معرفی
Thomas Cokelaer is a researcher at the Institut Pasteur, affiliated with the Bioinformatics and Biostatistics HUB and based at the Platform Biomics. Since October 2018, he has led the SALSA (dry-lab) group, focusing on bioinformatics software development and data analysis. His interdisciplinary background spans astronomy, plant modeling, systems biology, and drug discovery.
- Institution: Institut Pasteur
- Unit: Bioinformatics and Biostatistics HUB
- Platform: Platform Biomics
- Group: SALSA (dry-lab group) leader
His research interests center on bioinformatics, next-generation sequencing (NGS) analysis, machine learning, data visualization, and reproducible research. He develops and maintains several widely used open-source tools including Sequana (NGS pipelines), BioServices (biological web services), Bioconvert (format conversion), Sequanix (GUI for Snakemake), and GDSCTools (pharmacogenomics). He is deeply committed to promoting reproducibility in computational research through initiatives like reprohackathons.
The recent publications reflect a strong trend in computational biology, with a focus on developing bioinformatics methodologies, improving data analysis workflows, and applying these tools to diverse biological problems such as fungal pathogenesis, cancer pharmacogenomics, mitochondrial metabolism, and viral evolution. The work spans genomics, transcriptomics, systems biology, and software engineering.
He has contributed to numerous scientific software projects as Principal Investigator, including Sequana, Bioconvert, GDSCTools, DREAMTools, and Sequanix. He has also taught courses in scientific programming with Python and reproducible data analysis at the Institut Pasteur.
His collaborative network includes researchers from EMBL-EBI, Sanger Institute, INRIA, and international partners within the Pasteur Network. The SALSA group hosts master’s students and visiting researchers annually.
