Julia V. Ponomarenko

This study benchmarks four commercial LR snRNA-seq workflows, finding 10x Genomics 3' and 5' to be the most balanced for isoform-resolved single-nucleus transcriptomics.

AMaNITA provides an end-to-end workflow for analyzing nanopore native tRNA sequencing data, enabling differential abundance and modification stoichiometry analysis.

SeqTagger demultiplexes direct RNA nanopore sequencing datasets with high precision and recall, supporting multiple chemistries and library types.

ExOrthist infers exon orthologies across species by analyzing exon sequences and their surrounding intron context, enabling analysis at any evolutionary distance.

This paper presents a high-sensitivity targeted method to measure pri-miRNA processing efficiency in clinical samples and identifies 24 microRNAs with significant changes in processing efficiency between normal liver and hepatocellular carcinoma.

The paper introduces a scalable workflow for analyzing Oxford Nanopore direct RNA sequencing data, enabling RNA modification detection and polyA tail length estimation.