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Predictions of time to HIV viral rebound following ART suspension that incorporate personal biomarkers.

Conway JM, Perelson AS, Li JZ.

PLoS Comput Biol. 2019 Jul 24;15(7):e1007229. doi: 10.1371/journal.pcbi.1007229. eCollection 2019 Jul.


Modeling the Effects of Morphine-Altered Virus Specific Antibody Responses on HIV/SIV Dynamics.

Mutua JM, Perelson AS, Kumar A, Vaidya NK.

Sci Rep. 2019 Apr 1;9(1):5423. doi: 10.1038/s41598-019-41751-8.


Regulation of T cell expansion by antigen presentation dynamics.

Mayer A, Zhang Y, Perelson AS, Wingreen NS.

Proc Natl Acad Sci U S A. 2019 Mar 26;116(13):5914-5919. doi: 10.1073/pnas.1812800116. Epub 2019 Mar 8.


Probabilistic control of HIV latency and transactivation by the Tat gene circuit.

Cao Y, Lei X, Ribeiro RM, Perelson AS, Liang J.

Proc Natl Acad Sci U S A. 2018 Dec 4;115(49):12453-12458. doi: 10.1073/pnas.1811195115. Epub 2018 Nov 19.


Determinants of the efficacy of HIV latency-reversing agents and implications for drug and treatment design.

Ke R, Conway JM, Margolis DM, Perelson AS.

JCI Insight. 2018 Oct 18;3(20). pii: 123052. doi: 10.1172/jci.insight.123052.


CD8+ lymphocyte control of SIV infection during antiretroviral therapy.

Cao Y, Cartwright EK, Silvestri G, Perelson AS.

PLoS Pathog. 2018 Oct 11;14(10):e1007350. doi: 10.1371/journal.ppat.1007350. eCollection 2018 Oct.


No recovery of replication-competent HIV-1 from human liver macrophages.

Kandathil AJ, Sugawara S, Goyal A, Durand CM, Quinn J, Sachithanandham J, Cameron AM, Bailey JR, Perelson AS, Balagopal A.

J Clin Invest. 2018 Oct 1;128(10):4501-4509. doi: 10.1172/JCI121678. Epub 2018 Sep 10.


Mathematical modeling of within-host Zika virus dynamics.

Best K, Perelson AS.

Immunol Rev. 2018 Sep;285(1):81-96. doi: 10.1111/imr.12687. Review.


Introduction to modeling viral infections and immunity.

Perelson AS, Ribeiro RM.

Immunol Rev. 2018 Sep;285(1):5-8. doi: 10.1111/imr.12700. No abstract available.


Variation in cell-associated unspliced HIV RNA on antiretroviral therapy is associated with the circadian regulator brain-and-muscle-ARNT-like-1.

Chang CC, Naranbhai V, Stern J, Roche M, Dantanarayana A, Ke R, Tennakoon S, Solomon A, Hoh R, Hartogensis W, Hecht FM, Sikaris K, Price DJ, Elliott JH, Deeks SG, Churchill M, Cameron PU, Hengartner N, Perelson AS, Lewin SR.

AIDS. 2018 Sep 24;32(15):2119-2128. doi: 10.1097/QAD.0000000000001937. Erratum in: AIDS. 2018 Nov 13;32(17):2643-2647.


Superinfection and cure of infected cells as mechanisms for hepatitis C virus adaptation and persistence.

Ke R, Li H, Wang S, Ding W, Ribeiro RM, Giorgi EE, Bhattacharya T, Barnard RJO, Hahn BH, Shaw GM, Perelson AS.

Proc Natl Acad Sci U S A. 2018 Jul 24;115(30):E7139-E7148. doi: 10.1073/pnas.1805267115. Epub 2018 Jul 9.


Correlation Between Anti-gp41 Antibodies and Virus Infectivity Decay During Primary HIV-1 Infection.

Vaidya NK, Ribeiro RM, Liu P, Haynes BF, Tomaras GD, Perelson AS.

Front Microbiol. 2018 Jun 20;9:1326. doi: 10.3389/fmicb.2018.01326. eCollection 2018.


A New Age-Structured Multiscale Model of the Hepatitis C Virus Life-Cycle During Infection and Therapy With Direct-Acting Antiviral Agents.

Quintela BM, Conway JM, Hyman JM, Guedj J, Dos Santos RW, Lobosco M, Perelson AS.

Front Microbiol. 2018 Apr 4;9:601. doi: 10.3389/fmicb.2018.00601. eCollection 2018.


Acute hepatitis B virus infection in humanized chimeric mice has multiphasic viral kinetics.

Ishida Y, Chung TL, Imamura M, Hiraga N, Sen S, Yokomichi H, Tateno C, Canini L, Perelson AS, Uprichard SL, Dahari H, Chayama K.

Hepatology. 2018 Aug;68(2):473-484. doi: 10.1002/hep.29891. Epub 2018 Jun 6.


Intracellular Hepatitis C Virus Modeling Predicts Infection Dynamics and Viral Protein Mechanisms.

Aunins TR, Marsh KA, Subramanya G, Uprichard SL, Perelson AS, Chatterjee A.

J Virol. 2018 May 14;92(11). pii: e02098-17. doi: 10.1128/JVI.02098-17. Print 2018 Jun 1.


A pharmacokinetic/viral kinetic model to evaluate treatment of chronic HCV infection with a non-nucleoside polymerase inhibitor.

Canini L, Lemenuel-Diot A, Brennan BJ, Smith PF, Perelson AS.

Antivir Ther. 2018;23(4):353-361. doi: 10.3851/IMP3216.


Early HIV infection predictions: role of viral replication errors.

Conway JM, Perelson AS.

SIAM J Appl Math. 2018;78(4):1863-1890. doi: 10.1137/17M1134019. Epub 2018 Jul 3.


The Role of Infected Cell Proliferation in the Clearance of Acute HBV Infection in Humans.

Goyal A, Ribeiro RM, Perelson AS.

Viruses. 2017 Nov 18;9(11). pii: E350. doi: 10.3390/v9110350.


Modelling the effects of phylogeny and body size on within-host pathogen replication and immune response.

Banerjee S, Perelson AS, Moses M.

J R Soc Interface. 2017 Nov;14(136). pii: 20170479. doi: 10.1098/rsif.2017.0479.


Nonlatching positive feedback enables robust bimodality by decoupling expression noise from the mean.

Razooky BS, Cao Y, Hansen MMK, Perelson AS, Simpson ML, Weinberger LS.

PLoS Biol. 2017 Oct 18;15(10):e2000841. doi: 10.1371/journal.pbio.2000841. eCollection 2017 Oct.


A strongly selected mutation in the HIV-1 genome is independent of T cell responses and neutralizing antibodies.

Liu D, Wang C, Hora B, Zuo T, Goonetilleke N, Liu MKP, Berrong M, Ferrari G, McMichael AJ, Bhattacharya T, Perelson AS, Gao F.

Retrovirology. 2017 Oct 10;14(1):46. doi: 10.1186/s12977-017-0371-4.


How Germinal Centers Evolve Broadly Neutralizing Antibodies: the Breadth of the Follicular Helper T Cell Response.

De Boer RJ, Perelson AS.

J Virol. 2017 Oct 27;91(22). pii: e00983-17. doi: 10.1128/JVI.00983-17. Print 2017 Nov 15.


The paradox of highly effective sofosbuvir-based combination therapy despite slow viral decline: can we still rely on viral kinetics?

Nguyen THT, Guedj J, Uprichard SL, Kohli A, Kottilil S, Perelson AS.

Sci Rep. 2017 Aug 31;7(1):10233. doi: 10.1038/s41598-017-09776-z.


Zika plasma viral dynamics in nonhuman primates provides insights into early infection and antiviral strategies.

Best K, Guedj J, Madelain V, de Lamballerie X, Lim SY, Osuna CE, Whitney JB, Perelson AS.

Proc Natl Acad Sci U S A. 2017 Aug 15;114(33):8847-8852. doi: 10.1073/pnas.1704011114. Epub 2017 Aug 1.


On the Death Rate of Abortively Infected Cells: Estimation from Simian-Human Immunodeficiency Virus Infection.

Ke R, Cong ME, Li D, GarcĂ­a-Lerma JG, Perelson AS.

J Virol. 2017 Aug 24;91(18). pii: e00352-17. doi: 10.1128/JVI.00352-17. Print 2017 Sep 15.


Treatment with integrase inhibitor suggests a new interpretation of HIV RNA decay curves that reveals a subset of cells with slow integration.

Cardozo EF, Andrade A, Mellors JW, Kuritzkes DR, Perelson AS, Ribeiro RM.

PLoS Pathog. 2017 Jul 5;13(7):e1006478. doi: 10.1371/journal.ppat.1006478. eCollection 2017 Jul.


Editorial: Transplant Rejection and Tolerance-Advancing the Field through Integration of Computational and Experimental Investigation.

Raimondi G, Wood KJ, Perelson AS, Arciero JC.

Front Immunol. 2017 May 30;8:616. doi: 10.3389/fimmu.2017.00616. eCollection 2017. No abstract available.


NS5A inhibitors unmask differences in functional replicase complex half-life between different hepatitis C virus strains.

Benzine T, Brandt R, Lovell WC, Yamane D, Neddermann P, De Francesco R, Lemon SM, Perelson AS, Ke R, McGivern DR.

PLoS Pathog. 2017 Jun 8;13(6):e1006343. doi: 10.1371/journal.ppat.1006343. eCollection 2017 Jun.


Reply to Padmanabhan and Dixit: Hepatitis C virus entry inhibitors for optimally boosting direct-acting antiviral-based treatments.

Ohashi H, Koizumi Y, Fukano K, Wakita T, Perelson AS, Iwami S, Watashi K.

Proc Natl Acad Sci U S A. 2017 Jun 6;114(23):E4527-E4529. doi: 10.1073/pnas.1705234114. Epub 2017 May 16. No abstract available.


Zika Virus Persistence in the Central Nervous System and Lymph Nodes of Rhesus Monkeys.

Aid M, Abbink P, Larocca RA, Boyd M, Nityanandam R, Nanayakkara O, Martinot AJ, Moseley ET, Blass E, Borducchi EN, Chandrashekar A, Brinkman AL, Molloy K, Jetton D, Tartaglia LJ, Liu J, Best K, Perelson AS, De La Barrera RA, Lewis MG, Barouch DH.

Cell. 2017 May 4;169(4):610-620.e14. doi: 10.1016/j.cell.2017.04.008. Epub 2017 Apr 27.


Prevalence of end of treatment RNA-positive/sustained viral response in HCV patients treated with sofosbuvir combination therapies.

Malespin M, Benyashvili T, Uprichard SL, Perelson AS, Dahari H, Cotler SJ.

Therap Adv Gastroenterol. 2017 Jan;10(1):68-73. doi: 10.1177/1756283X16672392. Epub 2016 Oct 17.


Quantifying antiviral activity optimizes drug combinations against hepatitis C virus infection.

Koizumi Y, Ohashi H, Nakajima S, Tanaka Y, Wakita T, Perelson AS, Iwami S, Watashi K.

Proc Natl Acad Sci U S A. 2017 Feb 21;114(8):1922-1927. doi: 10.1073/pnas.1610197114. Epub 2017 Feb 7. Erratum in: Proc Natl Acad Sci U S A. 2017 Mar 21;114(12 ):E2540-E2541.


Corrigendum: Zika viral dynamics and shedding in rhesus and cynomolgus macaques.

Osuna CE, Lim SY, Deleage C, Griffin BD, Stein D, Schroeder LT, Omage R, Best K, Luo M, Hraber PT, Andersen-Elyard H, Ojeda EF, Huang S, Vanlandingham DL, Higgs S, Perelson AS, Estes JD, Safronetz D, Lewis MG, Whitney JB.

Nat Med. 2017 Feb 7;23(2):264. doi: 10.1038/nm0217-264b. No abstract available.


Efficacy and safety of 3-week response-guided triple direct-acting antiviral therapy for chronic hepatitis C infection: a phase 2, open-label, proof-of-concept study.

Lau G, Benhamou Y, Chen G, Li J, Shao Q, Ji D, Li F, Li B, Liu J, Hou J, Sun J, Wang C, Chen J, Wu V, Wong A, Wong CL, Tsang ST, Wang Y, Bassit L, Tao S, Jiang Y, Hsiao HM, Ke R, Perelson AS, Schinazi RF.

Lancet Gastroenterol Hepatol. 2016 Oct;1(2):97-104. Epub 2016 Jul 25.


Transmission of Multiple HIV-1 Subtype C Transmitted/founder Viruses into the Same Recipients Was not Determined by Modest Phenotypic Differences.

Song H, Hora B, Giorgi EE, Kumar A, Cai F, Bhattacharya T, Perelson AS, Gao F.

Sci Rep. 2016 Dec 2;6:38130. doi: 10.1038/srep38130.


Zika viral dynamics and shedding in rhesus and cynomolgus macaques.

Osuna CE, Lim SY, Deleage C, Griffin BD, Stein D, Schroeder LT, Omange RW, Best K, Luo M, Hraber PT, Andersen-Elyard H, Ojeda EF, Huang S, Vanlandingham DL, Higgs S, Perelson AS, Estes JD, Safronetz D, Lewis MG, Whitney JB.

Nat Med. 2016 Dec;22(12):1448-1455. doi: 10.1038/nm.4206. Epub 2016 Oct 3. Erratum in: Nat Med. 2017 Feb 7;23 (2):264.


Modeling the Effects of Morphine on Simian Immunodeficiency Virus Dynamics.

Vaidya NK, Ribeiro RM, Perelson AS, Kumar A.

PLoS Comput Biol. 2016 Sep 26;12(9):e1005127. doi: 10.1371/journal.pcbi.1005127. eCollection 2016 Sep.


Modeling Viral Spread.

Graw F, Perelson AS.

Annu Rev Virol. 2016 Sep 29;3(1):555-572. Epub 2016 Aug 31. Review.


Reply to: Danoprevir pharmacokinetic/viral kinetic model for treating chronic HCV - some considerations.

Canini L, Guedj J, Perelson AS.

Antivir Ther. 2016;21(7):648-649. doi: 10.3851/IMP3045. Epub 2016 Apr 1. No abstract available.


Hepatitis C virus dynamics and cellular gene expression in uPA-SCID chimeric mice with humanized livers during intravenous silibinin monotherapy.

DebRoy S, Hiraga N, Imamura M, Hayes CN, Akamatsu S, Canini L, Perelson AS, Pohl RT, Persiani S, Uprichard SL, Tateno C, Dahari H, Chayama K.

J Viral Hepat. 2016 Sep;23(9):708-17. doi: 10.1111/jvh.12551. Epub 2016 Jun 8.


Molecular clock of HIV-1 envelope genes under early immune selection.

Park SY, Love TM, Perelson AS, Mack WJ, Lee HY.

Retrovirology. 2016 Jun 1;13(1):38. doi: 10.1186/s12977-016-0269-6.


Estimating biologically relevant parameters under uncertainty for experimental within-host murine West Nile virus infection.

Banerjee S, Guedj J, Ribeiro RM, Moses M, Perelson AS.

J R Soc Interface. 2016 Apr;13(117). pii: 20160130. doi: 10.1098/rsif.2016.0130. Epub 2016 Apr 13.


Viral dynamic modelling of Hepatitis C and resistance-associated variants in haemophiliacs.

Sherman KE, Ke R, Rouster SD, Abdel-Hameed EA, Park C, Palascak J, Perelson AS.

Haemophilia. 2016 Jul;22(4):543-8. doi: 10.1111/hae.12918. Epub 2016 Mar 3.


Residual Viremia in Treated HIV+ Individuals.

Conway JM, Perelson AS.

PLoS Comput Biol. 2016 Jan 6;12(1):e1004677. doi: 10.1371/journal.pcbi.1004677. eCollection 2016 Jan.


SPMM: estimating infection duration of multivariant HIV-1 infections.

Love TM, Park SY, Giorgi EE, Mack WJ, Perelson AS, Lee HY.

Bioinformatics. 2016 May 1;32(9):1308-15. doi: 10.1093/bioinformatics/btv749. Epub 2015 Dec 31.


Recombination Enhances HIV-1 Envelope Diversity by Facilitating the Survival of Latent Genomic Fragments in the Plasma Virus Population.

Immonen TT, Conway JM, Romero-Severson EO, Perelson AS, Leitner T.

PLoS Comput Biol. 2015 Dec 22;11(12):e1004625. doi: 10.1371/journal.pcbi.1004625. eCollection 2015 Dec.


Early HIV RNA decay during raltegravir-containing regimens exhibits two distinct subphases (1a and 1b).

Andrade A, Guedj J, Rosenkranz SL, Lu D, Mellors J, Kuritzkes DR, Perelson AS, Ribeiro RM; ACTG A5249s protocol team.

AIDS. 2015 Nov 28;29(18):2419-26. doi: 10.1097/QAD.0000000000000843.


Modelling the interaction between danoprevir and mericitabine in the treatment of chronic HCV infection.

Canini L, Guedj J, Chatterjee A, Lemenuel-Diot A, Smith PF, Perelson AS.

Antivir Ther. 2016;21(4):297-306. doi: 10.3851/IMP3006. Epub 2015 Nov 10.


Modeling the Effects of Vorinostat In Vivo Reveals both Transient and Delayed HIV Transcriptional Activation and Minimal Killing of Latently Infected Cells.

Ke R, Lewin SR, Elliott JH, Perelson AS.

PLoS Pathog. 2015 Oct 23;11(10):e1005237. doi: 10.1371/journal.ppat.1005237. eCollection 2015 Oct.


Single-Genome Sequencing of Hepatitis C Virus in Donor-Recipient Pairs Distinguishes Modes and Models of Virus Transmission and Early Diversification.

Li H, Stoddard MB, Wang S, Giorgi EE, Blair LM, Learn GH, Hahn BH, Alter HJ, Busch MP, Fierer DS, Ribeiro RM, Perelson AS, Bhattacharya T, Shaw GM.

J Virol. 2015 Oct 14;90(1):152-66. doi: 10.1128/JVI.02156-15. Print 2016 Jan 1.

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