T. N. Nguyen

The T Cell Receptor beta Chain Repertoire of Tumor Infiltrating Lymphocytes Improves Neoantigen Prediction and Prioritization

This paper develops a machine learning model that integrates TCRβ and pHLA binding data to improve neoantigen prioritization in colorectal cancer, showing better performance than existing tools.

Genomic islands of speciation harbor genes underlying coloration differences in a pair of Neotropical seedeaters

The paper identifies genomic regions associated with coloration differences between two Neotropical seedeaters, suggesting these genes contribute to reproductive isolation.

Control of mitophagy initiation and progression by the TBK1 adaptors NAP1 and SINTBAD

This study identifies NAP1 and SINTBAD as regulators of mitophagy, inhibiting OPTN-driven initiation while promoting NDP52-driven progression.

A single-dose intramuscular immunization of pigs with lipid-nanoparticle DNA vaccines based on the hemagglutinin antigen confers complete protection against challenge infection with the homologous influenza virus strain

This study shows that lipid-nanoparticle DNA vaccines encoding hemagglutinin protect pigs fully against homologous IAV-S challenge with minimal viral shedding.

Improvement in Neoantigen Prediction via Integration of RNA Sequencing Data for Variant Calling

This study improves neoantigen prediction by integrating RNA sequencing data with DNA sequencing to identify more immunogenic neoantigens in colorectal cancer patients.

Structure and activation of the human autophagy-initiating ULK1C:PI3KC3-C1 supercomplex

The paper determines the cryo-EM structure of the human ULK1C core and its complex with PI3KC3-C1, revealing structural changes that suggest a mechanism for autophagy initiation through supercomplex formation.

The Genetic Landscape of a Metabolic Interaction

The paper quantifies how DHFR mutations affect TYMS growth rates using deep mutational scanning, revealing metabolic context's role in enzyme mutational tolerance.

Temporal landscape of mitochondrial proteostasis governed by the UPRmt

This study develops MitoPQ, a functional proteomics framework, to analyze how the UPRmt maintains mitochondrial proteostasis during stress and identifies oxidative phosphorylation as a key target.

Unconventional Initiation of PINK1/Parkin Mitophagy by Optineurin

This study identifies an unconventional mechanism by which OPTN initiates mitophagy through TBK1 and the class III phosphatidylinositol 3-kinase complex I, distinct from the FIP200-ULK1/2 pathway.

Postural Sway is not affected by estrogen fluctuations during the menstrual cycle

This study examines the relationship between estrogen levels and postural sway in women, finding no significant effect of menstrual cycle phase or estradiol levels on sway.

Structural basis for ATG9A recruitment to the ULK1 complex in mitophagy initiation

The paper determines the structure of ATG9A's C-terminal tail interacting with the ULK1 complex's ATG13:ATG101 HORMA dimer, revealing how this interaction facilitates mitophagy.

Single-Cell Stochastic Modeling of the Action of Antimicrobial Peptides on Bacteria

This study develops a stochastic model to analyze how antimicrobial peptides neutralize bacteria, showing that both entry and inhibition processes are critical for their effectiveness.

Atg4 family proteins drive phagophore growth independently of the LC3/GABARAP lipidation system

This study reveals that Atg4 family proteins drive autophagosome formation independently of Atg8 lipidation and protease activity, using AI-driven 3D electron microscopy.

ACE2-Variants Indicate Potential SARS-CoV-2-Susceptibility in Animals: An Extensive Molecular Dynamics Study

The paper uses molecular dynamics simulations to analyze SARS-CoV-2 ACE2 variants and predicts susceptibility in red squirrels and specific mutations in dogs, rats, and mice.

Unveiling Prognostics Biomarkers of Tyrosine Metabolism Reprogramming in Liver Cancer by Cross-platform Gene Expression Analyses

This study identifies five downregulated tyrosine catabolic enzymes in HCC and links their low expression to poorer patient survival.

BiasDB: A Comprehensive Database for Biased GPCR Ligands

BiasDB compiles and analyzes known biased GPCR ligands, offering a resource for medicinal chemistry and pharmacology.

Genomic surveillance for hypervirulence and multi-drug resistance in invasive Klebsiella pneumoniae from south and southeast Asia.

This study identifies diverse antimicrobial resistant and hypervirulent Klebsiella pneumoniae strains in South and Southeast Asia, highlighting the convergence of AMR and virulence genes.