Shane R. Byrne

Oncogenes have the most distinct codon biases in the genome and codon signatures that oppose tumor suppressor genes

The paper compares codon usage bias between oncogenes and tumor suppressor genes in humans and mice, finding distinct patterns in humans and less distinct in mice.

Synonymous codon usage defines functional gene families

The paper defines functional gene families in S. cerevisiae by analyzing codon usage patterns using a new statistical method called ASCS.

Phosphorothioate DNA modification by BREX Type 4 systems in the human gut microbiome

The paper identifies new phosphorothioate DNA modification systems in the human gut microbiome using genomic and mass spectrometric analysis.

Temporal dynamics and metagenomics of phosphorothioate epigenomes in the human gut microbiome

The paper characterizes phosphorothioate (PT) modifications in the human gut microbiome using metagenomics and mass spectrometry, revealing temporal dynamics and species-specific patterns.

Genes and Pathways Comprising the Human and Mouse ORFeomes Display Distinct Codon Bias Signatures that Can Regulate Protein Levels

The paper analyzes codon bias in human and mouse ORFeomes to identify species-specific pathways regulated by translation, showing that extreme codon bias affects protein levels in transcription factors.

PT-seq: A method for metagenomic analysis of phosphorothioate epigenetics in complex microbial communities

PT-seq is a high-sensitivity method for mapping phosphorothioate DNA modifications in complex microbial communities and metagenomic identification of PT-containing microbes.

Translational response to mitochondrial stresses is orchestrated by tRNA modifications.

The paper shows that tRNA modifications regulate the translational response to mitochondrial stress by altering codon decoding and pathway activity.