About me

I'm about to start a postdoc in Martin Steinegger's Lab at Seoul National University. I recently defended my PhD in computer science at Univ Lille, supervised by Camille Marchet.

My research focuses on algorithmic bioinformatics: designing and implementing fast algorithms for sequencing data. I work on k-mer data structures, sketching and sampling methods, and SIMD-accelerated sequence processing.

Before that, I studied at ENS Rennes, completed the MPRI master's in theoretical computer science, and spent a semester at EPFL. (More details in my resume, French version)

News

• Nov 2026 - New preprint on fast long-read RNA-seq mapping to a transcriptome!
• Sep 2026 - I successfully defended my PhD!
• Jun 2026 - My PhD thesis is now available online and as pdf version!
• Jun 2026 - Our paper on accelerated sequence filtering using minimizers has been published in Peer Community Journal!
• May 2026 - Talk at RECOMB 2026 on multiminimizers
• May 2026 - Talk at RECOMB-Arch 2026 on helicase

See all news

Publications

• Helicase: Vectorized parsing and bitpacking of genomic sequences, with Loup Lobet, Camille Marchet & Charles Paperman, accepted to RECOMB-Arch 2026
  [to be published] • [preprint] • [slides] • [code]
• Minimizer Density revisited: Models and Multiminimizers, with Florian Ingels, Lucas Robidou, Camille Marchet & Antoine Limasset, RECOMB 2026
  [paper] • [preprint] • [slides] • [code]
• Accelerating k-mer-based sequence filtering, with Léa Vandamme, Bede Constantinides, Bastien Cazaux, Charles Paperman & Antoine Limasset
  [paper] • [preprint] • [code]
• SimdMinimizers: Computing random minimizers, fast, with Ragnar Groot Koerkamp, SEA 2025
  [paper] • [slides] • [preprint] • [code]
• Hyper-k-mers: efficient streaming k-mers representation, with Lucas Robidou, Yoshihiro Shibuya & Antoine Limasset, RECOMB 2025
  [short paper] • [slides] • [preprint] • [code]
• Conway-Bromage-Lyndon (CBL): an exact, dynamic representation of k-mer sets, with Bastien Cazaux, Antoine Limasset & Camille Marchet, ISMB 2024
  [paper] • [slides] • [preprint] • [code]
• Fractional hitting sets for efficient multiset sketching, with Timothé Rouzé, Camille Marchet & Antoine Limasset, Algorithms for Molecular Biology
  [paper] • [code]
• Fractional hitting sets for efficient and lightweight genomic data sketching, with Timothé Rouzé, Camille Marchet & Antoine Limasset, WABI 2023
  [paper] • [slides] • [poster] • [preprint] • [code]

Thesis

PhD: Algorithm design and implementation for the scale of sequencing data
[online] • [pdf] • [sources] • [slides]

Preprints

• spearfish: ultrafast Δ-mapping of long reads to redundant transcriptomes, with Hesham Abdelgawad, Camille Marchet & Rob Patro
  [preprint] • [code]
• Brisk: Exact resource-efficient dictionary for k-mers, with Caleb Smith, Antoine Limasset & Yoann Dufresne
  [preprint] • [code]
• Constrained enumeration of k-mers from a collection of references with metadata, with Florian Ingels, Mikaël Salson & Camille Marchet
  [preprint] • [code]

Recent projects

Some projects I've been contributing to lately:

• helicase, a vectorized parsing library for FASTA/Q that supports on-the-fly bitpacking
• zefiro, a fast parallel decompression library for zstd
• simd-minimizers, a SIMD-accelerated library to quickly compute minimizers & syncmers
• KFC, a fast k-mer counter based on hyper-k-mers (it has a cute logo too!)

Teaching

• [2025-2026] Teaching assistant: Algorithms & Complexity
• [2024-2025] Teaching assistant: Algorithms & Complexity
• [2023-2024] Teaching assistant: Information theory
• [2023-2024] Teaching assistant: Javascript