Group & supervision
I co-lead the Atelier de Bioinformatique team of ISYEB with Lucie Bittner.
PhD students
Jeremy Rousseau (2023 – ) — Structural and functional annotation of dinoflagellate sequences. PhD funding from the Institute of Computing and Data Sciences (ISCD), Sorbonne Université. Co-supervised with Lucie Bittner.
Martin Romei (2018 – 2021) — Structural evolution of proteins. PhD funding from the Interface Pour le Vivant programme, Sorbonne Université. Co-supervised with Guillaume Lecointre and Jacques Chomilier. Two publications came out of it, in Evolution (2022) and the Journal of Molecular Evolution (2023).
Postdoctoral and engineering staff
Hugo Talibart (2021 – 2022), postdoctoral researcher — Potts models for sequence–structure alignment of proteins. Funded by the Émergence programme, Sorbonne Université.
Suvethigaa Shanthirabalan (2016 – 2017), research engineer — A statistical potential for simulating protein evolution. Funded by ANR TempoMut. Led to a publication in Proteins (2018).
Internships supervised
| Year | Student | Level | Topic | Co-supervisor |
|---|---|---|---|---|
| 2026 | Defne Ozguven | MSc MIND, Sorbonne Université | Clustering large protein graphs | H. Naacke |
| 2026 | Salma Mbarki | MSc Bioinformatics, Paris-Saclay | Genomic analysis-based serotyping method development | E. Duchaud, P Debeljak |
| 2025 | Timéo Hennebelle | MSc AMI2B, Paris-Saclay & AgroParisTech | Identifying novel protein structures in teleosts | G. Lecointre |
| 2025 | Rim Kais | MSc BIM, Sorbonne Université | Epistasis in protein sequences: can different types of constraint be distinguished? | G. Achaz |
| 2024 | Christophe Ye | IMT Nord Europe, 2nd year | Deep learning structure prediction for analysing fold distribution | |
| 2024 | Rim Kais | MSc1 BIM, Sorbonne Université | Analysing and predicting the effect of mutations on structures | |
| 2024 | Loralie Rigaud | MSc1 BIM, Sorbonne Université | Protein structure alignment | |
| 2023 | Jeremy Rousseau | MSc2, Université de Rennes 1 | Distribution of protein folds in metagenomes | L. Bittner |
| 2022 | Clara Toussaint | MSc1, Université Paris-Saclay | Distribution of amino acid co-occurrences | |
| 2022 | Jeremy Rousseau | MSc1, Université de Rennes 1 | Distribution of protein folds in metagenomes | L. Bittner |
| 2022 | Pauline Turk | MSc AMI2B, Paris-Saclay & AgroParisTech | Deep learning and protein evolution | |
| 2022 | Sophie Chareyre | L3, CNAM | Superposition of protein structures | |
| 2021 | Théo Jamay | MSc1 Bioinformatics, Université de Paris | Distribution of protein folds in the tree of life | |
| 2020 | Nicolas Dibot | MSc1 Bioinformatics, Université de Nantes | Effect of point mutations on protein structures | J. Chomilier |
| 2020 | Pierre Imbert | MSc1 Bioinformatics, Université de Paris | Combination of structural domains in genomes | |
| 2020 | Miara Rakotomavo | MSc2 Bioinformatics, Université de Paris | Conservation of contacts in protein structures | |
| 2019 | Emile Faure | MSc1 BIM, Sorbonne Université | HMM computation for fold recognition | |
| 2019 | Huiyuan Li | 2nd-year BSc computer science, Sorbonne Université | Adapting the KMR motif-search algorithm to contact maps | |
| 2018 | Ophélie Foucault & André Lanrezac | MSc1 BIM, Sorbonne Université | Improving Yakusa, a structural BLAST | |
| 2018 | Martin Romei | MSc2 BIM, UPMC | Structural evolution of proteins | G. Lecointre |
| 2018 | Mojgan Karimi | MSc2 BIM, UPMC | Identifying horizontal transfers in Penicillium | |
| 2017 | Clément Joubert | MSc2 BIM, UPMC | Evolution of protein dynamics | |
| 2016 | Steven Fletcher | MSc2 BIM, UPMC | Structural study of co-evolution in proteins | |
| 2016 | Mojgan Karimi | MSc1 BIM, UPMC | Testing a new method for detecting horizontal transfers | |
| 2015 | Benjamin Roques | MSc1, AgroParisTech | Exact multiple sequence alignment method | G. Achaz |
| 2015 | Baptiste Mossoti | MSc1 BIM, UPMC | Structural motif search in viral metagenomes | |
| 2013 | Meriem Aziz | MSc1 ISSD, Paris 7 | Structural study of insertions and deletions in proteins | |
| 2012 | Damien Monet | 3rd-year BSc PIMA (mathematics & computer science) | Exact multiple sequence alignment method | G. Achaz |
| 2007 | Stéphane Peugeot | MSc2, Master Biologie Informatique, Paris 7 | Functional annotation of orphan genes in Plasmodium falciparum |
Committees and juries
- Member of PhD advisory committees, as doctoral school representative for ED227 (3) or as an invited member (2).
- Member of PhD juries as examiner (3) or reviewer (1), and of one habilitation jury.
Interested in an internship?
Every year I host master’s-level interns, and occasionally undergraduates, on topics related to the evolution of protein structures, structural and functional annotation, or alignment methods. A dual background in biology and computer science is not required, but a genuine appetite for programming is.
Write to me with a CV and a few lines on what interests you in these topics — that last part matters most.