Jan Fostier

The paper identifies trans-eQTL hotspots in T. urticae linked to host plant fitness using a multiparental RNA-seq approach.

This paper introduces HaploDetox, a method for de novo bacterial haplotype reconstruction using a Conditional Random Field approach on de Bruijn graphs, achieving improved SNP phasing accuracy.

Columba is a high-performance lossless aligner for Illumina sequencing data that outperforms existing tools in speed and memory efficiency, particularly for large datasets.

This paper introduces a run-length compressed metagenomic read classification method that outperforms existing tools in accuracy and runtime while maintaining efficient memory usage.

The paper introduces b-move, a bidirectional extension of the move structure for run-length compressed indices, achieving faster character extensions than existing methods while maintaining memory efficiency.

elPrep 5 improves variant calling speed by parallelizing the GATK Best Practices pipeline, achieving 8-16x faster runtime than GATK 4 on whole-exome and whole-genome data.

elPrep 4 is a multithreaded framework for processing sequence alignment files, offering faster and more efficient variant calling preparation steps compared to GATK 4, SAMtools, and Picard.