DahariLAB
Mathematical/Computational Virology & Medicine
2024
2023
October 2023
Hepatitis D Virus and HBsAg Dynamics in the era of new Antiviral Treatments
Shekhtman, L., et al.
Current Gastroenterology Reports
January 2023
Modeling-Based Response-Guided Hepatitis C Treatment during Pregnancy and Postpartum
Kushner, T., et al.
OPEN FORUM INFECTIOUS DISEASES
June 2023
Treatment of Chronic Hepatitis D with Peginterferon Lambda - The Phase 2 LIMT-1 Clinical Trial
Etzion O., et al.
HEPATOLOGY
2022
December
Hepatitis B and Hepatitis D Viruses:
A Comprehensive Update with an Immunological Focus
Sausen D., et al.
INTERNATIONAL JOURNAL OF MOELCULAR SCIENCES
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June
Advances in Parameter Estimation and Learning from Data for Mathematical Models of Hepatitis C Viral Kinetics
Reinharz V., et al.
MATHEMATICS
January
Mathematical modeling suggests that entry-inhibitor Bulevirtide may interfere with hepatitis D virus clearance from circulation
Shekhtman L., et al.
JOURNAL OF HEPATOLOGY
November
Epstein–Barr Virus (EBV) Epithelial Associated Malignancies: Exploring
Pathologies and Current Treatments
Shechter O., et al.
INTERNATIONAL JOURNAL OF MOELCULAR SCIENCES
March
Modeling-based response-guided DAA therapy for chronic hepatitis C to identify individuals for shortening treatment duration
Goyal A., et al.
OPEN FORUM INFECTIOUS DISEASES
January
Machine learning for mathematical models of HCV kinetics during antiviral therapy
Churkin A., et al.
MATHEMATICAL BIOSCIENCES
October
Modeling the Interplay between HDV and HBV in Chronic HDV/HBV Patients
Mhlanga A., et al.
MATHEMATICS
March
January
2021
December
A Mathematical Model for early HBV and -HDV Kinetics during Anti-HDV Treatment
Zakh R., et al.
MATHEMATICS
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July
HCV spread kinetics reveal varying contributions of transmission modes to infection dynamics
Durso-Cain, K., et al.
VIRUSES
January
Understanding the antiviral effects of RNAi-based therapy on chronic hepatitis B infection
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Kadelka S., et al.
SCIENTIFIC REPORTS
November
September
Letter to the Editor: Examining HBV RNA kinetics during NA treatment - are NA multifunctional antiviral agents?
Dahari H., et al
HEPATOLOGY
April
Understanding hepatitis B virus dynamics and the antiviral effect of interferon-a treatment in humanized chimeric mice
Reinharz V., et al.
JOURNAL OF VIROLOGY
September
Ginkgolic acid inhibits Coronavirus strain 229E infection of human epithelial lung cells
Bhutta M. S., et al
PHARMACEUTICALS
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January
Early HBV RNA kinetics under NA treatment may reveal new insights into HBV RNA dynamics and NA mode of action-more detailed kinetic studies are needed
Dahari H., et al.
JOURNAL OF VIRAL HEPATITIS
2020
October
Response guided therapy for reducing duration of direct acting antivirals in chronic hepatitis C infected patients: a Pilot study
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Etzion O., et al.
SCIENTIFIC REPORTS
June
Modeling based response guided therapy in subjects with recent hepatitis C infection
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Gorstein E., et al.
ANTIVIRAL RESEARCH
April
Modeling-based response-guided therapy for chronic hepatitis C under glecaprevir/pibrentasvir may identify patients for ultra-short treatment duration
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Dasgupta S, et al.
JOURNAL OF INFECTIOUS DISEASES
August
Efficient Methods for Parameter Estimation of Ordinary and Partial Differential Equation Models of Viral Hepatitis Kinetics
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Churkin A., et al.
MATHEMATICS
May
Evaluation of short-course direct-acting antivirals and ezetimibe to prevent HCV infection in recipients of organs from HCV-infected donors: A single-centre, open-label study
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Feld J.J., et al.
THE LANCET GASTROENTEROLOGY & HEPATOLOGY
April
Sustained Virological Response Following an 11 Day Course of Direct Acting Antiviral Therapy for Hepatitis C Infection
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Yardeni D, et al.
JOURNAL OF GASTROINTESTINAL AND LIVER DISEASES
July
HCVMultiscaleFit: A Simulator for Parameter Estimation in Multiscale Models of Hepatitis C Virus Dynamics
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Churkin A., et al.
AIP CONFERENCE PROCEEDINGS
April
Modelling hepatitis D virus RNA and HBsAg dynamics during nucleic acid polymer monotherapy suggest rapid turnover of HBsAg
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Shekhtman L, et al.
SCIENTIFIC REPORTS
January
Modeling Challenges of Ebola Virus -Host Dynamics during Infection and Treatment
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Chertow D.S., et al.
VIRUSES
2019
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July
A Parameter Estimation Method for Multiscale Models of Hepatitis C Virus Dynamics
Reinharz V, et al.
BULLETIN OF MATHEMATICAL BIOLOGY
May
Early HCV viral kinetics under DAAs may optimize duration of therapy in patients with compensated cirrhosis
Gambato M, et al.
LIVER INTERNATIONAL
March
A randomized, proof-of-concept clinical trial on repurposing chlorcyclizine for the treatment of chronic hepatitis C
Koh C, et al.
ANTIVIRAL RESEARCH
July
Plasma hepatitis E virus kinetics in solid organ transplant patients receiving ribavirin
Lhomme S, et al.
VIRUSES
January
Modeling suggests that microliter volumes of contaminated blood caused an outbreak of hepatitis C during computerized tomography
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Shteyer E, et al.
PLOS ONE
June
Multi-objective model exploration of hepatitis C elimination in an agent-based model of people who inject drugs
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Tatara E, et al.
WINTER SIMULATION CONFERENCE
2018
August 2018
Acute hepatitis B virus infection in humanized chimeric mice has multiphasic viral kinetics
Ishida Y, et al.
HEPATOLOGY
April 2018
Accounting for Space--Quantification of Cell-to-Cell Transmission Kinetics Using Virus Dynamics Models
Kumberger P, et al.
VIRUSES
July 2018
Modeling of patient virus titers suggests that availability of a vaccine could reduce hepatitis C virus transmission among injecting drug users
Major M, et al.
SCIENCE TRANSLATIONAL MEDICINE
February 2018
How to eliminate HCV in people who inject drugs in the USA
Dahari H, et al.
THE LANCET INFECTIOUS DISEASES
June 2018
Numerical schemes for solving and optimizing multiscale models with age of hepatitis C virus dynamics
Reinharz V, et al.
MATHEMATICAL BIOSCIENCES
February 2018
High-Risk Geographic Mobility Patterns among Young Urban and Suburban Persons who Inject Drugs and their Injection Networks Members
Boodram B, et al.
J URBAN HEALTH
2017
June 2017
Pharmacokinetics and pharmacodynamics modeling of lonafarnib in patients with chronic hepatitis delta virus infection
Canini L, et al.
HEPATOLOGY COMMUNICATIONS
October 2017
A Robust and Efficient Numerical Method for RNA-Mediated Viral Dynamics
Reinharz V, et al.
FRONTIERS IN APPLIED MATHEMATICS AND STATISTICS
May 2017
End of treatment RNA-positive/sustained viral response in an individual with acute HCV infection treated with direct-acting antivirals
Shtyer E, et al.
THERAPEUTIC ADVANCES IN GASTROENTEROLOGY
August 2017
Modeling HCV cure after an ultra-short duration of therapy with direct acting agents
Goyal A, et al.
ANTIVIRAL RESEARCH
January 2017
​Prevalence of End of Treatment RNA-Positivity/Sustained Viral Response in HCV Patients Treated with Sofosbuvir Combination Therapies
Malespin M, et al.
THERAPEUTIC ADVANCES IN GASTROENTEROLOGY
2016
June 2016
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September 2016
Resurrection of response-guided therapy for sofosbuvir combination therapies
Dahari H, et al.
J HEPATOLOGY
September 2016
HCV dynamics and cellular gene expression in uPA-SCID chimeric mice with humanized livers during intravenous silibinin monotherapy
DebRoy S, et al.
J VIRAL HEPATITIS
July 2016
Hepatitis C virus cure after direct acting antiviral-related drug-induced liver injury: Case report
Hasin Y, et al.
WORLD JOURNAL HEPATOLOGY
2015
October 2015
Oral Prenylation Inhibition with Lonafarnib in Chronic Hepatitis D Infection: a randomized, double-blinded, placebo controlled phase 2a trial
Koh C, et al.
LANCET INFECTIOUS DISEASES
July 2015
Quantification of HCV cell-to-cell spread using a stochastic modeling approach
Graw F, et al.
J VIROLOGY
January 2015
Severity of liver disease affects HCV kinetics in patients treated with intravenous silibinin monotherapy
Canini L, et al.
ANTIVIRAL THERAPY
September 2015
August 2015
February 2015
Sustained virological response with intravenous silibinin: individualized IFN-free therapy via real-time modeling of HCV kinetics
Dahari H, et al.
LIVER INTERNATIONAL
2014
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Guedj J, Rotman Y, Cotler S.J, Schmid P, Albrecht J, Haynes-Williams V, Liang T.J, Hoofnagle J.H, Heller T, Dahari H. Understanding early hepatitis D virus and hepatitis B surface antigen kinetics during pegylated interferon-alpha therapy via mathematical modeling. Hepatology (2014); 60(6):1902-10; [Pubmed]
Rong L, Guedj J, Dahari H, Perelson AS. Treatment of hepatitis C with an interferon-based lead-in phase: A perspective from mathematical modeling. Antiviral Therapy (2014) 19:469-477; [Pubmed]
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Rotman Y, Noureddin M, Feld JJ, Guedj J, Witthaus M, Han H, Park Y, Park SH, Heller T, Ghany MG, Doo E, Koh C, Abdalla A, Gara N, Sarkar S, Thomas E, Ahlenstiel G, Edlich B, Titerence R, Hogdal L, Rehermann B, Dahari H, Perelson AS, Hoofnagle JH and Liang TJ. Effect of Ribavirin on Viral Kinetics and Liver Gene Expression in Chronic Hepatitis C. Gut (2014) Jan;63(1):161-9; [Pubmed]
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Dahari H & Cotler SJ. Individualized treatment for patients with low HCV load (genotype 1): A viral kinetic approach. Hepatology (2014) Jun;59(6):2422-3; [Pubmed]
2013
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Guedj J*, Dahari H*, Rong L, Sansone N, Nettles RE, Cotler SJ, Layden JE, Uprichard SL, Perelson AS. Modeling shows that the NS5A inhibitor daclatasvir has two modes of action and yields a new estimate of the hepatitis C virus half-life. Proc Natl Acad Sci U S A. (2013) Mar 5;110(10):3991-6 (* equal contributors). Selected by Faculty of 1000; [Pubmed]
Zhang J, Lipton HL, Perelson AS, Dahari H. Modeling the acute and chronic phases of Theiler murine encephalomyelitis virus infection. J Virology (2013) April;87(7):4052-4059; [Pubmed]
Gutfraind A, Boodram B, Ouellet LJ, Prachand N, Perelson AS, Feinstone S, Novak RM, Mniszewski SM, Del Valle SY, Dahari H, Major M. Implementing a data-driven model of hepatitis C infections in metropolitan Chicago: a concept paper. Accepted at the Proceedings of the 8th INFORMS Workshop on Data Mining and Health Informatics 2013.
Rong L*, Guedj J*, Dahari H*, Smith P, Perelson AS. Multiscale modeling approach predicts that the protease inhibitor danoprevir blocks several distinct stages of the HCV replication in vivo. PLoS Comp Bio (2013) Mar;9(3):e1002959 (* equal contributors); [Pubmed]
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Guedj J, Dahari H, Uprichard SL, Perelson AS. The HCV NS5A inhibitor daclatasvir has dual mode of action and reveals a shorter HCV half-life estimate. Expert Rev Gastroentrol Hepatol. (2013) Jul;7(5):397-9; [Pubmed]
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Polyak SJ, Oberlies NH, Pécheur E, Dahari H, Ferenci P, Pawlotsky JM. Silymarin for HCV infection. Antiviral Therapy (2013) 18:141-147; [Pubmed]
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Dahari H, Cotler SJ, Layden TJ, Perelson AS. Understanding triphasic HCV decline during treatment in the era of IL28B polymorphisms and direct acting antiviral agents via mathematical modeling. J Hepatology (2013) vol. 58:831–843; [Pubmed]
2012
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Guedj J*, Dahari H*, Pohl RT, Ferenci P, Perelson AS Understanding silibinin's modes of action against HCV using viral kinetic modeling. J Hepatology (2012) 56: 1019-1024 (*equal contributors); [Pubmed]
Guedj J, Dahari H, Shudo E, Smith P, Perelson AS. Hepatitis C viral kinetics with the nucleoside polymerase inhibitor mericitabine (RG7128). Hepatology (2012) 55(4):1030-7; [Pubmed]
2011
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Araújo ESA*, Dahari H*, Cotler SJ, Layden TJ, Neumann AU, Melo CE, Tatsch FF, Barone AA. Pharmacodynamics of PEG-IFN alpha-2a and HCV response as a function of IL28B polymorphism in HIV/HCV co-infected patients. J Acquir Immune Defic Syndr (2011); 56:95–99 (* equal contributors); [Pubmed]
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Evaldo S.A. Araújo, Harel Dahari , Avidan U. Neumann , Norma de Paula Cavalheiro, Carlos Eduardo Melo,Evandro Sobroza de Melo, Thomas J. Layden, Scott J. Cotler, Antônio Alci Barone. Very early prediction of response to HCV treatment with peg-IFN-alfa-2a and ribavirin in HIV/HCV coinfected patients. J Viral Hepatitis (2011); Apr;18(4):e52-60; [Pubmed]
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Dahari H, Guedj J, Perelson AS, Layden TJ. Hepatitis C viral kinetics in the era of direct acting antiviral agents and IL28B. Current Hepatitis Reports (2011) Volume 10, Number 3, 214-227; [Pubmed]
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Dahari H, Guedj J, Perelson AS. Silibinin’s mode of action against HCV: A controversy yet to be resolved. Hepatology (2011) Aug;54(2):749; [Pubmed]
Guedj J, Dahari H, Perelson AS. Understanding the nature of early HCV RNA blips and the use of mathematical modeling of viral kinetics during IFN-based therapy. Proc Natl Acad Sci U S A. (2011) Jul 19;108(29):E302; [Pubmed]
Dahari H, Rong L, Layden TJ, Cotler SJ. Hepatocyte proliferation and hepatitis C virus (HCV) kinetics. Clinical Pharmacology & Therapeutics (2011) Mar;89(3):353-4; [Pubmed]
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2010
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L. Rong, H. Dahari, R.M. Ribeiro, A.S. Perelson. Rapid emergence of hepatitis C virus protease inhibitor resistance. Science Translational Medicine (AAAS) (2010) 2, 30ra32; [Pubmed]
Harel Dahari, Stephen Feinstone, Marian Major. Quantitative evaluation of HCV vaccine success: a meta-analysis. Gastroenterology (2010); Sep 139:965-974; [Pubmed]
Harel Dahari, Evaldo S. Affonso de Araujo, Bart L. Haagmans, Thomas J. Layden, Scott J. Cotler, Antonio A. Barone, Avidan U. Neumann. Pharmacodynamics of PEG-IFN alpha-2a in HIV/HCV co-infected patients: Implications for treatment outcomes. J Hepatology (2010); 53: 460-467. (see Editorial on pages 418-420); [Pubmed]
Ali Sabahi, Katherine A. Marsh, Harel Dahari, Peter Corcoran, Jennifer M. Lamora, Xuemei Yu, Robert F. Garry, Susan L. Uprichard. The rate of hepatitis C virus infection initiation in vitro is directly related to particle density. Virology (2010) Nov 10;407(1):110-9; [Pubmed]
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Marianna Halasi, Huiping Zhao, Harel Dahari, Uppoor G. Bhat, Erick B. Gonzalez, Aleksander V. Lyubimov, Debra A. Tonetti, Andrei L. Gartel. Thiazole antibiotics against breast cancer. Cell Cycle 2010; Mar; 9(6):1214-1217; [Pubmed]
Neumann AU, Phillips S, Levine I, Ijaz S, Dahari H, Eren R, Dagan S, Naoumov NV. Novel mechanism of antibodies to hepatitis B virus in blocking viral particle release from cells. Hepatology (2010); Sep;52(3):875-85; [Pubmed]
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Guedj J, Rong R, Dahari H, Perelson AS. A perspective on modeling hepatitis C virus infection. J Viral Hepatitis (2010); 17, 825–833; [Pubmed]
2009
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Dahari H, Sainz Jr. B, Perelson AS, Uprichard SL. Modeling subgenomic HCV RNA kinetics during interferon-a treatment. J Virology (2009) Jul;83(13):6383-90; [Pubmed]
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Burg D, Libin R, Neumann AU, Dahari H. Mathematical modeling of viral kinetics under immune control during primary HIV-1 infection. Journal Theoretical Biology (2009) Aug 21;259(4):751-9; [Pubmed]
Dahari H, Shudo E, Cotler SJ, Layden TJ, Perelson AS. Modeling HCV kinetics: The relationship between the infected cell loss rate and the final slope of viral decay. Antiviral Therapy (2009) 14(3):459-64; [Pubmed]
Dahari H, Layden-Almer JE, Kallwitz E, Ribeiro RM, Cotler SJ, Layden TJ, Perelson AS. A mathematical model of hepatitis C virus dynamics in patients with high baseline viral loads or advanced liver disease. Gastroenterology (2009) Apr;136(4):1402-9; [Pubmed]
Dahari H, Shudo E, Ribeiro RM, Perelson AS. Modeling complex decay profiles of hepatitis B virus during antiviral therapy. Hepatology (2009) Jan;49(1):32-38; [Pubmed]
Dahari H, Shudo E, Ribeiro RM, Perelson AS. Mathematical modeling of HCV infection and treatment. Hepatitis C Protocols. 2nd ed. NJ: Humana Press (2009): 439-453. Also published in Methods Mol Biol. 2009;510:439-53; [Pubmed]
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Reluga T, Dahari H, Perelson AS. Analysis of hepatitis C virus infection models with hepatocyte homeostasis. SIAM Journal on Applied mathematics (2009) 69(4): 999-1023; [Pubmed]
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Dahari H, Cotler SJ, Layden TJ, Perelson AS. Hepatitis B virus clearance rate estimates. Hepatology (2009) Apr 2;49(5):1779-1780; [Pubmed]
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2008
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Dahari H, Layden-Almer JE, Perelson AS, Layden TJ. Hepatitis C viral kinetics in special populations. Current Hepatitis Reports (2008) Volume 7, Issue 3: 97-105; [Pubmed]
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2007
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Dahari H, Ribeiro RM, Perelson AS. Triphasic decline of HCV RNA during antiviral therapy. Hepatology (2007) Jul;46(1):16-21. (Selected by Faculty of 1000 Biology: Factor 6.0 = Must Read); [Pubmed]
Dahari H, Lo A, Ribeiro RM, Perelson AS. Modeling HCV Dynamics: Liver regeneration and critical drug efficacy. Journal Theoretical Biology (2007) Jul 21;247(2):371-81; [Pubmed]
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Dahari H, Markatou M, Zeremski M, Haller I, Ribeiro RM, Licholai T, Perelson AS, Talal AH. Early ribavirin pharmacokinetics, HCV RNA and alanine aminotransferase kinetics in HIV/HCV co-infected patients during treatment with pegylated Interferon and ribavirin. J Hepatology (2007) July 47(1):23-30. (see Editorial July 47(1):1-3); [Pubmed]
Dahari H, Ribeiro RM, Rice CM, Perelson AS. Mathematical modeling of subgenomic hepatitis C viral replication in Huh-7 cells. J Virology (2007) Jan;81(2):750-60; [Pubmed]
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Dahari H & Perelson AS. Hepatitis C virus RNA kinetics: Drug efficacy and the rate of HCV-infected cells loss. World Journal Gastroenterology (2007):13(21):3020-21; [Pubmed]
Dahari H & Perelson AS. Hepatitis C virus kinetics in chimeric mice during antiviral therapy. Hepatology (2007) Oct 12;46(6):2048-2049; [Pubmed]
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2006
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Dahari H, Forns X, Neumann AU, Perelson AS. The extrahepatic contribution to HCV plasma viremia. J Hepatology (2006) Oct 45(4):626-7; [Pubmed]
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2005
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Dahari H, Major M, Zhang X, Mihalik K, Rice CM, Perelson AS, Feinstone SM, Neumann AU. Mathematical Modeling of Primary Hepatitis C Infection: Non-cytolytic clearance and early blockage of virion production. Gastroenterology (2005); 128(4): 1056-1066; [Pubmed]
Dahari H, Feliu A, Garcia-Retortillo M, Forns X, Neumann AU. Second Hepatitis C Compartment Indicated by Viral Dynamics during Liver Transplantation. J Hepatology (2005) April 42(4): 491-498. (see Editorial April 42(4):441-443); [Pubmed]
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2004
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Major ME, Dahari H, Mihalik K, Puig M, Rice CM, Neumann AU, Feinstone SM. Hepatitis C Virus Kinetics and Host Responses Associated with Disease and Outcome of Infection. Hepatology (2004) Jun;39(6):1709-20; [Pubmed]
Pawlotsky JM, Dahari H, Neumann AU, Hezode C, Germanidis G, Lonjon I, Castera L, Dhumeaux D. Antiviral Action of Ribavirin in Chronic Hepatitis C. Gastroenterology (2004) 126(3):703-14; [Pubmed]
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2002
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Bouvier-Alias M, Patel K, Dahari H, Beaucourt S, Larderie P, Blatt L, Hezode C, Picchio G, Dhumeaux D, Neumann AU, McHutchison JG, Pawlotsky JM.. Clinical utility of total HCV core antigen quantification: a new indirect marker of HCV replication. Hepatology (2002) 36(1): 211-218; [Pubmed]
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2000
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Neumann AU, Lam NP, Dahari H, Davidian M, Wiley TE, Mika BP, Perelson AS, Layden TJ. Differences in viral dynamics between genotypes 1 and 2 of hepatitis C virus. J Infectious Diseases. (2000) July 182(1):28-35; [Pubmed]
1998
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Neumann AU, Lam NP, Dahari H, Gretch DR, Wiley TE, Layden TJ, Perelson AS. Hepatitis C viral dynamics in vivo and the antiviral efficacy of interferon-alpha therapy. Science (AAAS) (1998) 282:103-7; [Pubmed]