Maxwell Lewis Neal

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.

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.

CD4-mediated immunity shapes neutrophil-driven tuberculous pathology

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

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.

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.

NLIMED: Natural Language Interface for ModelEntity Discovery in Biosimulation ModelRepositories

NLIMED converts natural language queries into SPARQL to discover model entities from biosimulation model repositories.

SBMate: A Framework for Evaluating Quality of Annotations in Systems Biology Models

SBMate evaluates annotation quality in systems biology models using coverage, consistency, and specificity metrics on 1,000 BioModels repository models.

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.

Model Annotation and Discovery with the Physiome Model Repository

The paper annotates biological models with semantic annotations and develops a web tool to help users discover relevant models in the Physiome Model Repository.