Publications

@inproceedings{ limasset20261,
  title = { { ZOR Filters: Fast and Smaller Than Fuse Filters } },
  author = { Limasset, Antoine },
  year = { 2026 },
  doi = { 10.4230/LIPIcs.SEA.2026.24 },
  url = { https://doi.org/10.4230/LIPIcs.SEA.2026.24 },
  booktitle = { 24th International Symposium on Experimental Algorithms (SEA 2026) },
  series = { Leibniz International Proceedings in Informatics (LIPIcs) },
  volume = { 371 },
  pages = { 24:1--24:17 },
  publisher = { Schloss Dagstuhl – Leibniz-Zentrum für Informatik },
}

@misc{ ingels20252,
  title = { { Compressed inverted indexes for scalable sequence similarity } },
  author = { Ingels, Florian and Vandamme, Léa and Girard, Mathilde and Agret, Clément and Cazaux, Bastien and Limasset, Antoine },
  year = { 2025 },
  doi = { 10.1101/2025.11.21.689685 },
  url = { https://doi.org/10.1101/2025.11.21.689685 },
  howpublished = { bioRxiv preprint },
  note = { Presented at RECOMB 2026 },
}

@misc{ ingels20253,
  title = { { Minimizer Density revisited: Models and Multiminimizers } },
  author = { Ingels, Florian and Robidou, Lucas and Martayan, Igor and Marchet, Camille and Limasset, Antoine },
  year = { 2025 },
  doi = { 10.1101/2025.11.21.689688 },
  url = { https://doi.org/10.1101/2025.11.21.689688 },
  howpublished = { bioRxiv preprint },
  note = { Presented at RECOMB 2026 },
}

@misc{ conchonkerjan20264,
  title = { { Super Bloom: Fast and precise filter for streaming k-mer queries } },
  author = { Conchon-Kerjan, Étienne and Rouzé, Timothé and Robidou, Lucas and Ingels, Florian and Limasset, Antoine },
  year = { 2026 },
  doi = { 10.64898/2026.03.17.712354 },
  url = { https://doi.org/10.64898/2026.03.17.712354 },
  howpublished = { bioRxiv preprint },
  note = { Presented at RECOMB-Seq 2026 },
}

@article{ martayan20265,
  title = { { Accelerating k-mer-based sequence filtering } },
  author = { Martayan, Igor and Vandamme, Léa and Constantinides, Bede and Cazaux, Bastien and Paperman, Charles and Limasset, Antoine },
  year = { 2026 },
  doi = { 10.24072/pcjournal.735 },
  url = { https://doi.org/10.24072/pcjournal.735 },
  journal = { Peer Community Journal },
  volume = { 6 },
  eid = { e55 },
}

@misc{ rouze20256,
  title = { { Inverted colored de Bruijn Graph for practical kmer sets storage } },
  author = { Rouzé, Timothé and Chikhi, Rayan and Limasset, Antoine },
  year = { 2025 },
  doi = { 10.64898/2025.12.08.692073 },
  url = { https://doi.org/10.64898/2025.12.08.692073 },
  howpublished = { bioRxiv preprint },
}

@article{ rouze20257,
  title = { { Fractional hitting sets for efficient multiset sketching } },
  author = { Rouzé, Timothé and Martayan, Igor and Marchet, Camille and Limasset, Antoine },
  year = { 2025 },
  doi = { 10.1186/s13015-024-00268-0 },
  url = { https://doi.org/10.1186/s13015-024-00268-0 },
  journal = { Algorithms for Molecular Biology },
  volume = { 20 },
  number = { 1 },
  eid = { 1 },
}

@inproceedings{ hernandezcourbevoie20258,
  title = { { REINDEER2: Practical Abundance Index at Scale } },
  author = { Hernandez-Courbevoie, Yohan and Salson, Mikaël and Bessière, Chloé and Xue, Haoliang and Gautheret, Daniel and Marchet, Camille and Limasset, Antoine },
  year = { 2025 },
  doi = { 10.1007/978-3-032-05228-5_14 },
  url = { https://doi.org/10.1007/978-3-032-05228-5_14 },
  booktitle = { String Processing and Information Retrieval },
  pages = { 156--171 },
  publisher = { Springer Nature },
  series = { Lecture Notes in Computer Science },
  volume = { 16073 },
}

@article{ girard20259,
  title = { { OReO: optimizing read order for practical compression } },
  author = { Girard, Mathilde and Vandamme, Léa and Cazaux, Bastien and Limasset, Antoine },
  year = { 2025 },
  doi = { 10.1093/bioadv/vbaf128 },
  url = { https://doi.org/10.1093/bioadv/vbaf128 },
  journal = { Bioinformatics Advances },
  volume = { 5 },
  number = { 1 },
  eid = { vbaf128 },
}

@article{ vandamme202510,
  title = { { K2R: Tinted de Bruijn graphs implementation for efficient read extraction from sequencing datasets } },
  author = { Vandamme, Léa and Cazaux, Bastien and Limasset, Antoine },
  year = { 2025 },
  doi = { 10.1093/bioadv/vbaf111 },
  url = { https://doi.org/10.1093/bioadv/vbaf111 },
  journal = { Bioinformatics Advances },
  volume = { 5 },
  number = { 1 },
  eid = { vbaf111 },
}

@inproceedings{ martayan202511,
  title = { { Hyper-k-mers: Efficient Streaming k-mers Representation } },
  author = { Martayan, Igor and Robidou, Lucas and Shibuya, Yoshihiro and Limasset, Antoine },
  year = { 2025 },
  doi = { 10.1007/978-3-031-90252-9_33 },
  url = { https://doi.org/10.1007/978-3-031-90252-9_33 },
  booktitle = { Research in Computational Molecular Biology },
  pages = { 330--335 },
  publisher = { Springer Nature },
  series = { Lecture Notes in Computer Science },
  volume = { 15647 },
}

@article{ rohmer202412,
  title = { { Automated evaluation of multiple sequence alignment methods to handle third generation sequencing errors } },
  author = { Rohmer, Coralie and Touzet, Hélène and Limasset, Antoine },
  year = { 2024 },
  doi = { 10.7717/peerj.17731 },
  url = { https://doi.org/10.7717/peerj.17731 },
  journal = { PeerJ },
  volume = { 12 },
  pages = { e17731 },
  eid = { e17731 },
}

@article{ martayan202413,
  title = { { Conway–Bromage–Lyndon (CBL): an exact, dynamic representation of k-mer sets } },
  author = { Martayan, Igor and Cazaux, Bastien and Limasset, Antoine and Marchet, Camille },
  year = { 2024 },
  doi = { 10.1093/bioinformatics/btae217 },
  url = { https://doi.org/10.1093/bioinformatics/btae217 },
  journal = { Bioinformatics },
  volume = { 40 },
  pages = { i48--i57 },
  number = { Suppl. 1 },
}

@misc{ smith202414,
  title = { { Brisk: Exact resource-efficient dictionary for k-mers } },
  author = { Smith, Caleb and Martayan, Igor and Limasset, Antoine and Dufresne, Yoann },
  year = { 2024 },
  doi = { 10.1101/2024.11.26.625346 },
  url = { https://doi.org/10.1101/2024.11.26.625346 },
  howpublished = { bioRxiv preprint },
}

@misc{ agret202415,
  title = { { Evaluating k-mer Transformations for Cache Coherence and Uniformity } },
  author = { Agret, Clément and Chateau, Annie and Marchet, Camille and Mancheron, Alban and Limasset, Antoine },
  year = { 2024 },
  doi = { 10.5281/zenodo.10870713 },
  url = { https://doi.org/10.5281/zenodo.10870713 },
  howpublished = { Zenodo preprint },
}

@article{ pibiri202316,
  title = { { Locality-preserving minimal perfect hashing of k-mers } },
  author = { Pibiri, Giulio Ermanno and Shibuya, Yoshihiro and Limasset, Antoine },
  year = { 2023 },
  doi = { 10.1093/bioinformatics/btad219 },
  url = { https://doi.org/10.1093/bioinformatics/btad219 },
  journal = { Bioinformatics },
  volume = { 39 },
  pages = { i534--i543 },
  number = { Suppl. 1 },
}

@article{ marchet202317,
  title = { { Scalable sequence database search using partitioned aggregated Bloom comb trees } },
  author = { Marchet, Camille and Limasset, Antoine },
  year = { 2023 },
  doi = { 10.1093/bioinformatics/btad225 },
  url = { https://doi.org/10.1093/bioinformatics/btad225 },
  journal = { Bioinformatics },
  volume = { 39 },
  pages = { i252--i259 },
  number = { Suppl. 1 },
}

@inproceedings{ rouze202318,
  title = { { Fractional Hitting Sets for Efficient and Lightweight Genomic Data Sketching } },
  author = { Rouzé, Timothé and Martayan, Igor and Marchet, Camille and Limasset, Antoine },
  year = { 2023 },
  doi = { 10.4230/LIPIcs.WABI.2023.15 },
  url = { https://doi.org/10.4230/LIPIcs.WABI.2023.15 },
  booktitle = { 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023) },
  series = { Leibniz International Proceedings in Informatics (LIPIcs) },
  volume = { 273 },
  pages = { 15:1--15:27 },
  publisher = { Schloss Dagstuhl – Leibniz-Zentrum für Informatik },
}

@inproceedings{ agret202219,
  title = { { Toward Optimal Fingerprint Indexing for Large Scale Genomics } },
  author = { Agret, Clément and Cazaux, Bastien and Limasset, Antoine },
  year = { 2022 },
  doi = { 10.4230/LIPIcs.WABI.2022.25 },
  url = { https://doi.org/10.4230/LIPIcs.WABI.2022.25 },
  booktitle = { 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022) },
  series = { Leibniz International Proceedings in Informatics (LIPIcs) },
  volume = { 242 },
  pages = { 25:1--25:15 },
  publisher = { Schloss Dagstuhl – Leibniz-Zentrum für Informatik },
}

@article{ meyer202220,
  title = { { Critical Assessment of Metagenome Interpretation: the second round of challenges } },
  author = { Meyer, Fernando and Fritz, Adrian and Deng, Zhi-Luo and Koslicki, David and Lesker, Till Robin and Gurevich, Alexey and Robertson, Gary and Alser, Mohammed and Antipov, Dmitry and Beghini, Francesco and Bertrand, Denis and Brito, Jaqueline J. and Brown, C. Titus and Buchmann, Jan and Buluç, Aydin and Chen, Bo and Chikhi, Rayan and Clausen, Philip T. L. C. and Cristian, Alexandru and Dabrowski, Piotr Wojciech and Darling, Aaron E. and Egan, Rob and Eskin, Eleazar and Georganas, Evangelos and Goltsman, Eugene and Gray, Melissa A. and Hansen, Lars Hestbjerg and Hofmeyr, Steven and Huang, Pingqin and Irber, Luiz and Jia, Huijue and Jørgensen, Tue Sparholt and Kieser, Silas D. and Klemetsen, Terje and Kola, Axel and Kolmogorov, Mikhail and Korobeynikov, Anton and Kwan, Jason and LaPierre, Nathan and Lemaitre, Claire and Li, Chenhao and Limasset, Antoine and Malcher-Miranda, Fabio and Mangul, Serghei and Marcelino, Vanessa R. and Marchet, Camille and Marijon, Pierre and Meleshko, Dmitry and Mende, Daniel R. and Milanese, Alessio and Nagarajan, Niranjan and Nissen, Jakob and Nurk, Sergey and Oliker, Leonid and Paoli, Lucas and Peterlongo, Pierre and Piro, Vitor C. and Porter, Jacob S. and Rasmussen, Simon and Rees, Evan R. and Reinert, Knut and Renard, Bernhard and Robertsen, Espen Mikal and Rosen, Gail L. and Ruscheweyh, Hans-Joachim and Sarwal, Varuni and Segata, Nicola and Seiler, Enrico and Shi, Lizhen and Sun, Fengzhu and Sunagawa, Shinichi and Sørensen, Søren Johannes and Thomas, Ashleigh and Tong, Chengxuan and Trajkovski, Mirko and Tremblay, Julien and Uritskiy, Gherman and Vicedomini, Riccardo and Wang, Zhengyang and Wang, Ziye and Wang, Zhong and Warren, Andrew and Willassen, Nils Peder and Yelick, Katherine and You, Ronghui and Zeller, Georg and Zhao, Zhengqiao and Zhu, Shanfeng and Zhu, Jie and Garrido-Oter, Ruben and Gastmeier, Petra and Hacquard, Stephane and Häußler, Susanne and Khaledi, Ariane and Maechler, Friederike and Mesny, Fantin and Radutoiu, Simona and Schulze-Lefert, Paul and Smit, Nathiana and Strowig, Till and Bremges, Andreas and Sczyrba, Alexander and McHardy, Alice Carolyn },
  year = { 2022 },
  doi = { 10.1038/s41592-022-01431-4 },
  url = { https://doi.org/10.1038/s41592-022-01431-4 },
  journal = { Nature Methods },
  volume = { 19 },
  pages = { 429--440 },
  number = { 4 },
}

@article{ simion202121,
  title = { { Chromosome-level genome assembly reveals homologous chromosomes and recombination in asexual rotifer Adineta vaga } },
  author = { Simion, Paul and Narayan, Jitendra and Houtain, Antoine and Derzelle, Alessandro and Baudry, Lyam and Nicolas, Emilien and Arora, Rohan and Cariou, Marie and Cruaud, Corinne and Gaudray, Florence Rodriguez and Gilbert, Clément and Guiglielmoni, Nadège and Hespeels, Boris and Kozlowski, Djampa K. L. and Labadie, Karine and Limasset, Antoine and Llirós, Marc and Marbouty, Martial and Terwagne, Matthieu and Virgo, Julie and Cordaux, Richard and Danchin, Etienne G. J. and Hallet, Bernard and Koszul, Romain and Lenormand, Thomas and Flot, Jean-Francois and Van Doninck, Karine },
  year = { 2021 },
  doi = { 10.1126/sciadv.abg4216 },
  url = { https://doi.org/10.1126/sciadv.abg4216 },
  journal = { Science Advances },
  volume = { 7 },
  number = { 41 },
  eid = { eabg4216 },
}

@article{ quince202122,
  title = { { STRONG: metagenomics strain resolution on assembly graphs } },
  author = { Quince, Christopher and Nurk, Sergey and Raguideau, Sebastien and James, Robert and Soyer, Orkun S. and Summers, J. Kimberly and Limasset, Antoine and Eren, A. Murat and Chikhi, Rayan and Darling, Aaron E. },
  year = { 2021 },
  doi = { 10.1186/s13059-021-02419-7 },
  url = { https://doi.org/10.1186/s13059-021-02419-7 },
  journal = { Genome Biology },
  volume = { 22 },
  number = { 1 },
  eid = { 214 },
}

@article{ marchet202123,
  title = { { BLight: efficient exact associative structure for k-mers } },
  author = { Marchet, Camille and Kerbiriou, Mael and Limasset, Antoine },
  year = { 2021 },
  doi = { 10.1093/bioinformatics/btab217 },
  url = { https://doi.org/10.1093/bioinformatics/btab217 },
  journal = { Bioinformatics },
  volume = { 37 },
  pages = { 2858--2865 },
  number = { 18 },
}

@article{ morisse202124,
  title = { { Scalable long read self-correction and assembly polishing with multiple sequence alignment } },
  author = { Morisse, Pierre and Marchet, Camille and Limasset, Antoine and Lecroq, Thierry and Lefebvre, Arnaud },
  year = { 2021 },
  doi = { 10.1038/s41598-020-80757-5 },
  url = { https://doi.org/10.1038/s41598-020-80757-5 },
  journal = { Scientific Reports },
  volume = { 11 },
  number = { 1 },
  eid = { 761 },
}

@article{ limasset202025,
  title = { { Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs } },
  author = { Limasset, Antoine and Flot, Jean-François and Peterlongo, Pierre },
  year = { 2020 },
  doi = { 10.1093/bioinformatics/btz102 },
  url = { https://doi.org/10.1093/bioinformatics/btz102 },
  journal = { Bioinformatics },
  volume = { 36 },
  pages = { 1374--1381 },
  number = { 5 },
}

@article{ marchet202026,
  title = { { ELECTOR: evaluator for long reads correction methods } },
  author = { Marchet, Camille and Morisse, Pierre and Lecompte, Lolita and Lefebvre, Arnaud and Lecroq, Thierry and Peterlongo, Pierre and Limasset, Antoine },
  year = { 2020 },
  doi = { 10.1093/nargab/lqz015 },
  url = { https://doi.org/10.1093/nargab/lqz015 },
  journal = { NAR Genomics and Bioinformatics },
  volume = { 2 },
  number = { 1 },
  eid = { lqz015 },
}

@article{ marchet202027,
  title = { { A resource-frugal probabilistic dictionary and applications in bioinformatics } },
  author = { Marchet, Camille and Lecompte, Lolita and Limasset, Antoine and Bittner, Lucie and Peterlongo, Pierre },
  year = { 2020 },
  doi = { 10.1016/j.dam.2018.03.035 },
  url = { https://doi.org/10.1016/j.dam.2018.03.035 },
  journal = { Discrete Applied Mathematics },
  volume = { 274 },
  pages = { 92--102 },
}

@misc{ marchet201928,
  title = { { Read correction for non-uniform coverages } },
  author = { Marchet, Camille and Dufresne, Yoann and Limasset, Antoine },
  year = { 2019 },
  doi = { 10.1101/673624 },
  url = { https://doi.org/10.1101/673624 },
  howpublished = { bioRxiv preprint },
}

@inproceedings{ limasset201729,
  title = { { Fast and Scalable Minimal Perfect Hashing for Massive Key Sets } },
  author = { Limasset, Antoine and Rizk, Guillaume and Chikhi, Rayan and Peterlongo, Pierre },
  year = { 2017 },
  doi = { 10.4230/LIPIcs.SEA.2017.25 },
  url = { https://doi.org/10.4230/LIPIcs.SEA.2017.25 },
  booktitle = { 16th International Symposium on Experimental Algorithms (SEA 2017) },
  series = { Leibniz International Proceedings in Informatics (LIPIcs) },
  volume = { 75 },
  pages = { 25:1--25:16 },
  publisher = { Schloss Dagstuhl – Leibniz-Zentrum für Informatik },
}

@article{ chikhi201630,
  title = { { Compacting de Bruijn graphs from sequencing data quickly and in low memory } },
  author = { Chikhi, Rayan and Limasset, Antoine and Medvedev, Paul },
  year = { 2016 },
  doi = { 10.1093/bioinformatics/btw279 },
  url = { https://doi.org/10.1093/bioinformatics/btw279 },
  journal = { Bioinformatics },
  volume = { 32 },
  pages = { i201--i208 },
  number = { 12 },
}

@article{ limasset201631,
  title = { { Read mapping on de Bruijn graphs } },
  author = { Limasset, Antoine and Cazaux, Bastien and Rivals, Eric and Peterlongo, Pierre },
  year = { 2016 },
  doi = { 10.1186/s12859-016-1103-9 },
  url = { https://doi.org/10.1186/s12859-016-1103-9 },
  journal = { BMC Bioinformatics },
  volume = { 17 },
  number = { 1 },
  eid = { 237 },
}

@inproceedings{ marchet201632,
  title = { { A Resource-frugal Probabilistic Dictionary and Applications in (Meta)Genomics } },
  author = { Marchet, Camille and Limasset, Antoine and Bittner, Lucie and Peterlongo, Pierre },
  year = { 2016 },
  url = { https://psc.fit.cvut.cz/papers/PSC2016.pdf#page=95 },
  booktitle = { Proceedings of the Prague Stringology Conference 2016 },
  pages = { 85--98 },
  publisher = { Czech Technical University in Prague },
  editor = { Holub, Jan and Žďárek, Jan },
}

@article{ chikhi201533,
  title = { { On the Representation of De Bruijn Graphs } },
  author = { Chikhi, Rayan and Limasset, Antoine and Jackman, Shaun and Simpson, Jared T. and Medvedev, Paul },
  year = { 2015 },
  doi = { 10.1089/cmb.2014.0160 },
  url = { https://doi.org/10.1089/cmb.2014.0160 },
  journal = { Journal of Computational Biology },
  volume = { 22 },
  pages = { 336--352 },
  number = { 5 },
}

@inproceedings{ chikhi201434,
  title = { { On the Representation of de Bruijn Graphs } },
  author = { Chikhi, Rayan and Limasset, Antoine and Jackman, Shaun and Simpson, Jared T. and Medvedev, Paul },
  year = { 2014 },
  doi = { 10.1007/978-3-319-05269-4_4 },
  url = { https://doi.org/10.1007/978-3-319-05269-4_4 },
  booktitle = { Research in Computational Molecular Biology },
  pages = { 35--55 },
  publisher = { Springer Nature },
  series = { Lecture Notes in Computer Science },
  volume = { 8394 },
}