Alice Cleynen

T2G converts transcriptome-aligned BAM files to genome coordinates, improving specificity and splice junction accuracy across RNA sequencing technologies.

The paper integrates multi-omic data from yeast to identify translational programs during glucose starvation, revealing convergent cis-regulatory mechanisms in repressed genes.

The paper updates a yeast reference transcriptome using direct RNA sequencing to improve UTR annotation and provides a reusable pipeline for future updates.

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

VX provides a genome and transcriptome viewer with an embedded API and analysis framework enabling script and AI agent interaction.

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

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 paper develops a method to identify prognostic copy-number alterations by integrating segmentation and lasso regularization, showing improved recovery of significant regions and survival prediction in multiple myeloma.