DahariLAB
Mathematical/Computational Virology & Medicine
Publications
2019
Gambato M, Canini L, Lens S, Graw F, Perpiñan E, Londoño MC, Uprichard SL, Mariño Z, Reverter E, Bartres C, González P, Pla A, Costa J, Burra P, Cotler SJ, Forns X, Dahari H. Early HCV viral kinetics under DAAs may optimize duration of therapy in patients with compensated cirrhosis. Liver International. May 2019; 39(5):826-834. doi: 10.1111/liv.14014; [Pubmed, Editorial]
Echevarria D, Gutfraind A, Boodram B, Layden J, Ozik J, Page K, Cotler SJ, Major M, Dahari H. Modeling indicates efficient vaccine-based interventions for the elimination of hepatitis C virus among persons who inject drugs in metropolitan Chicago. Vaccine. April 2019. Vol(37), Issue 19, 2608-2616. doi: 10.1016/j.vaccine.2019.02.081; [Full Text, Pubmed]
Tsuge M, Uchida T, Walsh K, Ishida Y, Tateno C, Kumar U, Glenn JS, Koh C, Heller T, Uprichard SL, Dahari H, Chayama K. Early Multiphasic HBV Infection Initiation Kinetics Is Not Clone-Specific and Is Not Affected by Hepatitis D Virus (HDV) Infection. Viruses. March 2019. 15;11(3). doi: 10.3390/v11030263. [Full Text, Pubmed]
Koh C, Dubey P, Han MAT, Walter PJ, Garraffo HM, Surana P, Southall NT, Borochov N, Uprichard SL, Cotler SJ, Etzion O, Heller T, Dahari H, Liang TJ. A randomized, proof-of-concept clinical trial on repurposing chlorcyclizine for the treatment of chronic hepatitis C. Antiviral Research. March 2019; Vol(163):149-155. doi: 10.1016/j.antiviral.2019.01.017. [Pubmed]
Shteyer E, Shekhtman L, Zinger T, Harari S, Gafanovich I, Wolf D, Ivgi H, Barsuk R, Dery I, Armoni D, Rivkin M, Pipalia R, Cohen Eliav M, Skorochod Y, Breuer GS, Tur-Kaspa R, Weil Wiener Y, Stern A, Cotler SJ, Dahari H, Lurie Y. Modeling suggests that microliter volumes of contaminated blood caused an outbreak of hepatitis C during computerized tomography. PLoS One. January 2019. 15;14(1): doi: 10.1371/journal.pone.0210173. [Full Text, Additional Figure, Pubmed]
2018
Marian Major, Alexander Gutfraind, Louis Shekhtman, Qingwen Cui, Alla Kachko, Scott J. Cotler, Behzad Hajarizadeh, Rachel Sacks-Davis, Kimberly Page, Basmattee Boodram and Harel Dahari. Modeling of patient virus titers suggests that availability of a vaccine could reduce hepatitis C virus transmission among injecting drug users. Science Translational Medicine, 11 July 2018; Vol(10) 449: [Abstract, Reprint, Full Text, Pubmed]
Dahari H and Boodram B. How to eliminate HCV in people who inject drugs in the USA. Lancet Infectious Diseases. 2018 Feb;18(2):134-135. doi: 10.1016/S1473-3099(17)30678-3; [Pubmed]
Boodram B, Hotton AL, Shekhtman L, Gutfraind A, Dahari H. High-Risk Geographic Mobility Patterns among Young Urban and Suburban Persons who Inject Drugs and their Injection Networks Members. J Urban Health. 2018 Feb;95(1):71-82. doi: 10.1007/s11524-017-0185-7; [Pubmed]
Kumberger P, Durso-Cain K, Uprichard SL, Dahari H, Graw F. Accounting for Space--Quantification of Cell-to-Cell Transmission Kinetics Using Virus Dynamics Models. Viruses 2018 April 17; 10(4). doi: 10.3390/v10040200; [Pubmed]
Reinharz V, Dahari H, Barash D. Numerical schemes for solving and optimizing multiscale models with age of hepatitis C virus dynamics. Mathematical Biosciences. 2018 Jun;300:1-13. doi: 10.1016/j.mbs.2018.03.011; [Pubmed]
Ishida Y, Chung TL, Imamura M, Hiraga N, Sen S, Yokomichi H, Tateno C, Canini L, Perelson AS, Uprichard SL, Dahari H, Chayama K. Acute hepatitis B virus infection in humanized chimeric mice has multiphasic viral kinetics. Hepatology. 2018 Aug;68(2):473-484. doi: 10.1002/hep.29891; [Pubmed]
2017
Ashish Goyal, Yoav Lurie, Eric G. Meissner, Marian Major, Natasha Sansone, Susan L. Uprichard, Scott J. Cotler, Harel Dahari. Modeling HCV cure after an ultra-short duration of therapy with direct acting agents. Antiviral Research, 2017; 144: 281-285: [Pubmed]
Laetitia Canini, Christopher Koh, Scott J. Cotler, Susan L. Uprichard, Mark A. Winters, Ma Ai Thanda Han, David E. Kleiner, Ramazan Idilman, Cihan Yurdaydin, Jeffrey S. Glenn, Theo Heller, Harel Dahari. Pharmacokinetics and pharmacodynamics modeling of lonafarnib in patients with chronic hepatitis delta virus infection. Hepatology Communications, 2017; vol.1: 288-292 [the newest open access journal of the American Association for the Study of Liver Diseases]: [Pubmed]
Vladimir Reinharz, Alexander Churkin, Harel Dahari, Danny Barash. A Robust and Efficient Numerical Method for RNA-Mediated Viral Dynamics. Frontiers in Applied Mathematics and Statistics, Oct 31, 2017; doi: 10.3389/fams.2017.00020; [Pubmed]
Malespin M, Uprichard SL, Perelson AS, Dahari H, Cotler SJ. Prevalence of End of Treatment RNA-
Positivity/Sustained Viral Response in HCV Patients Treated with Sofosbuvir Combination Therapies. Therapeutic Advances in Gastroenterology, 2017; Jan:10(1):68-73 [Pubmed]
Shteyer E, Dahari H, Gafanovich I, Dery I, Wolf D, Cotler SJ, Lurie Y. End of treatment RNA-positive/sustained viral response in an individual with acute HCV infection treated with direct-acting antivirals. Therapeutic Advances in Gastroenterology (2017) Vol. 10(5): 429-430; [Pubmed]
2016
Dahari H, Canini L, Graw F, Uprichard SL, Arau´jo ESA, Penaranda G, Coquet E, Chiche L, Riso A, Renou C, Bourliere M, Cotler SJ, Halfon P. HCV Kinetic and modeling analyses indicate similar time to cure among sofosbuvir combination regimens with daclatasvir, simeprevir or ledipasvir. J Hepatology, 2016; 64(6):1232-9. [Pubmed]
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*. HCV dynamics and cellular gene expression in uPA-SCID chimeric mice with humanized livers during intravenous silibinin monotherapy. J Viral Hepatitis, 2016; Sep;23(9):708-17 (*equal senior contributors) [Pubmed]
Hasin Y, Shteingart S, Dahari H, Gafanovich I, Floru S, Braun M, Shlomai A, Verstanding A, Deri I, Uprichard SL, Cotler SJ, Lurie Y. Hepatitis C virus cure after direct acting antiviral-related drug-induced liver injury: Case report. World Journal Hepatology 2016; 8(20):858-862; [Pubmed]
Dahari H, Halfon P, Cotler SJ. Resurrection of response-guided therapy for sofosbuvir combination therapies. J Hepatology (2016) Sep;65(3):462-4; [Pubmed]
Dahari H, Cotler SJ, Feld JJ. Cure prevents more than HCV transmission. Hepatology (2016) Sep;64(3):1003-4; [Pubmed]
2015
Gutfraind A, Boodram B, Prachand N, Hailegiorgis A, Dahari H*, Major M*. Agent-based model forecasts aging of the population of people who inject drugs in metropolitan Chicago and changing prevalence of hepatitis C infections. PLoS One (2015); Sep 30;10(9):e0137993 (*equal senior contributors) [Paper, Pubmed]
Echevarria D, Gutfraind A, Boodram B, Major M, Del Valle S, Cotler SJ, Dahari H. Mathematical modeling of hepatitis C prevalence reduction with antiviral treatment scale-up in persons who inject drugs in metropolitan Chicago. PLoS One (2015); Aug 21;10(8):e0135901; [Paper, Pubmed]
Christopher Koh, Laetitia Canini; Harel Dahari, Xiongce Zhao, Susan L Uprichard, Vanessa Haynes-Williams, Mark A Winters, Gitanjali Subramanya, Stewart L Cooper, Peter Pinto, Erin F Wolff, Rachel Bishop, Ma Ai Thanda Han, Scott J Cotler, David E Kleiner, Onur Keskin, Ramazan Idilman, Cihan Yurdaydin, Jeffrey S Glenn, Theo Heller. Oral Prenylation Inhibition with Lonafarnib in Chronic Hepatitis D Infection: a randomized, double-blinded, placebo controlled phase 2a trial. Lancet Infectious Diseases (2015); Oct;15(10):1167-74; [Pubmed]
Graw F, Martin DN, Perelson AS, Uprichard SL, . Quantification of HCV cell-to-cell spread using a stochastic modeling approach. J Virol (2015); Jul;89(13):6551-61; [Pubmed]
Dahari H, Shteingart S, Gafanovich I, Cotler SJ, D’Amato M, Pohl RT, Weiss G, Ashkenazi YJ, Tichler T, Goldin E, Lurie Y. Sustained virological response with intravenous silibinin: individualized IFN-free therapy via real-time modeling of HCV kinetics. Liver International (2015); 35(2):289-294; NIHMSID #630488 [Featured in Debates in Hepatology with two commentaries: Meissner EG. 35(2):295-296 ; Guedj G & Nguyen T. 35(2):297-298]; [Pubmed]
Canini L, DebRoy S, Mariño Z, Crespo G, Navasa M, D’Amato M, Ferenci P, Cotler SJ, Forns X, Perelson AS, Dahari H. Severity of liver disease affects HCV kinetics in patients treated with intravenous silibinin monotherapy. Antiviral Therapy (2015); 20(2):149-55; [Pubmed]
Guedj J, Canini L, Cotler SJ, Dahari H. Reply: Effect of interferon-alfa therapy on hepatitis D virus. Hepatology (2015) Jun;61(6):2118-9; [Pubmed]
2014
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]
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]
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
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]
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]
Polyak SJ, Oberlies NH, Pécheur E, Dahari H, Ferenci P, Pawlotsky JM. Silymarin for HCV infection. Antiviral Therapy (2013) 18:141-147; [Pubmed]
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
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
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]
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]
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]
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]
2010
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]
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]
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
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]
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]
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]
Dahari H, Cotler SJ, Layden TJ, Perelson AS. Hepatitis B virus clearance rate estimates. Hepatology (2009) Apr 2;49(5):1779-1780; [Pubmed]
2008
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]
2007
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]
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]
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]
2006
Dahari H, Forns X, Neumann AU, Perelson AS. The extrahepatic contribution to HCV plasma viremia. J Hepatology (2006) Oct 45(4):626-7; [Pubmed]
2005
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]
2004
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]
2002
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]
2000
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
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]
