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Changes in the Plasticity of HIV-1 Nef RNA during the Evolution of the North American Epidemic.

Manzourolajdad A, Gonzalez M, Spouge JL.

PLoS One. 2016 Sep 29;11(9):e0163688. doi: 10.1371/journal.pone.0163688.


HCVIVdb: The hepatitis-C IRES variation database.

Floden EW, Khawaja A, Vopálenský V, Pospíšek M.

BMC Microbiol. 2016 Aug 15;16(1):187. doi: 10.1186/s12866-016-0804-6.


Features of Recently Transmitted HIV-1 Clade C Viruses that Impact Antibody Recognition: Implications for Active and Passive Immunization.

Rademeyer C, Korber B, Seaman MS, Giorgi EE, Thebus R, Robles A, Sheward DJ, Wagh K, Garrity J, Carey BR, Gao H, Greene KM, Tang H, Bandawe GP, Marais JC, Diphoko TE, Hraber P, Tumba N, Moore PL, Gray GE, Kublin J, McElrath MJ, Vermeulen M, Middelkoop K, Bekker LG, Hoelscher M, Maboko L, Makhema J, Robb ML, Abdool Karim S, Abdool Karim Q, Kim JH, Hahn BH, Gao F, Swanstrom R, Morris L, Montefiori DC, Williamson C.

PLoS Pathog. 2016 Jul 19;12(7):e1005742. doi: 10.1371/journal.ppat.1005742.


Defective HIV-1 proviruses produce novel protein-coding RNA species in HIV-infected patients on combination antiretroviral therapy.

Imamichi H, Dewar RL, Adelsberger JW, Rehm CA, O'Doherty U, Paxinos EE, Fauci AS, Lane HC.

Proc Natl Acad Sci U S A. 2016 Aug 2;113(31):8783-8. doi: 10.1073/pnas.1609057113.


Longitudinal Antigenic Sequences and Sites from Intra-Host Evolution (LASSIE) Identifies Immune-Selected HIV Variants.

Hraber P, Korber B, Wagh K, Giorgi EE, Bhattacharya T, Gnanakaran S, Lapedes AS, Learn GH, Kreider EF, Li Y, Shaw GM, Hahn BH, Montefiori DC, Alam SM, Bonsignori M, Moody MA, Liao HX, Gao F, Haynes BF.

Viruses. 2015 Oct 21;7(10):5443-75. doi: 10.3390/v7102881.


The Number and Complexity of Pure and Recombinant HIV-1 Strains Observed within Incident Infections during the HIV and Malaria Cohort Study Conducted in Kericho, Kenya, from 2003 to 2006.

Billings E, Sanders-Buell E, Bose M, Bradfield A, Lei E, Kijak GH, Arroyo MA, Kibaya RM, Scott PT, Wasunna MK, Sawe FK, Shaffer DN, Birx DL, McCutchan FE, Michael NL, Robb ML, Kim JH, Tovanabutra S.

PLoS One. 2015 Aug 19;10(8):e0135124. doi: 10.1371/journal.pone.0135124.


Multiplexed highly-accurate DNA sequencing of closely-related HIV-1 variants using continuous long reads from single molecule, real-time sequencing.

Dilernia DA, Chien JT, Monaco DC, Brown MP, Ende Z, Deymier MJ, Yue L, Paxinos EE, Allen S, Tirado-Ramos A, Hunter E.

Nucleic Acids Res. 2015 Nov 16;43(20):e129. doi: 10.1093/nar/gkv630.


Advanced molecular surveillance of hepatitis C virus.

Rossi LM, Escobar-Gutierrez A, Rahal P.

Viruses. 2015 Mar 13;7(3):1153-88. doi: 10.3390/v7031153. Review.


Strong epistatic selection on the RNA secondary structure of HIV.

Assis R.

PLoS Pathog. 2014 Sep 11;10(9):e1004363. doi: 10.1371/journal.ppat.1004363.


Evolution of HIV-1 coreceptor usage and coreceptor switching during pregnancy.

Ransy DG, Motorina A, Merindol N, Akouamba BS, Samson J, Lie Y, Napolitano LA, Lapointe N, Boucher M, Soudeyns H.

AIDS Res Hum Retroviruses. 2014 Mar;30(3):312-24. doi: 10.1089/AID.2013.0155. Erratum in: AIDS Res Hum Retroviruses. 2014 May;30(5):509.


HIV N-linked glycosylation site analyzer and its further usage in anchored alignment.

Shaw TI, Zhang M.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W454-8. doi: 10.1093/nar/gkt472.


Integrating genealogical and dynamical modelling to infer escape and reversion rates in HIV epitopes.

Palmer D, Frater J, Phillips R, McLean AR, McVean G.

Proc Biol Sci. 2013 May 15;280(1762):20130696. doi: 10.1098/rspb.2013.0696.


Interplay between HIV-1 and Host Genetic Variation: A Snapshot into Its Impact on AIDS and Therapy Response.

Sampathkumar R, Shadabi E, Luo M.

Adv Virol. 2012;2012:508967. doi: 10.1155/2012/508967.


The LANL hemorrhagic fever virus database, a new platform for analyzing biothreat viruses.

Kuiken C, Thurmond J, Dimitrijevic M, Yoon H.

Nucleic Acids Res. 2012 Jan;40(Database issue):D587-92. doi: 10.1093/nar/gkr898.


Genetic signatures in the envelope glycoproteins of HIV-1 that associate with broadly neutralizing antibodies.

Gnanakaran S, Daniels MG, Bhattacharya T, Lapedes AS, Sethi A, Li M, Tang H, Greene K, Gao H, Haynes BF, Cohen MS, Shaw GM, Seaman MS, Kumar A, Gao F, Montefiori DC, Korber B.

PLoS Comput Biol. 2010 Oct 7;6(10):e1000955. doi: 10.1371/journal.pcbi.1000955.


Epitopes for broad and potent neutralizing antibody responses during chronic infection with human immunodeficiency virus type 1.

Nandi A, Lavine CL, Wang P, Lipchina I, Goepfert PA, Shaw GM, Tomaras GD, Montefiori DC, Haynes BF, Easterbrook P, Robinson JE, Sodroski JG, Yang X; NIAID Center for HIV/AIDS Vaccine Immunology..

Virology. 2010 Jan 20;396(2):339-48. doi: 10.1016/j.virol.2009.10.044.


Valinomycin biosynthetic gene cluster in Streptomyces: conservation, ecology and evolution.

Matter AM, Hoot SB, Anderson PD, Neves SS, Cheng YQ.

PLoS One. 2009 Sep 29;4(9):e7194. doi: 10.1371/journal.pone.0007194.


Antibody binding is a dominant determinant of the efficiency of human immunodeficiency virus type 1 neutralization.

Yang X, Lipchina I, Cocklin S, Chaiken I, Sodroski J.

J Virol. 2006 Nov;80(22):11404-8.

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