My NCBISign In
Massively parallel pyrosequencing highlights minority variants in the HIV-1 env quasispecies deriving from lymphomonocyte sub-populations
Gabriella Rozera, Isabella Abbate, Alessandro Bruselles, Crhysoula Vlassi, Gianpiero D'Offizi, Pasquale Narciso, Giovanni Chillemi, Mattia Prosperi, Giuseppe Ippolito, Maria R Capobianchi
Retrovirology. 2009; 6: 15. Published online 2009 February 12. doi: 10.1186/1742-4690-6-15
PMCID:
PMC2660291
Abstract Full Text PDF–1.1M Supplementary Material

Is Cited by the Following 25 Articles in this Archive:

Dynamics of Hepatitis B Virus Quasispecies in Association with Nucleos(t)ide Analogue Treatment Determined by Ultra-Deep Sequencing
Norihiro Nishijima, Hiroyuki Marusawa, Yoshihide Ueda, Ken Takahashi, Akihiro Nasu, Yukio Osaki, Tadayuki Kou, Shujiro Yazumi, Takeshi Fujiwara, Soken Tsuchiya, Kazuharu Shimizu, Shinji Uemoto, Tsutomu Chiba
PLoS One. 2012; 7(4): e35052. Published online 2012 April 16. doi: 10.1371/journal.pone.0035052
PMCID:
PMC3327662
Abstract Full Text PDF–233K Supplementary Material
Analysis of high-depth sequence data for studying viral diversity: a comparison of next generation sequencing platforms using Segminator II
John Archer, Greg Baillie, Simon J Watson, Paul Kellam, Andrew Rambaut, David L Robertson
BMC Bioinformatics. 2012; 13: 47. Published online 2012 March 23. doi: 10.1186/1471-2105-13-47
PMCID:
PMC3359224
Abstract Full Text PDF–2.2M
Experimental Analysis of Sources of Error in Evolutionary Studies Based on Roche/454 Pyrosequencing of Viral Genomes
Ericka A. Becker, Charles M. Burns, Enrique J. León, Saravanan Rajabojan, Robert Friedman, Thomas C. Friedrich, Shelby L. O'Connor, Austin L. Hughes
Genome Biol Evol. 2012; 4(4): 457–465. Published online 2012 March 20. doi: 10.1093/gbe/evs029
PMCID:
PMC3342875
Abstract Full Text PDF–142K
Highly Sensitive and Specific Detection of Rare Variants in Mixed Viral Populations from Massively Parallel Sequence Data
Alexander R. Macalalad, Michael C. Zody, Patrick Charlebois, Niall J. Lennon, Ruchi M. Newman, Christine M. Malboeuf, Elizabeth M. Ryan, Christian L. Boutwell, Karen A. Power, Doug E. Brackney, Kendra N. Pesko, Joshua Z. Levin, Gregory D. Ebel, Todd M. Allen, Bruce W. Birren, Matthew R. Henn
PLoS Comput Biol. 2012 March; 8(3): e1002417. Published online 2012 March 15. doi: 10.1371/journal.pcbi.1002417
PMCID:
PMC3305335
Abstract Full Text PDF–462K Supplementary Material
Dynamics of Envelope Evolution in Clade C SHIV-Infected Pig-Tailed Macaques during Disease Progression Analyzed by Ultra-Deep Pyrosequencing
For Yue Tso, Damien C. Tully, Sandra Gonzalez, Christopher Quince, On Ho, Patricia Polacino, Ruth M. Ruprecht, Shiu-Lok Hu, Charles Wood
PLoS One. 2012; 7(3): e32827. Published online 2012 March 12. doi: 10.1371/journal.pone.0032827
PMCID:
PMC3299704
Abstract Full Text PDF–1.3M Supplementary Material
A Comparison of Parallel Pyrosequencing and Sanger Clone-Based Sequencing and Its Impact on the Characterization of the Genetic Diversity of HIV-1
Binhua Liang, Ma Luo, Joel Scott-Herridge, Christina Semeniuk, Mark Mendoza, Rupert Capina, Brent Sheardown, Hezhao Ji, Joshua Kimani, Blake T. Ball, Gary Van Domselaar, Morag Graham, Shane Tyler, Steven J. M. Jones, Francis A. Plummer
PLoS One. 2011; 6(10): e26745. Published online 2011 October 21. doi: 10.1371/journal.pone.0026745
PMCID:
PMC3198814
Abstract Full Text PDF–114K Supplementary Material
Evaluation of High-Throughput Sequencing for Identifying Known and Unknown Viruses in Biological Samples
Justine Cheval, Virginie Sauvage, Lionel Frangeul, Laurent Dacheux, Ghislaine Guigon, Nicolas Dumey, Kevin Pariente, Claudine Rousseaux, Fabien Dorange, Nicolas Berthet, Sylvain Brisse, Ivan Moszer, Hervé Bourhy, Claude Jean Manuguerra, Marc Lecuit, Ana Burguiere, Valérie Caro, Marc Eloit
J Clin Microbiol. 2011 September; 49(9): 3268–3275. doi: 10.1128/JCM.00850-11
PMCID:
PMC3165575
Abstract Full Text PDF–163K Supplementary Material
Identification of HIV Superinfection in Seroconcordant Couples in Rakai, Uganda, by Use of Next-Generation Deep Sequencing
Andrew D. Redd, Aleisha Collinson-Streng, Craig Martens, Stacy Ricklefs, Caroline E. Mullis, Jordyn Manucci, Aaron A. R. Tobian, Ethan J. Selig, Oliver Laeyendecker, Nelson Sewankambo, Ronald H. Gray, David Serwadda, Maria J. Wawer, Stephen F. Porcella, Thomas C. Quinn
J Clin Microbiol. 2011 August; 49(8): 2859–2867. doi: 10.1128/JCM.00804-11
PMCID:
PMC3147722
Abstract Full Text PDF–1.9M Supplementary Material
Performance of Ultra-Deep Pyrosequencing in Analysis of HIV-1 pol Gene Variation
Mattias Mild, Charlotte Hedskog, Johanna Jernberg, Jan Albert
PLoS One. 2011; 6(7): e22741. Published online 2011 July 25. doi: 10.1371/journal.pone.0022741
PMCID:
PMC3143174
Abstract Full Text PDF–495K Supplementary Material
Analysis of HIV-1 Expression Level and Sense of Transcription by High-Throughput Sequencing of the Infected Cell
Gregory Lefebvre, Sébastien Desfarges, Frédéric Uyttebroeck, Miguel Muñoz, Niko Beerenwinkel, Jacques Rougemont, Amalio Telenti, Angela Ciuffi
J Virol. 2011 July; 85(13): 6205–6211. doi: 10.1128/JVI.00252-11
PMCID:
PMC3126515
Abstract Full Text PDF–738K Supplementary Material
Cellular HIV-1 DNA levels in patients receiving antiretroviral therapy strongly correlate with therapy initiation timing but not with therapy duration
Dai Watanabe, Shiro Ibe, Tomoko Uehira, Rumi Minami, Atsushi Sasakawa, Keishiro Yajima, Hitoshi Yonemoto, Hiroki Bando, Yoshihiko Ogawa, Tomohiro Taniguchi, Daisuke Kasai, Yasuharu Nishida, Masahiro Yamamoto, Tsuguhiro Kaneda, Takuma Shirasaka
BMC Infect Dis. 2011; 11: 146. Published online 2011 May 24. doi: 10.1186/1471-2334-11-146
PMCID:
PMC3112100
Abstract Full Text PDF–424K
Replicative phenotyping adds value to genotypic resistance testing in heavily pre-treated HIV-infected individuals - the Swiss HIV Cohort Study
Jan Fehr, Tracy R Glass, Séverine Louvel, François Hamy, Hans H Hirsch, Viktor von Wyl, Jürg Böni, Sabine Yerly, Philippe Bürgisser, Matthias Cavassini, Christoph A Fux, Bernard Hirschel, Pietro Vernazza, Gladys Martinetti, Enos Bernasconi, Huldrych F Günthard, Manuel Battegay, Heiner C Bucher, Thomas Klimkait
J Transl Med. 2011; 9: 14. Published online 2011 January 21. doi: 10.1186/1479-5876-9-14
PMCID:
PMC3032678
Abstract Full Text PDF–254K
The Evolutionary Analysis of Emerging Low Frequency HIV-1 CXCR4 Using Variants through Time—An Ultra-Deep Approach
John Archer, Andrew Rambaut, Bruce E. Taillon, P. Richard Harrigan, Marilyn Lewis, David L. Robertson
PLoS Comput Biol. 2010 December; 6(12): e1001022. Published online 2010 December 16. doi: 10.1371/journal.pcbi.1001022
PMCID:
PMC3002995
Abstract Full Text PDF–1.3M Supplementary Material
Beyond the Consensus: Dissecting Within-Host Viral Population Diversity of Foot-and-Mouth Disease Virus by Using Next-Generation Genome Sequencing
Caroline F. Wright, Marco J. Morelli, Gaël Thébaud, Nick J. Knowles, Pawel Herzyk, David J. Paton, Daniel T. Haydon, Donald P. King
J Virol. 2011 March; 85(5): 2266–2275. Published online 2010 December 15. doi: 10.1128/JVI.01396-10
PMCID:
PMC3067773
Abstract Full Text PDF–1.9M Supplementary Material
Massively parallel sequencing for monitoring genetic consistency and quality control of live viral vaccines
Alexander Neverov, Konstantin Chumakov
Proc Natl Acad Sci U S A. 2010 November 16; 107(46): 20063–20068. Published online 2010 November 1. doi: 10.1073/pnas.1012537107
PMCID:
PMC2993378
Abstract Full Text PDF–475K
Development of a Low Bias Method for Characterizing Viral Populations Using Next Generation Sequencing Technology
Stephanie M. Willerth, Hélder A. M. Pedro, Lior Pachter, Laurent M. Humeau, Adam P. Arkin, David V. Schaffer
PLoS One. 2010; 5(10): e13564. Published online 2010 October 22. doi: 10.1371/journal.pone.0013564
PMCID:
PMC2962647
Abstract Full Text PDF–1.4M Supplementary Material
Exposing malaria in-host diversity and estimating population diversity by capture-recapture using massively parallel pyrosequencing
Jonathan J. Juliano, Kimberly Porter, Victor Mwapasa, Rithy Sem, William O. Rogers, Frédéric Ariey, Chansuda Wongsrichanalai, Andrew Read, Steven R. Meshnick
Proc Natl Acad Sci U S A. 2010 November 16; 107(46): 20138–20143. Published online 2010 October 19. doi: 10.1073/pnas.1007068107
PMCID:
PMC2993407
Abstract Full Text PDF–420K Supplementary Material
Tracking the Evolution of Multiple In Vitro Hepatitis C Virus Replicon Variants under Protease Inhibitor Selection Pressure by 454 Deep Sequencing
Thierry Verbinnen, Herwig Van Marck, Ina Vandenbroucke, Leen Vijgen, Marijke Claes, Tse-I Lin, Kenneth Simmen, Johan Neyts, Gregory Fanning, Oliver Lenz
J Virol. 2010 November; 84(21): 11124–11133. Published online 2010 August 25. doi: 10.1128/JVI.01217-10
PMCID:
PMC2953167
Abstract Full Text PDF–1.1M
A Maraviroc-Resistant HIV-1 with Narrow Cross-Resistance to Other CCR5 Antagonists Depends on both N-Terminal and Extracellular Loop Domains of Drug-Bound CCR5
John C. Tilton, Craig B. Wilen, Chukwuka A. Didigu, Rohini Sinha, Jessamina E. Harrison, Caroline Agrawal-Gamse, Elizabeth A. Henning, Frederick D. Bushman, Jeffrey N. Martin, Steven G. Deeks, Robert W. Doms
J Virol. 2010 October; 84(20): 10863–10876. Published online 2010 August 11. doi: 10.1128/JVI.01109-10
PMCID:
PMC2950574
Abstract Full Text PDF–1.4M
Drug-Class Specific Impact of Antivirals on the Reproductive Capacity of HIV
Max von Kleist, Stephan Menz, Wilhelm Huisinga
PLoS Comput Biol. 2010 March; 6(3): e1000720. Published online 2010 March 26. doi: 10.1371/journal.pcbi.1000720
PMCID:
PMC2845651
Abstract Full Text PDF–684K Supplementary Material
HIV Drug Resistance Surveillance Using Pooled Pyrosequencing
Hezhao Ji, Nathalie Massé, Shaun Tyler, Ben Liang, Yang Li, Harriet Merks, Morag Graham, Paul Sandstrom, James Brooks
PLoS One. 2010; 5(2): e9263. Published online 2010 February 17. doi: 10.1371/journal.pone.0009263
PMCID:
PMC2822863
Abstract Full Text PDF–468K Supplementary Material
Phylogenetic Analysis of Population-Based and Deep Sequencing Data to Identify Coevolving Sites in the nef Gene of HIV-1
Art F.Y. Poon, Luke C. Swenson, Winnie W.Y. Dong, Wenjie Deng, Sergei L. Kosakovsky Pond, Zabrina L. Brumme, James I. Mullins, Douglas D. Richman, P. Richard Harrigan, Simon D.W. Frost
Mol Biol Evol. 2010 April; 27(4): 819–832. Published online 2009 December 2. doi: 10.1093/molbev/msp289
PMCID:
PMC2877536
Abstract Full Text PDF–666K Supplementary Material
Unique features of HLA-mediated HIV evolution in a Mexican cohort: a comparative study
Santiago Avila-Rios, Christopher E Ormsby, Jonathan M Carlson, Humberto Valenzuela-Ponce, Juan Blanco-Heredia, Daniela Garrido-Rodriguez, Claudia Garcia-Morales, David Heckerman, Zabrina L Brumme, Simon Mallal, Mina John, Enrique Espinosa, Gustavo Reyes-Teran
Retrovirology. 2009; 6: 72. Published online 2009 August 10. doi: 10.1186/1742-4690-6-72
PMCID:
PMC2734549
Abstract Full Text PDF–4.2M Supplementary Material
Next-generation sequencing: a transformative tool for vaccinology
Neelam Dhiman, David I Smith, Gregory A Poland
Expert Rev Vaccines. Author manuscript; available in PMC 2010 August 1.
Published in final edited form as: Expert Rev Vaccines. 2009 August; 8(8): 963–967. doi: 10.1586/erv.09.67
PMCID:
PMC2843135
Full Text PDF–91K
The co-receptor signaling model of HIV-1 pathogenesis in peripheral CD4 T cells
Yuntao Wu
Retrovirology. 2009; 6: 41. Published online 2009 May 1. doi: 10.1186/1742-4690-6-41
PMCID:
PMC2679705
Abstract Full Text PDF–300K
You are here: NCBI > Literature > PubMed Central (PMC)
Write to the Help Desk