution in 2D
-
Vrancken, B.; Lemey, P. High-throughput HIV sequencing: Evolution in 2D. Future Virol. 2011, 6, 417-420.
-
(2011)
Future Virol
, vol.6
, pp. 417-420
-
-
Vrancken, B.1
Lemey, P.2
-
32
-
-
15544376129
-
Effect of oligonucleotide primers in determining viral variability within hosts
-
Bracho, M.A.; García-Robles, I.; Jiménez, N.; Torres-Puente, M.; Moya, A.; González-Candelas, F. Effect of oligonucleotide primers in determining viral variability within hosts. Virol. J. 2004, 1, doi:10.1186/ 1743-422X-1-13.
-
(2004)
Virol. J
, vol.1
-
-
Bracho, M.A.1
García-Robles, I.2
Jiménez, N.3
Torres-Puente, M.4
Moya, A.5
González-Candelas, F.6
-
33
-
-
77952299935
-
Phylogenetic analysis of population-based and deep sequencing data to identify coevolving sites in the nef gene of HIV-1
-
Poon, A.F.Y.; Swenson, L.C.; Dong, W.W.Y.; Deng, W.; Kosakovsky Pond, S.L.; Brumme, Z.L.; Mullins, J.I.; Richman, D.D.; Harrigan, P.R.; Frost, S.D.W. Phylogenetic analysis of population-based and deep sequencing data to identify coevolving sites in the nef gene of HIV-1. Mol. Biol. Evol. 2010, 27, 819-832.
-
(2010)
Mol. Biol. Evol
, vol.27
, pp. 819-832
-
-
Poon, A.F.Y.1
Swenson, L.C.2
Dong, W.W.Y.3
Deng, W.4
Kosakovsky Pond, S.L.5
Brumme, Z.L.6
Mullins, J.I.7
Richman, D.D.8
Harrigan, P.R.9
Frost, S.D.W.10
-
34
-
-
77949451392
-
HIV-1 V3 envelope deep sequencing for clinical plasma specimens failing in phenotypic tropism assays
-
Vandenbroucke, I.; Marck, H.V.; Mostmans, W.; Eygen, V.V.; Rondelez, E.; Thys, K.; van Baelen, K.; Fransen, K.; Vaira, D.; Kabeya, K.; et al. HIV-1 V3 envelope deep sequencing for clinical plasma specimens failing in phenotypic tropism assays. AIDS Res. Ther. 2010, 7, doi:10.1186/1742-6405-7-4.
-
(2010)
AIDS Res. Ther
, vol.7
-
-
Vandenbroucke, I.1
Marck, H.V.2
Mostmans, W.3
Eygen, V.V.4
Rondelez, E.5
Thys, K.6
van Baelen, K.7
Fransen, K.8
Vaira, D.9
Kabeya, K.10
-
35
-
-
77955883388
-
Biases in Illumina transcriptome sequencing caused by random hexamer priming
-
Hansen, K.D.; Brenner, S.E.; Dudoit, S. Biases in Illumina transcriptome sequencing caused by random hexamer priming. Nucleic Acids Res. 2010, 38, doi:10.1093/nar/gkq224.
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Hansen, K.D.1
Brenner, S.E.2
Dudoit, S.3
-
36
-
-
84897466729
-
Non-random DNA fragmentation in next-generation sequencing
-
Poptsova, M.S.; Il'icheva, I.A.; Nechipurenko, D.Y.; Panchenko, L.A.; Khodikov, M.V.; Oparina, N.Y.; Polozov, R.V.; Nechipurenko, Y.D.; Grokhovsky, S.L. Non-random DNA fragmentation in next-generation sequencing. Sci. Rep. 2014, 4, doi:10.1038/srep04532.
-
(2014)
Sci. Rep
, vol.4
-
-
Poptsova, M.S.1
Il'icheva, I.A.2
Nechipurenko, D.Y.3
Panchenko, L.A.4
Khodikov, M.V.5
Oparina, N.Y.6
Polozov, R.V.7
Nechipurenko, Y.D.8
Grokhovsky, S.L.9
-
37
-
-
83055180102
-
Evaluation of a transposase protocol for rapid generation of shotgun high-throughput sequencing libraries from nanogram quantities of DNA
-
Marine, R.; Polson, S.W.; Ravel, J.; Hatfull, G.; Russell, D.; Sullivan, M.; Syed, F.; Dumas, M.;Wommack, K.E. Evaluation of a transposase protocol for rapid generation of shotgun high-throughput sequencing libraries from nanogram quantities of DNA. Appl. Environ. Microbiol. 2011, 77, 8071-8079.
-
(2011)
Appl. Environ. Microbiol
, vol.77
, pp. 8071-8079
-
-
Marine, R.1
Polson, S.W.2
Ravel, J.3
Hatfull, G.4
Russell, D.5
Sullivan, M.6
Syed, F.7
Dumas, M.8
Wommack, K.E.9
-
38
-
-
67650082453
-
Novel recombinant virus assay for measuring susceptibility of human immunodeficiency virus type 1 group M subtypes to clinically approved drugs
-
Covens, K.; Dekeersmaeker, N.; Schrooten, Y.; Weber, J.; Schols, D.; Quiñones-Mateu, M.E.; Vandamme, A.M.; van Laethem, K. Novel recombinant virus assay for measuring susceptibility of human immunodeficiency virus type 1 group M subtypes to clinically approved drugs. J. Clin. Microbiol. 2009, 47, 2232-2242.
-
(2009)
J. Clin. Microbiol
, vol.47
, pp. 2232-2242
-
-
Covens, K.1
Dekeersmaeker, N.2
Schrooten, Y.3
Weber, J.4
Schols, D.5
Quiñones-Mateu, M.E.6
Vandamme, A.M.7
van Laethem, K.8
-
39
-
-
22144494590
-
Optimization of a genotypic assay applicable to all human immunodeficiency virus type 1 protease and reverse transcriptase subtypes
-
Snoeck, J.; Riva, C.; Steegen, K.; Schrooten, Y.; Maes, B.; Vergne, L.; van Laethem, K.; Peeters, M.; Vandamme, A.M. Optimization of a genotypic assay applicable to all human immunodeficiency virus type 1 protease and reverse transcriptase subtypes. J. Virol. Methods 2005, 128, 47-53.
-
(2005)
J. Virol. Methods
, vol.128
, pp. 47-53
-
-
Snoeck, J.1
Riva, C.2
Steegen, K.3
Schrooten, Y.4
Maes, B.5
Vergne, L.6
van Laethem, K.7
Peeters, M.8
Vandamme, A.M.9
-
40
-
-
53049097137
-
A genotypic assay for the amplification and sequencing of integrase from diverse HIV-1 group M subtypes
-
Van Laethem, K.; Schrooten, Y.; Covens, K.; Dekeersmaeker, N.; de Munter, P.; van Wijngaerden, E.; van Ranst, M.; Vandamme, A.M. A genotypic assay for the amplification and sequencing of integrase from diverse HIV-1 group M subtypes. J. Virol. Methods 2008, 153, 176-181.
-
(2008)
J. Virol. Methods
, vol.153
, pp. 176-181
-
-
Van Laethem, K.1
Schrooten, Y.2
Covens, K.3
Dekeersmaeker, N.4
de Munter, P.5
van Wijngaerden, E.6
van Ranst, M.7
Vandamme, A.M.8
-
41
-
-
32344453358
-
A genotypic assay for the amplification and sequencing of gag and protease from diverse human immunodeficiency virus type 1 group M subtypes
-
Van Laethem, K.; Schrooten, Y.; Dedecker, S.; van Heeswijck, L.; Deforche, K.; van Wijngaerden, E.; van Ranst, M.; Vandamme, A.M. A genotypic assay for the amplification and sequencing of gag and protease from diverse human immunodeficiency virus type 1 group M subtypes. J. Virol. Methods 2006, 132, 181-186.
-
(2006)
J. Virol. Methods
, vol.132
, pp. 181-186
-
-
Van Laethem, K.1
Schrooten, Y.2
Dedecker, S.3
van Heeswijck, L.4
Deforche, K.5
van Wijngaerden, E.6
van Ranst, M.7
Vandamme, A.M.8
-
43
-
-
84954413370
-
Transmission cluster of dual-class resistant HIV-1 in untreated patients
-
Lisbon, Portugal, 9-14 September
-
Van Laethem, K.; Schrooten, Y.; Lemey, P.; Covens, K.; Dekeersmaeker, N.; van Ranst, M.; van Wijngaerden, E.; Vandamme, A.M. Transmission cluster of dual-class resistant HIV-1 in untreated patients. In Proceedings of The 13th International BioInformatics Workshop on Virus Evolution and Molecular Epidemiology, Lisbon, Portugal, 9-14 September 2007.
-
(2007)
Proceedings of The 13th International BioInformatics Workshop on Virus Evolution and Molecular Epidemiology
-
-
Van Laethem, K.1
Schrooten, Y.2
Lemey, P.3
Covens, K.4
Dekeersmaeker, N.5
van Ranst, M.6
van Wijngaerden, E.7
Vandamme, A.M.8
-
44
-
-
84907987051
-
-
(accessed on 6 January 2016)
-
Bioinformatics at COMAV. Available online: https://bioinf.comav.upv.es/ (accessed on 6 January 2016).
-
Bioinformatics at COMAV
-
-
-
45
-
-
84858739096
-
Analysis of high-depth sequence data for studying viral diversity: A comparison of next generation sequencing platforms using Segminator II
-
Archer, J.; Baillie, G.;Watson, S.J.; Kellam, P.; Rambaut, A.; Robertson, D.L. Analysis of high-depth sequence data for studying viral diversity: A comparison of next generation sequencing platforms using Segminator II. BMC Bioinform. 2012, 13, doi:10.1186/1471-2105-13-47.
-
(2012)
BMC Bioinform
, vol.13
-
-
Archer, J.1
Baillie, G.2
Watson, S.J.3
Kellam, P.4
Rambaut, A.5
Robertson, D.L.6
-
46
-
-
84866113768
-
De novo assembly of highly diverse viral populations
-
Yang, X.; Charlebois, P.; Gnerre, S.; Coole, M.G.; Lennon, N.J.; Levin, J.Z.; Qu, J.; Ryan, E.M.; Zody, M.C.; Henn, M.R. De novo assembly of highly diverse viral populations. BMC Genom. 2012, 13, doi:10.1186/ 1471-2164-13-475.
-
(2012)
BMC Genom
, vol.13
-
-
Yang, X.1
Charlebois, P.2
Gnerre, S.3
Coole, M.G.4
Lennon, N.J.5
Levin, J.Z.6
Qu, J.7
Ryan, E.M.8
Zody, M.C.9
Henn, M.R.10
-
47
-
-
70350294348
-
Systematic artifacts in metagenomes from complex microbial communities
-
Gomez-Alvarez, V.; Teal, T.K.; Schmidt, T.M. Systematic artifacts in metagenomes from complex microbial communities. ISME J. 2009, 3, 1314-1317.
-
(2009)
ISME J.
, vol.3
, pp. 1314-1317
-
-
Gomez-Alvarez, V.1
Teal, T.K.2
Schmidt, T.M.3
-
48
-
-
79956044149
-
Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing
-
Gilles, A.; Meglécz, E.; Pech, N.; Ferreira, S.; Malausa, T.; Martin, J.F. Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing. BMC Genom. 2011, 12, doi:10.1186/1471-2164-12-245.
-
(2011)
BMC Genom
, vol.12
-
-
Gilles, A.1
Meglécz, E.2
Pech, N.3
Ferreira, S.4
Malausa, T.5
Martin, J.F.6
-
49
-
-
33748879209
-
Rationale and uses of a public HIV drug-resistance database
-
Shafer, R.W. Rationale and uses of a public HIV drug-resistance database. J. Infect. Dis. 2006, 194, S51-S58.
-
(2006)
J. Infect. Dis
, vol.194
, pp. S51-S58
-
-
Shafer, R.W.1
-
50
-
-
62749200513
-
Drug resistance mutations for surveillance of transmitted HIV-1 drug-resistance: 2009 Update
-
Bennett, D.E.; Camacho, R.J.; Otelea, D.; Kuritzkes, D.R.; Fleury, H.; Kiuchi, M.; Heneine, W.; Kantor, R.; Jordan, M.R.; Schapiro, J.M.; et al. Drug resistance mutations for surveillance of transmitted HIV-1 drug-resistance: 2009 Update. PLoS ONE 2009, 4, doi:10.1371/journal.pone.0004724.
-
(2009)
PLoS ONE
, vol.4
-
-
Bennett, D.E.1
Camacho, R.J.2
Otelea, D.3
Kuritzkes, D.R.4
Fleury, H.5
Kiuchi, M.6
Heneine, W.7
Kantor, R.8
Jordan, M.R.9
Schapiro, J.M.10
-
51
-
-
84893495651
-
Detection of low-frequency HIV type 1 reverse transcriptase drug resistance mutations by ultradeep sequencing in naive HIV type 1-infected individuals
-
Bellecave, P.; Recordon-Pinson, P.; Papuchon, J.; Vandenhende, M.A.; Reigadas, S.; Tauzin, B.; Fleury, H. Detection of low-frequency HIV type 1 reverse transcriptase drug resistance mutations by ultradeep sequencing in naive HIV type 1-infected individuals. AIDS Res. Hum. Retroviruses 2014, 30, 170-173.
-
(2014)
AIDS Res. Hum. Retroviruses
, vol.30
, pp. 170-173
-
-
Bellecave, P.1
Recordon-Pinson, P.2
Papuchon, J.3
Vandenhende, M.A.4
Reigadas, S.5
Tauzin, B.6
Fleury, H.7
-
52
-
-
84884530557
-
Evaluation of the Roche prototype 454 HIV-1 ultradeep sequencing drug resistance assay in a routine diagnostic laboratory
-
Garcia-Diaz, A.; Guerrero-Ramos, A.; McCormick, A.L.; Macartney, M.; Conibear, T.; Johnson, M.A.; Haque, T.;Webster, D.P. Evaluation of the Roche prototype 454 HIV-1 ultradeep sequencing drug resistance assay in a routine diagnostic laboratory. J. Clin. Virol. 2013, 58, 468-473.
-
(2013)
J. Clin. Virol
, vol.58
, pp. 468-473
-
-
Garcia-Diaz, A.1
Guerrero-Ramos, A.2
McCormick, A.L.3
Macartney, M.4
Conibear, T.5
Johnson, M.A.6
Haque, T.7
Webster, D.P.8
-
53
-
-
84905098081
-
Deep sequencing: Becoming a critical tool in clinical virology
-
Quiñones-Mateu, M.E.; Avila, S.; Reyes-Teran, G.; Martinez, M.A. Deep sequencing: Becoming a critical tool in clinical virology. J. Clin. Virol. 2014, 61, 9-19.
-
(2014)
J. Clin. Virol
, vol.61
, pp. 9-19
-
-
Quiñones-Mateu, M.E.1
Avila, S.2
Reyes-Teran, G.3
Martinez, M.A.4
-
54
-
-
84934909975
-
HIV-1 genotypic drug resistance testing: Digging deep, reaching wide?
-
Van Laethem, K.; Theys, K.; Vandamme, A.M. HIV-1 genotypic drug resistance testing: Digging deep, reaching wide? Curr. Opin. Virol. 2015, 14, 16-23.
-
(2015)
Curr. Opin. Virol
, vol.14
, pp. 16-23
-
-
Van Laethem, K.1
Theys, K.2
Vandamme, A.M.3
-
55
-
-
82355193803
-
Systematic comparison of three methods for fragmentation of long-range PCR products for next generation sequencing
-
Knierim, E.; Lucke, B.; Schwarz, J.M.; Schuelke, M.; Seelow, D. Systematic comparison of three methods for fragmentation of long-range PCR products for next generation sequencing. PLoS ONE 2011, 6, doi:10.1371/journal.pone.0028240.
-
(2011)
PLoS ONE
, vol.6
-
-
Knierim, E.1
Lucke, B.2
Schwarz, J.M.3
Schuelke, M.4
Seelow, D.5
-
56
-
-
84055200527
-
Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer ID
-
Jabara, C.B.; Jones, C.D.; Roach, J.; Anderson, J.A.; Swanstrom, R. Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer ID. Proc. Natl. Acad. Sci. USA 2011, 108, 20166-20171.
-
(2011)
Proc. Natl. Acad. Sci. USA
, vol.108
, pp. 20166-20171
-
-
Jabara, C.B.1
Jones, C.D.2
Roach, J.3
Anderson, J.A.4
Swanstrom, R.5
-
57
-
-
84865979581
-
Detection of ultra-rare mutations by next-generation sequencing
-
Schmitt, M.W.; Kennedy, S.R.; Salk, J.J.; Fox, E.J.; Hiatt, J.B.; Loeb, L.A. Detection of ultra-rare mutations by next-generation sequencing. Proc. Natl. Acad. Sci. USA 2012, 109, 14508-14513.
-
(2012)
Proc. Natl. Acad. Sci. USA
, vol.109
, pp. 14508-14513
-
-
Schmitt, M.W.1
Kennedy, S.R.2
Salk, J.J.3
Fox, E.J.4
Hiatt, J.B.5
Loeb, L.A.6
-
58
-
-
84889659729
-
High-throughput DNA sequencing errors are reduced by orders of magnitude using circle sequencing
-
Lou, D.I.; Hussmann, J.A.; McBee, R.M.; Acevedo, A.; Andino, R.; Press, W.H.; Sawyer, S.L. High-throughput DNA sequencing errors are reduced by orders of magnitude using circle sequencing. Proc. Natl. Acad. Sci. USA 2013, 110, 19872-19877.
-
(2013)
Proc. Natl. Acad. Sci. USA
, vol.110
, pp. 19872-19877
-
-
Lou, D.I.1
Hussmann, J.A.2
McBee, R.M.3
Acevedo, A.4
Andino, R.5
Press, W.H.6
Sawyer, S.L.7
-
59
-
-
84907436128
-
Library preparation for highly accurate population sequencing of RNA viruses
-
Acevedo, A.; Andino, R. Library preparation for highly accurate population sequencing of RNA viruses. Nat. Protoc. 2014, 9, 1760-1769.
-
(2014)
Nat. Protoc
, vol.9
, pp. 1760-1769
-
-
Acevedo, A.1
Andino, R.2
-
60
-
-
84882832047
-
A glimpse into past, present, and future DNA sequencing
-
Morey, M.; Fernández-Marmiesse, A.; Castiñeiras, D.; Fraga, J.M.; Couce, M.L.; Cocho, J.A. A glimpse into past, present, and future DNA sequencing. Mol. Genet. Metab. 2013, 110, 3-24.
-
(2013)
Mol. Genet. Metab
, vol.110
, pp. 3-24
-
-
Morey, M.1
Fernández-Marmiesse, A.2
Castiñeiras, D.3
Fraga, J.M.4
Couce, M.L.5
Cocho, J.A.6
-
61
-
-
77956873627
-
Tackling the widespread and critical impact of batch effects in high-throughput data
-
Leek, J.T.; Scharpf, R.B.; Bravo, H.C.; Simcha, D.; Langmead, B.; Johnson, W.E.; Geman, D.; Baggerly, K.; Irizarry, R.A. Tackling the widespread and critical impact of batch effects in high-throughput data. Nat. Rev. Genet. 2010, 11, 733-739.
-
(2010)
Nat. Rev. Genet
, vol.11
, pp. 733-739
-
-
Leek, J.T.1
Scharpf, R.B.2
Bravo, H.C.3
Simcha, D.4
Langmead, B.5
Johnson, W.E.6
Geman, D.7
Baggerly, K.8
Irizarry, R.A.9
-
62
-
-
84890565382
-
The role of replicates for error mitigation in next-generation sequencing
-
Robasky, K.; Lewis, N.E.; Church, G.M. The role of replicates for error mitigation in next-generation sequencing. Nat. Rev. Genet. 2014, 15, 56-62.
-
(2014)
Nat. Rev. Genet
, vol.15
, pp. 56-62
-
-
Robasky, K.1
Lewis, N.E.2
Church, G.M.3
-
63
-
-
84894259565
-
Low-frequency nevirapine (NVP)-resistant HIV-1 variants are not associated with failure of antiretroviral therapy in women without prior exposure to single-dose NVP
-
Boltz, V.F.; Bao, Y.; Lockman, S.; Halvas, E.K.; Kearney, M.F.; McIntyre, J.A.; Schooley, R.T.; Hughes, M.D.; Coffin, J.M.; Mellors, J.W.; et al. Low-frequency nevirapine (NVP)-resistant HIV-1 variants are not associated with failure of antiretroviral therapy in women without prior exposure to single-dose NVP. J. Infect. Dis. 2014, 209, 703-710.
-
(2014)
J. Infect. Dis
, vol.209
, pp. 703-710
-
-
Boltz, V.F.1
Bao, Y.2
Lockman, S.3
Halvas, E.K.4
Kearney, M.F.5
McIntyre, J.A.6
Schooley, R.T.7
Hughes, M.D.8
Coffin, J.M.9
Mellors, J.W.10
-
64
-
-
67349096369
-
Prevalence of minor variants of HIV strains at reverse transcriptase position 103 in therapy-naïve patients and their impact on the virological failure
-
Balduin, M.; Oette, M.; Däumer, M.P.; Hoffmann, D.; Pfister, H.J.; Kaiser, R. Prevalence of minor variants of HIV strains at reverse transcriptase position 103 in therapy-naïve patients and their impact on the virological failure. J. Clin. Virol. 2009, 45, 34-38.
-
(2009)
J. Clin. Virol
, vol.45
, pp. 34-38
-
-
Balduin, M.1
Oette, M.2
Däumer, M.P.3
Hoffmann, D.4
Pfister, H.J.5
Kaiser, R.6
-
65
-
-
84875676262
-
Pre-existing mutations in the rilpivirine Phase III trials ECHO and THRIVE: Prevalence and impact on virological response
-
Vingerhoets, J.; Rimsky, L.; van Eygen, V.; Nijs, S.; Vanveggel, S.; Boven, K.; Picchio, G. Pre-existing mutations in the rilpivirine Phase III trials ECHO and THRIVE: Prevalence and impact on virological response. Antivir. Ther. 2013, 18, 253-256.
-
(2013)
Antivir. Ther
, vol.18
, pp. 253-256
-
-
Vingerhoets, J.1
Rimsky, L.2
van Eygen, V.3
Nijs, S.4
Vanveggel, S.5
Boven, K.6
Picchio, G.7
-
66
-
-
84905735621
-
2014 Update of the drug resistance mutations in HIV-1
-
Wensing, A.M.; Calvez, V.; Günthard, H.F.; Johnson, V.A.; Paredes, R.; Pillay, D.; Shafer, R.W.; Richman, D.D. 2014 Update of the drug resistance mutations in HIV-1. Top Antivir. Med. 2014, 22, 642-650.
-
(2014)
Top Antivir. Med
, vol.22
, pp. 642-650
-
-
Wensing, A.M.1
Calvez, V.2
Günthard, H.F.3
Johnson, V.A.4
Paredes, R.5
Pillay, D.6
Shafer, R.W.7
Richman, D.D.8
-
67
-
-
79953745195
-
Low-frequency HIV-1 drug resistance mutations and risk of NNRTI-based antiretroviral treatment failure: A systematic review and pooled analysis
-
Li, J.Z.; Paredes, R.; Ribaudo, H.J.; Svarovskaia, E.S.; Metzner, K.J.; Kozal, M.J.; Hullsiek, K.H.; Balduin, M.; Jakobsen, M.R.; Geretti, A.M.; et al. Low-frequency HIV-1 drug resistance mutations and risk of NNRTI-based antiretroviral treatment failure: A systematic review and pooled analysis. JAMA 2011, 305, 1327-1335.
-
(2011)
JAMA
, vol.305
, pp. 1327-1335
-
-
Li, J.Z.1
Paredes, R.2
Ribaudo, H.J.3
Svarovskaia, E.S.4
Metzner, K.J.5
Kozal, M.J.6
Hullsiek, K.H.7
Balduin, M.8
Jakobsen, M.R.9
Geretti, A.M.10
-
68
-
-
78650657286
-
New technology to detect low-level drug-resistant HIV variants
-
Gega, A.; Kozal, M.J. New technology to detect low-level drug-resistant HIV variants. Future Virol. 2011, 6, 17-26.
-
(2011)
Future Virol
, vol.6
, pp. 17-26
-
-
Gega, A.1
Kozal, M.J.2
-
69
-
-
77955690396
-
Minority variants of drug-resistant HIV
-
Gianella, S.; Richman, D.D. Minority variants of drug-resistant HIV. J. Infect. Dis. 2010, 202, 657-666.
-
(2010)
J. Infect. Dis
, vol.202
, pp. 657-666
-
-
Gianella, S.1
Richman, D.D.2
-
70
-
-
79955943288
-
Added value of deep sequencing relative to population sequencing in heavily pre-treated HIV-1-infected subjects
-
Codoñer, F.M.; Pou, C.; Thielen, A.; García, F.; Delgado, R.; Dalmau, D.; Álvarez-Tejado, M.; Ruiz, L.; Clotet, B.; Paredes, R. Added value of deep sequencing relative to population sequencing in heavily pre-treated HIV-1-infected subjects. PLoS ONE 2011, 6, doi:10.1371/journal.pone.0019461.
-
(2011)
PLoS ONE
, vol.6
-
-
Codoñer, F.M.1
Pou, C.2
Thielen, A.3
García, F.4
Delgado, R.5
Dalmau, D.6
Álvarez-Tejado, M.7
Ruiz, L.8
Clotet, B.9
Paredes, R.10
-
71
-
-
84922481959
-
Comparison of ultra-deep versus Sanger sequencing detection of minority mutations on the HIV-1 drug resistance interpretations after virological failure
-
Mohamed, S.; Penaranda, G.; Gonzalez, D.; Camus, C.; Khiri, H.; Boulmé, R.; Sayada, C.; Philibert, P.; Olive, D.; Halfon, P. Comparison of ultra-deep versus Sanger sequencing detection of minority mutations on the HIV-1 drug resistance interpretations after virological failure. AIDS 2014, 28, 1315-1324.
-
(2014)
AIDS
, vol.28
, pp. 1315-1324
-
-
Mohamed, S.1
Penaranda, G.2
Gonzalez, D.3
Camus, C.4
Khiri, H.5
Boulmé, R.6
Sayada, C.7
Philibert, P.8
Olive, D.9
Halfon, P.10
-
72
-
-
84929732555
-
Improved detection of resistance at failure to a tenofovir, emtricitabine and efavirenz regimen by ultradeep sequencing
-
Todesco, E.; Rodriguez, C.; Morand-Joubert, L.; Mercier-Darty, M.; Desire, N.; Wirden, M.; Girard, P.M.; Katlama, C.; Calvez, V.; Marcelin, A.G. Improved detection of resistance at failure to a tenofovir, emtricitabine and efavirenz regimen by ultradeep sequencing. J. Antimicrob. Chemother. 2015, 70, 1503-1506.
-
(2015)
J. Antimicrob. Chemother
, vol.70
, pp. 1503-1506
-
-
Todesco, E.1
Rodriguez, C.2
Morand-Joubert, L.3
Mercier-Darty, M.4
Desire, N.5
Wirden, M.6
Girard, P.M.7
Katlama, C.8
Calvez, V.9
Marcelin, A.G.10
-
73
-
-
84904981928
-
Improved prediction of salvage antiretroviral therapy outcomes using ultrasensitive HIV-1 drug resistance testing
-
Pou, C.; Noguera-Julian, M.; Pérez-Álvarez, S.; García, F.; Delgado, R.; Dalmau, D.; Álvarez-Tejado, M.; Gonzalez, D.; Sayada, C.; Chueca, N.; et al. Improved prediction of salvage antiretroviral therapy outcomes using ultrasensitive HIV-1 drug resistance testing. Clin. Infect. Dis. 2014, 59, 578-588.
-
(2014)
Clin. Infect. Dis
, vol.59
, pp. 578-588
-
-
Pou, C.1
Noguera-Julian, M.2
Pérez-Álvarez, S.3
García, F.4
Delgado, R.5
Dalmau, D.6
Álvarez-Tejado, M.7
Gonzalez, D.8
Sayada, C.9
Chueca, N.10
-
74
-
-
84864505786
-
Human immunodeficiency virus gag and protease: Partners in resistance
-
Fun, A.; Wensing, A.M.J.; Verheyen, J.; Nijhuis, M. Human immunodeficiency virus gag and protease: Partners in resistance. Retrovirology 2012, 9, doi:10.1186/1742-4690-9-63.
-
(2012)
Retrovirology
, vol.9
-
-
Fun, A.1
Wensing, A.M.J.2
Verheyen, J.3
Nijhuis, M.4
-
75
-
-
84929497885
-
Deep sequencing of protease inhibitor resistant HIV patient isolates reveals patterns of correlated mutations in Gag and protease
-
Flynn, W.F.; Chang, M.W.; Tan, Z.; Oliveira, G.; Yuan, J.; Okulicz, J.F.; Torbett, B.E.; Levy, R.M. Deep sequencing of protease inhibitor resistant HIV patient isolates reveals patterns of correlated mutations in Gag and protease. PLoS Comput. Biol. 2015, 11, doi:10.1371/journal.pcbi.1004249.
-
(2015)
PLoS Comput. Biol
, vol.11
-
-
Flynn, W.F.1
Chang, M.W.2
Tan, Z.3
Oliveira, G.4
Yuan, J.5
Okulicz, J.F.6
Torbett, B.E.7
Levy, R.M.8
-
76
-
-
84867060060
-
Read length versus depth of coverage for viral quasispecies reconstruction
-
Zagordi, O.; Däumer, M.; Beisel, C.; Beerenwinkel, N. Read length versus depth of coverage for viral quasispecies reconstruction. PLoS ONE 2012, 7, doi:10.1371/journal.pone.0047046.
-
(2012)
PLoS ONE
, vol.7
-
-
Zagordi, O.1
Däumer, M.2
Beisel, C.3
Beerenwinkel, N.4
-
77
-
-
84906220576
-
Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations
-
Giallonardo, F.D.; Töpfer, A.; Rey, M.; Prabhakaran, S.; Duport, Y.; Leemann, C.; Schmutz, S.; Campbell, N.K.; Joos, B.; Lecca, M.R.; et al. Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations. Nucleic Acids Res. 2014, 42, doi:10.1093/nar/gku537.
-
(2014)
Nucleic Acids Res
, vol.42
-
-
Giallonardo, F.D.1
Töpfer, A.2
Rey, M.3
Prabhakaran, S.4
Duport, Y.5
Leemann, C.6
Schmutz, S.7
Campbell, N.K.8
Joos, B.9
Lecca, M.R.10
-
78
-
-
84875002547
-
Analysis of 454 sequencing error rate, error sources, and artifact recombination for detection of Low-frequency drug resistance mutations in HIV-1 DNA
-
Shao, W.; Boltz, V.F.; Spindler, J.E.; Kearney, M.F.; Maldarelli, F.; Mellors, J.W.; Stewart, C.; Volfovsky, N.; Levitsky, A.; Stephens, R.M.; et al. Analysis of 454 sequencing error rate, error sources, and artifact recombination for detection of Low-frequency drug resistance mutations in HIV-1 DNA. Retrovirology 2013, 10, doi: 10.1186/1742-4690-10-18.
-
(2013)
Retrovirology
, vol.10
-
-
Shao, W.1
Boltz, V.F.2
Spindler, J.E.3
Kearney, M.F.4
Maldarelli, F.5
Mellors, J.W.6
Stewart, C.7
Volfovsky, N.8
Levitsky, A.9
Stephens, R.M.10
-
79
-
-
79960714085
-
Performance of ultra-deep pyrosequencing in analysis of HIV-1 pol gene variation
-
Mild, M.; Hedskog, C.; Jernberg, J.; Albert, J. Performance of ultra-deep pyrosequencing in analysis of HIV-1 pol gene variation. PLoS ONE 2011, 6, doi:10.1371/journal.pone.0022741.
-
(2011)
PLoS ONE
, vol.6
-
-
Mild, M.1
Hedskog, C.2
Jernberg, J.3
Albert, J.4
|