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Genome Assembly and Analysis of the North American Mountain Goat ( Oreamnos americanus ) Reveals Species-Level Responses to Extreme Environments

 Daria Martchenko , Rayan Chikhi , Aaron Shafer
G3, 2020, 10 (2), pp.437-442. ⟨10.1534/g3.119.400747⟩
Article dans une revue hal-03165277v1

On the readability of overlap digraphs

 Rayan Chikhi , Paul Medvedev , Martin Milanic , Sofya Raskhodnikova
26th Annual Symposium on Combinatorial Pattern Matching, 2015, Ischia Porto, Italy. ⟨10.1007/978-3-319-19929-0_11⟩
Communication dans un congrès hal-01236007v1

RecoverY: k-mer-based read classification for Y-chromosome-specific sequencing and assembly

 Samarth Rangavittal , Robert Harris , Monika Cechova , Marta Tomaszkiewicz , Rayan Chikhi , et al.
Bioinformatics, 2017, ⟨10.1093/bioinformatics/btx771⟩
Article dans une revue hal-01729744v1
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GATB: Genome Assembly & Analysis Tool Box

 Erwan Drezen , Guillaume Rizk , Rayan Chikhi , Charles Deltel , Claire Lemaitre , et al.
Bioinformatics, 2014, 30, pp.2959 - 2961. ⟨10.1093/bioinformatics/btu406⟩
Article dans une revue hal-01088571v1
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Computational methods for de novo assembly of next-generation genome sequencing data

 Rayan Chikhi
Other [cs.OH]. École normale supérieure de Cachan - ENS Cachan, 2012. English. ⟨NNT : 2012DENS0033⟩
Thèse tel-00752033v1

Using Minimum Path Cover to Boost Dynamic Programming on DAGs: Co-Linear Chaining Extended

 Anna Kuosmanen , Topi Paavilainen , Travis Gagie , Rayan Chikhi , Alexandru Ioan Tomescu , et al.
RECOMB 2018 - 22nd Annual International Conference on Research in Computational Molecular Biology, Apr 2018, Paris, France
Communication dans un congrès hal-01935568v1
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Practical dynamic de Bruijn graphs

 Alan Kuhnle , Victoria G. Crawford , Christina Boucher , Rayan Chikhi , Travis Gagie
Bioinformatics, 2018, ⟨10.1093/bioinformatics/bty500⟩
Article dans une revue hal-01935559v1
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Fast and scalable minimal perfect hashing for massive key sets

 Antoine Limasset , Guillaume Rizk , Rayan Chikhi , Pierre Peterlongo
16th International Symposium on Experimental Algorithms, Jun 2017, London, United Kingdom. pp.1 - 11
Communication dans un congrès hal-01566246v1
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Debugging long-read genome and metagenome assemblies using string graph analysis

 Pierre Marijon , Jean-Stéphane Varré , Rayan Chikhi
JOBIM 2017- Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2017, Lille, France.
Poster de conférence hal-01574824v1

Parallel decompression of gzip-compressed files and random access to DNA sequences

 Mael Kerbiriou , Rayan Chikhi
2019 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), May 2019, Rio de Janeiro, France. pp.209-217, ⟨10.1109/IPDPSW.2019.00042⟩
Communication dans un congrès hal-03165281v1
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Localized genome assembly from reads to scaffolds: practical traversal of the paired string graph

 Rayan Chikhi , Dominique Lavenier
WABI 2011, Sep 2011, Sarrebruck, Germany. ⟨10.1007/978-3-642-23038-7_4⟩
Communication dans un congrès inria-00637535v1
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Parallel and memory-efficient reads indexing for genome assembly

 Rayan Chikhi , Guillaume Chapuis , Dominique Lavenier
Parallel Bio-Computing 2011, Sep 2011, torun, Poland
Communication dans un congrès inria-00637536v1
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Compareads: comparing huge metagenomic experiments

 Nicolas Maillet , Claire Lemaitre , Rayan Chikhi , Dominique Lavenier , Pierre Peterlongo
BMC Bioinformatics, 2012, 13 (Suppl 19), pp.S10. ⟨10.1186/1471-2105-13-S19-S10⟩
Article dans une revue hal-00784394v1
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GATB: a software toolbox for genome assembly and analysis

 Erwan Drezen , Guillaume Rizk , Rayan Chikhi , Charles Deltel , Claire Lemaitre , et al.
Bio-IT World Conference, Apr 2014, Boston, United States
Poster de conférence hal-01088641v1

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

 Chikhi Rayan , Steven Derrien , Noumsi Auguste , Patrice Quinton
International Journal of Electronics, 2008, 95 (7), pp.621-635(15)
Article dans une revue inria-00453946v1
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Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

 Keith Bradnam , Joseph Fass , Anton Alexandrov , Paul Baranay , Michael Bechner , et al.
GigaScience, 2013, 2 (1), pp.10. ⟨10.1186/2047-217X-2-10⟩
Article dans une revue hal-00868822v1
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REINDEER: efficient indexing of k-mer presence and abundance in sequencing datasets

 Camille Marchet , Zamin Iqbal , Daniel Gautheret , Mikaël Salson , Rayan Chikhi
Bioinformatics, 2020, 36 (Supplement_1), pp.i177-i185. ⟨10.1093/bioinformatics/btaa487⟩
Article dans une revue hal-03413006v1

Disk Compression of k-mer Sets

 Amatur Rahman , Rayan Chikhi , Paul Medvedev
WABI 2020, Sep 2020, Pisa, Italy
Communication dans un congrès hal-03165270v1
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Critical Assessment of Metagenome Interpretation: the second round of challenges

 Fernando Meyer , Adrian Fritz , Zhi-Luo Deng , David Koslicki , Till Robin Lesker , et al.
Nature Methods, 2022, 19 (4), pp.429-440. ⟨10.1038/s41592-022-01431-4⟩
Article dans une revue hal-03832903v1

New developments in KisSplice: Combining local and global transcriptome assemblers to decipher splicing in RNA-seq data

 Alice Julien-Laferriere , Gustavo Sacomoto , Rayan Chikhi , Erwan Scaon , David P. Parsons , et al.
Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM), Jul 2013, Toulouse, France
Communication dans un congrès hal-02069363v1
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On the readability of overlap digraphs

 Rayan Chikhi , Paul Medvedev , Martin Milanič , Sofya Raskhodnikova
Discrete Applied Mathematics, 2016, 205, pp.35-44. ⟨10.1016/j.dam.2015.12.009⟩
Article dans une revue hal-01729749v1
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A Graph-Theoretic Barcode Ordering Model for Linked-Reads

 Yoann Dufresne , Chen Sun , Pierre Marijon , Dominique Lavenier , Cedric Chauve , et al.
WABI 2020 - 20th Workshop on Algorithms in Bioinformatics, Sep 2020, Pisa, Italy. pp.11 - 12, ⟨10.4230/LIPIcs.WABI.2020.11⟩
Communication dans un congrès hal-03008334v1
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kmdiff, large-scale and user-friendly differential k-mer analyses

 Téo Lemane , Rayan Chikhi , Pierre Peterlongo
Bioinformatics, 2022, 38 (24), pp.5443-5445. ⟨10.1093/bioinformatics/btac689⟩
Article dans une revue hal-03885124v1
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Mapsembler, targeted assembly of larges genomes on a desktop computer

 Pierre Peterlongo , Rayan Chikhi
[Research Report] RR-7565, INRIA. 2011, pp.17
Rapport inria-00577218v1
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Strainberry: automated strain separation in low-complexity metagenomes using long reads

 Riccardo Vicedomini , Christopher Quince , Aaron Darling , Rayan Chikhi
Nature Communications, 2021, 12 (1), pp.4485. ⟨10.1038/s41467-021-24515-9⟩
Article dans une revue hal-03412884v1

Genome scaffolding with PE-contaminated mate-pair libraries

 Kristoffer Sahlin , Rayan Chikhi , Lars Arvestad.
WABI 2015, 2015, Atlanta, United States. ⟨10.1101/025650⟩
Communication dans un congrès hal-01236176v1

A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y

 Marta Tomaszkiewicz , Samarth Rangavittal , Monika Cechova , Rebeca Campos Sanchez , Howard William Fescemyer , et al.
Genome Research, 2016, 26 (4), pp.530 - 540. ⟨10.1101/gr.199448.115⟩
Article dans une revue hal-01395702v1

Bipartite Graphs of Small Readability

 Rayan Chikhi , Vladan Jovičić , Stefan Kratsch , Paul Medvedev , Martin Milanic , et al.
COCOON 2018 - The 24th International Computing and Combinatorics Conference, Jul 2018, Qingdao, China
Communication dans un congrès hal-01935562v1
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Space-efficient and exact de Bruijn graph representation based on a Bloom filter

 Rayan Chikhi , Guillaume Rizk
WABI 2012, Sep 2012, Ljubljana, Slovenia. pp 236-248, ⟨10.1007/978-3-642-33122-0_19⟩
Communication dans un congrès hal-00753930v1

On the Representation of De Bruijn Graphs

 Rayan Chikhi , Antoine Limasset , Shaun Jackman , Jared T. Simpson , Paul Medvedev
Journal of Computational Biology, 2015, 22 (5), pp.336 - 352. ⟨10.1089/cmb.2014.0160⟩
Article dans une revue hal-01524525v1
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