Alan S. Perelson

According to our database, Alan S. Perelson authored at least 53 papers between 1976 and 2024.

Collaborative distances:

• Dijkstra number of three.
• Erdős number of four.

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

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, Maura Dandri, Koichi Watashi, Yasuhito Tanaka, Shingo Iwami

PLoS Comput. Biol., 2024

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

2023

Erratum: On Identifiability of Nonlinear ODE Models and Applications in Viral Dynamics.

Hongyu Miao, Alan S. Perelson, Hulin Wu

SIAM Rev., August, 2023

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

2022

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

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

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

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

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, 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

CoRR, 2021

2020

Mathematical modeling of hepatitis C RNA replication, exosome secretion and virus release.

Carolin Zitzmann, Lars Kaderali, Alan S. Perelson

PLoS Comput. Biol., November, 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, Grant Lythe, John N. Barr, Carmen Molina-París

PLoS Comput. Biol., November, 2020

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

2019

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

2018

Early HIV Infection Predictions: Role of Viral Replication Errors.

Jessica M. Conway, Alan S. Perelson

SIAM J. Appl. Math., 2018

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

Residual Viremia in Treated HIV⁺ Individuals.

Jessica M. Conway, Alan S. Perelson

PLoS Comput. Biol., 2016

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

2015

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

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

A Hepatitis C Virus Infection Model with Time-Varying Drug Effectiveness: Solution and Analysis.

Jessica M. Conway, Alan S. Perelson

PLoS Comput. Biol., 2014

Antibody Responses during Hepatitis B Viral Infection.

Stanca M. Ciupe, Ruy M. Ribeiro, Alan S. Perelson

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

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

2013

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

2012

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

2011

On Identifiability of Nonlinear ODE Models and Applications in Viral Dynamics.

Hongyu Miao, Xiaohua Xia, Alan S. Perelson, Hulin Wu

SIAM Rev., 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

Stochastic Theory of Early Viral Infection: Continuous versus Burst Production of Virions.

John E. Pearson, Paul Krapivsky, Alan S. Perelson

PLoS Comput. Biol., 2011

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

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

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

BMC Bioinform., 2010

2009

Analysis of Hepatitis C Virus Infection Models with Hepatocyte Homeostasis.

Timothy C. Reluga, Harel Dahari, Alan S. Perelson

SIAM J. Appl. Math., 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

Agent-based modeling of host-pathogen systems: The successes and challenges.

Amy L. Bauer, Catherine Beauchemin, Alan S. Perelson

Inf. Sci., 2009

2008

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

2007

Mathematical Analysis of Age-Structured HIV-1 Dynamics with Combination Antiretroviral Therapy.

Libin Rong, Zhilan Feng, Alan S. Perelson

SIAM J. Appl. Math., 2007

2006

Viral and Latent Reservoir Persistence in HIV-1-Infected Patients on Therapy.

Hwijin Kim, Alan S. Perelson

PLoS Comput. Biol., 2006

2005

Human Immunodeficiency Virus: Quasi-Species and Drug Resistance.

John M. Murray, Alan S. Perelson

Multiscale Model. Simul., 2005

Optimization of Influenza Vaccine Selection.

Joseph T. Wu, Lawrence M. Wein, Alan S. Perelson

Oper. Res., 2005

2004

An Overview of Computational and Theoretical Immunology.

Alan S. Perelson

Proceedings of the Artificial Immune Systems, Third International Conference, 2004

2003

Stochastic Stage-structured Modeling of the Adaptive Immune System.

Dennis L. Chao, Miles P. Davenport, Stephanie Forrest, Alan S. Perelson

Proceedings of the 2nd IEEE Computer Society Bioinformatics Conference, 2003

1999

Mathematical Analysis of HIV-1 Dynamics in Vivo.

Alan S. Perelson, Patrick W. Nelson

SIAM Rev., 1999

Some design principles for immune system recognition.

Alan S. Perelson, Frederik W. Wiegel

Complex., 1999

1996

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

1995

The Evolution of Emergent Organization in Immune System Gene Libraries.

Ron R. Hightower, Stephanie Forrest, Alan S. Perelson

Proceedings of the 6th International Conference on Genetic Algorithms, 1995

1994

Self-nonself discrimination in a computer.

Stephanie Forrest, Alan S. Perelson, Lawrence Allen, Rajesh Cherukuri

Proceedings of the 1994 IEEE Computer Society Symposium on Research in Security and Privacy, 1994

1993

Searching for Diverse, Cooperative Populations with Genetic Algorithms.

Robert E. Smith, Stephanie Forrest, Alan S. Perelson

Evol. Comput., 1993

Using Genetic Algorithms to Explore Pattern Recognition in the Immune System.

Stephanie Forrest, Robert E. Smith, Brenda Javornik, Alan S. Perelson

Evol. Comput., 1993

1992

Population Diversity in an Immune System Model: Implications for Genetic Search.

Robert E. Smith, Stephanie Forrest, Alan S. Perelson

Proceedings of the Second Workshop on Foundations of Genetic Algorithms. Vail, 1992

1990

Genetic Algorithms and the Immune System.

Stephanie Forrest, Alan S. Perelson

Proceedings of the Parallel Problem Solving from Nature, 1st Workshop, 1990

1976

Review of "Introduction to Bond Graphs and Their Applications" by J. U. Thoma.

Alan S. Perelson

IEEE Trans. Syst. Man Cybern., 1976

Review of "System Dynamics: A Unified Approach" by Dean C. Karnopp and Ronald C. Rosenberg.

Alan S. Perelson

IEEE Trans. Syst. Man Cybern., 1976