K. E. Johnson

Optimized Quantification of Intrahost Viral Diversity in SARS-CoV-2 and Influenza Virus Sequence Data

This study evaluates variant calling tools for detecting minority variants in viral sequencing data and provides guidance for accurate quantification of intrahost viral diversity.

Mapping the evolutionary landscape of Zika virus infection in immunocompromised mice.

This study establishes a ZIKV transmission model in immunocompromised mice to investigate factors influencing viral evolution and DVG production.

The industrial solvent trichloroethylene induces LRRK2 kinase activity and dopaminergic neurodegeneration in a rat model of Parkinson's disease

This study shows that trichloroethylene exposure activates LRRK2 kinase and causes dopaminergic neurodegeneration in rats, linking environmental toxins to Parkinson's disease risk.

Integrating multimodal data sets into a mathematical framework to describe and predict therapeutic resistance in cancer

This paper develops a framework integrating single-cell transcriptomic data with longitudinal treatment response data to predict drug resistance in breast cancer, achieving higher predictive accuracy with integrated data.

Expressed barcodes enable clonal characterization of chemotherapeutic responses in chronic lymphocytic leukemia

This paper develops a method to study clonal responses to chemotherapy in CLL by combining barcoding with single-cell RNA sequencing, revealing that rare drug-tolerant clones dominate post-treatment populations.

Stochastic Models for Revealing the Dynamics of the Growth of Small Tumor Populations

This paper presents a stochastic modeling framework to study altered growth dynamics in small tumor populations using high-throughput data.

Cancer cell population growth kinetics at low densities deviate from the exponential growth model and suggest an Allee effect

This paper investigates cancer cell growth at low densities and finds that an Allee effect model better describes growth kinetics than exponential growth, suggesting cooperative behavior among cells.

Thrombocyte inhibition restores protective immunity to mycobacterial infection

This study shows that inhibiting thrombocyte activation improves control of mycobacterial infection by reducing thrombocyte-macrophage interactions and restoring macrophage immunity.