Alan S. Perelson

55 papers A 2Journal 49Unranked 4

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	A multiscale model of the action of a capsid assembly modulator for the treatment of chronic hepatitis B. PLoS Comput. Biol. Sarafa A. Iyaniwura, Tyler Cassidy, Ruy M. Ribeiro, Alan S. Perelson
2025	J	`jnl`	Prediction of cccDNA dynamics in hepatitis B patients by a combination of serum surrogate markers. PLoS Comput. Biol. 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, Takara Nishiyama, Naotoshi Nakamura, Yasuhisa Fujita, Eiryo Kawakami, Shinji Nakaoka, Masamichi Muramatsu, Kazuyuki Aihara, Takaji Wakita, Alan S. Perelson, Maura Dandri, Koichi Watashi, Shingo Iwami, Yasuhito Tanaka
2024	J	`jnl`	How robust are estimates of key parameters in standard viral dynamic models? PLoS Comput. Biol. Carolin Zitzmann, Ruian Ke, Ruy M. Ribeiro, Alan S. Perelson
2024	J	`jnl`	Modeling resistance to the broadly neutralizing antibody PGT121 in people living with HIV-1. PLoS Comput. Biol. Tyler Cassidy, Kathryn E. Stephenson, Dan H. Barouch, Alan S. Perelson
2024	J	`jnl`	Multiscale modeling of HBV infection integrating intra- and intercellular viral propagation to analyze extracellular viral markers. PLoS Comput. Biol. 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, Maura Dandri, Koichi Watashi, Yasuhito Tanaka, Shingo Iwami
2023	J	`jnl`	Erratum: On Identifiability of Nonlinear ODE Models and Applications in Viral Dynamics. SIAM Rev. Hongyu Miao, Alan S. Perelson, Hulin Wu
2023	J	`jnl`	Mathematical modeling of plus-strand RNA virus replication to identify broad-spectrum antiviral treatment strategies. PLoS Comput. Biol. 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
2022	J	`jnl`	Antithetic effect of interferon-α on cell-free and cell-to-cell HIV-1 infection. PLoS Comput. Biol. 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
2021	J	`jnl`	Challenges in cybersecurity: Lessons from biological defense systems. CoRR Edward C. Schrom II, Ann Kinzig, Stephanie Forrest, Andrea L. Graham, Simon A. Levin, Carl T. Bergstrom, Carlos Castillo-Chavez, James P. Collins, Rob J. De Boer, Adam Doupé, Roya Ensafi, Stuart I. Feldman, Bryan T. Grenfell, J. Alex Halderman, Silvie Huijben, Carlo C. Maley, Melanie E. Moses, Alan S. Perelson, Charles Perrings, Joshua B. Plotkin, Jennifer Rexford, Mohit Tiwari
2021	J	`jnl`	Mechanistic basis of post-treatment control of SIV after anti-α4β7 antibody therapy. PLoS Comput. Biol. 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
2021	J	`jnl`	Success of prophylactic antiviral therapy for SARS-CoV-2: Predicted critical efficacies and impact of different drug-specific mechanisms of action. PLoS Comput. Biol. Peter Czuppon, Florence Débarre, António Gonçalves, Olivier Tenaillon, Alan S. Perelson, Jérémie Guedj, François Blanquart
2021	J	`jnl`	Zika virus dynamics: Effects of inoculum dose, the innate immune response and viral interference. PLoS Comput. Biol. Katharine Best, Dan H. Barouch, Jérémie Guedj, Ruy M. Ribeiro, Alan S. Perelson
2020	J	`jnl`	Mathematical modeling of hepatitis C RNA replication, exosome secretion and virus release. PLoS Comput. Biol. Carolin Zitzmann, Lars Kaderali, Alan S. Perelson
2020	J	`jnl`	Models of SIV rebound after treatment interruption that involve multiple reactivation events. PLoS Comput. Biol. Christiaan H. van Dorp, Jessica M. Conway, Dan H. Barouch, James B. Whitney, Alan S. Perelson
2020	J	`jnl`	Quantification of Ebola virus replication kinetics in vitro. PLoS Comput. Biol. 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, Grant Lythe, John N. Barr, Carmen Molina-París
2019	J	`jnl`	Predictions of time to HIV viral rebound following ART suspension that incorporate personal biomarkers. PLoS Comput. Biol. Jessica M. Conway, Alan S. Perelson, Jonathan Z. Li
2018	J	`jnl`	Early HIV Infection Predictions: Role of Viral Replication Errors. SIAM J. Appl. Math. Jessica M. Conway, Alan S. Perelson
2016	J	`jnl`	Modeling the Effects of Morphine on Simian Immunodeficiency Virus Dynamics. PLoS Comput. Biol. Naveen K. Vaidya, Ruy M. Ribeiro, Alan S. Perelson, Anil Kumar
2016	J	`jnl`	Residual Viremia in Treated HIV PLoS Comput. Biol. Jessica M. Conway, Alan S. Perelson
2016	J	`jnl`	SPMM: estimating infection duration of multivariant HIV-1 infections. Bioinform. Tanzy M. T. Love, Sung Yong Park, Elena E. Giorgi, Wendy J. Mack, Alan S. Perelson, Ha Youn Lee
2015	J	`jnl`	Recombination Enhances HIV-1 Envelope Diversity by Facilitating the Survival of Latent Genomic Fragments in the Plasma Virus Population. PLoS Comput. Biol. Taina T. Immonen, Jessica M. Conway, Ethan O. Romero-Severson, Alan S. Perelson, Thomas Leitner
2014	J	`jnl`	A Hepatitis C Virus Infection Model with Time-Varying Drug Effectiveness: Solution and Analysis. PLoS Comput. Biol. Jessica M. Conway, Alan S. Perelson
2014	J	`jnl`	Antibody Responses during Hepatitis B Viral Infection. PLoS Comput. Biol. Stanca M. Ciupe, Ruy M. Ribeiro, Alan S. Perelson
2014	J	`jnl`	Impact of Different Oseltamivir Regimens on Treating Influenza A Virus Infection and Resistance Emergence: Insights from a Modelling Study. PLoS Comput. Biol. Laetitia Canini, Jessica M. Conway, Alan S. Perelson, Fabrice Carrat
2014	J	`jnl`	Inferring Viral Dynamics in Chronically HCV Infected Patients from the Spatial Distribution of Infected Hepatocytes. PLoS Comput. Biol. Frederik Graw, Ashwin Balagopal, Abraham J. Kandathil, Stuart C. Ray, David L. Thomas, Ruy M. Ribeiro, Alan S. Perelson
2014	J	`jnl`	Quantifying the Turnover of Transcriptional Subclasses of HIV-1-Infected Cells. PLoS Comput. Biol. Christian L. Althaus, Beda Joos, Alan S. Perelson, Huldrych F. Günthard
2013	J	`jnl`	Analysis of Hepatitis C Virus Decline during Treatment with the Protease Inhibitor Danoprevir Using a Multiscale Model. PLoS Comput. Biol. Libin Rong, Jérémie Guedj, Harel Dahari, Daniel J. Coffield Jr., Micha Levi, Patrick Smith, Alan S. Perelson
2012	J	`jnl`	Modeling Within-Host Dynamics of Influenza Virus Infection Including Immune Responses. PLoS Comput. Biol. Kasia A. Pawelek, Giao T. Huynh, Michelle Quinlivan, Ann Cullinane, Libin Rong, Alan S. Perelson
2011	J	`jnl`	Effect of 1918 PB1-F2 Expression on Influenza A Virus Infection Kinetics. PLoS Comput. Biol. Amber M. Smith, Frederick R. Adler, Julie L. McAuley, Ryan N. Gutenkunst, Ruy M. Ribeiro, Jonathan A. McCullers, Alan S. Perelson
2011	J	`jnl`	On Identifiability of Nonlinear ODE Models and Applications in Viral Dynamics. SIAM Rev. Hongyu Miao, Xiaohua Xia, Alan S. Perelson, Hulin Wu
2011	J	`jnl`	Stochastic Theory of Early Viral Infection: Continuous versus Burst Production of Virions. PLoS Comput. Biol. John E. Pearson, Paul Krapivsky, Alan S. Perelson
2010	J	`jnl`	Current Estimates for HIV-1 Production Imply Rapid Viral Clearance in Lymphoid Tissues. PLoS Comput. Biol. Rob J. De Boer, Ruy M. Ribeiro, Alan S. Perelson
2010	J	`jnl`	Estimating time since infection in early homogeneous HIV-1 samples using a poisson model. BMC Bioinform. Elena E. Giorgi, Bob Funkhouser, Gayathri Athreya, Alan S. Perelson, Bette T. Korber, Tanmoy Bhattacharya
2010	J	`jnl`	Treatment-Mediated Alterations in HIV Fitness Preserve CD4 PLoS Comput. Biol. Naveen K. Vaidya, Libin Rong, Vincent C. Marconi, Daniel R. Kuritzkes, Steven G. Deeks, Alan S. Perelson
2009	J	`jnl`	Agent-based modeling of host-pathogen systems: The successes and challenges. Inf. Sci. Amy L. Bauer, Catherine Beauchemin, Alan S. Perelson
2009	J	`jnl`	Analysis of Hepatitis C Virus Infection Models with Hepatocyte Homeostasis. SIAM J. Appl. Math. Timothy C. Reluga, Harel Dahari, Alan S. Perelson
2009	J	`jnl`	Modeling Latently Infected Cell Activation: Viral and Latent Reservoir Persistence, and Viral Blips in HIV-infected Patients on Potent Therapy. PLoS Comput. Biol. Libin Rong, Alan S. Perelson
2008	J	`jnl`	Dynamic Correlation between Intrahost HIV-1 Quasispecies Evolution and Disease Progression. PLoS Comput. Biol. Ha Youn Lee, Alan S. Perelson, Su-Chan Park, Thomas Leitner
2007	J	`jnl`	Mathematical Analysis of Age-Structured HIV-1 Dynamics with Combination Antiretroviral Therapy. SIAM J. Appl. Math. Libin Rong, Zhilan Feng, Alan S. Perelson
2006	J	`jnl`	Viral and Latent Reservoir Persistence in HIV-1-Infected Patients on Therapy. PLoS Comput. Biol. Hwijin Kim, Alan S. Perelson
2005	J	`jnl`	Human Immunodeficiency Virus: Quasi-Species and Drug Resistance. Multiscale Model. Simul. John M. Murray, Alan S. Perelson
2005	J	`jnl`	Optimization of Influenza Vaccine Selection. Oper. Res. Joseph T. Wu, Lawrence M. Wein, Alan S. Perelson
2004	—	`conf`	An Overview of Computational and Theoretical Immunology. ICARIS Alan S. Perelson
2003	—	`conf`	Stochastic Stage-structured Modeling of the Adaptive Immune System. CSB Dennis L. Chao, Miles P. Davenport, Stephanie Forrest, Alan S. Perelson
1999	J	`jnl`	Mathematical Analysis of HIV-1 Dynamics in Vivo. SIAM Rev. Alan S. Perelson, Patrick W. Nelson
1999	J	`jnl`	Some design principles for immune system recognition. Complex. Alan S. Perelson, Frederik W. Wiegel
1996	J	`jnl`	Base Pairing Probabilities in a Complete HIV-1 RNA. J. Comput. Biol. Martijn A. Huynen, Alan S. Perelson, W. A. Vieira, Peter F. Stadler
1995	—	`conf`	The Evolution of Emergent Organization in Immune System Gene Libraries. ICGA Ron R. Hightower, Stephanie Forrest, Alan S. Perelson
1994	—	`conf`	Self-nonself discrimination in a computer. S&P Stephanie Forrest, Alan S. Perelson, Lawrence Allen, Rajesh Cherukuri
1993	J	`jnl`	Searching for Diverse, Cooperative Populations with Genetic Algorithms. Evol. Comput. Robert E. Smith, Stephanie Forrest, Alan S. Perelson
1993	J	`jnl`	Using Genetic Algorithms to Explore Pattern Recognition in the Immune System. Evol. Comput. Stephanie Forrest, Robert E. Smith, Brenda Javornik, Alan S. Perelson
1992	A	`conf`	Population Diversity in an Immune System Model: Implications for Genetic Search. FOGA Robert E. Smith, Stephanie Forrest, Alan S. Perelson
1990	A	`conf`	Genetic Algorithms and the Immune System. PPSN Stephanie Forrest, Alan S. Perelson
1976	J	`jnl`	Review of "Introduction to Bond Graphs and Their Applications" by J. U. Thoma. IEEE Trans. Syst. Man Cybern. Alan S. Perelson
1976	J	`jnl`	Review of "System Dynamics: A Unified Approach" by Dean C. Karnopp and Ronald C. Rosenberg. IEEE Trans. Syst. Man Cybern. Alan S. Perelson