Mark Helm

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.

DModE provides an end-to-end framework for analyzing Nanopore DRS data, enabling integrated differential expression and modification analysis with automated reporting.

The paper identifies sex-specific changes in the tRNA epitranscriptome in Alzheimer's disease models and human tissue, and develops a tRNA modification score linked to disease severity.

This study introduces NanoRibolyzer, a long-read nanopore sequencing method to map pre-rRNA processing and modification at single-nucleotide resolution, revealing cleavage sites and modification patterns.

This paper demonstrates real-time transcriptomic analysis using nanopore sequencing for quality control and differential expression in various experimental conditions.

ViREn is a two-step method that purifies dengue virus RNA with high purity, revealing a 5-methylcytosine modification mediated by NSUN6 that affects RNA turnover.

This study evaluates improvements in direct RNA sequencing (DRS) using RNA004 chemistry and modified-base-calling models, showing enhanced throughput, accuracy, and detection of RNA modifications in clinical applications.

The paper provides a comprehensive analysis of tRNA modifications in Staphylococcus aureus, revealing species-specific features and decoding dynamics.

This study identifies potent DNMT2 inhibitors through DNA-encoded library screening, revealing a cryptic allosteric binding site and optimizing an inhibitor with low nanomolar affinity.

ModiDeC is a deep-learning classifier that identifies multiple RNA modifications from direct nanopore sequencing, validated on synthetic data and biological samples.

The paper shows that Pus7 mutations reduce tRNA-Asp levels, activating the integrated stress response and glycolytic reprogramming, which contributes to aggressive behavior.

The paper shows that m1A methylation of ND5 mRNA, catalyzed by TRMT10C, leads to translation repression and mitochondrial dysfunction in Alzheimer's disease.

The paper investigates 6mA DNA modification in drosophila, finding it present at very low levels and not erased by TET, suggesting TET acts non-enzymatically.

NanopoReaTA provides a user-friendly tool for real-time RNA-seq analysis of nanopore sequencing data, enabling interactive decision-making during sequencing.

The paper identifies sequence preferences of TET enzymes that target DNA demethylation to bHLH and bZIP transcription factor binding sites.

This study evaluates protein-based docking tools for RNA-ligand docking, identifying active compounds against the preQ1-riboswitch.

The paper identifies new RNA targets of ALKBH8, including additional tRNAs and non-coding RNAs, through transcriptome-wide analysis using HITS-CLIP-seq and RIP-seq.

This study shows that m5C RNA modification in C. elegans affects translation efficiency and adaptation to heat stress by modulating leucine and proline decoding.

The paper presents a comprehensive analysis of AATF's RNA interactions, revealing its role in ribosome biogenesis through binding to pre-rRNA and mRNAs of ribosome factors.

The paper develops a computational method to accurately call methylation in whole-transcriptome bisulfite sequencing data, revealing new methylation patterns in mouse RNAs.

This study shows that marbled crayfish, a parthenogenetic triploid, originated from P. fallax through autopolyploidy and is now an independent asexual species with distinct traits.