Alan S. Perelson

Alan S. Perelson, Stephanie Forrest, Dennis L. Chao, 2003, Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003.

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

Alan S. Perelson, Jessica M. Conway, A. Perelson, 2014, PLoS Comput. Biol..

SPMM: estimating infection duration of multivariant HIV-1 infections

Alan S. Perelson, Sung Yong Park, Ha Youn Lee, 2016, Bioinform..

Challenges in cybersecurity: Lessons from biological defense systems pdf

Joshua B. Plotkin, Alan S. Perelson, Jennifer Rexford, 2021, Mathematical biosciences.

Recent approaches to immune networks

Alan S. Perelson, Lee A. Segel, Gérard Weisbuch, 1993 .

Modeling the Acute and Chronic Phases of Theiler Murine Encephalomyelitis Virus Infection

Alan S. Perelson, Harel Dahari, A. Perelson, 2013, Journal of Virology.

Receptor clustering on a cell surface. III. theory of receptor cross-linking by multivalent ligands: description by ligand states

Alan S. Perelson, A. Perelson, 1981 .

Conclusions and Extensions

Alan S. Perelson, Catherine A. Macken, 1985 .

Early Low-Titer Neutralizing Antibodies Impede HIV-1 Replication and Select for Virus Escape

Alan S. Perelson, Feng Gao, Hui Li, 2012, PLoS pathogens.

Inferring HIV Escape Rates from Multi-Locus Genotype Data

Alan S. Perelson, Richard A. Neher, A. Perelson, 2013, Front. Immunol..

Modeling the Dynamics and Migratory Pathways of Virus-Specific Antibody-Secreting Cell Populations in Primary Influenza Infection

Alan S. Perelson, Hulin Wu, Martin S. Zand, 2014, PloS one.

Estimating division and death rates from CFSE data

Alan S. Perelson, Rob J. de Boer, A. Perelson, 2005 .

Corrigendum to “Modeling sequence evolution in acute HIV-1 infection” [J. Theor. Biol. 261 (2009) 341–360]

Alan S. Perelson, Tanmoy Bhattacharya, Eric Delwart, 2012 .

Modelling hepatitis C therapy—predicting effects of treatment

Alan S. Perelson, Jeremie Guedj, A. Perelson, 2015, Nature Reviews Gastroenterology &Hepatology.

RNA Structural Motifs

Alan S. Perelson, Ming Zhang, A. Perelson, 2011 .

Deriving Shape Space Parameters from Immunological Data for a Model of Cross-Reactive Memory

Alan S. Perelson, Stephanie Forrest, Ron R. Hightower, 1997 .

Analysis of hepatitis B viral load decline under potent therapy: Complex decay profiles observed

Alan S. Perelson, Scott Bowden, Ruy M. Ribeiro, 2001, Hepatology.

Growth and Recruitment in the Immune Network

Alan S. Perelson, Paulien Hogeweg, R. J. de Boer, 1992 .

KINETICS OF RED BLOOD CELL AGGREGATION: AN EXAMPLE OF GEOMETRIC POLYMERIZATION

Alan S. Perelson, A. Perelson, Richard W. Samsel, 1984 .

Rapid Emergence of Protease Inhibitor Resistance in Hepatitis C Virus

Alan S. Perelson, Libin Rong, Ruy M. Ribeiro, 2010, Science Translational Medicine.

Turnover of CD 4 1 and CD 8 1 T Lymphocytes in HIV-1 Infection as Measured by Ki-67 Antigen

Alan S. Perelson, Bernard Hirschel, Sabine Yerly, 1998 .

Multiplicity of Human Immunodeficiency Virus Infections in Lymphoid Tissue

Alan S. Perelson, Narendra M. Dixit, A. Perelson, 2004, Journal of Virology.

Mathematical Modeling of Subgenomic Hepatitis C Virus Replication in Huh-7 Cells

Alan S. Perelson, Ruy M. Ribeiro, Charles M. Rice, 2006, Journal of Virology.

Shape space analysis of immune networks

Alan S. Perelson, Lee A. Segel, L. Segel, 1989 .

Decay characteristics of HIV-1-infected compartments during combination therapy

Alan S. Perelson, A. Perelson, D. Ho, 1997, Nature.

Kinetics of Virus-Specific CD8+ T Cells and the Control of Human Immunodeficiency Virus Infection

Alan S. Perelson, Ruy M. Ribeiro, Miles P. Davenport, 2004, Journal of Virology.

Bulletin of Mathematical Biology Special Issue

Alan S. Perelson, A. Perelson, Leah Keshet, 2006 .

Virus Dynamics: Mathematical Principles of Immunology and Virology, Martin A. Nowak, Robert M. May. Oxford University Press, Oxford, 2000. $34.95 (paper), $70 (hardcover)

Alan S. Perelson, 2001 .

Competitive exclusion by autologous antibodies can prevent broad HIV-1 antibodies from arising

Alan S. Perelson, Shishi Luo, A. Perelson, 2015, Proceedings of the National Academy of Sciences.

Modeling deuterated glucose labeling of T-lymphocytes

Alan S. Perelson, Ruy M. Ribeiro, A. Perelson, 2002, Bulletin of mathematical biology.

Recruitment Times, Proliferation, and Apoptosis Rates during the CD8+ T-Cell Response to Lymphocytic Choriomeningitis Virus

Alan S. Perelson, Rustom Antia, Mihaela Oprea, 2001, Journal of Virology.

In a Subset of Subjects on Highly Active Antiretroviral Therapy, Human Immunodeficiency Virus Type 1 RNA in Plasma Decays from 50 to <5 Copies per Milliliter, with a Half-Life of 6 Months

Alan S. Perelson, Hui Zhang, Geethanjali Dornadula, 2003, Journal of Virology.

Computational Models of B cell and T cell Receptors

Alan S. Perelson, A. Perelson, H. Y. Lee, 2007 .

Low-dose rectal inoculation of rhesus macaques by SIVsmE660 or SIVmac251 recapitulates human mucosal infection by HIV-1

Alan S. Perelson, Hui Li, Gary J. Nabel, 2009, The Journal of experimental medicine.

How Antigen Quantity and Quality Determine T-Cell Decisions in Lymphoid Tissue

Alan S. Perelson, Arup K. Chakraborty, Sarah E. Henrickson, 2008, Molecular and Cellular Biology.

Increased Turnover of T Lymphocytes in HIV-1 Infection and Its Reduction by Antiretroviral Therapy

Alan S. Perelson, Ruy M. Ribeiro, L. Weinberger, 2001, The Journal of experimental medicine.

Dynamics of HIV Infection

Alan S. Perelson, A. Perelson, 2003 .

A New Age-Structured Multiscale Model of the Hepatitis C Virus Life-Cycle During Infection and Therapy With Direct-Acting Antiviral Agents

Alan S. Perelson, Marcelo Lobosco, James M. Hyman, 2018, Front. Microbiol..

Modeling the effects of prior infection on vaccine efficacy

David H. Ackley, Alan S. Perelson, Stephanie Forrest, 1997, 1997 IEEE International Conference on Systems, Man, and Cybernetics. Computational Cybernetics and Simulation.

Modeling and Simulation of Aggregation of Membrane Protein LAT with Molecular Variability in the Number of Binding Sites for Cytosolic Grb2-SOS1-Grb2

Alan S. Perelson, Byron Goldstein, Ambarish Nag, 2012, PloS one.

Emergence of HIV-1 Drug Resistance During Antiretroviral Treatment

Alan S. Perelson, Libin Rong, Zhilan Feng, 2007, Bulletin of mathematical biology.

Exploiting the diversity of time scales in the immune system: A B-cell antibody model

Alan S. Perelson, Lee A. Segel, L. Segel, 1991 .

Accelerated Immunodeficiency by Anti-CCR5 Treatment in HIV Infection

Alan S. Perelson, Ariel D. Weinberger, Leor S. Weinberger, 2009, PLoS computational biology.

Fitness Costs and Diversity of the Cytotoxic T Lymphocyte (CTL) Response Determine the Rate of CTL Escape during Acute and Chronic Phases of HIV Infection

Alan S. Perelson, Guido Ferrari, Vitaly V. Ganusov, 2011, Journal of Virology.

Characterizing T Cell Movement within Lymph Nodes in the Absence of Antigen1

Alan S. Perelson, Narendra M. Dixit, A. Perelson, 2007, The Journal of Immunology.

Branching Processes Applied to Cell Surface Aggregation Phenomena

Alan S. Perelson, Catherine A. Macken, 1985 .

13 Modelling the in vivo growth rate of HIV: implications for vaccination

Alan S. Perelson, Ruy M. Ribeiro, Narendra M. Dixit, 2005 .

A paradoxical instability caused by relatively short-range inhibition

Alan S. Perelson, Lee A. Segel, 1990 .

The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection

Alan S. Perelson, Tanmoy Bhattacharya, Guido Ferrari, 2009, The Journal of experimental medicine.

Evolution of Envelope Sequences of Human Immunodeficiency Virus Type 1 in Cellular Reservoirs in the Setting of Potent Antiviral Therapy

Alan S. Perelson, Douglas D. Richman, Simon D. W. Frost, 1999, Journal of Virology.

Elucidation of Hepatitis C Virus Transmission and Early Diversification by Single Genome Sequencing

Alan S. Perelson, Hui Li, Tanmoy Bhattacharya, 2012, PLoS pathogens.

A SIMPLE IDIOTYPIC NETWORK MODEL WITH COMPLEX DYNAMICS

Alan S. Perelson, Ioannis G. Kevrekidis, R. J. de Boer, 1990 .

Turnover of CD4+ and CD8+ T Lymphocytes in HIV-1 Infection as Measured by Ki-67 Antigen

Alan S. Perelson, Bernard Hirschel, Sabine Yerly, 1998, The Journal of experimental medicine.

Different Dynamics of CD4+ and CD8+ T Cell Responses During and After Acute Lymphocytic Choriomeningitis Virus Infection 1

Alan S. Perelson, Dirk Homann, A. Perelson, 2003, The Journal of Immunology.

Transmission of Single HIV-1 Genomes and Dynamics of Early Immune Escape Revealed by Ultra-Deep Sequencing

Alan S. Perelson, Timothy C. Wallstrom, Tanmoy Bhattacharya, 2010, PloS one.

The IgM-IgG switch looked at from a control theoretic viewpoint

Alan S. Perelson, A. Perelson, 1978 .

Effect of drug efficacy and the eclipse phase of the viral life cycle on estimates of HIV viral dynamic parameters.

Alan S. Perelson, John E. Mittler, Patrick W. Nelson, 2001 .

Naïve and Memory Cell Turnover as Drivers of CCR5-to-CXCR4 Tropism Switch in Human Immunodeficiency Virus Type 1: Implications for Therapy

Alan S. Perelson, Ruy M. Ribeiro, Miles P. Davenport, 2006, Journal of Virology.

Duration of an intermittent episode of viremia

Alan S. Perelson, Ora E. Percus, Jerome Percus, 2005, Bulletin of mathematical biology.

Kinetics of Acute Hepatitis B Virus Infection in Humans

Alan S. Perelson, Vincent C. Emery, John M. Murray, 2000, The Journal of experimental medicine.

Modeling and Simulation of Aggregation of Membrane Protein LAT with Molecular Variability in the Number of Binding Sites for Cytosolic Grb 2-SOS 1-Grb 2

Alan S. Perelson, Byron Goldstein, Ambarish Nag, 2012 .

Modeling Subgenomic Hepatitis C Virus RNA Kinetics during Treatment with Alpha Interferon

Alan S. Perelson, Harel Dahari, A. Perelson, 2009, Journal of Virology.

High Multiplicity Infection by HIV-1 in Men Who Have Sex with Men

Alan S. Perelson, Hui Li, Tanmoy Bhattacharya, 2010, PLoS pathogens.

Determination of virus burst size in vivo using a single-cycle SIV in rhesus macaques

Alan S. Perelson, A. Perelson, D. Ho, 2007, Proceedings of the National Academy of Sciences.

Opportunistic infection as a cause of transient viremia in chronically infected HIV patients under treatment with HAART

Alan S. Perelson, A. Perelson, Laura E. Jonesa, 2004, Bulletin of mathematical biology.

Analysis of Human Immunodeficiency Virus Cytopathicity by Using a New Method for Quantitating Viral Dynamics in Cell Culture

Alan S. Perelson, Mihaela Zavolan, Richard Siegel, 2005, Journal of Virology.

The decay of the latent reservoir of replication-competent HIV-1 is inversely correlated with the extent of residual viral replication during prolonged anti-retroviral therapy

Alan S. Perelson, John E. Mittler, Catherine A. Macken, 2000, Nature Medicine.

CD8+ Lymphocytes Control Viral Replication in SIVmac239-Infected Rhesus Macaques without Decreasing the Lifespan of Productively Infected Cells

Alan S. Perelson, Ruy M. Ribeiro, Nichole R. Klatt, 2010, PLoS pathogens.

Quantitative Image Analysis of HIV-1 Infection in Lymphoid Tissue

Alan S. Perelson, Ashley T. Haase, Peter J. Dailey, 1996, Science.

Dynamics of CD4+ T Cell Responses against Listeria monocytogenes

Alan S. Perelson, Paul M. Allen, Frederik Graw, 2012, The Journal of Immunology.

Second‐phase hepatitis C virus RNA decline during telaprevir‐based therapy increases with drug effectiveness: Implications for treatment duration

Alan S. Perelson, Jeremie Guedj, A. Perelson, 2011, Hepatology.

Modeling and Estimation of Replication Fitness of Human Immunodeficiency Virus Type 1 In Vitro Experiments by Using a Growth Competition Assay

Alan S. Perelson, Hulin Wu, Jingming Ma, 2006, Journal of Virology.

Estimating Lymphocyte Division and Death Rates from CFSE Data

Alan S. Perelson, Philip D. Hodgkin, Dejan Milutinović, 2006, Bulletin of mathematical biology.

Estimation of the Initial Viral Growth Rate and Basic Reproductive Number during Acute HIV-1 Infection

Alan S. Perelson, Ruy M. Ribeiro, Steven G. Self, 2010, Journal of Virology.

Hepatitis B virus clearance rate estimates

Alan S. Perelson, Harel Dahari, Scott J. Cotler, 2009, Hepatology.

An age-based multiscale mathematical model of the hepatitis C virus life-cycle during infection and therapy: Including translation and replication

Alan S. Perelson, Ruy Freitas Reis, Marcelo Lobosco, 2017 .

Some mathematical models of receptor clustering by multivalent ligands

Alan S. Perelson, A. Perelson, 1984 .

Quantifying Aggregation of IgE-FcϵRI by Multivalent Antigen

Alan S. Perelson, William S. Hlavacek, Richard G. Posner, 1999 .

Quantitative Biology: Theory, Computational Methods, and Models

Terrence J. Sejnowski, Alan S. Perelson, Marco S. Nobile, 2018 .

Dynamics of T Cells and TCR Excision Circles Differ After Treatment of Acute and Chronic HIV Infection1 2

Alan S. Perelson, Ruy M. Ribeiro, John Zaunders, 2002, The Journal of Immunology.

Stochastic Models of Lymphocyte Proliferation and Death

Alan S. Perelson, Vitaly V. Ganusov, Anton Zilman, 2010, PloS one.

Some design principles for immune system recognition

Alan S. Perelson, Frederik W. Wiegel, 1999 .

Stem Cell Proliferation and Differentiation

Alan S. Perelson, Catherine A. Macken, 1988 .

A Cayley tree immune network model with antibody dynamics

Alan S. Perelson, Russell W. Anderson, A. Perelson, 1993, Bulletin of mathematical biology.

Molecular evolution on rugged landscapes : proteins, RNA and the immune system : the proceedings of the Workshop on Applied Molecular Evolution and the Maturation of the Immune Response, held March, 1989 in Santa Fe, New Mexico

Alan S. Perelson, Stuart A. Kauffman, S. Kauffman, 1991 .

In vivo dynamics of T cell activation, proliferation, and death in HIV-1 infection: Why are CD4+ but not CD8+ T cells depleted?

Alan S. Perelson, Ruy M. Ribeiro, A. Perelson, 2002, Proceedings of the National Academy of Sciences of the United States of America.

776 MODELING INTERFERON-ALPHA MEDIATED INHIBITION KINETICS OF INTRACELLULAR AND EXTRACELLULAR HCVRNA DURING HCV INFECTION IN VITRO

Alan S. Perelson, Harel Dahari, Jeremie Guedj, 2011 .

Quantifying the Diversification of Hepatitis C Virus (HCV) during Primary Infection: Estimates of the In Vivo Mutation Rate

Alan S. Perelson, Hui Li, Tanmoy Bhattacharya, 2012, PLoS pathogens.

Hepatitis C Viral Dynamics in Vivo and the Antiviral Efficacy of Interferon-α Therapy

Alan S. Perelson, Harel Dahari, A. Perelson, 1998 .

Self-Organization in Nonequilibrium Systems. From Dissipative Structures to Order Through Fluctuations.G. Nicolis , I. Prigogine

Alan S. Perelson, A. Perelson, 1978 .

Quantification of Cell Turnover Kinetics Using 5-Bromo-2′-deoxyuridine1

Alan S. Perelson, Sebastian Bonhoeffer, A. Perelson, 2000, The Journal of Immunology.

Effects of Aging on Influenza Virus Infection Dynamics

Alan S. Perelson, Michael Meyer-Hermann, Esteban A. Hernandez-Vargas, 2014, Journal of Virology.

Pharmacodynamics of Antiretroviral Agents in HIV-1 Infected Patients: Using Viral Dynamic Models that Incorporate Drug Susceptibility and Adherence

Alan S. Perelson, Hulin Wu, Song Yu, 2006, Journal of Pharmacokinetics and Pharmacodynamics.

Estimating average cellular turnover from 5–bromo–2'–deoxyuridine (BrdU) measurements

Alan S. Perelson, A. Perelson, D. Ho, 2003, Proceedings of the Royal Society of London. Series B: Biological Sciences.

Two theoretical problems in immunology: AIDS and epitopes

Alan S. Perelson, 1999 .

Hepatitis C Viral Kinetics in the Era of Direct Acting Antiviral Agents and Interleukin-28B

Alan S. Perelson, Harel Dahari, Jeremie Guedj, 2011 .

Theoretical and Experimental Insights into Immunology

Alan S. Perelson, Gérard Weisbuch, G. Weisbuch, 1992, NATO ASI Series.

Probability of Self-Nonself Discrimination

Alan S. Perelson, Jerome K. Percus, Ora E. Percus, 1992 .

Applications of Optimal Control Theory to Immunology

Alan S. Perelson, A. Perelson, 1978 .

Proof-of-Principle for Immune Control of Global HIV-1 Reactivation In Vivo

Alan S. Perelson, Paul R. Grant, Deenan Pillay, 2015, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

Rapid Clearance of Simian Immunodeficiency Virus Particles from Plasma of Rhesus Macaques

Alan S. Perelson, Sebastian Bonhoeffer, Peter J. Dailey, 1999, Journal of Virology.

Turnover Rates of B Cells, T Cells, and NK Cells in Simian Immunodeficiency Virus-Infected and Uninfected Rhesus Macaques1

Alan S. Perelson, A. Perelson, D. Ho, 2003, The Journal of Immunology.

Multitype Branching Processes

Alan S. Perelson, Catherine A. Macken, A. Perelson, 1985 .

Viral Dynamics during Primary Simian Immunodeficiency Virus Infection: Effect of Time-Dependent Virus Infectivity

Alan S. Perelson, Ruy M. Ribeiro, Naveen K. Vaidya, 2010, Journal of Virology.

Modeling the effects of updating the influenza vaccine on the efficacy of repeated vaccination

Alan S. Perelson, Stephanie Forrest, Alan S. Lapedes, 2000 .

Viral kinetic modeling: state of the art

Alan S. Perelson, Laetitia Canini, A. Perelson, 2014, Journal of Pharmacokinetics and Pharmacodynamics.

Nonlinear dynamics of immunogenic tumors: Parameter estimation and global bifurcation analysis

Alan S. Perelson, A. Perelson, M. Taylor, 1994 .

Th1/Th2 differentiation and cross-regulation

Alan S. Perelson, Michael A. Fishman, A. Perelson, 1999, Bulletin of mathematical biology.

Viral Blip Dynamics during Highly Active Antiretroviral Therapy

Alan S. Perelson, Christine Hogan, A. Perelson, 2003, Journal of Virology.

Dynamics of one-pass germinal center models: Implications for affinity maturation

Alan S. Perelson, Mihaela Oprea, A. Perelson, 2000, Bulletin of mathematical biology.

Feedback regulation of T cell development: manifestations in aging

Alan S. Perelson, Ramit Mehr, A. Perelson, 1996, Mechanisms of Ageing and Development.

A Novel Antiviral Intervention Results in More Accurate Assessment of Human Immunodeficiency Virus Type 1 Replication Dynamics and T-Cell Decay In Vivo

Alan S. Perelson, A. Perelson, D. Ho, 2003, Journal of Virology.

Quantifying the Early Immune Response and Adaptive Immune Response Kinetics in Mice Infected with Influenza A Virus

Alan S. Perelson, Hulin Wu, Martin S. Zand, 2010, Journal of Virology.