Mikaël Salson

REINDEER2 provides a scalable, dynamic abundance index for RNA datasets, achieving faster construction and accurate abundance recovery.

This study evaluates eight long-read mapping tools for viral genomic data, finding that most struggle with read edges and performance decreases with default settings.

The paper introduces a framework to efficiently enumerate k-mers from a collection of references based on metadata constraints, using a specialized data structure and demonstrating it on microbial and RNA-seq data.

The paper introduces a k-mer-based method to quantify RNA sequences from large RNA-seq datasets, demonstrating its accuracy for variant RNA detection in cancer cell lines.

FiLT3r is an alignment-free algorithm that accurately detects FLT3-ITDs in HTS data with high precision and low resource usage.

The paper surveys computational methods for indexing and querying large sequencing datasets using k-mer-based data structures.

REINDEER indexes k-mer presence and abundance across large sequencing datasets efficiently, processing 2,585 human RNA-seq experiments in 45 hours with 56 GB RAM.

This paper introduces DE-kupl, a k-mer-based method to capture RNA variation without a reference, identifying novel transcripts and biological events from RNA-seq data.