Todd M. Lowe

The paper presents the first telomere-to-telomere diploid reference genome of the human embryonic stem cell line H9, revealing genomic features and ancestry.

RNAcentral integrates literature and gene-level data to enhance non-coding RNA sequence analysis and functional understanding.

This study examines tRNA and tRNA-derived RNA (tDR) expression and modification across 19 mouse tissues, revealing tissue-specific patterns and regulatory mechanisms.

This study examines how low-protein and high-fat diets affect tRNA abundance and modifications in multiple mouse tissues using RNA mass spectrometry and OTTR-seq.

This study shows that gammaherpesvirus infection leads to tRNA cleavage, producing tRNA fragments that are regulated by tRNA splicing factors and essential for viral replication.

This study identifies PAPI (encoded by pcnB) as essential for maintaining virulence and AMR plasmid copy number, stability, and bacterial virulence in Yersinia and Shigella.

This study profiles tRNA modifications across nine archaeal species using OTTR-seq, revealing coordinated methylation patterns and lineage-specific divergence in methyltransferase domains.

R2DT is a software platform for visualizing RNA secondary structures with enhanced features like SNP display and template-free visualization.

The paper identifies specialized tRNA-derived small RNAs (tDRs) in early human brain development using cerebral cortex organoids and ARM-seq, revealing dynamic expression patterns and sequence motifs associated with neural-specific tDRs.

The paper identifies the roles of TRMT1 and TRMT1L in tRNA modifications, showing their impact on tRNA stability and function, and links TRMT1 variants to disease.

The paper proposes a standardized ontology for naming tRNA-derived RNAs based on molecular origin to improve inter-study comparisons.

tRAX is a tool for analyzing tRNAs and tRNA-derived small RNAs, demonstrating its effectiveness in characterizing these transcriptomes in mouse tissues.

The paper improves tRNAscan-SE for better detection and classification of tRNA genes across diverse genomes and introduces mitochondrial tRNA detection.

R2DT generates standardised 2D RNA structure diagrams for diverse ncRNA types using a template library, producing a large dataset of visualisations.

The paper describes a SARS-CoV-2 genome browser that integrates molecular data from multiple sources for visualization and analysis.

The paper predicts tRNA gene activity using sequence and genomic context features, finding strong correlations with G+C content and CpG density.

The paper shows tRNA genes have much higher mutation rates than the genome average, driven by transcription-associated mutagenesis and purifying selection.

The paper analyzes antibiotic resistance gene distribution in E. coli isolates, identifying two distinct resistance gene clusters with functional redundancy and widespread horizontal transfer.

The paper analyzes 110 C/D box sRNA families in six Pyrobaculum species, revealing their genomic organization, evolutionary patterns, and functional features through computational and genomic methods.