Tamer Butto

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

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.

The paper shows that New1 prevents ribosomal collisions and subsequent mRNA degradation in yeast by no-go decay, protecting essential genes from downregulation.

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.

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

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

This study identifies mTORC1 as a transcriptional regulator of cholesterol biosynthesis genes in developing neurons, linking mTOR activity to cholesterol production and neurodevelopmental disorders.