Agin Ravindran

SWARM resolves nanopore signal interference between RNA modification types and reveals splicing-shaped pseudouridylation

SWARM improves detection of RNA modifications by reducing false positives and reveals new splicing-related pseudouridylation patterns.

FracFixR: A compositional statistical framework for absolute proportion estimation between fractions in RNA sequencing data

FracFixR estimates original RNA fraction proportions from fractionated sequencing data, correcting biases and enabling accurate differential expression analysis.

High-Accuracy RNA Integrity Definition for Unbiased Transcriptome Comparisons with INDEGRA

The paper introduces DTI, a new RNA integrity metric based on nanopore sequencing, and the INDEGRA package to correct biases and enable accurate transcriptome comparisons.

The conserved landscape of RNA modifications and transcript diversity across mammalian evolution

The paper presents a long-read RNA sequencing atlas across mammals, revealing conserved transcript complexity and m6A modifications, and their evolutionary roles.

Biochemical-free enrichment or depletion of RNA classes in real-time during direct RNA sequencing with RISER

RISER enables real-time RNA class enrichment or depletion during direct RNA sequencing, improving detection of low-abundance RNAs by reducing dominant RNA reads.

Prediction of m6A and m5C at single-molecule resolution reveals a cooccurrence of RNA modifications across the transcriptome

CHEUI predicts m6A and m5C modifications at single-molecule resolution, revealing co-occurrence of these modifications in mRNAs across cell lines and tissues.