Robert D. Patton

Gene expression inference from cell-free DNA using uncertainty-aware deep learning

This paper develops a deep learning framework to infer gene expression from cell-free DNA, improving reliability and enabling functional genomics in precision oncology.

PYM1 limits non-canonical Exon Junction Complex occupancy in a gene architecture dependent manner to tune mRNA expression

This study shows PYM1 regulates EJC occupancy in a gene architecture-dependent manner, affecting mRNA stability and decay, and is exploited by flaviviruses to alter host mRNA regulation.

Mammalian UPF3A and UPF3B activate NMD independently of their EJC binding

The paper shows that UPF3A and UPF3B can activate NMD independently of EJC binding in human cells, challenging the idea that UPF3 is solely a bridge between the EJC and UPF complex.

Stop codon-proximal 3′UTR introns in vertebrates can elicit EJC-dependent Nonsense-Mediated mRNA Decay

The paper identifies stop codon-proximal 3′UTR introns as a new class of EJC-regulated NMD targets that influence vertebrate development.

The exon junction complex undergoes a compositional switch that alters mRNP structure and nonsense-mediated mRNA decay activity

The paper shows the exon junction complex (EJC) undergoes a compositional switch from an SR-rich to an SR-devoid form, altering mRNP structure and NMD activity.