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hal-04670703

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⟩

hal-04287842

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⟩

hal-04831168

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⟩

pasteur-04915025

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⟩

hal-04765771

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⟩

pasteur-04778741

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⟩

hal-04489740

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⟩

cea-04321497

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

hal-04148201

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⟩

hal-04385612

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⟩

hal-03885124

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⟩

hal-04149122

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⟩

hal-03885245

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⟩

hal-03166007

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⟩

hal-03832903

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⟩

hal-03412884

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⟩

hal-03412939

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⟩

hal-03443171

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⟩

hal-03165261

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⟩

hal-03008334

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⟩

hal-03165270

Amatur Rahman, Rayan Chikhi, Paul Medvedev

Disk Compression of k-mer Sets

WABI 2020, Sep 2020, Pisa, Italy

hal-03413006

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⟩

hal-03165276

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⟩

hal-03165277

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⟩

hal-02414162

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

hal-02394395

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⟩

hal-03165281

Mael Kerbiriou, Rayan Chikhi

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⟩

hal-03165290

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⟩

hal-02167175

Pierre Marijon, Rayan Chikhi, Jean-Stéphane Varré

Graph analysis of fragmented long-read bacterial genome assemblies

Bioinformatics, 2019, ⟨10.1093/bioinformatics/btz219⟩

hal-01935566

Rayan Chikhi, Alexander Schönhuth

Dualities in Tree Representations

2018

hal-01935562

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

hal-01935559

Alan Kuhnle, Victoria G. Crawford, Christina Boucher, Rayan Chikhi, Travis Gagie

Practical dynamic de Bruijn graphs

Bioinformatics, 2018, ⟨10.1093/bioinformatics/bty500⟩

hal-01935568

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

hal-01728770

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⟩

hal-01729744

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⟩

hal-01574824

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.

hal-01566246

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

hal-01575350

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⟩

hal-01395704

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⟩

hal-01729749

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⟩

hal-01395702

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⟩

hal-01396904

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⟩

hal-01524525

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⟩

hal-01236176

Kristoffer Sahlin, Rayan Chikhi, Lars Arvestad.

Genome scaffolding with PE-contaminated mate-pair libraries

WABI 2015, 2015, Atlanta, United States. ⟨10.1101/025650⟩

hal-01236007

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⟩

hal-01081089

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⟩

hal-01083715

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⟩

hal-01087832

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

hal-01088683

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

hal-01088641

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

hal-01088571

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⟩

hal-00842027

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

hal-02069363

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

hal-00778473

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⟩

hal-00868805

Rayan Chikhi, Guillaume Rizk

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⟩

hal-00868822

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⟩

hal-00720951

Nicolas Maillet, Claire Lemaitre, Rayan Chikhi, Dominique Lavenier, Pierre Peterlongo

Compareads: comparing huge metagenomic experiments

RECOMB Comparative Genomics 2012, Oct 2012, Niterói, Brazil

hal-00753930

Rayan Chikhi, Guillaume Rizk

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⟩

hal-00760332

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

tel-00752033

Rayan Chikhi

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⟩

hal-00784394

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⟩

hal-00784408

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⟩

hal-00784407

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⟩

hal-00654249

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

inria-00637536

Rayan Chikhi, Guillaume Chapuis, Dominique Lavenier

Parallel and memory-efficient reads indexing for genome assembly

Parallel Bio-Computing 2011, Sep 2011, torun, Poland

inria-00637535

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⟩

inria-00577218

Pierre Peterlongo, Rayan Chikhi

Mapsembler, targeted assembly of larges genomes on a desktop computer

[Research Report] RR-7565, INRIA. 2011, pp.17

inria-00426856

Rayan Chikhi, Dominique Lavenier

Paired-end read length lower bounds for genome re-sequencing

BMC Bioinformatics, 2009, ⟨10.1186/1471-2105-10-S13-O2⟩

inria-00453946

Chikhi Rayan, Steven Derrien, Noumsi Auguste, Patrice Quinton

Combining flash memory and FPGAs to efficiently implement a massively parallel algorithm for content-based image retrieval

International Journal of Electronics, 2008, 95 (7), pp.621-635(15)

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