John D. Aitchison

Subunit vaccination enhances protection conferred by prior Mycobacterium tuberculosis exposure

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

Modulation of Ferroptosis During Early Mycobacterium tuberculosis Infection Contributes to Beijing Lineage Strain SA161 Virulence

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.

Host oxidative stress primes mycobacteria for rapid antibiotic resistance evolution

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

Single-cell profiling reveals that dynamic lung immune responses distinguish protection from susceptibility to tuberculosis

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

A Chemical-Genetic Interaction Matrix Reveals Drug Mechanism and Genetic Architecture

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

TOR and heat shock response pathways regulate peroxisome biogenesis during proteotoxic stress

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

APOE Protects Against Severe Infection with Mycobacterium tuberculosis by Restraining Production of Neutrophil Extracellular Traps

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

A Conditional Cas9 System for Stage-Specific Gene Editing in P. falciparum

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: Utilizing a compendium of yeast deletion strain transcriptomes to identify co-functional genes

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

Systems-level reconstruction of kinase phosphosignaling networks regulating endothelial barrier integrity using temporal data

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

Automated, image-based quantification of peroxisome characteristics with perox-per-cell

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

Multiple Receptor Tyrosine Kinases Regulate Dengue Infection of Hepatocytes

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

Predicting host-based, synthetic lethal antiviral targets from omics data

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.

Viral protein engagement of GBF1 induces host cell vulnerability through synthetic lethality

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

Cryomilling Tethered Chromatin Conformation Capture reveal new insights into inter-chromosomal interactions

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.

A system-level gene regulatory network model for Plasmodium falciparum

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.

An indicator cell assay for blood-based diagnostics

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.

Combining inferred regulatory and reconstructed metabolic networks enhances phenotype prediction in yeast

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.