Antoine Limasset
Chargé de recherche epst
Laboratoire / équipe
Publications
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"title_s":["lphash"],
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"Yoshihiro Shibuya",
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"citationFull_s":"Coralie Rohmer, Hélène Touzet, Antoine Limasset. Automated evaluation of multiple sequence alignment methods to handle third generation sequencing errors. 2023. <a target=\"_blank\" href=\"https://hal.science/hal-04288487\">⟨hal-04288487⟩</a>",
"title_s":["Automated evaluation of multiple sequence alignment methods to handle third generation sequencing errors"],
"authFullName_s":["Coralie Rohmer",
"Hélène Touzet",
"Antoine Limasset"],
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"citationFull_s":"Timothé Rouzé, Igor Martayan, Camille Marchet, Antoine Limasset. Fractional Hitting Sets for Efficient and Lightweight Genomic Data Sketching. <i>23rd International Workshop on Algorithms in Bioinformatics (WABI 2023</i>, Sep 2023, Houston, United States. <a target=\"_blank\" href=\"https://dx.doi.org/10.4230/LIPIcs.WABI.2023.15\">⟨10.4230/LIPIcs.WABI.2023.15⟩</a>. <a target=\"_blank\" href=\"https://hal.science/hal-04279798\">⟨hal-04279798⟩</a>",
"title_s":["Fractional Hitting Sets for Efficient and Lightweight Genomic Data Sketching"],
"authFullName_s":["Timothé Rouzé",
"Igor Martayan",
"Camille Marchet",
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"citationFull_s":"Antoine Limasset, Timothé Rouzé, Igor Martayan, Camille Marchet. supersampler\r\nFractionnal hitting set implementation for lightweight genomic data sketching. 2023, <a target=\"_blank\" style=\"word-break: break-all;\" href=\"https://archive.softwareheritage.org/browse/swh:1:dir:bb6dea99f95337e2bf26180f5242fa4b09b897f6;origin=https://hal.archives-ouvertes.fr/hal-04448163;visit=swh:1:snp:1f35ba3a6890c0ed7ca0e06e4662f5abc05db16c;anchor=swh:1:rel:42686bbd8658ab7a2a280c4dd46d8bd8223a0851;path=/\">⟨swh:1:dir:bb6dea99f95337e2bf26180f5242fa4b09b897f6;origin=https://hal.archives-ouvertes.fr/hal-04448163;visit=swh:1:snp:1f35ba3a6890c0ed7ca0e06e4662f5abc05db16c;anchor=swh:1:rel:42686bbd8658ab7a2a280c4dd46d8bd8223a0851;path=/⟩</a>. <a target=\"_blank\" href=\"https://hal.science/hal-04448163\">⟨hal-04448163⟩</a>",
"title_s":["supersampler Fractionnal hitting set implementation for lightweight genomic data sketching"],
"authFullName_s":["Antoine Limasset",
"Timothé Rouzé",
"Igor Martayan",
"Camille Marchet"],
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"citationRef_s":"<i>Bioinformatics</i>, 2023, 39 (Supplement_1), pp.i534-i543. <a target=\"_blank\" href=\"https://dx.doi.org/10.1093/bioinformatics/btad219\">⟨10.1093/bioinformatics/btad219⟩</a>",
"citationFull_s":"Giulio Ermanno Pibiri, Yoshihiro Shibuya, Antoine Limasset. Locality-preserving minimal perfect hashing of k -mers. <i>Bioinformatics</i>, 2023, 39 (Supplement_1), pp.i534-i543. <a target=\"_blank\" href=\"https://dx.doi.org/10.1093/bioinformatics/btad219\">⟨10.1093/bioinformatics/btad219⟩</a>. <a target=\"_blank\" href=\"https://hal.science/hal-04288471\">⟨hal-04288471⟩</a>",
"title_s":["Locality-preserving minimal perfect hashing of k -mers"],
"authFullName_s":["Giulio Ermanno Pibiri",
"Yoshihiro Shibuya",
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"citationFull_s":"Camille Marchet, Antoine Limasset. Scalable sequence database search using Partitioned Aggregated Bloom Comb-Trees. 2022. <a target=\"_blank\" href=\"https://hal.science/hal-03871213\">⟨hal-03871213⟩</a>",
"title_s":["Scalable sequence database search using Partitioned Aggregated Bloom Comb-Trees"],
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"citationFull_s":"Giulio Ermanno Pibiri, Yoshihiro Shibuya, Antoine Limasset. Locality-Preserving Minimal Perfect Hashing of k-mers. 2022. <a target=\"_blank\" href=\"https://hal.science/hal-03832901\">⟨hal-03832901⟩</a>",
"title_s":["Locality-Preserving Minimal Perfect Hashing of k-mers"],
"authFullName_s":["Giulio Ermanno Pibiri",
"Yoshihiro Shibuya",
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"citationFull_s":"Clément Agret, Bastien Cazaux, Antoine Limasset. Toward Optimal Fingerprint Indexing for Large Scale Genomics. <i>WABI 2022 - 22nd International Workshop on Algorithms in Bioinformatics</i>, Sep 2022, Postdam, Germany. pp.25:1-25:15, <a target=\"_blank\" href=\"https://dx.doi.org/10.4230/LIPIcs.WABI.2022.25\">⟨10.4230/LIPIcs.WABI.2022.25⟩</a>. <a target=\"_blank\" href=\"https://hal.science/hal-04121819\">⟨hal-04121819⟩</a>",
"title_s":["Toward Optimal Fingerprint Indexing for Large Scale Genomics"],
"authFullName_s":["Clément Agret",
"Bastien Cazaux",
"Antoine Limasset"],
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"citationRef_s":"<i>Recomb 2022- 26th Annual International Conference on Research in Computational Molecular Biology</i>, May 2022, La jolla, United States",
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"title_s":["Scalable sequence database search using Partitioned Aggregated Bloom Comb-Trees"],
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"citationRef_s":"<i>Nature Methods</i>, 2022, 19 (4), pp.429-440. <a target=\"_blank\" href=\"https://dx.doi.org/10.1038/s41592-022-01431-4\">⟨10.1038/s41592-022-01431-4⟩</a>",
"citationFull_s":"Fernando Meyer, Adrian Fritz, Zhi-Luo Deng, David Koslicki, Till Robin Lesker, et al.. Critical Assessment of Metagenome Interpretation: the second round of challenges. <i>Nature Methods</i>, 2022, 19 (4), pp.429-440. <a target=\"_blank\" href=\"https://dx.doi.org/10.1038/s41592-022-01431-4\">⟨10.1038/s41592-022-01431-4⟩</a>. <a target=\"_blank\" href=\"https://hal.science/hal-03832903\">⟨hal-03832903⟩</a>",
"title_s":["Critical Assessment of Metagenome Interpretation: the second round of challenges"],
"authFullName_s":["Fernando Meyer",
"Adrian Fritz",
"Zhi-Luo Deng",
"David Koslicki",
"Till Robin Lesker",
"Alexey Gurevich",
"Gary Robertson",
"Mohammed Alser",
"Dmitry Antipov",
"Francesco Beghini",
"Denis Bertrand",
"Jaqueline Brito",
"C. Titus Brown",
"Jan Buchmann",
"Aydin Buluç",
"Bo Chen",
"Rayan Chikhi",
"Philip Clausen",
"Alexandru Cristian",
"Piotr Wojciech Dabrowski",
"Aaron Darling",
"Rob Egan",
"Eleazar Eskin",
"Evangelos Georganas",
"Eugene Goltsman",
"Melissa Gray",
"Lars Hestbjerg Hansen",
"Steven Hofmeyr",
"Pingqin Huang",
"Luiz Irber",
"Huijue Jia",
"Tue Sparholt Jørgensen",
"Silas Kieser",
"Terje Klemetsen",
"Axel Kola",
"Mikhail Kolmogorov",
"Anton Korobeynikov",
"Jason Kwan",
"Nathan Lapierre",
"Claire Lemaitre",
"Chenhao Li",
"Antoine Limasset",
"Fabio Malcher-Miranda",
"Serghei Mangul",
"Vanessa Marcelino",
"Camille Marchet",
"Pierre Marijon",
"Dmitry Meleshko",
"Daniel Mende",
"Alessio Milanese",
"Niranjan Nagarajan",
"Jakob Nissen",
"Sergey Nurk",
"Leonid Oliker",
"Lucas Paoli",
"Vitor Piro",
"Jacob Porter",
"Simon Rasmussen",
"Evan Rees",
"Knut Reinert",
"Bernhard Renard",
"Espen Mikal Robertsen",
"Gail Rosen",
"Hans-Joachim Ruscheweyh",
"Varuni Sarwal",
"Nicola Segata",
"Enrico Seiler",
"Lizhen Shi",
"Fengzhu Sun",
"Shinichi Sunagawa",
"Søren Johannes Sørensen",
"Ashleigh Thomas",
"Chengxuan Tong",
"Mirko Trajkovski",
"Julien Tremblay",
"Gherman Uritskiy",
"Riccardo Vicedomini",
"Zhengyang Wang",
"Ziye Wang",
"Zhong Wang",
"Andrew Warren",
"Nils Peder Willassen",
"Katherine Yelick",
"Ronghui You",
"Georg Zeller",
"Zhengqiao Zhao",
"Shanfeng Zhu",
"Jie Zhu",
"Ruben Garrido-Oter",
"Petra Gastmeier",
"Stephane Hacquard",
"Susanne Häußler",
"Ariane Khaledi",
"Friederike Maechler",
"Fantin Mesny",
"Simona Radutoiu",
"Paul Schulze-Lefert",
"Nathiana Smit",
"Till Strowig",
"Andreas Bremges",
"Alexander Sczyrba",
"Alice Carolyn Mchardy",
"Pierre Peterlongo"],
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"citationFull_s":"Clément Agret, Bastien Cazaux, Antoine Limasset. NIQKI. 2022, <a target=\"_blank\" style=\"word-break: break-all;\" href=\"https://archive.softwareheritage.org/browse/swh:1:dir:4b130954e11adff2be9108f45c4181f972604407;origin=https://github.com/Malfoy/NIQKI;visit=swh:1:snp:65940e352a73e160a22b0e80a69d0b3964de4048;anchor=swh:1:rev:ac03f90a644e79c1a76a7e8d2dd0410470959a33\">⟨swh:1:dir:4b130954e11adff2be9108f45c4181f972604407;origin=https://github.com/Malfoy/NIQKI;visit=swh:1:snp:65940e352a73e160a22b0e80a69d0b3964de4048;anchor=swh:1:rev:ac03f90a644e79c1a76a7e8d2dd0410470959a33⟩</a>. <a target=\"_blank\" href=\"https://hal-lirmm.ccsd.cnrs.fr/lirmm-04121986\">⟨lirmm-04121986⟩</a>",
"title_s":["NIQKI"],
"authFullName_s":["Clément Agret",
"Bastien Cazaux",
"Antoine Limasset"],
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"citationFull_s":"Camille Marchet, Antoine Limasset. PAC (Partitionned Aggregated bloom Comb trees). 2021, <a target=\"_blank\" style=\"word-break: break-all;\" href=\"https://archive.softwareheritage.org/browse/swh:1:dir:71df7ad3c1d66b4989702820283a7cc3e9bfd5e5;origin=https://hal.archives-ouvertes.fr/hal-04441806;visit=swh:1:snp:5e96275dff1a0983e64f36993e8cfa6a2bf4ee9b;anchor=swh:1:rel:9d59c913641e1e548439d22aced030ded561a90e;path=/\">⟨swh:1:dir:71df7ad3c1d66b4989702820283a7cc3e9bfd5e5;origin=https://hal.archives-ouvertes.fr/hal-04441806;visit=swh:1:snp:5e96275dff1a0983e64f36993e8cfa6a2bf4ee9b;anchor=swh:1:rel:9d59c913641e1e548439d22aced030ded561a90e;path=/⟩</a>. <a target=\"_blank\" href=\"https://hal.science/hal-04441806\">⟨hal-04441806⟩</a>",
"title_s":["PAC (Partitionned Aggregated bloom Comb trees)"],
"authFullName_s":["Camille Marchet",
"Antoine Limasset"],
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"citationRef_s":"<i>Scientific Reports</i>, 2021, 11 (1), pp.1-13. <a target=\"_blank\" href=\"https://dx.doi.org/10.1038/s41598-020-80757-5\">⟨10.1038/s41598-020-80757-5⟩</a>",
"citationFull_s":"Pierre Morisse, Camille Marchet, Antoine Limasset, Thierry Lecroq, Arnaud Lefebvre. Scalable long read self-correction and assembly polishing with multiple sequence alignment. <i>Scientific Reports</i>, 2021, 11 (1), pp.1-13. <a target=\"_blank\" href=\"https://dx.doi.org/10.1038/s41598-020-80757-5\">⟨10.1038/s41598-020-80757-5⟩</a>. <a target=\"_blank\" href=\"https://cnrs.hal.science/hal-03210290\">⟨hal-03210290⟩</a>",
"title_s":["Scalable long read self-correction and assembly polishing with multiple sequence alignment"],
"authFullName_s":["Pierre Morisse",
"Camille Marchet",
"Antoine Limasset",
"Thierry Lecroq",
"Arnaud Lefebvre"],
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"citationRef_s":"<i>Science Advances </i>, 2021, 7 (41), pp.eabg4216. <a target=\"_blank\" href=\"https://dx.doi.org/10.1126/sciadv.abg4216\">⟨10.1126/sciadv.abg4216⟩</a>",
"citationFull_s":"Paul Simion, Jitendra Narayan, Antoine Houtain, Alessandro Derzelle, Lyam Baudry, et al.. Chromosome-level genome assembly reveals homologous chromosomes and recombination in asexual rotifer Adineta vaga. <i>Science Advances </i>, 2021, 7 (41), pp.eabg4216. <a target=\"_blank\" href=\"https://dx.doi.org/10.1126/sciadv.abg4216\">⟨10.1126/sciadv.abg4216⟩</a>. <a target=\"_blank\" href=\"https://hal.sorbonne-universite.fr/hal-03406292\">⟨hal-03406292⟩</a>",
"title_s":["Chromosome-level genome assembly reveals homologous chromosomes and recombination in asexual rotifer Adineta vaga"],
"authFullName_s":["Paul Simion",
"Jitendra Narayan",
"Antoine Houtain",
"Alessandro Derzelle",
"Lyam Baudry",
"Emilien Nicolas",
"Rohan Arora",
"Marie Cariou",
"Corinne Cruaud",
"Florence Rodriguez Gaudray",
"Clément Gilbert",
"Nadège Guiglielmoni",
"Boris Hespeels",
"Djampa K. L. Kozlowski",
"Karine Labadie",
"Antoine Limasset",
"Marc Llirós",
"Martial Marbouty",
"Matthieu Terwagne",
"Julie Virgo",
"Richard Cordaux",
"Etienne G. J. Danchin",
"Bernard Hallet",
"Romain Koszul",
"Thomas Lenormand",
"Jean-Francois Flot",
"Karine van Doninck"],
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"citationRef_s":"<i>Genome Biology</i>, 2021, 22 (1), <a target=\"_blank\" href=\"https://dx.doi.org/10.1186/s13059-021-02419-7\">⟨10.1186/s13059-021-02419-7⟩</a>",
"citationFull_s":"Antoine Limasset, Christopher Quince, Sergey Nurk, Sebastien Raguideau, Robert James, et al.. STRONG: metagenomics strain resolution on assembly graphs. <i>Genome Biology</i>, 2021, 22 (1), <a target=\"_blank\" href=\"https://dx.doi.org/10.1186/s13059-021-02419-7\">⟨10.1186/s13059-021-02419-7⟩</a>. <a target=\"_blank\" href=\"https://hal.science/hal-03443171\">⟨hal-03443171⟩</a>",
"title_s":["STRONG: metagenomics strain resolution on assembly graphs"],
"authFullName_s":["Antoine Limasset",
"Christopher Quince",
"Sergey Nurk",
"Sebastien Raguideau",
"Robert James",
"Orkun Soyer",
"J. Kimberly Summers",
"A. Murat Eren",
"Rayan Chikhi",
"Aaron Darling"],
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"citationRef_s":"2021",
"citationFull_s":"Camille Marchet, Yoann Dufresne, Antoine Limasset. Read correction for non-uniform coverages. 2021. <a target=\"_blank\" href=\"https://pasteur.hal.science/pasteur-03263392\">⟨pasteur-03263392⟩</a>",
"title_s":["Read correction for non-uniform coverages"],
"authFullName_s":["Camille Marchet",
"Yoann Dufresne",
"Antoine Limasset"],
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"citationRef_s":"<i>Bioinformatics</i>, 2021, 37 (18), pp.2858-2865. <a target=\"_blank\" href=\"https://dx.doi.org/10.1093/bioinformatics/btab217\">⟨10.1093/bioinformatics/btab217⟩</a>",
"citationFull_s":"Antoine Limasset, Camille Marchet, Mael Kerbiriou. BLight: efficient exact associative structure for k-mers. <i>Bioinformatics</i>, 2021, 37 (18), pp.2858-2865. <a target=\"_blank\" href=\"https://dx.doi.org/10.1093/bioinformatics/btab217\">⟨10.1093/bioinformatics/btab217⟩</a>. <a target=\"_blank\" href=\"https://hal.science/hal-03443183\">⟨hal-03443183⟩</a>",
"title_s":["BLight: efficient exact associative structure for k-mers"],
"authFullName_s":["Antoine Limasset",
"Camille Marchet",
"Mael Kerbiriou"],
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