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Elucidation of hepatitis C virus transmission and early diversification by single genome sequencing.

Li H, Stoddard MB, Wang S, Blair LM, Giorgi EE, Parrish EH, Learn GH, Hraber P, Goepfert PA, Saag MS, Denny TN, Haynes BF, Hahn BH, Ribeiro RM, Perelson AS, Korber BT, Bhattacharya T, Shaw GM.

PLoS Pathog. 2012;8(8):e1002880. doi: 10.1371/journal.ppat.1002880. Epub 2012 Aug 23.


From molecular genetics to phylodynamics: evolutionary relevance of mutation rates across viruses.

Sanjuán R.

PLoS Pathog. 2012;8(5):e1002685. doi: 10.1371/journal.ppat.1002685. Epub 2012 May 3.


Contribution of a mutational bias in hepatitis C virus replication to the genetic barrier in the development of drug resistance.

Powdrill MH, Tchesnokov EP, Kozak RA, Russell RS, Martin R, Svarovskaia ES, Mo H, Kouyos RD, Götte M.

Proc Natl Acad Sci U S A. 2011 Dec 20;108(51):20509-13. doi: 10.1073/pnas.1105797108. Epub 2011 Dec 1.


Upper limits of normal for alanine aminotransferase activity in the United States population.

Ruhl CE, Everhart JE.

Hepatology. 2012 Feb;55(2):447-54. doi: 10.1002/hep.24725.


Sequential bottlenecks drive viral evolution in early acute hepatitis C virus infection.

Bull RA, Luciani F, McElroy K, Gaudieri S, Pham ST, Chopra A, Cameron B, Maher L, Dore GJ, White PA, Lloyd AR.

PLoS Pathog. 2011 Sep;7(9):e1002243. doi: 10.1371/journal.ppat.1002243. Epub 2011 Sep 1.


Delayed induction, not impaired recruitment, of specific CD8⁺ T cells causes the late onset of acute hepatitis C.

Shin EC, Park SH, Demino M, Nascimbeni M, Mihalik K, Major M, Veerapu NS, Heller T, Feinstone SM, Rice CM, Rehermann B.

Gastroenterology. 2011 Aug;141(2):686-95, 695.e1. doi: 10.1053/j.gastro.2011.05.006. Epub 2011 May 18.


Estimating time since infection in early homogeneous HIV-1 samples using a poisson model.

Giorgi EE, Funkhouser B, Athreya G, Perelson AS, Korber BT, Bhattacharya T.

BMC Bioinformatics. 2010 Oct 25;11:532. doi: 10.1186/1471-2105-11-532.


Viral mutation rates.

Sanjuán R, Nebot MR, Chirico N, Mansky LM, Belshaw R.

J Virol. 2010 Oct;84(19):9733-48. doi: 10.1128/JVI.00694-10. Epub 2010 Jul 21. Review.


Mutational fitness effects in RNA and single-stranded DNA viruses: common patterns revealed by site-directed mutagenesis studies.

Sanjuán R.

Philos Trans R Soc Lond B Biol Sci. 2010 Jun 27;365(1548):1975-82. doi: 10.1098/rstb.2010.0063. Review.


Rapid emergence of protease inhibitor resistance in hepatitis C virus.

Rong L, Dahari H, Ribeiro RM, Perelson AS.

Sci Transl Med. 2010 May 5;2(30):30ra32. doi: 10.1126/scitranslmed.3000544.


Chemical genetics strategy identifies an HCV NS5A inhibitor with a potent clinical effect.

Gao M, Nettles RE, Belema M, Snyder LB, Nguyen VN, Fridell RA, Serrano-Wu MH, Langley DR, Sun JH, O'Boyle DR 2nd, Lemm JA, Wang C, Knipe JO, Chien C, Colonno RJ, Grasela DM, Meanwell NA, Hamann LG.

Nature. 2010 May 6;465(7294):96-100. doi: 10.1038/nature08960. Epub 2010 Apr 21.


Hepatitis C virus transmission bottlenecks analyzed by deep sequencing.

Wang GP, Sherrill-Mix SA, Chang KM, Quince C, Bushman FD.

J Virol. 2010 Jun;84(12):6218-28. doi: 10.1128/JVI.02271-09. Epub 2010 Apr 7.


Estimation of the initial viral growth rate and basic reproductive number during acute HIV-1 infection.

Ribeiro RM, Qin L, Chavez LL, Li D, Self SG, Perelson AS.

J Virol. 2010 Jun;84(12):6096-102. doi: 10.1128/JVI.00127-10. Epub 2010 Mar 31.


Genotype 1 and global hepatitis C T-cell vaccines designed to optimize coverage of genetic diversity.

Yusim K, Fischer W, Yoon H, Thurmond J, Fenimore PW, Lauer G, Korber B, Kuiken C.

J Gen Virol. 2010 May;91(Pt 5):1194-206. doi: 10.1099/vir.0.017491-0. Epub 2010 Jan 6.


Replication mode and landscape topology differentially affect RNA virus mutational load and robustness.

Sardanyés J, Solé RV, Elena SF.

J Virol. 2009 Dec;83(23):12579-89. doi: 10.1128/JVI.00767-09. Epub 2009 Sep 23.


Modeling sequence evolution in acute HIV-1 infection.

Lee HY, Giorgi EE, Keele BF, Gaschen B, Athreya GS, Salazar-Gonzalez JF, Pham KT, Goepfert PA, Kilby JM, Saag MS, Delwart EL, Busch MP, Hahn BH, Shaw GM, Korber BT, Bhattacharya T, Perelson AS.

J Theor Biol. 2009 Nov 21;261(2):341-60. doi: 10.1016/j.jtbi.2009.07.038. Epub 2009 Aug 4. Review. Erratum in: J Theor Biol. 2012 Mar 21;297:187.


Visualizing hepatitis C virus infections in human liver by two-photon microscopy.

Liang Y, Shilagard T, Xiao SY, Snyder N, Lau D, Cicalese L, Weiss H, Vargas G, Lemon SM.

Gastroenterology. 2009 Oct;137(4):1448-58. doi: 10.1053/j.gastro.2009.07.050. Epub 2009 Jul 24.


Effect of ribavirin on the mutation rate and spectrum of hepatitis C virus in vivo.

Cuevas JM, González-Candelas F, Moya A, Sanjuán R.

J Virol. 2009 Jun;83(11):5760-4. doi: 10.1128/JVI.00201-09. Epub 2009 Mar 25.


Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection.

Keele BF, Giorgi EE, Salazar-Gonzalez JF, Decker JM, Pham KT, Salazar MG, Sun C, Grayson T, Wang S, Li H, Wei X, Jiang C, Kirchherr JL, Gao F, Anderson JA, Ping LH, Swanstrom R, Tomaras GD, Blattner WA, Goepfert PA, Kilby JM, Saag MS, Delwart EL, Busch MP, Cohen MS, Montefiori DC, Haynes BF, Gaschen B, Athreya GS, Lee HY, Wood N, Seoighe C, Perelson AS, Bhattacharya T, Korber BT, Hahn BH, Shaw GM.

Proc Natl Acad Sci U S A. 2008 May 27;105(21):7552-7. doi: 10.1073/pnas.0802203105. Epub 2008 May 19.

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