Antoine Limasset

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Chargé de recherche CNRS · CRIStAL · Université de Lille
Bonsai team — Algorithms and data structures for sequence analysis

Publications · Software · Team · Funding · Teaching · Contact

About Me

I am a CNRS researcher in the Bonsai team at CRIStAL, Université de Lille. I design algorithms and data structures for large genomic and transcriptomic datasets, connecting theoretical computer science with practical bioinformatics.

My research focuses on sequence indexing, compact k-mer representations, compression, sketching and sequencing error correction. I develop open-source tools to make large-scale sequence analysis more efficient in both memory and computation.

I obtained my habilitation to direct research (HDR) at Université de Lille in September 2025.

Publications

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2026

• ZOR Filters: Fast and Smaller Than Fuse Filters
  24th International Symposium on Experimental Algorithms (SEA 2026), LIPIcs 371, 24:1–24:17. Schloss Dagstuhl – Leibniz-Zentrum für Informatik.
  DOI: 10.4230/LIPIcs.SEA.2026.24 · Software: ZOR

• Compressed inverted indexes for scalable sequence similarity
  RECOMB 2026. Available text: bioRxiv preprint, first posted in 2025.
  Preprint DOI: 10.1101/2025.11.21.689685 · RECOMB 2026 · Software: Onika

• Minimizer Density revisited: Models and Multiminimizers
  RECOMB 2026. Available text: bioRxiv preprint, first posted in 2025.
  Preprint DOI: 10.1101/2025.11.21.689688 · RECOMB 2026

• Super Bloom: Fast and precise filter for streaming k-mer queries
  RECOMB-Seq 2026 ; preprint bioRxiv.
  Preprint DOI: 10.64898/2026.03.17.712354 · Software: SuperBloom

• Accelerating k-mer-based sequence filtering
  Peer Community Journal, 6, e55.
  DOI: 10.24072/pcjournal.735 · Software: K2Rmini

2025

• Inverted colored de Bruijn Graph for practical kmer sets storage
  bioRxiv, preprint.
  Preprint DOI: 10.64898/2025.12.08.692073 · Software: KLOE

• Fractional hitting sets for efficient multiset sketching
  Algorithms for Molecular Biology, 20 (1), 1.
  DOI: 10.1186/s13015-024-00268-0 · Software: SuperSampler

• REINDEER2: Practical Abundance Index at Scale
  String Processing and Information Retrieval (SPIRE 2025), Lecture Notes in Computer Science 16073, 156–171. Springer Nature.
  DOI: 10.1007/978-3-032-05228-5_14 · Software: REINDEER2

• OReO: optimizing read order for practical compression
  Bioinformatics Advances, 5 (1), vbaf128.
  DOI: 10.1093/bioadv/vbaf128 · Software: OReO

• K2R: Tinted de Bruijn graphs implementation for efficient read extraction from sequencing datasets
  Bioinformatics Advances, 5 (1), vbaf111.
  DOI: 10.1093/bioadv/vbaf111 · Software: K2R

• Hyper-k-mers: Efficient Streaming k-mers Representation
  Research in Computational Molecular Biology (RECOMB 2025), Lecture Notes in Computer Science 15647, 330–335. Springer Nature.
  DOI: 10.1007/978-3-031-90252-9_33 · Software: KFC

2024

• Automated evaluation of multiple sequence alignment methods to handle third generation sequencing errors
  PeerJ, 12, e17731.
  DOI: 10.7717/peerj.17731 · Software: MSA-Limit

• Conway–Bromage–Lyndon (CBL): an exact, dynamic representation of k-mer sets
  Bioinformatics, 40 (Suppl. 1), i48–i57.
  DOI: 10.1093/bioinformatics/btae217 · Software: CBL

• Brisk: Exact resource-efficient dictionary for k-mers
  bioRxiv, preprint.
  Preprint DOI: 10.1101/2024.11.26.625346 · Software: Brisk

• Evaluating k-mer Transformations for Cache Coherence and Uniformity
  Zenodo, preprint.
  Preprint DOI: 10.5281/zenodo.10870713

2023

• Locality-preserving minimal perfect hashing of k-mers
  Bioinformatics, 39 (Suppl. 1), i534–i543.
  DOI: 10.1093/bioinformatics/btad219 · Software: LPHASH

• Scalable sequence database search using partitioned aggregated Bloom comb trees
  Bioinformatics, 39 (Suppl. 1), i252–i259.
  DOI: 10.1093/bioinformatics/btad225 · Software: PAC

• Fractional Hitting Sets for Efficient and Lightweight Genomic Data Sketching
  23rd International Workshop on Algorithms in Bioinformatics (WABI 2023), LIPIcs 273, 15:1–15:27. Schloss Dagstuhl – Leibniz-Zentrum für Informatik.
  DOI: 10.4230/LIPIcs.WABI.2023.15

2022

• Toward Optimal Fingerprint Indexing for Large Scale Genomics
  22nd International Workshop on Algorithms in Bioinformatics (WABI 2022), LIPIcs 242, 25:1–25:15. Schloss Dagstuhl – Leibniz-Zentrum für Informatik.
  DOI: 10.4230/LIPIcs.WABI.2022.25 · Software: NIQKI

2021

• BLight: efficient exact associative structure for k-mers
  Bioinformatics, 37 (18), 2858–2865.
  DOI: 10.1093/bioinformatics/btab217 · Software: BLight

• Scalable long read self-correction and assembly polishing with multiple sequence alignment
  Scientific Reports, 11 (1), 761.
  DOI: 10.1038/s41598-020-80757-5 · Software: CONSENT

2020

• Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs
  Bioinformatics, 36 (5), 1374–1381.
  DOI: 10.1093/bioinformatics/btz102 · Corrigendum · Software: BCOOL

• ELECTOR: evaluator for long reads correction methods
  NAR Genomics and Bioinformatics, 2 (1), lqz015.
  DOI: 10.1093/nargab/lqz015 · Software: ELECTOR

• A resource-frugal probabilistic dictionary and applications in bioinformatics
  Discrete Applied Mathematics, 274, 92–102.
  DOI: 10.1016/j.dam.2018.03.035 · Software: SRC

2019

• Read correction for non-uniform coverages
  bioRxiv, preprint.
  Preprint DOI: 10.1101/673624

2017

• Fast and Scalable Minimal Perfect Hashing for Massive Key Sets
  16th International Symposium on Experimental Algorithms (SEA 2017), LIPIcs 75, 25:1–25:16. Schloss Dagstuhl – Leibniz-Zentrum für Informatik.
  DOI: 10.4230/LIPIcs.SEA.2017.25 · Software: BBHash

2016

• Compacting de Bruijn graphs from sequencing data quickly and in low memory
  Bioinformatics, 32 (12), i201–i208.
  DOI: 10.1093/bioinformatics/btw279 · Software: BCALM2

• Read mapping on de Bruijn graphs
  BMC Bioinformatics, 17 (1), 237.
  DOI: 10.1186/s12859-016-1103-9 · Software: BGREAT

• A Resource-frugal Probabilistic Dictionary and Applications in (Meta)Genomics
  Proceedings of the Prague Stringology Conference 2016, 85–98. Jan Holub and Jan Žďárek (eds.), Czech Technical University in Prague.
  Proceedings, pp. 85–98

2015

• On the Representation of De Bruijn Graphs
  Journal of Computational Biology, 22 (5), 336–352.
  DOI: 10.1089/cmb.2014.0160

2014

• On the Representation of de Bruijn Graphs
  Research in Computational Molecular Biology (RECOMB 2014), Lecture Notes in Computer Science 8394, 35–55. Springer.
  DOI: 10.1007/978-3-319-05269-4_4

Collaborative Publications

2022

• Critical Assessment of Metagenome Interpretation: the second round of challenges
  Nature Methods, 19 (4), 429–440.
  DOI: 10.1038/s41592-022-01431-4

2021

• Chromosome-level genome assembly reveals homologous chromosomes and recombination in asexual rotifer Adineta vaga
  Science Advances, 7 (41), eabg4216.
  DOI: 10.1126/sciadv.abg4216

• STRONG: metagenomics strain resolution on assembly graphs
  Genome Biology, 22 (1), 214.
  DOI: 10.1186/s13059-021-02419-7 · Software: STRONG

Software

Team & Supervision

Current PhD Students

• Étienne Conchon-Kerjan — PhD director, 2026–present.

• Yohan Hernandez-Courbevoie — PhD director, 2024–present. Indexing global transcriptomic databases.

• Timothé Rouzé — PhD co-supervisor, 2023–present. Compression of large sequencing collections.

Research Staff

• Lucas Robidou — Research engineer, supervisor, 2026–present. Scalable genomic sequence analysis.

• Florian Ingels — Postdoctoral researcher, supervisor, 2025–2026. Minimizer schemes.

Former Students and Staff

• Léa Vandamme — PhD director, 2022–2025. Indexing third-generation sequencing datasets.

• Caleb Smith — Engineer, supervisor, 2023–2024. Compression of large sequencing collections.

• Coralie Rohmer — PhD co-supervisor, 2019–2023. Multiple sequence alignment algorithms for third-generation sequencing.

Education

• 2025 — Habilitation à diriger des recherches (HDR), Université de Lille. Defended on 4 September 2025.
• 2017 — PhD in Computer Science, Université de Rennes 1. Novel approaches for the exploitation of high throughput sequencing data. Supervised by Pierre Peterlongo and Dominique Lavenier; defended on 12 July 2017.
• 2014 — MSc in Computer Science, École Normale Supérieure de Rennes.
• 2012 — BSc in Computer Science, École Normale Supérieure de Cachan.

Professional Experience

• 2018–present — CNRS researcher, Bonsai team, CRIStAL, Lille, France.
• 2017 — Postdoctoral researcher, Université Libre de Bruxelles, Belgium. De novo assembly of heterozygous genomes.

Grants & Funding

• 2026 — ANR PRC GRANDSMERS, principal investigator, approximately €585k. Graph-based Research on Accurate Nucleotide Data via Scalable, Multi-scale, and Efficient RepresentationS.

• 2026 — ANR PRC PRO-K-MER, member. PRObabilistic K-MERs for environmental sequence analysis.

• 2024 — MIC INSERM, principal investigator, €554k. Analyse efficace et évolutive du cancer par exploration transcriptomique avancée à grande échelle.

• 2024 — ANR Shannon x Cray, member, €500k.

• 2021 — ANR JCJC, principal investigator, €227k. Adequate graph structures for third-generation sequencing data exploration.

• 2019 — Hauts-de-France Region PhD Grant, principal investigator, €150k.

• CDP PIE — Protein-Interaction-Evolution — Université de Lille Initiative d’Excellence. Total project funding: €1.5M over 4 years, renewable.

Teaching

• 2026 — Instructor, EMBO Practical Course on Pangenomics, Naples, Italy.
• 2026 — Training team and organiser, Scalable Genomics and Pangenomics, Wellcome Genome Campus, Hinxton, UK.
• 2020–2027 — Genome assembly course for master’s students, France.
• 2019–2026 — Genome assembly course, Evomics workshop, Czech Republic.
• 2023–2026 — Genome assembly course, CNRS Formation, France.
• 2015–2017 — Functional programming for bachelor’s students, France.

Professional Service

Conference Committees

• Program committees: RECOMB (2020–2026), ECCB/ISMB (2020–2026), SeqBim (2020–2025), ACM-BCB (2020–2024).
• Organizing committee: SPIRE (2021).

Reviewing

Nature Communications, Nature Methods, Genome Research, Genome Biology, Nucleic Acids Research, Bioinformatics, Scientific Reports, and other journals and conferences.

Thesis Committees

• Nastasija Mijovic — PhD committee, 2023–2025.
• Riku Walve — Examiner, 2022.
• Svitlana Lukicheva — PhD jury, 2021.
• Théo Lemane — PhD committee, 2020–2021.
• Nadege Guiglielmoni — PhD committee, 2019–2020.

Talks & Presentations

• 2026 — Invited keynote, JC2B — Junior Conference on Computational Biology, Gif-sur-Yvette, France.

• 2026 — RECOMB and RECOMB-Seq, Thessaloniki, Greece. RECOMB-Seq

• 2024 — EMBL-EBI K-mer/sequence indexing workshop, Cambridge, UK.

• 2024 — Kmer days, Dijon, France.

• 2023 — ISMB, Lyon, France.

• 2022 — RECOMB, San Diego, US.

• 2022 — DSB, Düsseldorf, Germany.

• 2022 — TUDASTIC, Lille, France.

• 2022 — Genopim kickoff, Rennes, France.

• 2021 — Kmer days, Marville, France.

• 2019 — Biata, Saint Petersburg, Russia. Conference abstracts DOI: 10.1186/s12859-019-3122-9

• 2018 — RECOMB, Paris, France.

Contact

Antoine Limasset
CRIStAL (UMR 9189), Université de Lille
Bâtiment ESPRIT, 59655 Villeneuve d’Ascq, France

antoine.limasset@univ-lille.fr · antoine.limasset@cnrs.fr