JoAnne L. Flynn

The paper introduces a method to predict longitudinal outcomes from single-timepoint data using a virtual library of granulomas, applied to tuberculosis in non-human primates.

This study shows that antiretroviral treatment (ART) does not prevent extrapulmonary tuberculosis in SIV/Mtb co-infected macaques, despite suppressing SIV replication.

The study shows that prior Mtb infection protects against reinfection with a genetically distinct strain in macaques, suggesting broad vaccine efficacy across Mtb lineages.

The paper investigates TB relapse in a macaque model, finding that complete sterilization protects against relapse but PET CT cannot predict it, and that Mtb dissemination originates from both lung and lymph nodes.

The paper profiles macrophage diversity in TB granulomas using single-cell RNA sequencing and immunofluorescence in nonhuman primates, identifying distinct subsets and their roles in Mtb infection.

The paper simulates TB antibiotic regimens in a computational model to show rankings are influenced by spatial scale, detection limit, and initial bacterial burden.

This study identifies hypoxia as a key driver of immune dysfunction in TB granulomas, correlating with bacterial persistence.

The paper shows that CD4 T cells and innate CD8+ lymphocytes are essential for IV BCG-induced protection against tuberculosis in macaques.

This paper develops an engineered Mycobacterium tuberculosis strain with kill switches for a safe TB human challenge model, showing rapid clearance and low escape rates.

This study develops a 'suicide' BCG strain that is safely eliminated in immunocompromised hosts but induces stronger immune responses and better protection against Mtb in macaques.

The paper uses Markov Fields to integrate multi-modal immune data from vaccinated macaques, identifying critical immune interactions and predicting perturbation effects.

This study compares intravenous and intradermal BCG vaccination in SIV-infected macaques, finding IV BCG induces stronger airway and lung immune responses, including TRM cells and polyfunctional T cells.

The paper shows that CD4+ T cells reduce inflammation and disease severity during Mtb reinfection by reprogramming CD8+ T cells and innate immune cells.

This study uses multi-omics approaches to analyze myeloid cell diversity in TB granulomas and identifies IFN-γ, TGF-β, and time as factors driving macrophage diversity.

This study shows antibiotic treatment after primary Mtb infection reduces lung inflammation but does not eliminate protection against reinfection in macaques.