Peter C. Dedon

This study examines how tRNA reprogramming and codon bias link translation to metabolic state in Enterococcus faecalis across growth phases.

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.

This paper develops an ion-pair-free capillary HILIC-MS workflow for RNA modification mapping, enabling sensitive detection of modifications in tRNAs and rRNAs without contaminating the MS system.

This study identifies MnmA as a key enzyme that regulates codon-dependent stress response systems in E. coli by affecting tRNA modifications and gene expression.

The paper benchmarks cross-platform RNA modification quantification using LC-MS/MS and finds that harmonized workflows and SILIS normalization improve reproducibility across different instrument types.

The paper benchmarks MS-Seq for human 28S rRNA analysis, showing reproducible results across platforms but highlighting gaps in coverage and ambiguity.

This paper evaluates standalone Oxford Nanopore sequencing for foodborne pathogen surveillance, showing it can achieve high accuracy with quality control tools like alpaqa.

This study maps tRNA modifications in Streptococcus mutans and S. pneumoniae, revealing shared losses and clade-specific adaptations in modification genes and metabolic strategies.

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

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

The paper describes the creation of SINERGY, a synthetic sourdough starter using engineered microbial consortia with division-of-labor modules for biosensing and drug delivery.

This study identifies artemisinin's mechanism by showing it disrupts tRNA modifications and biosynthesis in Plasmodium falciparum.

The paper profiles tRNA modifications in Pseudomonas aeruginosa to uncover regulatory networks and validate gene annotations.

The paper shows that loss of s2U tRNA modification in Yersinia pseudotuberculosis leads to antibiotic tolerance by reducing ribosomal protein translation.

This study investigates age- and pathology-dependent changes in the epitranscriptome and translational dysfunction in a tauopathy mouse model, revealing significant alterations in tRNA biology and codon usage patterns.

This paper identifies N6-methyladenosine (m6A) as a mechanism enabling malaria parasites to rapidly restructure protein synthesis during transmission, dependent on temperature changes and the m6A-binding protein YTH.2.

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

The paper develops a method to map 5'-aldehyde termini in DNA at single-nucleotide resolution, revealing a preference for adenine bases and linking these lesions to genomic features and chromatin accessibility.

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.

This study identifies genetic interactions among tRNA modification genes in E. coli K12, revealing synthetic lethal pairs and condition-dependent phenotypes.

This study identifies a unique evolutionary pathway in Bartonella henselae for queuosine salvage, showing it can use both preQ1 and q, unlike other pathogens.

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

This paper identifies a novel pathway for mnm5s2U synthesis in Gram-positive bacteria, revealing alternative biosynthetic mechanisms involving the MnmL enzyme.

The paper maps tRNA modifications and their synthesis genes in two Bartonella species, identifying gene reductions linked to reductive evolution.

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

This study shows that Angiogenin regulates mitochondrial stress and function by generating tRNA-derived fragments and altering tRNA modifications.

The paper shows that ROS-induced translational bias during brown adipogenesis supports mitochondrial biogenesis by preferentially translating G/C-ending codons through tRNA modification.

The paper shows that tRNA modifications influence tissue-specific mRNA translation and codon optimization by analyzing tRNA and mRNA data from seven mouse tissues.

The paper identifies four new 7-deazaguanine derivatives in phages and characterizes enzymes involved in their biosynthesis and insertion into DNA.

This study shows that m6A accumulation correlates more strongly with MAPT pathology than beta-amyloid in an Alzheimer's mouse model.