Language-Informed Basecalling Architecture for Nanopore Direct RNA Sequencing. - Alexandra Sneddon; Pablo Acera Mateos; Nikolay Shirokikh; Eduardo Eyras (MLCB, 2022)

Concepts and methods for transcriptome-wide prediction of chemical messenger RNA modifications with machine learning. - Pablo Acera Mateos; You Zhou; Kathi Zarnack; Eduardo Eyras (Briefings Bioinform., 2023)

R2Dtool: integration and visualization of isoform-resolved RNA features. - Aditya J. Sethi; Pablo Acera Mateos; Rippei Hayashi; Nikolay E. Shirokikh; Eduardo Eyras (Bioinform., 2024)