Program for Experimental and Theoretical Modeling (PETM)


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. PDF

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

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). PDF

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 PDF

Dahari H, Boodram B. How to eliminate HCV in people who inject drugs in the USA. Lancet Infect Dis. 2018 Feb;18(2):134-135. doi: 10.1016/S1473-3099(17)30678-3. PDF

Canini L, Imamura M, Kawakami Y, Uprichard SL, Cotler SJ, Dahari H*, Chayama K*. HCV kinetic and modeling analyses project shorter durations to cure under combined therapy with daclatasvir and asunaprevir in chronic HCV-infected patients. PLoS One. 2017 Dec 7;12(12):e0187409. Pubmed

Nguyen THT, Guedj J, Uprichard SL, Kohli A, Kottilil S, Perelson AS. The paradox of highly effective sofosbuvir-based combination therapy despite slow viral decline: can we still rely on viral kinetics? Sci Rep. 2017 Aug 31;7(1):10233. Pubmed

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]. PDF‌

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; 2016 Sep;23(9):708-17.  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.  PDF


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.  Pubmed.  PDF


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.  Pubmed.  PDF


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*, Dahari H*. Quantification of HCV cell-to-cell spread using a stochastic modeling approach. J Virology (2015); Jul;89(13):6551-61.  Pubmed.  PDF


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.  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, 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


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; Selected by Faculty of 1000.  Pubmed  PDF


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


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.  PDF


Rong L*, Guedj J*, Dahari H*, Smith P, Perelson AS. Analysis of hepatitis C virus decline during treatment with the protease inhibitor danoprevir using a multiscale model. PLoS Comp Bio (2013) Mar;9(3):e1002959.  Pubmed.  PDF


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.  PDF


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.  PDF

*equal contributors