Mario L. Arrieta‐Ortiz

Monocyte-amplified transcriptional signatures of human diseases

The paper introduces monocyteMINER, a method using monocyte transcriptomes to discover disease-specific biomarkers, showing improved performance for atherosclerosis and tuberculosis.

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.

Predictive regulatory and metabolic network models for systems analysis of Clostridioides difficile

The paper develops regulatory, metabolic, and integrated models for C. difficile to understand its colonization mechanisms and interactions with the gut microbiota.

MtrA regulation of essential peptidoglycan cleavage in Mycobacterium tuberculosis during infection

This study identifies MtrA as a critical regulator of peptidoglycan cleavage in Mtb, essential for survival under acidic stress and a potential drug target.

Quantitative prediction of conditional vulnerabilities in regulatory and metabolic networks of Mycobacterium tuberculosis

This paper introduces PRIME, a model predicting environment-specific vulnerabilities in Mtb's regulatory and metabolic networks, validated through genome-wide fitness screens.

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.

Disrupting the ArcA regulatory network increases tetracycline susceptibility of TetR Escherichia coli

This study shows that disrupting the ArcA regulatory network in TetR E. coli increases tetracycline susceptibility, suggesting a strategy to re-sensitize AMR pathogens.

Inference of bacterial small RNA regulatory networks and integration with transcription factor driven regulatory networks

The paper infers bacterial sRNA regulatory networks and integrates them with transcription factor networks, identifying novel sRNA-mRNA interactions in multiple bacterial species.

Intricate genetic programs controlling dormancy in Mycobacterium tuberculosis

The paper identifies a six-state genetic program in Mycobacterium tuberculosis that enables entry into and exit from hypoxia-induced dormancy through high-resolution transcriptional time-course analysis.