About

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

The team’s mission is to enable Tree of Life operations and research by providing data management, bioinformatics, and infrastructure solutions. We implement large-scale genome analysis pipelines for the faculty teams, maintain the production environment (application deployment and pipeline orchestration), and manage and curate metadata across our production systems.

My experience is in:

Software development
Project management and planning
Computational biology and genome analysis
Comparative genomics, evolution, phylogenetics
Sequence alignment, sequence classification, homology inference
Algorithmics and graph theory

I love:

🔭 Reconstruction of phylogenetic trees and inference of orthologies
🔮 Reconstruction of ancestral genomes
🌳 Tree of Life projects
👥 Whole-genome duplications
⚡ High-throughput computing
🧊 Algorithms for 3D rendering
🤖 Code optimisation and assembly

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 with the Dyogen group under the supervision of Hugues Roest Crollius, where I reconstructed gene order and chromosome structure of extinct vertebrate species. The method was validated with simulations; the results are available on the Genomicus browser and are updated with Ensembl releases. The algorithms are described in my 🎓 thesis (in French) and in this 📖 Nature Ecology & Evolution paper.

I joined the comparative-genomics team of the Ensembl project (Compara) in 2011 under the leadership of Javier Herrero. My initial focus was the pipeline that builds protein trees for Ensembl releases, but I later worked on all aspects of the Perl API and its pipelines. I also led the development of eHive, Ensembl’s system for creating and running pipelines on a distributed compute resource. I grew a deep expertise in it, contributed to its development and expansion within Ensembl. eHive was responsible for scheduling and executing in excess of 1,000 CPU years of compute per year.

I led the team from Javier’s departure in 2013 until 2019, overseeing automation of our production processes. In my final year I supported the transition to the next project leader as Principal Developer, continuing to oversee software development.

I joined the Wellcome Sanger Institute in 2021 to create the Informatics Infrastructure team for the Tree of Life programme. I helped shape the team into its current form.

Contact

Various profile pages with contact details 👋:

Send me a message in 🇬🇧 English or in 🇫🇷 French. Feel free to message me in English or French. My Spanish and Korean are limited for professional use.