Review of "System Dynamics: A Unified Approach" by Dean C. Karnopp and Ronald C. Rosenberg. - Alan S. Perelson (IEEE Trans. Syst. Man Cybern., 1976)

Review of "Introduction to Bond Graphs and Their Applications" by J. U. Thoma. - Alan S. Perelson (IEEE Trans. Syst. Man Cybern., 1976)

Genetic Algorithms and the Immune System. - Stephanie Forrest; Alan S. Perelson (PPSN, 1990)

Population Diversity in an Immune System Model: Implications for Genetic Search. - Robert E. Smith 001; Stephanie Forrest; Alan S. Perelson (FOGA, 1992)

Using Genetic Algorithms to Explore Pattern Recognition in the Immune System. - Stephanie Forrest; Robert E. Smith 001; Brenda Javornik; Alan S. Perelson (Evol. Comput., 1993)

Searching for Diverse, Cooperative Populations with Genetic Algorithms. - Robert E. Smith 001; Stephanie Forrest; Alan S. Perelson (Evol. Comput., 1993)

Self-nonself discrimination in a computer. - Stephanie Forrest; Alan S. Perelson; Lawrence Allen; Rajesh Cherukuri (S&P, 1994)

The Evolution of Emergent Organization in Immune System Gene Libraries. - Ron R. Hightower; Stephanie Forrest; Alan S. Perelson (ICGA, 1995)

Base Pairing Probabilities in a Complete HIV-1 RNA. - Martijn A. Huynen; Alan S. Perelson; W. A. Vieira; Peter F. Stadler (J. Comput. Biol., 1996)

Some design principles for immune system recognition. - Alan S. Perelson; Frederik W. Wiegel (Complex., 1999)

Mathematical Analysis of HIV-1 Dynamics in Vivo. - Alan S. Perelson; Patrick W. Nelson (SIAM Rev., 1999)

Stochastic Stage-structured Modeling of the Adaptive Immune System. - Dennis L. Chao; Miles P. Davenport; Stephanie Forrest; Alan S. Perelson (CSB, 2003)

An Overview of Computational and Theoretical Immunology. - Alan S. Perelson (ICARIS, 2004)

Optimization of Influenza Vaccine Selection. - Joseph T. Wu; Lawrence M. Wein; Alan S. Perelson (Oper. Res., 2005)

Human Immunodeficiency Virus: Quasi-Species and Drug Resistance. - John M. Murray; Alan S. Perelson (Multiscale Model. Simul., 2005)

Viral and Latent Reservoir Persistence in HIV-1-Infected Patients on Therapy. - Hwijin Kim; Alan S. Perelson (PLoS Comput. Biol., 2006)

Mathematical Analysis of Age-Structured HIV-1 Dynamics with Combination Antiretroviral Therapy. - Libin Rong; Zhilan Feng; Alan S. Perelson (SIAM J. Appl. Math., 2007)

Dynamic Correlation between Intrahost HIV-1 Quasispecies Evolution and Disease Progression. - Ha Youn Lee; Alan S. Perelson; Su-Chan Park; Thomas Leitner (PLoS Comput. Biol., 2008)

Agent-based modeling of host-pathogen systems: The successes and challenges. - Amy L. Bauer; Catherine Beauchemin; Alan S. Perelson (Inf. Sci., 2009)

Modeling Latently Infected Cell Activation: Viral and Latent Reservoir Persistence, and Viral Blips in HIV-infected Patients on Potent Therapy. - Libin Rong; Alan S. Perelson (PLoS Comput. Biol., 2009)

Analysis of Hepatitis C Virus Infection Models with Hepatocyte Homeostasis. - Timothy C. Reluga; Harel Dahari; Alan S. Perelson (SIAM J. Appl. Math., 2009)

Estimating time since infection in early homogeneous HIV-1 samples using a poisson model. - Elena E. Giorgi; Bob Funkhouser; Gayathri Athreya; Alan S. Perelson; Bette T. Korber; Tanmoy Bhattacharya 001 (BMC Bioinform., 2010)

Current Estimates for HIV-1 Production Imply Rapid Viral Clearance in Lymphoid Tissues. - Rob J. De Boer; Ruy M. Ribeiro; Alan S. Perelson (PLoS Comput. Biol., 2010)

Treatment-Mediated Alterations in HIV Fitness Preserve CD4+ T Cell Counts but Have Minimal Effects on Viral Load. - Naveen K. Vaidya; Libin Rong; Vincent C. Marconi; Daniel R. Kuritzkes; Steven G. Deeks; Alan S. Perelson (PLoS Comput. Biol., 2010)

Stochastic Theory of Early Viral Infection: Continuous versus Burst Production of Virions. - John E. Pearson; Paul Krapivsky; Alan S. Perelson (PLoS Comput. Biol., 2011)

Effect of 1918 PB1-F2 Expression on Influenza A Virus Infection Kinetics. - Amber M. Smith; Frederick R. Adler; Julie L. McAuley; Ryan N. Gutenkunst; Ruy M. Ribeiro; Jonathan A. McCullers; Alan S. Perelson (PLoS Comput. Biol., 2011)

On Identifiability of Nonlinear ODE Models and Applications in Viral Dynamics. - Hongyu Miao 001; Xiaohua Xia; Alan S. Perelson; Hulin Wu (SIAM Rev., 2011)

Modeling Within-Host Dynamics of Influenza Virus Infection Including Immune Responses. - Kasia A. Pawelek; Giao T. Huynh; Michelle Quinlivan; Ann Cullinane; Libin Rong; Alan S. Perelson (PLoS Comput. Biol., 2012)

Analysis of Hepatitis C Virus Decline during Treatment with the Protease Inhibitor Danoprevir Using a Multiscale Model. - Libin Rong; Jérémie Guedj; Harel Dahari; Daniel J. Coffield Jr.; Micha Levi; Patrick Smith; Alan S. Perelson (PLoS Comput. Biol., 2013)

Quantifying the Turnover of Transcriptional Subclasses of HIV-1-Infected Cells. - Christian L. Althaus; Beda Joos; Alan S. Perelson; Huldrych F. Günthard (PLoS Comput. Biol., 2014)

Impact of Different Oseltamivir Regimens on Treating Influenza A Virus Infection and Resistance Emergence: Insights from a Modelling Study. - Laetitia Canini; Jessica M. Conway; Alan S. Perelson; Fabrice Carrat (PLoS Comput. Biol., 2014)

Antibody Responses during Hepatitis B Viral Infection. - Stanca M. Ciupe; Ruy M. Ribeiro; Alan S. Perelson (PLoS Comput. Biol., 2014)

A Hepatitis C Virus Infection Model with Time-Varying Drug Effectiveness: Solution and Analysis. - Jessica M. Conway; Alan S. Perelson (PLoS Comput. Biol., 2014)

Inferring Viral Dynamics in Chronically HCV Infected Patients from the Spatial Distribution of Infected Hepatocytes. - Frederik Graw; Ashwin Balagopal; Abraham J. Kandathil; Stuart C. Ray; David L. Thomas; Ruy M. Ribeiro; Alan S. Perelson (PLoS Comput. Biol., 2014)

Recombination Enhances HIV-1 Envelope Diversity by Facilitating the Survival of Latent Genomic Fragments in the Plasma Virus Population. - Taina T. Immonen; Jessica M. Conway; Ethan O. Romero-Severson; Alan S. Perelson; Thomas Leitner (PLoS Comput. Biol., 2015)

SPMM: estimating infection duration of multivariant HIV-1 infections. - Tanzy M. T. Love; Sung Yong Park; Elena E. Giorgi; Wendy J. Mack; Alan S. Perelson; Ha Youn Lee (Bioinform., 2016)

Residual Viremia in Treated HIV+ Individuals. - Jessica M. Conway; Alan S. Perelson (PLoS Comput. Biol., 2016)

Modeling the Effects of Morphine on Simian Immunodeficiency Virus Dynamics. - Naveen K. Vaidya; Ruy M. Ribeiro; Alan S. Perelson; Anil Kumar (PLoS Comput. Biol., 2016)

Early HIV Infection Predictions: Role of Viral Replication Errors. - Jessica M. Conway; Alan S. Perelson (SIAM J. Appl. Math., 2018)

Predictions of time to HIV viral rebound following ART suspension that incorporate personal biomarkers. - Jessica M. Conway; Alan S. Perelson; Jonathan Z. Li (PLoS Comput. Biol., 2019)

Models of SIV rebound after treatment interruption that involve multiple reactivation events. - Christiaan H. van Dorp; Jessica M. Conway; Dan H. Barouch; James B. Whitney; Alan S. Perelson (PLoS Comput. Biol., 2020)

Quantification of Ebola virus replication kinetics in vitro. - Laura E. Liao; Jonathan Carruthers; Sophie J. Smither; Simon A. Weller; Diane Williamson; Thomas R. Laws; Isabel García-Dorival; Julian A. Hiscox; Benjamin P. Holder; Catherine A. A. Beauchemin; Alan S. Perelson; Martín López-García; et al. (PLoS Comput. Biol., 2020)

Mathematical modeling of hepatitis C RNA replication, exosome secretion and virus release. - Carolin Zitzmann; Lars Kaderali; Alan S. Perelson (PLoS Comput. Biol., 2020)

Challenges in cybersecurity: Lessons from biological defense systems. - Edward C. Schrom II; Ann Kinzig; Stephanie Forrest; Andrea L. Graham; Simon A. Levin; Carl T. Bergstrom; Carlos Castillo-Chavez; James P. Collins 002; Rob J. De Boer; Adam Doupé; Roya Ensafi; Stuart I. Feldman; et al. (CoRR, 2021)

Zika virus dynamics: Effects of inoculum dose, the innate immune response and viral interference. - Katharine Best; Dan H. Barouch; Jérémie Guedj; Ruy M. Ribeiro; Alan S. Perelson (PLoS Comput. Biol., 2021)

Success of prophylactic antiviral therapy for SARS-CoV-2: Predicted critical efficacies and impact of different drug-specific mechanisms of action. - Peter Czuppon; Florence Débarre; António Gonçalves; Olivier Tenaillon; Alan S. Perelson; Jérémie Guedj; François Blanquart (PLoS Comput. Biol., 2021)

Mechanistic basis of post-treatment control of SIV after anti-α4β7 antibody therapy. - Chad R. Wells; Youfang Cao; David P. Durham; Siddappa N. Byrareddy; Aftab A. Ansari; Nancy H. Ruddle; Jeffrey P. Townsend; Alison P. Galvani; Alan S. Perelson (PLoS Comput. Biol., 2021)

Antithetic effect of interferon-α on cell-free and cell-to-cell HIV-1 infection. - Ryuichi Kumata; Shoya Iwanami; Katrina B. Mar; Yusuke Kakizoe; Naoko Misawa; Shinji Nakaoka; Yoshio Koyanagi; Alan S. Perelson; John W. Schoggins; Shingo Iwami; Kei Sato (PLoS Comput. Biol., 2022)

Mathematical modeling of plus-strand RNA virus replication to identify broad-spectrum antiviral treatment strategies. - Carolin Zitzmann; Christopher Dächert; Bianca Schmid; Hilde van der Schaar; Martijn van Hemert; Alan S. Perelson; Frank J. M. van Kuppeveld; Ralf Bartenschlager; Marco Binder; Lars Kaderali (PLoS Comput. Biol., 2023)

Erratum: On Identifiability of Nonlinear ODE Models and Applications in Viral Dynamics. - Hongyu Miao 001; Alan S. Perelson; Hulin Wu (SIAM Rev., 2023)

Modeling resistance to the broadly neutralizing antibody PGT121 in people living with HIV-1. - Tyler Cassidy; Kathryn E. Stephenson; Dan H. Barouch; Alan S. Perelson (PLoS Comput. Biol., 2024)

Multiscale modeling of HBV infection integrating intra- and intercellular viral propagation to analyze extracellular viral markers. - Kosaku Kitagawa; Kwang Su Kim; Masashi Iwamoto; Sanae Hayashi; Hyeongki Park; Takara Nishiyama; Naotoshi Nakamura; Yasuhisa Fujita; Shinji Nakaoka; Kazuyuki Aihara; Alan S. Perelson; Lena Allweiss; et al. (PLoS Comput. Biol., 2024)

How robust are estimates of key parameters in standard viral dynamic models? - Carolin Zitzmann; Ruian Ke; Ruy M. Ribeiro; Alan S. Perelson (PLoS Comput. Biol., 2024)

Prediction of cccDNA dynamics in hepatitis B patients by a combination of serum surrogate markers. - Kwang Su Kim; Masashi Iwamoto; Kosaku Kitagawa; Hyeongki Park; Sanae Hayashi; Senko Tsukuda; Takeshi Matsui; Masanori Atsukawa; Kentaro Matsuura; Natthaya Chuaypen; Pisit Tangkijvanich; Lena Allweiss; et al. (PLoS Comput. Biol., 2025)