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
- I'm visiting Rob Patro's lab at the University of Maryland from February to April 2025!
- [03/2025] Our paper on simd-minimizers has been accepted to SEA 2025!
- [01/2025] New preprint on simd-minimizers, a SIMD-accelerated library to compute random minimizers!
- [12/2024] Our paper on hyper-k-mers has been accepted to RECOMB 2025!
- [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
More
- [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!
- [09/2023] Talk at WABI 2023 in Houston about fractional hitting sets
- [06/2023] Our paper on fractional hitting sets has been accepted to WABI!
- [03/2023] I'm joining Camille Marchet and Antoine Limasset to work on locality-preserving representation of k-mer sets!
- [06/2022] I did a semester project supervised by Ola Svensson on the forest augmentation problem. [slides]
- [12/2021] I did a semester project with Erwan Le Merrer and Gilles Trédan on the indistinguishability of black-box recommenders outputs.
- [07/2021] I did my first research internship with Dominique Lavenier in the GenScale team. I've been working on a new algorithm for aligning long genomic sequences in the consensus problem. [report] [slides]
Publications
- SimdMinimizers: Computing random minimizers, fast, with Ragnar Groot Koerkamp, SEA 2025
[preprint] - Hyper-k-mers: efficient streaming k-mers representation, with Lucas Robidou, Yoshihiro Shibuya & Antoine Limasset, RECOMB 2025
[preprint] - Fractional hitting sets for efficient multiset sketching, with Timothé Rouzé, Camille Marchet & Antoine Limasset, Algorithms for Molecular Biology
[paper] - 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
- Brisk: Exact resource-efficient dictionary for k-mers, with Caleb Smith, Antoine Limasset & Yoann Dufresne
[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 projects I've been contributing to lately:
- simd-minimizers, a SIMD-accelerated library to quickly compute (canonical) minimizers
- minimizer-iter, a user-friendly library to iterate over (mod) minimizers
- KFC, a fast k-mer counter based on hyper-k-mers (it has a cute logo too!)
