Balyn W. Zaro

Ninhydrin as a covalent warhead for chemical proteomic-enabled discovery and selective engagement of reactive arginines

This paper introduces a ninhydrin-based warhead for selectively modifying arginine residues, enabling chemical proteomic studies and therapeutic targeting of reactive arginines.

Resolution of recursive data corruption to transform T-cell epitope discovery

The paper identifies methodological errors in epitope discovery that inflate in silico benchmarks and introduces a model trained on clean data that outperforms existing methods.

Integrative analysis of mRNA stability regulation uncovers a metastasis-suppressive program in breast cancer

The paper identifies a metastasis-suppressive regulatory axis involving RBMS3 and TXNIP by analyzing mRNA stability in breast cancer using a deep-learning framework.

Alveolar Type II Cell-derived MMP1high basal cells promote destructive microcysts in idiopathic pulmonary fibrosis.

The paper identifies MMP1high basal cells derived from alveolar type II cells that contribute to microcyst formation in IPF, suggesting a therapeutic target through MMP inhibition or WNT modulation.

C-terminal tagging, transmembrane domain hydrophobicity, and an ER retention motif influence the secretory trafficking of the inner nuclear membrane protein emerin

The paper identifies sequences affecting emerin's secretory trafficking, showing C-terminal tags and hydrophobic domains influence its lysosomal fate, while an ER retention motif stabilizes it.

Neutrophil TLR2 signaling promotes lipid accumulation and vascular plaque growth

This study shows that neutrophil TLR2 signaling promotes lipid uptake and storage, contributing to atherosclerotic plaque growth.

Phenotypic landscape of a fungal meningitis pathogen reveals its unique biology

The paper characterizes the phenotypic landscape of Cryptococcus neoformans by analyzing gene deletions and their fitness under various conditions, revealing novel biological insights.

Macrophages redeploy functional cancer cell surface proteins following phagocytosis

This study shows that macrophages transfer intact cancer cell surface proteins to their own surface after phagocytosis, which may affect their function and metabolism.

P66 is a bacterial mimic of CD47 that binds the anti-phagocytic receptor SIRPα and facilitates macrophage evasion by Borrelia burgdorferi

This study identifies P66, a bacterial protein mimicking CD47, which binds SIRPα to evade macrophage phagocytosis, and shows its role in Lyme Disease pathogenesis.

Perturbation-aware predictive modeling of RNA splicing using bidirectional transformers

The paper trains bidirectional transformer models to predict RNA splicing using perturbative RNA data, achieving state-of-the-art performance in splice junction prediction.