R. Ke

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.

Influenza A Viral Burst Size from Thousands of Infected Single Cells Using Droplet Quantitative PCR (dqPCR)

This study measures viral burst sizes in thousands of infected cells using dqPCR, finding significant variation in H3N2 and H1N1 strains with a small fraction of cells producing most viruses.

Stratification of viral shedding patterns in saliva of COVID-19 patients

This study stratifies SARS-CoV-2 viral shedding patterns in saliva into three groups with distinct durations using a mathematical model and clustering, but finds no clear clinical or miRNA biomarkers explaining the differences.

Modeling the emergence of viral resistance for SARS-CoV-2 during treatment with an anti-spike monoclonal antibody

This paper models viral resistance emergence in SARS-CoV-2 treated with anti-spike monoclonal antibodies, showing that target cell replenishment mechanisms can explain high viral rebounds.

How reliable are estimates of key parameters in viral dynamic models?

This study evaluates how reliable parameter estimates are in viral dynamic models when pre-peak viral load data are missing, finding that some parameters are less sensitive to data gaps than others.

Transcriptional Feedback Disruption Yields Escape-Resistant Antivirals

This paper develops feedback-circuit disruptors that inhibit viral replication and prevent resistance evolution in herpesviruses.

A common pattern of influenza A virus single cell gene expression heterogeneity governs the innate antiviral response to infection

This study identifies a common pattern of viral gene expression heterogeneity in influenza A virus that influences host antiviral responses across subtypes.

Report on the spatial spread of defective interfering particles and its role in suppressing infectious particles

The paper develops a spatio-temporal model to study how defective interfering particles suppress infectious virus spread within host tissues.

Coinfection of semi-infectious particles can contribute substantially to influenza infection dynamics

The paper models the role of semi-infectious particles and coinfection in influenza dynamics, finding SIPs significantly contribute to viral load and co-infection is frequent during early infection.

The dynamics of the HIV-1 latent reservoir - considering the heterogeneous subpopulations

This paper develops a mathematical model of HIV-1 latent reservoir subpopulations to explain clinical observations and predict therapeutic interventions.