Antoine Limasset

Chargé de recherche CNRS
I am a research associate in BONSAI team (Lille, France). My work focuses on methods and data structures in sequence bioinformatics

Experience

• 2018 current: Researcher at CNRS, CRIStAL, Lille.
  Role: Chargé de recherche au sein de l’equipe Bonsai

• 2017 2018: PostDoctoral researcher at Université Libre de Bruxelles, Belgique.
  Project: de novo assembly of heterozygous genomes

  • 2014 2017: Ph.D in Computer Science, Université de Rennes 1. Supervised by Pierre Peterlongo and Dominique Lavenier.
    Title: Novel approaches for the exploitation of high throughput sequencing data

Publications

• 2023: Locality-Preserving Minimal Perfect Hashing of k-mers, ISMB
• 2023: Scalable sequence database search using Partitioned Aggregated Bloom Comb-Trees, ISMB/Recomb-Seq
• 2022: Toward optimal fingerprint indexing for large scale genomics, WABI
• 2022: Critical Assessment of Metagenome Interpretation: the second round of challenges, Nature Methods
• 2021: STRONG: metagenomics strain resolution on assembly graphs, Genome Biology
• 2021: BLight: Efficient exact associative structure for k-mers, Recomb-seq/Bioinformatics
• 2021: Scalable long read self-correction and assembly polishing with multiple sequence alignment, Recomb-seq/Scientific report
• 2020: Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs, Recomb-seq/Bioinformatics
• 2020: ELECTOR: evaluator for long reads correction methods, NAR Genomics and Bioinformatics
• 2017: Fast and scalable minimal perfect hashing for massive key sets, Symposium on Experimental Algorithms
• 2016: Compacting de Bruijn graphs from sequencing data quickly and in low memory, ISMB/Bioinformatics
• 2016: Read mapping on de Bruijn graphs, BMC Bioinformatics
• 2016: A resource-frugal probabilistic dictionary and applications in bioinformatics, Discrete Applied Mathematics
• 2014: On the representation of De Bruijn graph, RECOMB

Supervising

• 2019 - current: Ph.D student, Coralie Rohmer.
  Project: Working on multiple alignment algorithms adapted to third generation sequencing
• 2022 - current: Ph.D student, Léa Vandamme.
  Project: Working on Third generation sequencing datasets indexing

Conference committee

• 2021: Organizational committee, SPIRE
• 2020-2023: Program committee, RECOMB
• 2020-2023: Program committee, ACM-BCB
• 2020-2023: Program committee, ECCB/ISMB

Grant

• 2021: ANR JCJC (young researchers).
  Project: Adequate graph structures for third-generation sequencing data exploration