John D. Aitchison

This study shows that subunit vaccination provides better protection than BCG in Mtb-exposed individuals, supported by mouse models and human data.

This study shows that ferroptosis, a form of cell death, is enhanced by a virulent Mtb strain, SA161, and inhibiting it reduces bacterial spread in mice.

This study shows that host oxidative stress primes Mycobacterium tuberculosis for rapid antibiotic resistance evolution by creating permissive genomic backgrounds that accelerate resistance mutations.

This study uses single-cell RNA sequencing to identify immune dynamics distinguishing protection from susceptibility to tuberculosis in mice.

The paper presents a chemical-genetic interaction matrix derived from CRISPR/Cas9 screens, revealing drug mechanisms and genetic architecture in human cells.

This study shows that TOR and heat shock pathways regulate peroxisome biogenesis during proteotoxic stress in yeast and human cells.

This study shows that prior immunity influences tuberculosis lesion structure by modulating neutrophil and T cell responses, leading to different pathological outcomes.

This study shows that APOE protects against severe tuberculosis by limiting neutrophil extracellular trap formation, which exacerbates infection in Apoe-/- mice.

This paper develops a conditional Cas9 system for stage-specific gene editing in P. falciparum, demonstrating its use in disrupting uncharacterized genes and identifying stage-specific phenotypes.

DeleteomeTools predicts gene function by analyzing yeast deletion strain transcriptomes, identifying co-functional genes and confirming novel functional relationships.

The paper uses two computational methods to reconstruct kinase phosphosignaling networks regulating endothelial barrier integrity from temporal data.

perox-per-cell automates image-based quantification of peroxisome features in yeast cells, matching manual counts and enabling high-throughput analysis.

The paper identifies receptor tyrosine kinases (RTKs) that regulate dengue virus infection in hepatocytes and shows their potential as therapeutic targets.

The paper predicts synthetic lethal antiviral targets by analyzing omics data and CRISPR KO screens, finding common targets across SARS-CoV-2 and influenza infections.

The paper demonstrates that viral-induced hypomorphs of GBF1 can be targeted using synthetic lethality to selectively kill virus-infected cells.

This paper introduces CTCC, a method using cryomilling to map chromatin interactions, showing it can generate global contact maps similar to Hi-C but with enhanced signal for stable inter-chromosomal contacts.

The paper develops a gene regulatory network model for Plasmodium falciparum using machine learning, showing it predicts gene expression and identifies correlates of artemisinin resistance.

The paper introduces an Indicator Cell Assay Platform (iCAP) for blood-based diagnostics, demonstrating its ability to detect pre-symptomatic diseases in animal models and early-stage Alzheimer's in humans with high accuracy.

The paper introduces IDREAM, a method that combines gene regulatory and metabolic networks to improve phenotype prediction in yeast, showing better accuracy than existing methods.