Charlotte Capitanchik

Parnet is a CLIP-seq-based foundation model for RNA sequence representation learning that outperforms existing methods in binding profile prediction and generalizes across tasks.

This study shows PRMT activity regulates 3' UTR shortening in proliferating cells through alternative polyadenylation, impacting cancer and immune-related diseases.

Flow provides a web platform and database for managing and analyzing large-scale bioinformatics data, addressing challenges in data processing, quality, and accessibility.

clipplotr is a command-line tool for visualizing and comparing CLIP data with annotations and functional genomic data, producing publication-quality figures.

The paper introduces PEKA, a tool for analyzing CLIP data to assess motif specificity, and shows that technical biases affect motif detection.

The paper introduces Nanocompore, a method to detect RNA modifications using Nanopore direct RNA sequencing, validated on human polyA+ RNAs and non-coding RNAs.

psiCLIP identifies dynamic RNA binding patterns of spliceosomal helicases before and after exon ligation, revealing their interactions with auxiliary factors.