About me

I'm a PhD student in computer science supervised by Camille Marchet and Jean-Stéphane Varré in the Bonsai team at Univ Lille. I was previously a student at ENS Rennes, I completed a Master's degree in theoretical computer science in the MPRI and also spent a semester at EPFL. (More details in my resume, French version)

I'm interested in algorithmic bioinformatics, with a focus on randomized algorithms and space-efficient data structures. I'm currently working on representations of k-mer sets that preserve locality.

News

• [11/2024] New preprint on hyper-k-mers, a more efficient alternative to super-k-mers!
• [07/2024] Talk at ISMB 2024 in Montreal on CBL, a dynamic index for k-mer sets
• [06/2024] New preprint on constrained enumeration of k-mers using CBL!
• [03/2024] Talk at DSB 2024 in Montpellier about CBL, a dynamic k-mer index
• [01/2024] New preprint on fully dynamic sets of k-mers with high locality!
• [12/2023] Talk at the seminar on Lyndon words (as part of the Lyndex project) at Univ Rouen about using necklaces to build a locality-preserving k-mer index
• [11/2023] Talk at the SeqBIM days in Lille about a dynamic and locality-preserving data structure for k-mer sets
• [11/2023] Talk at the RT MIA workshop on dimensionality reduction at ENS Lyon about locality-preserving representation of sparse k-mer sets
• [10/2023] I'm starting my PhD in the Bonsai team!

Publications

• Conway-Bromage-Lyndon (CBL): an exact, dynamic representation of k-mer sets, with Bastien Cazaux, Antoine Limasset & Camille Marchet, ISMB 2024
  [paper] [slides] [preprint]
• Fractional Hitting Sets for Efficient and Lightweight Genomic Data Sketching, with Timothé Rouzé, Camille Marchet & Antoine Limasset, WABI 2023
  [paper] [slides] [poster]

Preprints

• Hyper-k-mers: efficient streaming k-mers representation, with Lucas Robidou, Yoshihiro Shibuya & Antoine Limasset
  [preprint]
• Constrained enumeration of k-mers from a collection of references with metadata, with Florian Ingels, Mikaël Salson & Camille Marchet
  [preprint]

Teaching

• [2024-2025] Teaching assistant: Algorithms & Complexity
• [2023-2024] Teaching assistant: Information theory
• [2023-2024] Teaching assistant: Javascript

Recent projects

Some of the things I've been developing lately:

• a Rust library to iterate over (mod) minimizers in a DNA sequence
• a Rust library providing fast set operations on sorted iterators
• a Rust library providing a flat hashmap that supports multiple entries per key
• a Rust library providing fully dynamic sets of k-mers with high locality
• a Rust tool for correcting long reads with k-mers
• a Python library to reconstruct the social graph of Mastodon