Rayan Chikhi
Chargé de recherche epst
Laboratoire / équipe
Publications
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"citationFull_s":"Riccardo Vicedomini, Francesco Andreace, Yoann Dufresne, Rayan Chikhi, Camila Duitama González. MUSET: set of utilities for constructing abundance unitig matrices from sequencing data [sequence analysis]. <i>Bioinformatics</i>, 2025, 41 (3), pp.1-5. <a target=\"_blank\" href=\"https://dx.doi.org/10.1093/bioinformatics/btaf054\">⟨10.1093/bioinformatics/btaf054⟩</a>. <a target=\"_blank\" href=\"https://hal.science/hal-04831168v2\">⟨hal-04831168v2⟩</a>",
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"citationRef_s":"<i>Nature Microbiology</i>, 2024, 9, pp.3345-3361. <a target=\"_blank\" href=\"https://dx.doi.org/10.1038/s41564-024-01859-8\">⟨10.1038/s41564-024-01859-8⟩</a>",
"citationFull_s":"Lukas Hafner, Enzo Gadin, Lei Huang, Arthur Frouin, Fabien Laporte, et al.. Differential stress responsiveness determines intraspecies virulence heterogeneity and host adaptation in Listeria monocytogenes. <i>Nature Microbiology</i>, 2024, 9, pp.3345-3361. <a target=\"_blank\" href=\"https://dx.doi.org/10.1038/s41564-024-01859-8\">⟨10.1038/s41564-024-01859-8⟩</a>. <a target=\"_blank\" href=\"https://pasteur.hal.science/pasteur-04804169v1\">⟨pasteur-04804169⟩</a>",
"title_s":["Differential stress responsiveness determines intraspecies virulence heterogeneity and host adaptation in Listeria monocytogenes"],
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"citationFull_s":"Rayan Chikhi, Yoann Dufresne, Paul Medvedev. Constructing and personalizing population pangenome graphs. <i>Nature Methods</i>, 2024, 21 (11), pp.1980-1981. <a target=\"_blank\" href=\"https://dx.doi.org/10.1038/s41592-024-02402-7\">⟨10.1038/s41592-024-02402-7⟩</a>. <a target=\"_blank\" href=\"https://pasteur.hal.science/pasteur-04915025v1\">⟨pasteur-04915025⟩</a>",
"title_s":["Constructing and personalizing population pangenome graphs"],
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"citationFull_s":"Chloé Bessière, Haoliang Xue, Benoit Guibert, Anthony Boureux, Florence Rufflé, et al.. Transipedia.org: k-mer-based exploration of large RNA sequencing datasets and application to cancer data. <i>Genome Biology</i>, 2024, 25 (1), pp.266. <a target=\"_blank\" href=\"https://dx.doi.org/10.1186/s13059-024-03413-5\">⟨10.1186/s13059-024-03413-5⟩</a>. <a target=\"_blank\" href=\"https://hal.science/hal-04765771v1\">⟨hal-04765771⟩</a>",
"title_s":["Transipedia.org: k-mer-based exploration of large RNA sequencing datasets and application to cancer data"],
"authFullName_s":["Chloé Bessière","Haoliang Xue","Benoit Guibert","Anthony Boureux","Florence Rufflé","Julien Viot","Rayan Chikhi","Mikaël Salson","Camille Marchet","Thérèse Commes","Daniel Gautheret"],
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"citationFull_s":"Kristen D Curry, Feiqiao Brian Yu, Summer E Vance, Santiago Segarra, Devaki Bhaya, et al.. Reference-free structural variant detection in microbiomes via long-read co-assembly graphs. <i>Bioinformatics</i>, 2024, 40, pp.i58 - i67. <a target=\"_blank\" href=\"https://dx.doi.org/10.1093/bioinformatics/btae224\">⟨10.1093/bioinformatics/btae224⟩</a>. <a target=\"_blank\" href=\"https://pasteur.hal.science/pasteur-04778741v1\">⟨pasteur-04778741⟩</a>",
"title_s":["Reference-free structural variant detection in microbiomes via long-read co-assembly graphs"],
"authFullName_s":["Kristen D Curry","Feiqiao Brian Yu","Summer E Vance","Santiago Segarra","Devaki Bhaya","Rayan Chikhi","Eduardo P. C. Rocha","Todd J Treangen"],
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"title_s":["Statistical signature of subtle behavioural changes in large-scale behavioural assays"],
"authFullName_s":["Alexandre Blanc","François Laurent","Alex Barbier--Chebbah","Benjamin Cocanougher","Benjamin M.W. Jones","Peter Hague","Marta Zlatic","Rayan Chikhi","Christian Vestergaard","Tihana Jovanic","Jean-Baptiste Masson","Chloé Barré"],
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"citationFull_s":"Téo Lemane, Nolan Lezzoche, Julien Lecubin, Eric Pelletier, Magali Lescot, et al.. Indexing and real-time user-friendly queries in terabyte-sized complex genomic datasets with kmindex and ORA. <i>Nature Computational Science</i>, 2024, 4 (2), pp.104-109. <a target=\"_blank\" href=\"https://dx.doi.org/10.1038/s43588-024-00596-6\">⟨10.1038/s43588-024-00596-6⟩</a>. <a target=\"_blank\" href=\"https://hal.science/hal-04489740v1\">⟨hal-04489740⟩</a>",
"title_s":["Indexing and real-time user-friendly queries in terabyte-sized complex genomic datasets with kmindex and ORA"],
"authFullName_s":["Téo Lemane","Nolan Lezzoche","Julien Lecubin","Eric Pelletier","Magali Lescot","Rayan Chikhi","Pierre Peterlongo"],
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"citationFull_s":"Karel Břinda, Leandro Lima, Simone Pignotti, Natalia Quinones-Olvera, Kamil Salikhov, et al.. Efficient and Robust Search of Microbial Genomes via Phylogenetic Compression. 2024. <a target=\"_blank\" href=\"https://hal.science/hal-04287842v2\">⟨hal-04287842v2⟩</a>",
"title_s":["Efficient and Robust Search of Microbial Genomes via Phylogenetic Compression"],
"authFullName_s":["Karel Břinda","Leandro Lima","Simone Pignotti","Natalia Quinones-Olvera","Kamil Salikhov","Rayan Chikhi","Gregory Kucherov","Zamin Iqbal","Michael Baym"],
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"title_s":["kmindex and ORA: indexing and real-time user-friendly queries in terabyte-sized complex genomic datasets"],
"authFullName_s":["Téo Lemane","Nolan Lezzoche","Julien Lecubin","Eric Pelletier","Magali Lescot","Rayan Chikhi","Pierre Peterlongo"],
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"citationRef_s":"<i>Nature Methods</i>, 2023, 20 (4), pp.550-558. <a target=\"_blank\" href=\"https://dx.doi.org/10.1038/s41592-022-01674-1\">⟨10.1038/s41592-022-01674-1⟩</a>",
"citationFull_s":"Luca Denti, Parsoa Khorsand, Paola Bonizzoni, Fereydoun Hormozdiari, Rayan Chikhi. SVDSS: structural variation discovery in hard-to-call genomic regions using sample-specific strings from accurate long reads. <i>Nature Methods</i>, 2023, 20 (4), pp.550-558. <a target=\"_blank\" href=\"https://dx.doi.org/10.1038/s41592-022-01674-1\">⟨10.1038/s41592-022-01674-1⟩</a>. <a target=\"_blank\" href=\"https://hal.science/hal-04148201v1\">⟨hal-04148201⟩</a>",
"title_s":["SVDSS: structural variation discovery in hard-to-call genomic regions using sample-specific strings from accurate long reads"],
"authFullName_s":["Luca Denti","Parsoa Khorsand","Paola Bonizzoni","Fereydoun Hormozdiari","Rayan Chikhi"],
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"citationRef_s":"<i>Bioinformatics Advances</i>, 2023, 3 (1), <a target=\"_blank\" href=\"https://dx.doi.org/10.1093/bioadv/vbad108\">⟨10.1093/bioadv/vbad108⟩</a>",
"citationFull_s":"Lorraine a K Ayad, Rayan Chikhi, Solon P Pissis. Seedability: optimizing alignment parameters for sensitive sequence comparison. <i>Bioinformatics Advances</i>, 2023, 3 (1), <a target=\"_blank\" href=\"https://dx.doi.org/10.1093/bioadv/vbad108\">⟨10.1093/bioadv/vbad108⟩</a>. <a target=\"_blank\" href=\"https://inria.hal.science/hal-04385612v1\">⟨hal-04385612⟩</a>",
"title_s":["Seedability: optimizing alignment parameters for sensitive sequence comparison"],
"authFullName_s":["Lorraine a K Ayad","Rayan Chikhi","Solon P Pissis"],
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"citationRef_s":"<i>Bioinformatics</i>, 2022, 38 (24), pp.5443-5445. <a target=\"_blank\" href=\"https://dx.doi.org/10.1093/bioinformatics/btac689\">⟨10.1093/bioinformatics/btac689⟩</a>",
"citationFull_s":"Téo Lemane, Rayan Chikhi, Pierre Peterlongo. kmdiff, large-scale and user-friendly differential k-mer analyses. <i>Bioinformatics</i>, 2022, 38 (24), pp.5443-5445. <a target=\"_blank\" href=\"https://dx.doi.org/10.1093/bioinformatics/btac689\">⟨10.1093/bioinformatics/btac689⟩</a>. <a target=\"_blank\" href=\"https://inria.hal.science/hal-03885124v1\">⟨hal-03885124⟩</a>",
"title_s":["kmdiff, large-scale and user-friendly differential k-mer analyses"],
"authFullName_s":["Téo Lemane","Rayan Chikhi","Pierre Peterlongo"],
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"citationRef_s":"<i>iScience</i>, 2022, 25 (11), pp.105305. <a target=\"_blank\" href=\"https://dx.doi.org/10.1016/j.isci.2022.105305\">⟨10.1016/j.isci.2022.105305⟩</a>",
"citationFull_s":"Luc Blassel, Paul Medvedev, Rayan Chikhi. Mapping-friendly sequence reductions: Going beyond homopolymer compression. <i>iScience</i>, 2022, 25 (11), pp.105305. <a target=\"_blank\" href=\"https://dx.doi.org/10.1016/j.isci.2022.105305\">⟨10.1016/j.isci.2022.105305⟩</a>. <a target=\"_blank\" href=\"https://hal.science/hal-04149122v1\">⟨hal-04149122⟩</a>",
"title_s":["Mapping-friendly sequence reductions: Going beyond homopolymer compression"],
"authFullName_s":["Luc Blassel","Paul Medvedev","Rayan Chikhi"],
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"citationRef_s":"<i>Bioinformatics</i>, 2022, 38 (18), pp.4423-4425. <a target=\"_blank\" href=\"https://dx.doi.org/10.1093/bioinformatics/btac528\">⟨10.1093/bioinformatics/btac528⟩</a>",
"citationFull_s":"Yoann Dufresne, Teo Lemane, Pierre Marijon, Pierre Peterlongo, Amatur Rahman, et al.. The K-mer File Format: a standardized and compact disk representation of sets of k-mers. <i>Bioinformatics</i>, 2022, 38 (18), pp.4423-4425. <a target=\"_blank\" href=\"https://dx.doi.org/10.1093/bioinformatics/btac528\">⟨10.1093/bioinformatics/btac528⟩</a>. <a target=\"_blank\" href=\"https://inria.hal.science/hal-03885245v1\">⟨hal-03885245⟩</a>",
"title_s":["The K-mer File Format: a standardized and compact disk representation of sets of k-mers"],
"authFullName_s":["Yoann Dufresne","Teo Lemane","Pierre Marijon","Pierre Peterlongo","Amatur Rahman","Marek Kokot","Paul Medvedev","Sebastian Deorowicz","Rayan Chikhi"],
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"citationRef_s":"<i>Bioinformatics Advances</i>, 2022, <a target=\"_blank\" href=\"https://dx.doi.org/10.1093/bioadv/vbac029\">⟨10.1093/bioadv/vbac029⟩</a>",
"citationFull_s":"Téo Lemane, Paul Medvedev, Rayan Chikhi, Pierre Peterlongo. kmtricks: Efficient construction of Bloom filters for large sequencing data collections. <i>Bioinformatics Advances</i>, 2022, <a target=\"_blank\" href=\"https://dx.doi.org/10.1093/bioadv/vbac029\">⟨10.1093/bioadv/vbac029⟩</a>. <a target=\"_blank\" href=\"https://inria.hal.science/hal-03166007v1\">⟨hal-03166007⟩</a>",
"title_s":["kmtricks: Efficient construction of Bloom filters for large sequencing data collections"],
"authFullName_s":["Téo Lemane","Paul Medvedev","Rayan Chikhi","Pierre Peterlongo"],
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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-03832903v1\">⟨hal-03832903⟩</a>",
"title_s":["Critical Assessment of Metagenome Interpretation: the second round of challenges"],
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"citationRef_s":"<i>Nature Communications</i>, 2021, 12 (1), pp.4485. <a target=\"_blank\" href=\"https://dx.doi.org/10.1038/s41467-021-24515-9\">⟨10.1038/s41467-021-24515-9⟩</a>",
"citationFull_s":"Riccardo Vicedomini, Christopher Quince, Aaron Darling, Rayan Chikhi. Strainberry: automated strain separation in low-complexity metagenomes using long reads. <i>Nature Communications</i>, 2021, 12 (1), pp.4485. <a target=\"_blank\" href=\"https://dx.doi.org/10.1038/s41467-021-24515-9\">⟨10.1038/s41467-021-24515-9⟩</a>. <a target=\"_blank\" href=\"https://hal.science/hal-03412884v1\">⟨hal-03412884⟩</a>",
"title_s":["Strainberry: automated strain separation in low-complexity metagenomes using long reads"],
"authFullName_s":["Riccardo Vicedomini","Christopher Quince","Aaron Darling","Rayan Chikhi"],
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"citationFull_s":"Robert Edgar, Jeff Taylor, Victor Lin, Tomer Altman, Pierre Barbera, et al.. Petabase-scale sequence alignment catalyses viral discovery. 2021. <a target=\"_blank\" href=\"https://hal.science/hal-03412952v1\">⟨hal-03412952⟩</a>",
"title_s":["Petabase-scale sequence alignment catalyses viral discovery"],
"authFullName_s":["Robert Edgar","Jeff Taylor","Victor Lin","Tomer Altman","Pierre Barbera","Dmitry Meleshko","Dan Lohr","Gherman Novakovsky","Benjamin Buchfink","Basem Al-Shayeb","Jillian Banfield","Marcos de La Peña","Anton Korobeynikov","Rayan Chikhi","Artem Babaian"],
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"citationRef_s":"<i>Cell Systems</i>, 2021, 12 (10), pp.958-968.e6. <a target=\"_blank\" href=\"https://dx.doi.org/10.1016/j.cels.2021.08.009\">⟨10.1016/j.cels.2021.08.009⟩</a>",
"citationFull_s":"Bariş Ekim, Bonnie Berger, Rayan Chikhi. Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer. <i>Cell Systems</i>, 2021, 12 (10), pp.958-968.e6. <a target=\"_blank\" href=\"https://dx.doi.org/10.1016/j.cels.2021.08.009\">⟨10.1016/j.cels.2021.08.009⟩</a>. <a target=\"_blank\" href=\"https://hal.science/hal-03412939v1\">⟨hal-03412939⟩</a>",
"title_s":["Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer"],
"authFullName_s":["Bariş Ekim","Bonnie Berger","Rayan Chikhi"],
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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-03443171v1\">⟨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":"<i>Genome Research</i>, 2021, 31 (1), pp.1-12. <a target=\"_blank\" href=\"https://dx.doi.org/10.1101/gr.260604.119\">⟨10.1101/gr.260604.119⟩</a>",
"citationFull_s":"Camille Marchet, Christina Boucher, Simon Puglisi, Paul Medvedev, Mikaël Salson, et al.. Data structures based on k -mers for querying large collections of sequencing data sets. <i>Genome Research</i>, 2021, 31 (1), pp.1-12. <a target=\"_blank\" href=\"https://dx.doi.org/10.1101/gr.260604.119\">⟨10.1101/gr.260604.119⟩</a>. <a target=\"_blank\" href=\"https://hal.science/hal-03165261v1\">⟨hal-03165261⟩</a>",
"title_s":["Data structures based on k -mers for querying large collections of sequencing data sets"],
"authFullName_s":["Camille Marchet","Christina Boucher","Simon Puglisi","Paul Medvedev","Mikaël Salson","Rayan Chikhi"],
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"citationRef_s":"<i>WABI 2020 - 20th Workshop on Algorithms in Bioinformatics</i>, Sep 2020, Pisa, Italy. pp.11 - 12, <a target=\"_blank\" href=\"https://dx.doi.org/10.4230/LIPIcs.WABI.2020.11\">⟨10.4230/LIPIcs.WABI.2020.11⟩</a>",
"citationFull_s":"Yoann Dufresne, Chen Sun, Pierre Marijon, Dominique Lavenier, Cedric Chauve, et al.. A Graph-Theoretic Barcode Ordering Model for Linked-Reads. <i>WABI 2020 - 20th Workshop on Algorithms in Bioinformatics</i>, Sep 2020, Pisa, Italy. pp.11 - 12, <a target=\"_blank\" href=\"https://dx.doi.org/10.4230/LIPIcs.WABI.2020.11\">⟨10.4230/LIPIcs.WABI.2020.11⟩</a>. <a target=\"_blank\" href=\"https://hal.science/hal-03008334v1\">⟨hal-03008334⟩</a>",
"title_s":["A Graph-Theoretic Barcode Ordering Model for Linked-Reads"],
"authFullName_s":["Yoann Dufresne","Chen Sun","Pierre Marijon","Dominique Lavenier","Cedric Chauve","Rayan Chikhi"],
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