Alexander McKim

A module-based approach for post-omics, post-GWAS network-based gene classification

The paper introduces ModGenePlexus, a network-based gene classification method that improves disease gene discovery by decomposing gene lists into modules and combining module-specific classifiers.

amR: an R package suite to predict antimicrobial resistance in bacterial pathogens

The paper introduces amR, an R package suite for predicting antimicrobial resistance in bacterial pathogens using genome data and interpretable machine learning models.

A genetically informed atlas of transcriptomic programs from massive human RNA-seq compendia

CLAMP integrates genetic associations and drug signatures with large-scale RNA-seq data to identify interpretable gene modules linked to complex diseases.

A network-based approach for isolating the chronic inflammation gene signatures underlying complex diseases towards finding new treatment opportunities

The paper presents a computational approach to identify gene signatures of chronic inflammation in complex diseases and prioritize drugs for new therapeutic opportunities.