Alan S. Perelson

Defective Viral Genomes Reveal History-dependent Self-regulation of Type I Interferon Dynamics

The paper develops a Bayesian model to show that defective viral genomes modulate type I interferon dynamics by both inducing and suppressing IFN through cumulative exposure, explaining how pandemic viruses evade innate immunity.

A mechanistic basis for CD8+ T cell expansion sensitivity as a predictor of HIV post-treatment control

The paper develops a mechanistic model linking CD8+ T cell expansion sensitivity to HIV post-treatment control, showing strong correlations with Ki-67 and TCF-1 levels.

A generalized resource-allocation growth law reveals mechanisms of differential responses to intermittent androgen deprivation therapy in prostate cancer

This paper develops a generalized resource-allocation growth law to model prostate cancer responses to intermittent androgen deprivation therapy, showing it predicts treatment outcomes and adapts to different schedules.

AZD5582 robustly reactivates latently infected cells and clears the majority of those reactivated from the SIV reservoir

This study quantifies AZD5582's effect on SIV reservoirs in macaques, showing it reactivates 25% of latent cells per dose and clears 60-79% of reactivated cells.

Modeling Phage Therapy

The paper develops a mathematical model to simulate phage therapy success by considering bacterial resistance dynamics and cocktail composition.

A multiscale model of the action of a capsid assembly modulator for the treatment of chronic hepatitis B

The paper develops a multiscale model of CAM treatment in chronic HBV infection, showing HBV RNA is more sensitive to CAM effectiveness than HBV DNA.

Modeling suggests SARS-CoV-2 rebound after nirmatrelvir-ritonavir treatment is driven by target cell preservation coupled with incomplete viral clearance

The paper models viral rebound after nirmatrelvir-ritonavir treatment, finding that target cell preservation and incomplete viral clearance drive rebound, with extended treatment reducing this risk.

Quantification of heterogeneity in human CD8+ T cell responses to vaccine antigens: an HLA-guided perspective

The paper introduces metrics to quantify CD8+ T cell responses to vaccine antigens, considering HLA genetic variation and viral evolution, using Ebola, SARS-CoV-2, and Burkholderia pseudomallei as examples.

Understanding early HIV-1 rebound dynamics following antiretroviral therapy interruption: The importance of effector cell expansion

The paper uses dynamic models to analyze viral rebound after HIV-1 treatment interruption, showing effector cell expansion rate distinguishes post-treatment controllers from non-controllers.

Understanding hepatitis B virus dynamics and the antiviral effect of interferon-alpha treatment in humanized chimeric mice

The paper models HBV kinetics in humanized mice treated with interferon-alpha, lamivudine, or both, revealing biphasic viral decline and distinct treatment effects on HBV DNA synthesis.

Non-latching positive feedback enables robust bimodality by de-coupling expression noise from the mean

The paper investigates how HIV's Tat protein generates bimodal expression through non-latching positive feedback, decoupling noise from mean expression to maintain stochastic bimodality.