About

I lead the Informatics Infrastructure team of the Tree of Life programme of the Wellcome Sanger Institute.

The team’s mission is to enable Tree of Life operations and research by providing data management, informatics, and infrastructure solutions. We oversee the implementation and delivery of the genome assembly pipelines, implement large-scale genome analyses for the faculty teams, and curate the metadata held in the various production systems.

My experience is in:

Software development
Computational biology, Genome analysis.
Comparative genomics, Evolution, Phylogenetics.
Genome assembly and annotation
Sequence alignment, Sequence classification, Homology inference.
Algorithmics, Graph theory, Code optimization.
Algorithms for 3D rendering.
Project management

And I love:

🔭 Reconstruction of protein phylogenetic trees and inference of orthologies
🔮 Reconstruction of ancestral genomes
🌳 Tree of Life projects
👥 Whole genome duplications
⚡ High-throughput computing

Background

I graduated in 2006 from both the Institut d'Informatique d'Entreprise and the Université d'Évry. I completed in 2010 a PhD in bioinformatics in the Dyogen group under the supervision of Hugues Roest Crollius, reconstructing the gene order and the chromosome structure of extinct vertebrate species. The method was validated using simulations, and the results are available on the Genomicus browser and updated with the Ensembl releases. The algorithms are described in my 🎓 thesis (in French).

I joined the comparative-genomics team of the Ensembl project (aka Compara) in 2011, under the leadership of Javier Herrero. My initial focus was the pipeline that builds protein-trees for the Ensembl release, but I since worked on every aspect of the Perl API and every pipeline, and I gained extensive knowledge of the eHive workflow manager.

I led the team from Javier's departure in 2013 to 2019, leading a profound automation of all our production processes. I then acted as a Principal Developer, overseeing and guiding the software development, during a transition phase with the new management.

I joined the Wellcome Sanger Institute in 2021 to create the Informatics Infrastructure team of the Tree of Life programme.

Contact

Various profile pages with contact details 👋:

Send me a message in 🇬🇧 English or in 🇫🇷 French. Unfortunately, my notions of 🇪🇸 Spanish and 🇰🇷 Korean are too limited for professional settings.