Rayan Chikhi
Publications
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
Statistical signature of subtle behavioural changes in large-scale behavioural assays
PLoS Computational Biology, 2025, 21 (4), pp.e1012990. ⟨10.1371/journal.pcbi.1012990⟩
Karel Břinda, Leandro Lima, Simone Pignotti, Natalia Quinones-Olvera, Kamil Salikhov, Rayan Chikhi, Gregory Kucherov, Zamin Iqbal, Michael Baym
Efficient and robust search of microbial genomes via phylogenetic compression
Nature Methods, 2025, 22, pp.692-697. ⟨10.1038/s41592-025-02625-2⟩
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]
Bioinformatics, 2025, 41 (3), pp.1-5. ⟨10.1093/bioinformatics/btaf054⟩
Lukas Hafner, Enzo Gadin, Lei Huang, Arthur Frouin, Fabien Laporte, Charlotte Gaultier, Afonso Vieira, Claire Maudet, Hugo Varet, Alexandra Moura, Hélène Bracq-Dieye, Nathalie Tessaud-Rita, Mylène Maury, Melody Dazas, Rachel Legendre, Pauline Gastineau, Yu-Huan Tsai, Jean-Yves Coppée, Caroline Charlier, Etienne Patin, Rayan Chikhi, Eduardo Rocha, Alexandre Leclercq, Olivier Disson, Hugues Aschard, Marc Lecuit
Differential stress responsiveness determines intraspecies virulence heterogeneity and host adaptation in Listeria monocytogenes
Nature Microbiology, 2024, 9, pp.3345-3361. ⟨10.1038/s41564-024-01859-8⟩
Rayan Chikhi, Yoann Dufresne, Paul Medvedev
Constructing and personalizing population pangenome graphs
Nature Methods, 2024, 21 (11), pp.1980-1981. ⟨10.1038/s41592-024-02402-7⟩
Chloé Bessière, Haoliang Xue, Benoit Guibert, Anthony Boureux, Florence Rufflé, Julien Viot, Rayan Chikhi, Mikaël Salson, Camille Marchet, Thérèse Commes, Daniel Gautheret
Transipedia.org: k-mer-based exploration of large RNA sequencing datasets and application to cancer data
Genome Biology, 2024, 25 (1), pp.266. ⟨10.1186/s13059-024-03413-5⟩
Kristen D Curry, Feiqiao Brian Yu, Summer E Vance, Santiago Segarra, Devaki Bhaya, Rayan Chikhi, Eduardo P. C. Rocha, Todd J Treangen
Reference-free structural variant detection in microbiomes via long-read co-assembly graphs
Bioinformatics, 2024, 40, pp.i58 - i67. ⟨10.1093/bioinformatics/btae224⟩
Téo Lemane, Nolan Lezzoche, Julien Lecubin, Eric Pelletier, Magali Lescot, Rayan Chikhi, Pierre Peterlongo
Indexing and real-time user-friendly queries in terabyte-sized complex genomic datasets with kmindex and ORA
Nature Computational Science, 2024, 4 (2), pp.104-109. ⟨10.1038/s43588-024-00596-6⟩
Téo Lemane, Nolan Lezzoche, Julien Lecubin, Eric Pelletier, Magali Lescot, Rayan Chikhi, Pierre Peterlongo
kmindex and ORA: indexing and real-time user-friendly queries in terabyte-sized complex genomic datasets
2023
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
Nature Methods, 2023, 20 (4), pp.550-558. ⟨10.1038/s41592-022-01674-1⟩
Lorraine a K Ayad, Rayan Chikhi, Solon P Pissis
Seedability: optimizing alignment parameters for sensitive sequence comparison
Bioinformatics Advances, 2023, 3 (1), ⟨10.1093/bioadv/vbad108⟩
Téo Lemane, Rayan Chikhi, Pierre Peterlongo
kmdiff, large-scale and user-friendly differential k-mer analyses
Bioinformatics, 2022, 38 (24), pp.5443-5445. ⟨10.1093/bioinformatics/btac689⟩
Luc Blassel, Paul Medvedev, Rayan Chikhi
Mapping-friendly sequence reductions: Going beyond homopolymer compression
iScience, 2022, 25 (11), pp.105305. ⟨10.1016/j.isci.2022.105305⟩
Yoann Dufresne, Teo Lemane, Pierre Marijon, Pierre Peterlongo, Amatur Rahman, Marek Kokot, Paul Medvedev, Sebastian Deorowicz, Rayan Chikhi
The K-mer File Format: a standardized and compact disk representation of sets of k-mers
Bioinformatics, 2022, 38 (18), pp.4423-4425. ⟨10.1093/bioinformatics/btac528⟩
Téo Lemane, Paul Medvedev, Rayan Chikhi, Pierre Peterlongo
kmtricks: Efficient construction of Bloom filters for large sequencing data collections
Bioinformatics Advances, 2022, ⟨10.1093/bioadv/vbac029⟩
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
Critical Assessment of Metagenome Interpretation: the second round of challenges
Nature Methods, 2022, 19 (4), pp.429-440. ⟨10.1038/s41592-022-01431-4⟩
Riccardo Vicedomini, Christopher Quince, Aaron Darling, Rayan Chikhi
Strainberry: automated strain separation in low-complexity metagenomes using long reads
Nature Communications, 2021, 12 (1), pp.4485. ⟨10.1038/s41467-021-24515-9⟩
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
Petabase-scale sequence alignment catalyses viral discovery
2021
Bariş Ekim, Bonnie Berger, Rayan Chikhi
Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer
Cell Systems, 2021, 12 (10), pp.958-968.e6. ⟨10.1016/j.cels.2021.08.009⟩
Antoine Limasset, Christopher Quince, Sergey Nurk, Sebastien Raguideau, Robert James, Orkun Soyer, J. Kimberly Summers, A. Murat Eren, Rayan Chikhi, Aaron Darling
STRONG: metagenomics strain resolution on assembly graphs
Genome Biology, 2021, 22 (1), ⟨10.1186/s13059-021-02419-7⟩
Camille Marchet, Christina Boucher, Simon Puglisi, Paul Medvedev, Mikaël Salson, Rayan Chikhi
Data structures based on k -mers for querying large collections of sequencing data sets
Genome Research, 2021, 31 (1), pp.1-12. ⟨10.1101/gr.260604.119⟩
Yoann Dufresne, Chen Sun, Pierre Marijon, Dominique Lavenier, Cedric Chauve, Rayan Chikhi
A Graph-Theoretic Barcode Ordering Model for Linked-Reads
WABI 2020 - 20th Workshop on Algorithms in Bioinformatics, Sep 2020, Pisa, Italy. pp.11 - 12, ⟨10.4230/LIPIcs.WABI.2020.11⟩
Amatur Rahman, Rayan Chikhi, Paul Medvedev
Disk Compression of k-mer Sets
WABI 2020, Sep 2020, Pisa, Italy
Camille Marchet, Zamin Iqbal, Daniel Gautheret, Mikaël Salson, Rayan Chikhi
REINDEER: efficient indexing of k-mer presence and abundance in sequencing datasets
Bioinformatics, 2020, 36 (Supplement_1), pp.i177-i185. ⟨10.1093/bioinformatics/btaa487⟩
Pierre Marijon, Rayan Chikhi, Jean-Stéphane Varré
yacrd and fpa: upstream tools for long-read genome assembly
Bioinformatics, 2020, 36 (12), pp.3894-3896. ⟨10.1093/bioinformatics/btaa262⟩
Daria Martchenko, Rayan Chikhi, Aaron Shafer
Genome Assembly and Analysis of the North American Mountain Goat ( Oreamnos americanus ) Reveals Species-Level Responses to Extreme Environments
G3, 2020, 10 (2), pp.437-442. ⟨10.1534/g3.119.400747⟩
Camille Marchet, Christina Boucher, Simon J Puglisi, Paul Medvedev, Mikaël Salson, Rayan Chikhi
Data structures based on k-mers for querying large collections of sequencing datasets
2019
Leandro Lima, Camille Marchet, Ségolène Caboche, Corinne da Silva, Benjamin Istace, Jean-Marc Aury, Hélène Touzet, Rayan Chikhi
Comparative assessment of long-read error correction software applied to Nanopore RNA-sequencing data
Briefings in Bioinformatics, 2019, pp.1-18. ⟨10.1093/bib/bbz058⟩
Parallel decompression of gzip-compressed files and random access to DNA sequences
2019 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), May 2019, Rio de Janeiro, France. pp.209-217, ⟨10.1109/IPDPSW.2019.00042⟩
Veli Mäkinen, Alexandru Tomescu, Anna Kuosmanen, Topi Paavilainen, Travis Gagie, Rayan Chikhi
Sparse Dynamic Programming on DAGs with Small Width
ACM Transactions on Algorithms, 2019, 15 (2), pp.1-21. ⟨10.1145/3301312⟩
Pierre Marijon, Rayan Chikhi, Jean-Stéphane Varré
Graph analysis of fragmented long-read bacterial genome assemblies
Bioinformatics, 2019, ⟨10.1093/bioinformatics/btz219⟩
Rayan Chikhi, Vladan Jovičić, Stefan Kratsch, Paul Medvedev, Martin Milanic, Sofya Raskhodnikova, Nithin Varma
Bipartite Graphs of Small Readability
COCOON 2018 - The 24th International Computing and Combinatorics Conference, Jul 2018, Qingdao, China
Alan Kuhnle, Victoria G. Crawford, Christina Boucher, Rayan Chikhi, Travis Gagie
Practical dynamic de Bruijn graphs
Bioinformatics, 2018, ⟨10.1093/bioinformatics/bty500⟩
Anna Kuosmanen, Topi Paavilainen, Travis Gagie, Rayan Chikhi, Alexandru Ioan Tomescu, Veli Makinen
Using Minimum Path Cover to Boost Dynamic Programming on DAGs: Co-Linear Chaining Extended
RECOMB 2018 - 22nd Annual International Conference on Research in Computational Molecular Biology, Apr 2018, Paris, France
Tobias Marschall, Manja Marz, Thomas Abeel, Louis Dijkstra, Bas E. Dutilh, Ali Ghaffaari, Paul Kersey, Wigard P. Kloosterman, Veli Makinen, Adam M. Novak, Benedict Paten, David Porubsky, Eric Rivals, Can Alkan, Jasmijn A. Baaijens, Paul I. W. de Bakker, Valentina Boeva, Raoul J. P. Bonnal, Francesca Chiaromonte, Rayan Chikhi, Francesca D. Ciccarelli, Robin Cijvat, Erwin Datema, Cornelia M. Van Duijn, Evan E. Eichler, Corinna Ernst, Eleazar Eskin, Erik Garrison, Mohammed El-Kebir, Gunnar W. Klau, Jan O. Korbel, Eric-Wubbo Lameijer, Benjamin Langmead, Marcel Martin, Paul Medvedev, John C. Mu, Pieter Neerincx, Klaasjan Ouwens, Pierre Peterlongo, Nadia Pisanti, Sven Rahmann, Ben Raphael, Knut Reinert, Dick de Ridder, Jeroen de Ridder, Matthias Schlesner, Ole Schulz-Trieglaff, Ashley D. Sanders, Siavash Sheikhizadeh, Carl Shneider, Sandra Smit, Daniel Valenzuela, Jiayin Wang, Lodewyk Wessels, Ying Zhang, Victor Guryev, Fabio Vandin, Kai Ye, Alexander Schönhuth
Computational pan-genomics: status, promises and challenges
Briefings in Bioinformatics, 2018, 19 (1), pp.118-135. ⟨10.1093/bib/bbw089⟩
Jérôme Audoux, Nicolas Philippe, Rayan Chikhi, Mikael Salson, Mélina Gallopin, Marc Gabriel, Jérémy Le Coz, Emilie Drouineau, Thérèse Commes, Daniel Gautheret
DE-kupl: exhaustive capture of biological variation in RNA-seq data through k-mer decomposition
Genome Biology, 2017, 18 (1), pp.1-15. ⟨10.1186/s13059-017-1372-2⟩
Samarth Rangavittal, Robert Harris, Monika Cechova, Marta Tomaszkiewicz, Rayan Chikhi, Kateryna Makova, Paul Medvedev
RecoverY: k-mer-based read classification for Y-chromosome-specific sequencing and assembly
Bioinformatics, 2017, ⟨10.1093/bioinformatics/btx771⟩
Alexander Sczyrba, Peter Hofmann, Peter Belmann, David Koslicki, Stefan Janssen, Johannes Dröge, Ivan Gregor, Stephan Majda, Jessika Fiedler, Eik Dahms, Andreas Bremges, Adrian Fritz, Ruben Garrido-Oter, Tue Sparholt Jørgensen, Nicole Shapiro, Philip D Blood, Alexey Gurevich, Yang Bai, Dmitrij Turaev, Matthew Z Demaere, Rayan Chikhi, Niranjan Nagarajan, Christopher Quince, Lars Hestbjerg Hansen, Søren J Sørensen, Burton K H Chia, Bertrand Denis, Jeff L Froula, Zhong Wang, Robert Egan, Dongwan Don Kang, Jeffrey J Cook, Charles Deltel, Michael Beckstette, Claire Lemaitre, Peter Peterlongo, Guillaume Rizk, Dominique Lavenier, Yu-Wei Wu, Steven W Singer, Chirag Jain, Marc Strous, Heiner Klingenberg, Peter Meinicke, Michael D Barton, Thomas Lingner, Hsin-Hung Lin, Yu-Chieh Liao, Genivaldo Gueiros Z Silva, Daniel A Cuevas, Robert A Edwards, Surya Saha, Vitor C Piro, Bernhard y Renard, Mihai Pop, Hans-Peter Klenk, Markus Göker, Nikos C Kyrpides, Tanja Woyke, Julia A Vorholt, Paul Schulze-Lefert, Edward M Rubin, Aaron E Darling, Thomas Rattei, Alice C Mchardy
Critical Assessment of Metagenome Interpretation – a benchmark of computational metagenomics software
Nature Methods, 2017, 14 (11), pp.1063 - 1071. ⟨10.1038/nmeth.4458⟩
Pierre Marijon, Jean-Stéphane Varré, Rayan Chikhi
Debugging long-read genome and metagenome assemblies using string graph analysis
JOBIM 2017- Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2017, Lille, France.
Antoine Limasset, Guillaume Rizk, Rayan Chikhi, Pierre Peterlongo
Fast and scalable minimal perfect hashing for massive key sets
16th International Symposium on Experimental Algorithms, Jun 2017, London, United Kingdom. pp.1 - 11
Chen Sun, Robert S. Harris, Rayan Chikhi, Paul Medvedev
AllSome Sequence Bloom Trees
RECOMB 2017 - 21st Annual International Conference on Research in Computational Molecular Biology, May 2017, Hong Kong, China. ⟨10.1007/978-3-319-56970-3_17⟩
Rayan Chikhi, Antoine Limasset, Paul Medvedev
Compacting de Bruijn graphs from sequencing data quickly and in low memory
Bioinformatics, 2016, 32 (12), pp.i201 - i208. ⟨10.1093/bioinformatics/btw279⟩
Rayan Chikhi, Paul Medvedev, Martin Milanič, Sofya Raskhodnikova
On the readability of overlap digraphs
Discrete Applied Mathematics, 2016, 205, pp.35-44. ⟨10.1016/j.dam.2015.12.009⟩
Morris Agaba, Edson Ishengoma, Webb Colby Miller, Barbara C. Mcgrath, Chelsea N. Hudson, Oscar C. Bedoya Reina, Aakrosh Ratan, Rico Burhans, Rayan Chikhi, Paul Medvedev, Craig Praul, Lan Cavener, Brendan Wood, Heather Robertson, Linda Penfold, Douglas R. Cavener
Giraffe genome sequence reveals clues to its unique morphology and physiology
Nature Communications, 2016, 7, ⟨10.1038/ncomms11519⟩
Marta Tomaszkiewicz, Samarth Rangavittal, Monika Cechova, Rebeca Campos Sanchez, Howard William Fescemyer, Robert Harris, Danling Ye, Patricia C.M. O'Brien, Rayan Chikhi, Oliver A. Ryder, Malcolm A. Ferguson-Smith, Paul Medvedev, Kateryna D. Makova
A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y
Genome Research, 2016, 26 (4), pp.530 - 540. ⟨10.1101/gr.199448.115⟩
Kristoffer Sahlin, Rayan Chikhi, Lars Arvestad
Assembly scaffolding with PE-contaminated mate-pair libraries
Bioinformatics, 2016, 32 (13), pp.1925 - 1932. ⟨10.1093/bioinformatics/btw064⟩
Rayan Chikhi, Antoine Limasset, Shaun Jackman, Jared T. Simpson, Paul Medvedev
On the Representation of De Bruijn Graphs
Journal of Computational Biology, 2015, 22 (5), pp.336 - 352. ⟨10.1089/cmb.2014.0160⟩
Kristoffer Sahlin, Rayan Chikhi, Lars Arvestad.
Genome scaffolding with PE-contaminated mate-pair libraries
WABI 2015, 2015, Atlanta, United States. ⟨10.1101/025650⟩
Rayan Chikhi, Paul Medvedev, Martin Milanic, Sofya Raskhodnikova
On the readability of overlap digraphs
26th Annual Symposium on Combinatorial Pattern Matching, 2015, Ischia Porto, Italy. ⟨10.1007/978-3-319-19929-0_11⟩
Guillaume Rizk, Anaïs Gouin, Rayan Chikhi, Claire Lemaitre
MindTheGap: integrated detection and assembly of short and long insertions
Bioinformatics, 2014, 30 (24), pp.3451 - 3457. ⟨10.1093/bioinformatics/btu545⟩
Raluca Uricaru, Guillaume Rizk, Vincent Lacroix, Elsa Quillery, Olivier Plantard, Rayan Chikhi, Claire Lemaitre, Pierre Peterlongo
Reference-free detection of isolated SNPs
Nucleic Acids Research, 2014, 43 (2), pp.e11. ⟨10.1093/nar/gku1187⟩
Guillaume Rizk, Anaïs Gouin, Rayan Chikhi, Claire Lemaitre
MindTheGap: integrated detection and assembly of short and long insertions
European Conference on Computational Biology (ECCB), Sep 2014, Strasbourg, France. , ECCB 2014, 2014
Erwan Drezen, Guillaume Rizk, Rayan Chikhi, Charles Deltel, Claire Lemaitre, Pierre Peterlongo, Dominique Lavenier
Speeding up NGS software development
Sequencing, Finishing and Analysis in the Future Meeting, May 2014, Santa Fé, United States
Erwan Drezen, Guillaume Rizk, Rayan Chikhi, Charles Deltel, Claire Lemaitre, Pierre Peterlongo, Dominique Lavenier
GATB: a software toolbox for genome assembly and analysis
Bio-IT World Conference, Apr 2014, Boston, United States
Erwan Drezen, Guillaume Rizk, Rayan Chikhi, Charles Deltel, Claire Lemaitre, Pierre Peterlongo, Dominique Lavenier
GATB: Genome Assembly & Analysis Tool Box
Bioinformatics, 2014, 30, pp.2959 - 2961. ⟨10.1093/bioinformatics/btu406⟩
Guillaume Collet, Guillaume Rizk, Rayan Chikhi, Dominique Lavenier
MINIA on a Raspberry Pi, Assembling a 100 Mbp Genome on a Credit Card Sized Computer
JOBIM - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2013, Toulouse, France. 2013
Alice Julien-Laferriere, Gustavo Sacomoto, Rayan Chikhi, Erwan Scaon, David P. Parsons, Marie-France Sagot, Pierre Peterlongo, Vincent Miele, Vincent Lacroix
New developments in KisSplice: Combining local and global transcriptome assemblers to decipher splicing in RNA-seq data
Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM), Jul 2013, Toulouse, France
Guillaume Rizk, Dominique Lavenier, Rayan Chikhi
DSK: k-mer counting with very low memory usage
Bioinformatics, 2013, 29 (5), pp.652-653. ⟨10.1093/bioinformatics/btt020⟩
Space-efficient and exact de Bruijn graph representation based on a Bloom filter
Algorithms for Molecular Biology, 2013, 8 (1), pp.22. ⟨10.1186/1748-7188-8-22⟩
Keith Bradnam, Joseph Fass, Anton Alexandrov, Paul Baranay, Michael Bechner, Inanç Birol, Sébastien Boisvert, Jarrod Chapman, Guillaume Chapuis, Rayan Chikhi, Hamidreza Chitsaz, Wen-Chi Chou, Jacques Corbeil, Cristian del Fabbro, T Roderick Docking, Richard Durbin, Dent Earl, Scott Emrich, Pavel Fedotov, Nuno Fonseca, Ganeshkumar Ganapathy, Richard Gibbs, Sante Gnerre, Élénie Godzaridis, Steve Goldstein, Matthias Haimel, Giles Hall, David Haussler, Joseph Hiatt, Isaac Ho, Jason Howard, Martin Hunt, Shaun Jackman, David Jaffe, Erich Jarvis, Huaiyang Jiang, Sergey Kazakov, Paul Kersey, Jacob Kitzman, James Knight, Sergey Koren, Tak-Wah Lam, Dominique Lavenier, François Laviolette, Yingrui Li, Zhenyu Li, Binghang Liu, Yue Liu, Ruibang Luo, Iain Maccallum, Matthew Macmanes, Nicolas Maillet, Sergey Melnikov, Delphine Naquin, Zemin Ning, Thomas Otto, Benedict Paten, Octávio Paulo, Adam Phillippy, Francisco Pina-Martins, Michael Place, Dariusz Przybylski, Xiang Qin, Carson Qu, Filipe Ribeiro, Stephen Richards, Daniel Rokhsar, J Graham Ruby, Simone Scalabrin, Michael Schatz, David Schwartz, Alexey Sergushichev, Ted Sharpe, Timothy Shaw, Jay Shendure, Yujian Shi, Jared Simpson, Henry Song, Fedor Tsarev, Francesco Vezzi, Riccardo Vicedomini, Bruno Vieira, Jun Wang, Kim Worley, Shuangye Yin, Siu-Ming Yiu, Jianying Yuan, Guojie Zhang, Hao Zhang, Shiguo Zhou, Ian Korf
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
GigaScience, 2013, 2 (1), pp.10. ⟨10.1186/2047-217X-2-10⟩
Nicolas Maillet, Claire Lemaitre, Rayan Chikhi, Dominique Lavenier, Pierre Peterlongo
Compareads: comparing huge metagenomic experiments
RECOMB Comparative Genomics 2012, Oct 2012, Niterói, Brazil
Space-efficient and exact de Bruijn graph representation based on a Bloom filter
WABI 2012, Sep 2012, Ljubljana, Slovenia. pp 236-248, ⟨10.1007/978-3-642-33122-0_19⟩
Nicolas Maillet, Claire Lemaitre, Rayan Chikhi, Dominique Lavenier, Pierre Peterlongo
Compareads: comparing huge metagenomic experiments
13e édition des Journées Ouvertes en Biologie, Informatique et Mathématiques - JOBIM 2012, Jul 2012, Rennes, France. 2012
Computational methods for de novo assembly of next-generation genome sequencing data
Other [cs.OH]. École normale supérieure de Cachan - ENS Cachan, 2012. English. ⟨NNT : 2012DENS0033⟩
Nicolas Maillet, Claire Lemaitre, Rayan Chikhi, Dominique Lavenier, Pierre Peterlongo
Compareads: comparing huge metagenomic experiments
BMC Bioinformatics, 2012, 13 (Suppl 19), pp.S10. ⟨10.1186/1471-2105-13-S19-S10⟩
Pierre Peterlongo, Rayan Chikhi
Mapsembler, targeted and micro assembly of large NGS datasets on a desktop computer
BMC Bioinformatics, 2012, 13 (1), pp.48. ⟨10.1186/1471-2105-13-48⟩
Gustavo Sacomoto, Janice Kielbassa, Rayan Chikhi, Raluca Uricaru, Pavlos Antoniou, Marie-France Sagot, Pierre Peterlongo, Vincent Lacroix
KISSPLICE: de-novo calling alternative splicing events from RNA-seq data
BMC Bioinformatics, 2012, 13 (Suppl 6), pp.S5. ⟨10.1186/1471-2105-13-S6-S5⟩
Gustavo Akio Tominaga Sacomoto, J. Kielbassa, Pavlos Antoniou, Rayan Chikhi, Raluca Uricaru, Marie-France Sagot, Pierre Peterlongo, Vincent Lacroix
kisSplice, détection d'évènements d'épissages alternatifs dans les données RNA-seq
[Research Report] RR-7852, INRIA. 2011, pp.12
Dent A. Earl, Keith Bradnam, John St. John, Aaron Darling, Dawei Lin, Joseph Faas, Hung On Ken Yu, Buffalo Vince, Daniel R. Zerbino, Mark Diekhans, Ngan Nguyen, Pramila Nuwantha, Ariyaratne Wing-Kin Sung, Zemin Ning, Matthias Haimel, Jared T. Simpson, Nuno A. Fronseca, Inanç Birol, T. Roderick Docking, Isaac Y. Ho, Daniel S Rokhsar, Rayan Chikhi, Dominique Lavenier, Guillaume Chapuis, Delphine Naquin, Nicolas Maillet, Michael C. Schatz, David R. Kelly, Adam M. Phillippy, Sergey Koren, Shiaw-Pyng Yang, Wei Wu, Wen-Chi Chou, Anuj Srivastava, Timothy I. Shaw, J. Graham Ruby, Peter Skewes-Cox, Miguel Betegon, Michelle T. Dimon, Victor Solovyev, Petr Kosarev, Denis Vorobyev, Ricardo Ramirez-Gonzalez, Richard Leggett, Dan Maclean, Fangfang Xia, Ruibang Luo, Zhenyu Li, Yinlong Xie, Binghang Liu, Sante Gnerre, Iain Maccallum, Dariusz Przybylski, Filipe J. Ribeiro, Shuangye Yin, Ted Sharpe, Giles Hall, Paul J. Kersey, Richard Durbin, Shaun D. Jackman, Jarrod A. Chapman, Xiaoqiu Huang, Joseph L. Derisi, Mario Caccamo, Yingrui Li, David B. Jaffe, Richard M. Green, David Haussler, Ian Korf, Benedict Paten
Assemblathon 1: A competitive assessment of de novo short read assembly methods
Genome Research, 2011, ⟨10.1101/gr.126599.111⟩
Rayan Chikhi, Guillaume Chapuis, Dominique Lavenier
Parallel and memory-efficient reads indexing for genome assembly
Parallel Bio-Computing 2011, Sep 2011, torun, Poland
Rayan Chikhi, Dominique Lavenier
Localized genome assembly from reads to scaffolds: practical traversal of the paired string graph
WABI 2011, Sep 2011, Sarrebruck, Germany. ⟨10.1007/978-3-642-23038-7_4⟩
Pierre Peterlongo, Rayan Chikhi
Mapsembler, targeted assembly of larges genomes on a desktop computer
[Research Report] RR-7565, INRIA. 2011, pp.17
Rayan Chikhi, Dominique Lavenier
Paired-end read length lower bounds for genome re-sequencing
BMC Bioinformatics, 2009, ⟨10.1186/1471-2105-10-S13-O2⟩
Chikhi Rayan, Steven Derrien, Noumsi Auguste, Patrice Quinton
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