454 Life Sciences

Tracking the evolution of multiple in vitro HCV replicon variants under protease inhibitor selection pressure by 454 deep sequencing.  Verbinnen T, Van Marck H, Vandenbroucke I, Vijgen L, Claes M, Lin TI, Simmen K, Neyts J, Fanning G, Lenz O. (9/1/2010) Journal of Virology ePub:
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Analysis of co-receptor usage of circulating viral and proviral HIV genome quasispecies by ultra-deep pyrosequencing in patients candidate to CCR5 antagonist treatment.  Abbate I, Rozera G, Tommasi C, Bruselles A, Bartolini B, Chillemi G, Nicastri E, Narciso P, Ippolito G, Capobianchi MR. (8/20/2010) Clin Microbiol Infect ePub:
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Transmission of Single HIV-1 Genomes and Dynamics of Early Immune Escape Revealed by Ultra-Deep Sequencing.  Fischer W, Ganusov VV, Giorgi EE, Hraber PT, Keele BF, Leitner T, Han CS, Gleasner CD, Green L, Lo CC, Nag A, Wallstrom TC, Wang S, McMichael AJ, Haynes BF, Hahn BH, Perelson AS, Borrow P, Shaw GM, Bhattacharya T, Korber BT. (8/20/2010) PLoS One 5(8): e12303.
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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.  Tilton JC, Wilen CB, Didigu CA, Sinha R, Harrison JE, Agrawal-Gamse C, Henning EA, Bushman FD, Martin JN, Deeks SG, Doms RW. (8/11/2010) Journal of Virology ePub:
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Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies.  Zagordi O, Klein R, Däumer M, Beerenwinkel N. (7/28/2010) Nucleic Acids Research ePub:
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Dynamics of HIV-1 Quasispecies during Antiviral Treatment Dissected Using Ultra-Deep Pyrosequencing.  Hedskog C, Mild M, Jernberg J, Sherwood E, Bratt G, Leitner T, Lundeberg J, Andersson B, Albert J. (7/7/2010) PLoS One 5(7): e11345.
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Prevalence and clinical significance of HIV drug resistance mutations by ultra-deep sequencing in antiretroviral-naïve subjects in the CASTLE study.  Lataillade M, Chiarella J, Yang R, Schnittman S, Wirtz V, Uy J, Seekins D, Krystal M, Mancini M, McGrath D, Simen B, Egholm M, Kozal M. (6/3/2010) PLoS One 5(6): e10952.
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Hepatitis C virus transmission bottlenecks analyzed by deep sequencing.  Wang GP, Sherrill-Mix SA, Chang KM, Quince C, Bushman FD. (6/1/2010) Journal of Virology 84(12): 6218-28.
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Improved Detection of CXCR4-Using HIV by V3 Genotyping: Application of Population-Based and "Deep" Sequencing to Plasma RNA and Proviral DNA.  Swenson LC, Moores A, Low AJ, Thielen A, Dong W, Woods C, Jensen MA, Wynhoven B, Chan D, Glascock C, Harrigan PR. (5/27/2010) Journal of AIDS 54(5): 506-10.
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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.  Love TM, Thurston SW, Keefer MC, Dewhurst S, Lee HY. (3/24/2010) Journal of Virology 84(11): 5802-14.
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HIV Drug Resistance Surveillance Using Pooled Pyrosequencing.  Ji H, Massé N, Tyler S, Liang B, Li Y, Merks H, Graham M, Sandstrom P, Brooks J. (2/17/2010) PLoS One 5(2): e9263.
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Dynamics of Haplotype Frequency Change in a CD8+TL Epitope of Simian Immunodeficiency Virus.  Hughes AL, O'Connor S, Dudley DM, Burwitz BJ, Bimber BN, O'Connor D. (2/8/2010) Infect Genet Evol 10(4): 555-60.
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Lens epithelium-derived growth factor fusion proteins redirect HIV-1 DNA integration.  Ferris AL, Wu X, Hughes CM, Stewart C, Smith SJ, Milne TA, Wang GG, Shun MC, Allis CD, Engelman A, Hughes SH. (2/1/2010) PNAS 107(7): 3135-40.
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HIV Sequence Variation Associated With env Antisense Adoptive T-cell Therapy in the hNSG Mouse Model.  Mukherjee R, Plesa G, Sherrill-Mix S, Richardson MW, Riley JL, Bushman FD. (1/26/2010) Molecular Therapy 18(4): 803-11.
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Phylogenetic Analysis of Population-Based and Deep Sequencing Data to Identify Coevolving Sites in the nef Gene of HIV-1.  Poon AF, Swenson LC, Dong WW, Deng W, Kosakovsky Pond SL, Brumme ZL, Mullins JI, Richman DD, Harrigan PR, Frost SD. (12/2/2009) Molecular Biology and Evolution 27(4): 819-32.
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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.  Varghese V, Shahriar R, Rhee SY, Liu T, Simen BB, Egholm M, Hanczaruk B, Blake LA, Gharizadeh B, Babrzadeh F, Bachmann MH, Fessel WJ, Shafer RW. (9/3/2009) AIDS 52(3): 309-15.
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Use of massive parallel pyrosequencing for near full-length characterization of a unique HIV Type 1 BF recombinant associated with a fatal primary infection.  Bruselles A, Rozera G, Bartolini B, Prosperi M, Del Nonno F, Narciso P, Capobianchi MR, Abbate I. (9/1/2009) AIDS Research and Human Retroviruses 25(9): 937-42.
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Ultradeep pyrosequencing detects complex patterns of CD8+ T-lymphocyte escape in simian immunodeficiency virus-infected macaques.  Bimber BN, Burwitz BJ, O'Connor S, Detmer A, Gostick E, Lank SM, Price DA, Hughes A, O'Connor D. (8/1/2009) Journal of Virology 83(16): 8247-53.
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Low-abundance HIV drug-resistant viral variants in treatment-experienced persons correlate with historical antiretroviral use.  Le T, Chiarella J, Simen BB, Hanczaruk B, Egholm M, Landry ML, Dieckhaus K, Rosen MI, Kozal MJ. (6/29/2009) PLoS One 4(6): e6079.
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HIV integration site distributions in resting and activated CD4+ T cells infected in culture.  Brady T, Agosto LM, Malani N, Berry CC, Doherty U, Bushman F. (6/20/2009) AIDS 23(12): 1461-71.
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Quantitative deep sequencing reveals dynamic HIV-1 escape and large population shifts during CCR5 antagonist therapy in vivo.  Tsibris AM, Korber B, Arnaout R, Russ C, Lo CC, Leitner T, Gaschen B, Theiler J, Paredes R, Su Z, Hughes MD, Gulick RM, Greaves W, Coakley E, Flexner C, Nusbaum C, Kuritzkes DR. (5/25/2009) PLoS ONE 4(5): e5683.
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Detection of low-frequency pretherapy chemokine (CXC motif) receptor 4 (CXCR4)-using HIV-1 with ultra-deep pyrosequencing.  Archer J, Braverman MS, Taillon BE, Desany B, James I, Harrigan PR, Lewis M, Robertson DL. (5/6/2009) AIDS 23(10): 1209-18.
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Analysis of lentiviral vector integration in HIV+ study subjects receiving autologous infusions of gene modified CD4+ T cells.  Wang GP, Levine BL, Binder GK, Berry CC, Malani N, McGarrity G, Tebas P, June CH, Bushman FD. (5/1/2009) Molecular Therapy 17(5): 844-50.
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Long-term control of HIV by CCR5 Delta32/Delta32 stem-cell transplantation.  Hütter G, Nowak D, Mossner M, Ganepola S, Müssig A, Allers K, Schneider T, Hofmann J, Kücherer C, Blau O, Blau IW, Hofmann WK, Thiel E. (2/12/2009) New England Journal of Medicine 360(7): 692-8.
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Low-Abundance Drug-Resistant Viral Variants in Chronically HIV-Infected, Antiretroviral Treatment–Naive Patients Significantly Impact Treatment Outcomes.  Simen B, Simons J, Hullsiek K, Novak R, MacArthur R, Baxter J, Huang C, Lubeski C, Turenchalk G, Braverman M, Desany B, Rothberg J, Egholm M, and Kozal M. (2/12/2009) Journal of Infectious Diseases 199(5): 693-701
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Massively parallel pyrosequencing highlights minority variants in the HIV-1 env quasispecies deriving from lymphomonocyte sub-populations.  Rozera G, Abbate I, Bruselles A, Vlassi C, D'Offizi G, Narciso P, Chillemi G, Prosperi M, Ippolito G, Capobianchi MR. (2/12/2009) Retrovirology 6(1): 15
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Minority HIV-1 Variants in Antiretroviral Naive Persons with Reverse Transcriptase Codon 215 Revertant Mutations.  Mitsuya Y, Varghese V, Wang C, Liu TF, Holmes SP, Jayakumar R, Gharizadeh B, Ronaghi M, Klein D, Fessel WJ, Shafer RW. (10/1/2008) Journal of Virology 82: 10747-55
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Establishment of HIV-1 resistance in CD4+ T cells by genome editing using zinc-finger nucleases.  Perez EE, Wang J, Miller JC, Jouvenot Y, Kim KA, Liu O, Wang N, Lee G, Bartsevich VV, Lee YL, Guschin DY, Rupniewski I, Waite AJ, Carpenito C, Carroll RG, Orange JS, Urnov FD, Rebar EJ, Ando D, Gregory PD, Riley JL, Holmes MC, June CH. (7/1/2008) Nature Biotechnology 26: 808-16
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Characterization of mutation spectra with ultra-deep pyrosequencing: Application to HIV-1 drug resistance  Chunlin Wang, Yumi Mitsuya, Baback Gharizadeh, Mostafa Ronaghi and Robert W. Shafer (8/1/2007) Genome Research 17: 1195-1201
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DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations  Christian Hoffmann1, Nana Minkah1, Jeremy Leipzig1, Gary Wang1, Max Q. Arens3, Pablo Tebas and Frederic D. Bushman (6/18/2007) Nucleic Acids Research 35:
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