Nitin S. Baliga

The paper shows adenylyl cyclase agonists inhibit Mtb growth by rerouting carbon to virulence lipids through ETC blockade and cAMP-driven metabolic remodeling.

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

The paper uses controlled enrichments along ecological gradients to uncover eco-evolutionary forces shaping microbial biodiversity in subsurface sediment.

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

The paper investigates heat-induced alternative splicing changes in the coral Acropora cervicornis under different thermal stress conditions and finds that 40% of genes undergo alternative splicing, with intron retention dominating responses.

This study identifies pathway partitioning as a mechanism for complete denitrification in microbial communities and shows how imbalances in substrate utilization can disrupt cooperativity and lead to nitrous oxide emissions.

The paper shows how gene regulatory network topology in glioma stem-like cells influences drug resistance and treatment escape, suggesting strategies to overcome resistance through combinatorial therapies.

The paper uses microbial community-scale metabolic models to predict C. difficile engraftment risk and assess probiotic therapy efficacy in the human gut.

This study integrates omics data to reveal post-transcriptional regulation mechanisms in Halobacterium salinarum NRC-1, showing 54% of genes are regulated by multiple mechanisms and 7% show conditional regulation.

The paper uses single-cell analysis of GBM patient samples and xenografts to identify regulatory networks driving treatment-induced tumor evolution and proposes a framework for precision medicine.

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

The paper identifies 141 genetic programs in multiple myeloma that predict disease outcomes and reveal mechanisms of relapse and therapy response.

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

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

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 identifies a plastid antiporter in Thalassiosira pseudonana that shows differential transcript levels under elevated CO2, suggesting it could serve as a bioindicator of diatom resilience.

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

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

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.

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.

The paper builds genome-scale transcriptional regulatory networks for mouse and human striatum, identifying SMAD3 as a key regulator in Huntington’s disease.