-
1
-
-
0027265082
-
Analysis of heterogeneous viral populations by direct DNA sequencing
-
8363827 Epub 1993/07/01
-
Leitner T, Halapi E, Scarlatti G, Rossi P, Albert J, Fenyo EM, et al. Analysis of heterogeneous viral populations by direct DNA sequencing. BioTechniques. 1993;15(1):120-7. Epub 1993/07/01. PMID: 8363827.
-
(1993)
BioTechniques.
, vol.15
, Issue.1
, pp. 120-127
-
-
Leitner, T.1
Halapi, E.2
Scarlatti, G.3
Rossi, P.4
Albert, J.5
Fenyo, E.M.6
-
2
-
-
44649102135
-
Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection
-
18490657 Epub 2008/05/21, PubMed Central PMCID: PMC2387184
-
Keele BF, Giorgi EE, Salazar-Gonzalez JF, Decker JM, Pham KT, Salazar MG, et al. Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection. Proc Natl Acad Sci U S A. 2008;105(21):7552-7. Epub 2008/05/21. doi: 0802203105 [pii] doi: 10.1073/pnas. 0802203105 PMID: 18490657; PubMed Central PMCID: PMC2387184.
-
(2008)
Proc Natl Acad Sci U S A.
, vol.105
, Issue.21
, pp. 7552-7557
-
-
Keele, B.F.1
Giorgi, E.E.2
Salazar-Gonzalez, J.F.3
Decker, J.M.4
Pham, K.T.5
Salazar, M.G.6
-
3
-
-
33646481683
-
Selection and persistence of nonnucleoside reverse transcriptase inhibitor-resistant HIV-1 in patients starting and stopping non-nucleoside therapy
-
Epub 2006/03/04. 16514300
-
Palmer S, Boltz V, Maldarelli F, Kearney M, Halvas EK, Rock D, et al. Selection and persistence of nonnucleoside reverse transcriptase inhibitor-resistant HIV-1 in patients starting and stopping non-nucleoside therapy. AIDS. 2006;20(5):701-10. Epub 2006/03/04. doi: 10.1097/01.aids.0000216370.69066.7f 00002030-200603210-00009 [pii]. PMID: 16514300.
-
(2006)
AIDS.
, vol.20
, Issue.5
, pp. 701-710
-
-
Palmer, S.1
Boltz, V.2
Maldarelli, F.3
Kearney, M.4
Halvas, E.K.5
Rock, D.6
-
4
-
-
34547643929
-
Characterization of mutation spectra with ultra-deep pyrosequencing: Application to HIV-1 drug resistance
-
17600086
-
Wang C, Mitsuya Y, Gharizadeh B, Ronaghi M, Shafer RW. Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance. Genome Res. 2007;17(8):1195-201. PMID: 17600086.
-
(2007)
Genome Res.
, vol.17
, Issue.8
, pp. 1195-1201
-
-
Wang, C.1
Mitsuya, Y.2
Gharizadeh, B.3
Ronaghi, M.4
Shafer, R.W.5
-
5
-
-
70350534553
-
Minority variants associated with transmitted and acquired HIV-1 nonnucleoside reverse transcriptase inhibitor resistance: Implications for the use of second-generation nonnucleoside reverse transcriptase inhibitors
-
19734799 Epub 2009/09/08, PubMed Central PMCID: PMC2809083
-
Varghese V, Shahriar R, Rhee SY, Liu T, Simen BB, Egholm M, et al. Minority variants associated with transmitted and acquired HIV-1 nonnucleoside reverse transcriptase inhibitor resistance: implications for the use of second-generation nonnucleoside reverse transcriptase inhibitors. J Acquir Immune Defic Syndr. 2009;52(3):309-15. Epub 2009/09/08. doi: 10.1097/QAI.0b013e3181bca669 PMID: 19734799; PubMed Central PMCID: PMC2809083.
-
(2009)
J Acquir Immune Defic Syndr.
, vol.52
, Issue.3
, pp. 309-315
-
-
Varghese, V.1
Shahriar, R.2
Rhee, S.Y.3
Liu, T.4
Simen, B.B.5
Egholm, M.6
-
6
-
-
79953745195
-
Low-frequency HIV-1 drug resistance mutations and risk of NNRTI-based antiretroviral treatment failure: A systematic review and pooled analysis
-
21467286 Epub 2011/04/07
-
Li JZ, Paredes R, Ribaudo HJ, Svarovskaia ES, Metzner KJ, Kozal MJ, 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(13):1327-35. Epub 2011/04/07. doi: 305/13/1327 [pii] doi: 10. 1001/jama.2011.375 PMID: 21467286.
-
(2011)
JAMA.
, vol.305
, Issue.13
, 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
-
7
-
-
79952323624
-
Analysis of low-frequency mutations associated with drug resistance to raltegravir before antiretroviral treatment
-
21173185 Epub 2010/12/22, PubMed Central PMCID: PMC3067114
-
Liu J, Miller MD, Danovich RM, Vandergrift N, Cai F, Hicks CB, et al. Analysis of low-frequency mutations associated with drug resistance to raltegravir before antiretroviral treatment. Antimicrob Agents Chemother. 2011;55(3):1114-9. Epub 2010/12/22. doi: AAC.01492-10 [pii] doi: 10.1128/AAC.01492-10 PMID: 21173185; PubMed Central PMCID: PMC3067114.
-
(2011)
Antimicrob Agents Chemother.
, vol.55
, Issue.3
, pp. 1114-1119
-
-
Liu, J.1
Miller, M.D.2
Danovich, R.M.3
Vandergrift, N.4
Cai, F.5
Hicks, C.B.6
-
8
-
-
67749093395
-
Ultradeep pyrosequencing detects complex patterns of CD8+ T-lymphocyte escape in simian immunodeficiency virus-infected macaques
-
19515775 Epub 2009/06/12, PubMed Central PMCID: PMC2715741
-
Bimber BN, Burwitz BJ, O'Connor S, Detmer A, Gostick E, Lank SM, et al. Ultradeep pyrosequencing detects complex patterns of CD8+ T-lymphocyte escape in simian immunodeficiency virus-infected macaques. J Virol. 2009;83(16):8247-53. Epub 2009/06/12. doi: 10.1128/jvi.00897-09 PMID: 19515775; PubMed Central PMCID: PMC2715741.
-
(2009)
J Virol.
, vol.83
, Issue.16
, pp. 8247-8253
-
-
Bimber, B.N.1
Burwitz, B.J.2
O'Connor, S.3
Detmer, A.4
Gostick, E.5
Lank, S.M.6
-
9
-
-
78049524598
-
Whole-genome characterization of human and simian immunodeficiency virus intrahost diversity by ultradeep pyrosequencing
-
20844037 PubMed Central PMCID: PMC2977871
-
Bimber BN, Dudley DM, Lauck M, Becker EA, Chin EN, Lank SM, et al. Whole-genome characterization of human and simian immunodeficiency virus intrahost diversity by ultradeep pyrosequencing. J Virol. 2010;84(22):12087-92. doi: 10.1128/jvi.01378-10 PMID: 20844037; PubMed Central PMCID: PMC2977871.
-
(2010)
J Virol.
, vol.84
, Issue.22
, 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
-
10
-
-
77954713270
-
Vaccine-induced HIV seropositivity/reactivity in noninfected HIV vaccine recipients
-
20639561 PubMed Central PMCID: PMC3086635
-
Cooper CJ, Metch B, Dragavon J, Coombs RW, Baden LR, Force NHVTNV-IST. Vaccine-induced HIV seropositivity/reactivity in noninfected HIV vaccine recipients. JAMA: the journal of the American Medical Association. 2010;304(3):275-83. doi: 10.1001/jama.2010.926 PMID: 20639561; PubMed Central PMCID: PMC3086635.
-
(2010)
JAMA: The Journal of the American Medical Association
, vol.304
, Issue.3
, pp. 275-283
-
-
Force NHVTNV-IST1
Cooper, C.J.2
Metch, B.3
Dragavon, J.4
Coombs, R.W.5
Baden, L.R.6
-
11
-
-
77957901912
-
Transmission of single HIV-1 genomes and dynamics of early immune escape revealed by ultra-deep sequencing
-
20808830 Epub 2010/09/03, PubMed Central PMCID: PMC2924888
-
Fischer W, Ganusov VV, Giorgi EE, Hraber PT, Keele BF, Leitner T, et al. Transmission of single HIV-1 genomes and dynamics of early immune escape revealed by ultra-deep sequencing. PLoS One. 2010;5(8):e12303. Epub 2010/09/03. doi: 10.1371/journal.pone.0012303 PMID: 20808830; PubMed Central PMCID: PMC2924888.
-
(2010)
PLoS One.
, vol.5
, Issue.8
, pp. e12303
-
-
Fischer, W.1
Ganusov, V.V.2
Giorgi, E.E.3
Hraber, P.T.4
Keele, B.F.5
Leitner, T.6
-
12
-
-
77951980565
-
Mathematical modeling of ultradeep sequencing data reveals that acute CD8+ T-lymphocyte responses exert strong selective pressure in simian immunodeficiency virus-infected macaques but still fail to clear founder epitope sequences
-
20335256 PubMed Central PMCID: PMC2876615
-
Love TM, Thurston SW, Keefer MC, Dewhurst S, Lee HY. Mathematical modeling of ultradeep sequencing data reveals that acute CD8+ T-lymphocyte responses exert strong selective pressure in simian immunodeficiency virus-infected macaques but still fail to clear founder epitope sequences. J Virol. 2010;84(11):5802-14. doi: 10.1128/jvi.00117-10 PMID: 20335256; PubMed Central PMCID: PMC2876615.
-
(2010)
J Virol.
, vol.84
, Issue.11
, pp. 5802-5814
-
-
Love, T.M.1
Thurston, S.W.2
Keefer, M.C.3
Dewhurst, S.4
Lee, H.Y.5
-
13
-
-
84861214061
-
Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection
-
22412369 Epub 2012/03/14, PubMed Central PMCID: PMC3297584
-
Henn MR, Boutwell CL, Charlebois P, Lennon NJ, Power KA, Macalalad AR, 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(3):e1002529. Epub 2012/03/14. doi: 10.1371/journal.ppat. 1002529 PMID: 22412369; PubMed Central PMCID: PMC3297584.
-
(2012)
PLoS Pathog.
, vol.8
, Issue.3
, pp. e1002529
-
-
Henn, M.R.1
Boutwell, C.L.2
Charlebois, P.3
Lennon, N.J.4
Power, K.A.5
Macalalad, A.R.6
-
14
-
-
83355173006
-
Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies
-
22194782 Epub 2011/12/24, PubMed Central PMCID: PMC3237409
-
Schloss PD, Gevers D, Westcott SL. Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS ONE. 2011;6(12):e27310. Epub 2011/12/24. doi: 10.1371/journal.pone.0027310 PMID: 22194782; PubMed Central PMCID: PMC3237409.
-
(2011)
PLoS ONE.
, vol.6
, Issue.12
, pp. e27310
-
-
Schloss, P.D.1
Gevers, D.2
Westcott, S.L.3
-
15
-
-
84866065801
-
Groundtruthing next-gen sequencing for microbial ecology-biases and errors in community structure estimates from PCR amplicon pyrosequencing
-
22970184 Epub 2012/09/13, PubMed Central PMCID: PMC3435322
-
Lee CK, Herbold CW, Polson SW, Wommack KE, Williamson SJ, McDonald IR, et al. Groundtruthing next-gen sequencing for microbial ecology-biases and errors in community structure estimates from PCR amplicon pyrosequencing. PLoS ONE. 2012;7(9):e44224. Epub 2012/09/13. doi: 10.1371/journal.pone.0044224 PMID: 22970184; PubMed Central PMCID: PMC3435322.
-
(2012)
PLoS ONE.
, vol.7
, Issue.9
, pp. e44224
-
-
Lee, C.K.1
Herbold, C.W.2
Polson, S.W.3
Wommack, K.E.4
Williamson, S.J.5
McDonald, I.R.6
-
16
-
-
84865060813
-
PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets
-
22905208 Epub 2012/08/21, PubMed Central PMCID: PMC3419673
-
Pinto AJ, Raskin L. PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets. PLoS ONE. 2012;7(8):e43093. Epub 2012/08/21. doi: 10.1371/journal.pone.0043093 PMID: 22905208; PubMed Central PMCID: PMC3419673.
-
(2012)
PLoS ONE.
, vol.7
, Issue.8
, pp. e43093
-
-
Pinto, A.J.1
Raskin, L.2
-
17
-
-
84880760001
-
PCR-induced transitions are the major source of error in cleaned ultra-deep pyrosequencing data
-
23894647 Epub 2013/07/31, PubMed Central PMCID: PMC3720931
-
Brodin J, Mild M, Hedskog C, Sherwood E, Leitner T, Andersson B, et al. PCR-induced transitions are the major source of error in cleaned ultra-deep pyrosequencing data. PLoS ONE. 2013;8(7):e70388. Epub 2013/07/31. doi: 10.1371/journal.pone.0070388 PMID: 23894647; PubMed Central PMCID: PMC3720931.
-
(2013)
PLoS ONE.
, vol.8
, Issue.7
, pp. e70388
-
-
Brodin, J.1
Mild, M.2
Hedskog, C.3
Sherwood, E.4
Leitner, T.5
Andersson, B.6
-
18
-
-
84875002547
-
Analysis of 454 sequencing error rate, error sources, and artifact recombination for detection of Low-frequency drug resistance mutations in HIV-1 DNA
-
23402264 PubMed Central PMCID: PMC3599717
-
Shao W, Boltz VF, Spindler JE, Kearney MF, Maldarelli F, Mellors JW, 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;10:18. doi: 10.1186/1742-4690-10-18 PMID: 23402264; PubMed Central PMCID: PMC3599717.
-
(2013)
Retrovirology
, vol.10
, pp. 18
-
-
Shao, W.1
Boltz, V.F.2
Spindler, J.E.3
Kearney, M.F.4
Maldarelli, F.5
Mellors, J.W.6
-
19
-
-
84883532124
-
Quality score based identification and correction of pyrosequencing errors
-
24039850 Epub 2013/09/17, PubMed Central PMCID: PMC3764156
-
Iyer S, Bouzek H, Deng W, Larsen B, Casey E, Mullins JI. Quality score based identification and correction of pyrosequencing errors. PLoS One. 2013;8(9):e73015. Epub 2013/09/17. doi: 10.1371/journal. pone.0073015 PMID: 24039850; PubMed Central PMCID: PMC3764156.
-
(2013)
PLoS One.
, vol.8
, Issue.9
, pp. e73015
-
-
Iyer, S.1
Bouzek, H.2
Deng, W.3
Larsen, B.4
Casey, E.5
Mullins, J.I.6
-
20
-
-
84884847857
-
Improved detection of rare HIV-1 variants using 454 pyrosequencing
-
24098517 Epub 2013/10/08, PubMed Central PMCID: PMC3788733
-
Larsen BB, Chen L, Maust BS, Kim M, Zhao H, Deng W, et al. Improved detection of rare HIV-1 variants using 454 pyrosequencing. PLoS One. 2013;8(10):e76502. Epub 2013/10/08. doi: 10.1371/journal. pone.0076502 PMID: 24098517; PubMed Central PMCID: PMC3788733.
-
(2013)
PLoS One.
, vol.8
, Issue.10
, pp. e76502
-
-
Larsen, B.B.1
Chen, L.2
Maust, B.S.3
Kim, M.4
Zhao, H.5
Deng, W.6
-
21
-
-
0029817259
-
HIV quasispecies and resampling
-
8677432
-
Liu S-L, Rodrigo AG, Shankarappa R, Learn GH, Hsu L, Davidov O, et al. HIV quasispecies and resampling. Science. 1996;273(5274):415-6. PMID: 8677432
-
(1996)
Science.
, vol.273
, Issue.5274
, pp. 415-416
-
-
Liu, S.-L.1
Rodrigo, A.G.2
Shankarappa, R.3
Learn, G.H.4
Hsu, L.5
Davidov, O.6
-
22
-
-
0030977113
-
Quantitation of target molecules from polymerase chain reaction-based limiting dilution assays
-
Rodrigo AG, Goracke PC, Rowhanian K, Mullins JI. Quantitation of target molecules from polymerase chain reaction-based limiting dilution assays. AIDS Res and Hum Retrovir. 1997;13(9):737-42.
-
(1997)
AIDS Res and Hum Retrovir.
, vol.13
, Issue.9
, pp. 737-742
-
-
Rodrigo, A.G.1
Goracke, P.C.2
Rowhanian, K.3
Mullins, J.I.4
-
23
-
-
80054716265
-
Pcrefficiency: A Web tool for PCR amplification efficiency prediction
-
22014212 PubMed Central PMCID: PMC3234296
-
Mallona I, Weiss J, Egea-Cortines M. pcrEfficiency: a Web tool for PCR amplification efficiency prediction. BMC Bioinformatics. 2011;12:404. doi: 10.1186/1471-2105-12-404 PMID: 22014212; PubMed Central PMCID: PMC3234296.
-
(2011)
BMC Bioinformatics.
, vol.12
, pp. 404
-
-
Mallona, I.1
Weiss, J.2
Egea-Cortines, M.3
-
24
-
-
77955402078
-
Dynamics of HIV-1 quasispecies during antiviral treatment dissected using ultra-deep pyrosequencing
-
20628644 PubMed Central PMCID: PMC2898805
-
Hedskog C, Mild M, Jernberg J, Sherwood E, Bratt G, Leitner T, et al. Dynamics of HIV-1 quasispecies during antiviral treatment dissected using ultra-deep pyrosequencing. PLoS One. 2010;5(7):e11345. doi: 10.1371/journal.pone.0011345 PMID: 20628644; PubMed Central PMCID: PMC2898805.
-
(2010)
PLoS One.
, vol.5
, Issue.7
, pp. e11345
-
-
Hedskog, C.1
Mild, M.2
Jernberg, J.3
Sherwood, E.4
Bratt, G.5
Leitner, T.6
-
25
-
-
82355193803
-
Systematic comparison of three methods for fragmentation of long-range PCR products for next generation sequencing
-
22140562 Epub 2011/12/06, PubMed Central PMCID: PMC3227650
-
Knierim E, Lucke B, Schwarz JM, Schuelke M, Seelow D. Systematic comparison of three methods for fragmentation of long-range PCR products for next generation sequencing. PLoS ONE. 2011;6(11):e28240. Epub 2011/12/06. doi: 10.1371/journal.pone.0028240 PMID: 22140562; PubMed Central PMCID: PMC3227650.
-
(2011)
PLoS ONE.
, vol.6
, Issue.11
, pp. e28240
-
-
Knierim, E.1
Lucke, B.2
Schwarz, J.M.3
Schuelke, M.4
Seelow, D.5
-
26
-
-
79956044149
-
Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing
-
21592414 PubMed Central PMCID: PMC3116506
-
Gilles A, Meglecz E, Pech N, Ferreira S, Malausa T, Martin JF. Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing. BMC genomics. 2011;12:245. doi: 10.1186/1471-2164-12-245 PMID: 21592414; PubMed Central PMCID: PMC3116506.
-
(2011)
BMC Genomics
, vol.12
, pp. 245
-
-
Gilles, A.1
Meglecz, E.2
Pech, N.3
Ferreira, S.4
Malausa, T.5
Martin, J.F.6
-
27
-
-
84877074138
-
Single nucleotide polymorphism (SNP) detection and genotype calling from Massively parallel sequencing (MPS) data
-
24489615 Epub 2014/02/04, PubMed Central PMCID: PMC3905464
-
Li Y, Chen W, Liu EY, Zhou YH. Single Nucleotide Polymorphism (SNP) Detection and Genotype Calling from Massively Parallel Sequencing (MPS) Data. Statistics in biosciences. 2013;5(1):3-25. Epub 2014/02/04. doi: 10.1007/s12561-012-9067-4 PMID: 24489615; PubMed Central PMCID: PMC3905464.
-
(2013)
Statistics in Biosciences
, vol.5
, Issue.1
, pp. 3-25
-
-
Li, Y.1
Chen, W.2
Liu, E.Y.3
Zhou, Y.H.4
-
28
-
-
53649106195
-
Next-generation DNA sequencing
-
18846087 Epub 2008/10/11
-
Shendure J, Ji H. Next-generation DNA sequencing. Nat Biotechnol. 2008;26(10):1135-45. Epub 2008/10/11. doi: nbt1486 [pii] doi: 10.1038/nbt1486 PMID: 18846087.
-
(2008)
Nat Biotechnol.
, vol.26
, Issue.10
, pp. 1135-1145
-
-
Shendure, J.1
Ji, H.2
-
29
-
-
84865585233
-
Implications of pyrosequencing error correction for biological data interpretation
-
22952965 Epub 2012/09/07, PubMed Central PMCID: PMC3431371
-
Bakker MG, Tu ZJ, Bradeen JM, Kinkel LL. Implications of pyrosequencing error correction for biological data interpretation. PLoS ONE. 2012;7(8):e44357. Epub 2012/09/07. doi: 10.1371/journal.pone. 0044357 PMID: 22952965; PubMed Central PMCID: PMC3431371.
-
(2012)
PLoS ONE.
, vol.7
, Issue.8
, pp. e44357
-
-
Bakker, M.G.1
Tu, Z.J.2
Bradeen, J.M.3
Kinkel, L.L.4
-
30
-
-
84864085294
-
Experimental analysis of sources of error in evolutionary studies based on Roche/454 pyrosequencing of viral genomes
-
22436995 Epub 2012/03/23, PubMed Central PMCID: PMC3342875
-
Becker EA, Burns CM, Leon EJ, Rajabojan S, Friedman R, Friedrich TC, et al. Experimental analysis of sources of error in evolutionary studies based on Roche/454 pyrosequencing of viral genomes. Genome biology and evolution. 2012;4(4):457-65. Epub 2012/03/23. doi: 10.1093/gbe/evs029 PMID: 22436995; PubMed Central PMCID: PMC3342875.
-
(2012)
Genome Biology and Evolution
, vol.4
, Issue.4
, pp. 457-465
-
-
Becker, E.A.1
Burns, C.M.2
Leon, E.J.3
Rajabojan, S.4
Friedman, R.5
Friedrich, T.C.6
-
31
-
-
79960717109
-
Detection of minority resistance during early HIV-1 infection: Natural variation and spurious detection rather than transmission and evolution of multiple viral variants
-
21632754 Epub 2011/06/03, PubMed Central PMCID: PMC3147985
-
Gianella S, Delport W, Pacold ME, Young JA, Choi JY, Little SJ, et al. Detection of minority resistance during early HIV-1 infection: natural variation and spurious detection rather than transmission and evolution of multiple viral variants. J Virol. 2011;85(16):8359-67. Epub 2011/06/03. doi: 10.1128/JVI. 02582-10 PMID: 21632754; PubMed Central PMCID: PMC3147985.
-
(2011)
J Virol.
, vol.85
, Issue.16
, pp. 8359-8367
-
-
Gianella, S.1
Delport, W.2
Pacold, M.E.3
Young, J.A.4
Choi, J.Y.5
Little, S.J.6
-
32
-
-
77956204474
-
Nucleic acid template and the risk of a PCR-Induced HIV-1 drug resistance mutation
-
20539818 Epub 2010/06/12, PubMed Central PMCID: PMC2881873
-
Varghese V, Wang E, Babrzadeh F, Bachmann MH, Shahriar R, Liu T, et al. Nucleic acid template and the risk of a PCR-Induced HIV-1 drug resistance mutation. PLoS ONE. 2010;5(6):e10992. Epub 2010/06/12. doi: 10.1371/journal.pone.0010992 PMID: 20539818; PubMed Central PMCID: PMC2881873.
-
(2010)
PLoS ONE.
, vol.5
, Issue.6
, pp. e10992
-
-
Varghese, V.1
Wang, E.2
Babrzadeh, F.3
Bachmann, M.H.4
Shahriar, R.5
Liu, T.6
-
33
-
-
69549112742
-
Accurate determination of microbial diversity from 454 pyrosequencing data
-
19668203 Epub 2009/08/12
-
Quince C, Lanzen A, Curtis TP, Davenport RJ, Hall N, Head IM, et al. Accurate determination of microbial diversity from 454 pyrosequencing data. Nat Methods. 2009;6(9):639-41. Epub 2009/08/12. doi: 10.1038/nmeth.1361 PMID: 19668203.
-
(2009)
Nat Methods.
, vol.6
, Issue.9
, pp. 639-641
-
-
Quince, C.1
Lanzen, A.2
Curtis, T.P.3
Davenport, R.J.4
Hall, N.5
Head, I.M.6
-
34
-
-
78651228163
-
The evolutionary analysis of emerging low frequency HIV-1 CXCR4 using variants through time-an ultra-deep approach
-
21187908 Epub 2010/12/29, PubMed Central PMCID: PMC3002995
-
Archer J, Rambaut A, Taillon BE, Harrigan PR, Lewis M, Robertson DL. The evolutionary analysis of emerging low frequency HIV-1 CXCR4 using variants through time-an ultra-deep approach. PLoS Comput Biol. 2010;6(12):e1001022. Epub 2010/12/29. doi: 10.1371/journal.pcbi.1001022 PMID: 21187908; PubMed Central PMCID: PMC3002995.
-
(2010)
PLoS Comput Biol.
, vol.6
, Issue.12
, pp. e1001022
-
-
Archer, J.1
Rambaut, A.2
Taillon, B.E.3
Harrigan, P.R.4
Lewis, M.5
Robertson, D.L.6
-
35
-
-
81755185962
-
Ultra-deep sequencing for the analysis of viral populations
-
22440844 Epub 2012/03/24
-
Beerenwinkel N, Zagordi O. Ultra-deep sequencing for the analysis of viral populations. Current opinion in virology. 2011;1(5):413-8. Epub 2012/03/24. doi: 10.1016/j.coviro.2011.07.008 PMID: 22440844.
-
(2011)
Current Opinion in Virology
, vol.1
, Issue.5
, pp. 413-418
-
-
Beerenwinkel, N.1
Zagordi, O.2
-
36
-
-
78650798688
-
Combinatorial analysis and algorithms for quasispecies reconstruction using next-generation sequencing
-
21208435 Epub 2011/01/07, PubMed Central PMCID: PMC3022557
-
Prosperi MC, Prosperi L, Bruselles A, Abbate I, Rozera G, Vincenti D, et al. Combinatorial analysis and algorithms for quasispecies reconstruction using next-generation sequencing. BMC Bioinformatics. 2011;12:5. Epub 2011/01/07. doi: 10.1186/1471-2105-12-5 PMID: 21208435; PubMed Central PMCID: PMC3022557.
-
(2011)
BMC Bioinformatics.
, vol.12
, pp. 5
-
-
Prosperi, M.C.1
Prosperi, L.2
Bruselles, A.3
Abbate, I.4
Rozera, G.5
Vincenti, D.6
-
37
-
-
79251565226
-
Removing noise from pyrosequenced amplicons
-
21276213 Epub 2011/02/01, PubMed Central PMCID: PMC3045300
-
Quince C, Lanzen A, Davenport RJ, Turnbaugh PJ. Removing noise from pyrosequenced amplicons. BMC Bioinformatics. 2011;12:38. Epub 2011/02/01. doi: 10.1186/1471-2105-12-38 PMID: 21276213; PubMed Central PMCID: PMC3045300.
-
(2011)
BMC Bioinformatics.
, vol.12
, pp. 38
-
-
Quince, C.1
Lanzen, A.2
Davenport, R.J.3
Turnbaugh, P.J.4
-
38
-
-
79957814500
-
Correcting errors in short reads by multiple alignments
-
21471014 Epub 2011/04/08
-
Salmela L, Schröder J. Correcting errors in short reads by multiple alignments. Bioinformatics. 2011;27(11):1455-61. Epub 2011/04/08. doi: 10.1093/bioinformatics/btr170 PMID: 21471014.
-
(2011)
Bioinformatics.
, vol.27
, Issue.11
, pp. 1455-1461
-
-
Salmela, L.1
Schröder, J.2
-
39
-
-
79955125679
-
ShoRAH: Estimating the genetic diversity of a mixed sample from next-generation sequencing data
-
21521499 Epub 2011/04/28, PubMed Central PMCID: PMC3113935
-
Zagordi O, Bhattacharya A, Eriksson N, Beerenwinkel N. ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data. BMC Bioinformatics. 2011;12:119. Epub 2011/04/28. doi: 10.1186/1471-2105-12-119 PMID: 21521499; PubMed Central PMCID: PMC3113935.
-
(2011)
BMC Bioinformatics.
, vol.12
, pp. 119
-
-
Zagordi, O.1
Bhattacharya, A.2
Eriksson, N.3
Beerenwinkel, N.4
-
40
-
-
84861108474
-
Highly sensitive and specific detection of rare variants in mixed viral populations from Massively parallel sequence data
-
22438797
-
Macalalad AR, Zody MC, Charlebois P, Lennon NJ, Newman RM, Malboeuf CM, et al. Highly Sensitive and Specific Detection of Rare Variants in Mixed Viral Populations from Massively Parallel Sequence Data. PLoS Comput Biol. 2012;8(3):e1002417. doi: 10.1371/journal.pcbi.1002417 PMID: 22438797
-
(2012)
PLoS Comput Biol.
, vol.8
, Issue.3
, pp. e1002417
-
-
Macalalad, A.R.1
Zody, M.C.2
Charlebois, P.3
Lennon, N.J.4
Newman, R.M.5
Malboeuf, C.M.6
-
41
-
-
84855173088
-
QuRe: Software for viral quasispecies reconstruction from next-generation sequencing data
-
22088846 Epub 2011/11/18, PubMed Central PMCID: PMC3244773
-
Prosperi MC, Salemi M. QuRe: software for viral quasispecies reconstruction from next-generation sequencing data. Bioinformatics. 2012;28(1):132-3. Epub 2011/11/18. doi: 10.1093/bioinformatics/btr627 PMID: 22088846; PubMed Central PMCID: PMC3244773.
-
(2012)
Bioinformatics.
, vol.28
, Issue.1
, pp. 132-133
-
-
Prosperi, M.C.1
Salemi, M.2
-
42
-
-
84884874778
-
Indel and Carry forward Correction (ICC): A new analysis approach for processing 454 pyrosequencing data
-
23900188 Epub 2013/08/01, PubMed Central PMCID: PMC3777116
-
Deng W, Maust BS, Westfall DH, Chen L, Zhao H, Larsen BB, et al. Indel and Carryforward Correction (ICC): a new analysis approach for processing 454 pyrosequencing data. Bioinformatics. 2013;29(19):2402-9. Epub 2013/08/01. doi: 10.1093/bioinformatics/btt434 PMID: 23900188; PubMed Central PMCID: PMC3777116.
-
(2013)
Bioinformatics.
, vol.29
, Issue.19
, pp. 2402-2409
-
-
Deng, W.1
Maust, B.S.2
Westfall, D.H.3
Chen, L.4
Zhao, H.5
Larsen, B.B.6
-
43
-
-
77949508899
-
HIV drug resistance surveillance using pooled pyrosequencing
-
20174661 Epub 2010/02/23, PubMed Central PMCID: PMC2822863
-
Ji H, Masse N, Tyler S, Liang B, Li Y, Merks H, et al. HIV drug resistance surveillance using pooled pyrosequencing. PLoS ONE. 2010;5(2):e9263. Epub 2010/02/23. doi: 10.1371/journal.pone.0009263 PMID: 20174661; PubMed Central PMCID: PMC2822863.
-
(2010)
PLoS ONE.
, vol.5
, Issue.2
, pp. e9263
-
-
Ji, H.1
Masse, N.2
Tyler, S.3
Liang, B.4
Li, Y.5
Merks, H.6
-
44
-
-
79957970374
-
HIV-1 nucleotide mixture detection in the virco ((R)) TYPE HIV-1 genotyping assay: A comparison between Sanger sequencing and 454 pyrosequencing
-
21549149 Epub 2011/05/10
-
De Wolf H, Van Marck H, Mostmans W, Thys K, Vandenbroucke I, Van Eygen V, et al. HIV-1 nucleotide mixture detection in the virco ((R)) TYPE HIV-1 genotyping assay: a comparison between Sanger sequencing and 454 pyrosequencing. J Virol Methods. 2011;175(1):129-32. Epub 2011/05/10. doi: 10.1016/j.jviromet.2011.04.023 PMID: 21549149.
-
(2011)
J Virol Methods.
, vol.175
, Issue.1
, pp. 129-132
-
-
De Wolf, H.1
Van Marck, H.2
Mostmans, W.3
Thys, K.4
Vandenbroucke, I.5
Van Eygen, V.6
-
45
-
-
80955144081
-
Human immunodeficiency virus type 1 drug resistance testing: Evaluation of a new ultra-deep sequencing-based protocol and comparison with the TRUGENE HIV-1 Genotyping Kit
-
21907239 Epub 2011/09/13
-
Stelzl E, Proll J, Bizon B, Niklas N, Danzer M, Hackl C, et al. Human immunodeficiency virus type 1 drug resistance testing: Evaluation of a new ultra-deep sequencing-based protocol and comparison with the TRUGENE HIV-1 Genotyping Kit. J Virol Methods. 2011;178(1-2):94-7. Epub 2011/09/13. doi: 10.1016/j.jviromet.2011.08.020 PMID: 21907239.
-
(2011)
J Virol Methods.
, vol.178
, Issue.1-2
, pp. 94-97
-
-
Stelzl, E.1
Proll, J.2
Bizon, B.3
Niklas, N.4
Danzer, M.5
Hackl, C.6
-
46
-
-
84861205409
-
K65R in subtype C HIV-1 isolates from patients failing on a first-line regimen including d4T or AZT: Comparison of Sanger and UDP sequencing data
-
22615779 Epub 2012/05/23, PubMed Central PMCID: PMC3353948
-
Recordon-Pinson P, Papuchon J, Reigadas S, Deshpande A, Fleury H. K65R in subtype C HIV-1 isolates from patients failing on a first-line regimen including d4T or AZT: comparison of Sanger and UDP sequencing data. PLoS ONE. 2012;7(5):e36549. Epub 2012/05/23. doi: 10.1371/journal.pone. 0036549 PMID: 22615779; PubMed Central PMCID: PMC3353948.
-
(2012)
PLoS ONE.
, vol.7
, Issue.5
, pp. e36549
-
-
Recordon-Pinson, P.1
Papuchon, J.2
Reigadas, S.3
Deshpande, A.4
Fleury, H.5
-
47
-
-
84899506819
-
An international multicenter study on HIV-1 drug resistance testing by 454 ultra-deep pyrosequencing
-
24731928 Epub 2014/04/16
-
Simen BB, Braverman MS, Abbate I, Aerssens J, Bidet Y, Bouchez O, et al. An international multicenter study on HIV-1 drug resistance testing by 454 ultra-deep pyrosequencing. J Virol Methods. 2014;204:31-7. Epub 2014/04/16. doi: 10.1016/j.jviromet.2014.04.007 PMID: 24731928.
-
(2014)
J Virol Methods.
, vol.204
, pp. 31-37
-
-
Simen, B.B.1
Braverman, M.S.2
Abbate, I.3
Aerssens, J.4
Bidet, Y.5
Bouchez, O.6
-
48
-
-
80054839029
-
A comparison of parallel pyrosequencing and sanger clone-based sequencing and its impact on the characterization of the genetic diversity of HIV-1
-
22039546 Epub 2011/11/01, PubMed Central PMCID: PMC3198814
-
Liang B, Luo M, Scott-Herridge J, Semeniuk C, Mendoza M, Capina R, et al. A comparison of parallel pyrosequencing and sanger clone-based sequencing and its impact on the characterization of the genetic diversity of HIV-1. PLoS ONE. 2011;6(10):e26745. Epub 2011/11/01. doi: 10.1371/journal. pone.0026745 PMID: 22039546; PubMed Central PMCID: PMC3198814.
-
(2011)
PLoS ONE.
, vol.6
, Issue.10
, pp. e26745
-
-
Liang, B.1
Luo, M.2
Scott-Herridge, J.3
Semeniuk, C.4
Mendoza, M.5
Capina, R.6
-
49
-
-
84055200527
-
Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer ID
-
22135472 Epub 2011/12/03, PubMed Central PMCID: PMC3250168
-
Jabara CB, Jones CD, Roach J, Anderson JA, Swanstrom R. Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer ID. Proc Natl Acad Sci U S A. 2011;108(50):20166-71. Epub 2011/12/03. doi: 1110064108 [pii] doi: 10.1073/pnas.1110064108 PMID: 22135472; PubMed Central PMCID: PMC3250168.
-
(2011)
Proc Natl Acad Sci U S A.
, vol.108
, Issue.50
, pp. 20166-20171
-
-
Jabara, C.B.1
Jones, C.D.2
Roach, J.3
Anderson, J.A.4
Swanstrom, R.5
-
50
-
-
84904114340
-
HIV transmission. Selection bias at the heterosexual HIV-1 transmission bottleneck
-
25013080 Epub 2014/07/12
-
Carlson JM, Schaefer M, Monaco DC, Batorsky R, Claiborne DT, Prince J, et al. HIV transmission. Selection bias at the heterosexual HIV-1 transmission bottleneck. Science. 2014;345(6193):1254031. Epub 2014/07/12. doi: 10.1126/science.1254031 PMID: 25013080.
-
(2014)
Science.
, vol.345
, Issue.6193
, pp. 1254031
-
-
Carlson, J.M.1
Schaefer, M.2
Monaco, D.C.3
Batorsky, R.4
Claiborne, D.T.5
Prince, J.6
-
51
-
-
79952445068
-
Genetic impact of vaccination on breakthrough HIV-1 sequences from the STEP trial
-
21358627 Epub 2011/03/02, PubMed Central PMCID: PMC3053571
-
Rolland M, Tovanabutra S, De Camp AC, Frahm N, Gilbert PB, Sanders-Buell E, et al. Genetic impact of vaccination on breakthrough HIV-1 sequences from the STEP trial. Nature medicine. 2011;17(3):366-71. Epub 2011/03/02. doi: 10.1038/nm.2316 PMID: 21358627; PubMed Central PMCID: PMC3053571.
-
(2011)
Nature Medicine
, vol.17
, Issue.3
, pp. 366-371
-
-
Rolland, M.1
Tovanabutra, S.2
De Camp, A.C.3
Frahm, N.4
Gilbert, P.B.5
Sanders-Buell, E.6
-
52
-
-
56649105122
-
Efficacy assessment of a cell-mediated immunity HIV-1 vaccine (the Step Study): A double-blind, randomised, placebo-controlled, test-of-concept trial
-
19012954 Epub 2008/11/18
-
Buchbinder SP, Mehrotra DV, Duerr A, Fitzgerald DW, Mogg R, Li D, et al. Efficacy assessment of a cell-mediated immunity HIV-1 vaccine (the Step Study): a double-blind, randomised, placebo-controlled, test-of-concept trial. Lancet. 2008;372(9653):1881-93. Epub 2008/11/18. doi: S0140-6736 (08) 61591-3 [pii] doi: 10.1016/S0140-6736 (08) 61591-3 PMID: 19012954.
-
(2008)
Lancet.
, vol.372
, Issue.9653
, pp. 1881-1893
-
-
Buchbinder, S.P.1
Mehrotra, D.V.2
Duerr, A.3
Fitzgerald, D.W.4
Mogg, R.5
Li, D.6
-
53
-
-
56649114351
-
HIV-1 vaccine-induced immunity in the test-of-concept Step Study: A case-cohort analysis
-
19012957
-
McElrath MJ, De Rosa SC, Moodie Z, Dubey S, Kierstead L, Janes H, et al. HIV-1 vaccine-induced immunity in the test-of-concept Step Study: a case-cohort analysis. Lancet. 2008;372(9653):1894-905. PMID: 19012957. doi: 10.1016/S0140-6736 (08) 61592-5
-
(2008)
Lancet.
, vol.372
, Issue.9653
, pp. 1894-1905
-
-
McElrath, M.J.1
De Rosa, S.C.2
Moodie, Z.3
Dubey, S.4
Kierstead, L.5
Janes, H.6
-
54
-
-
77954067056
-
DIVEIN: A web server to analyze phylogenies, sequence divergence, diversity, and informative sites
-
20569214 PubMed Central PMCID: PMC3133969
-
Deng W, Maust BS, Nickle DC, Learn GH, Liu Y, Heath L, et al. DIVEIN: A Web Server to Analyze Phylogenies, Sequence Divergence, Diversity, and Informative Sites. Biotechniques. 2010;48(5):405-8. PubMed Central PMCID: PMC3133969. doi: 10.2144/000113370 PMID: 20569214
-
(2010)
Biotechniques.
, vol.48
, Issue.5
, pp. 405-408
-
-
Deng, W.1
Maust, B.S.2
Nickle, D.C.3
Learn, G.H.4
Liu, Y.5
Heath, L.6
-
55
-
-
84855692788
-
Amplification by PCR artificially reduces the proportion of the rare biosphere in microbial communities
-
22253843 Epub 2012/01/19, PubMed Central PMCID: PMC3256211
-
Gonzalez JM, Portillo MC, Belda-Ferre P, Mira A. Amplification by PCR artificially reduces the proportion of the rare biosphere in microbial communities. PLoS ONE. 2012;7(1):e29973. Epub 2012/01/19. doi: 10.1371/journal.pone.0029973 PMID: 22253843; PubMed Central PMCID: PMC3256211.
-
(2012)
PLoS ONE.
, vol.7
, Issue.1
, pp. e29973
-
-
Gonzalez, J.M.1
Portillo, M.C.2
Belda-Ferre, P.3
Mira, A.4
-
56
-
-
84908181086
-
Detecting ultralow-frequency mutations by duplex sequencing
-
25299156
-
Kennedy SR, Schmitt MW, Fox EJ, Kohrn BF, Salk JJ, Ahn EH, et al. Detecting ultralow-frequency mutations by Duplex Sequencing. Nat Protoc. 2014;9(11):2586-606. doi: 10.1038/nprot.2014.170 PMID: 25299156.
-
(2014)
Nat Protoc.
, vol.9
, Issue.11
, pp. 2586-2606
-
-
Kennedy, S.R.1
Schmitt, M.W.2
Fox, E.J.3
Kohrn, B.F.4
Salk, J.J.5
Ahn, E.H.6
|