Rayan Chikhi

ORCID

Publication Activity (10 Years)

Years Active: 2007-2024
Publications (10 Years): 32

Top Venues

École normale supérieure de Cachan, France (PHD)

Education History

École normale supérieure de Cachan, France

PHD

Publications

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. Nat. Comput. Sci. 4 (2) (2024)
Yoann Dufresne, Teo Lemane, Pierre Marijon, Pierre Peterlongo, Amatur Rahman, Marek Kokot, Paul Medvedev, Sebastian Deorowicz, Rayan Chikhi
-mers. Bioinform. 38 (18) (2022)
Teo Lemane, Rayan Chikhi, Pierre Peterlongo
-mer analyses. Bioinform. 38 (24) (2022)
Amatur Rahman, Rayan Chikhi, Paul Medvedev
Disk compression of k-mer sets. Algorithms Mol. Biol. 16 (1) (2021)
Rayan Chikhi, Jan Holub, Paul Medvedev
-long DNA Sequences. ACM Comput. Surv. 54 (1) (2021)
Rayan Chikhi
A Tale of Optimizing the Space Taken by de Bruijn Graphs. CiE (2021)
Camille Marchet, Zamin Iqbal, Daniel Gautheret, Mikaël Salson, Rayan Chikhi
REINDEER: efficient indexing of k-mer presence and abundance in sequencing datasets. Bioinform. 36 (Supplement-1) (2020)
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 Bioinform. 21 (4) (2020)
Yoann Dufresne, Chen Sun, Pierre Marijon, Dominique Lavenier, Cédric Chauve, Rayan Chikhi
A Graph-Theoretic Barcode Ordering Model for Linked-Reads. WABI (2020)
Amatur Rahman, Rayan Chikhi, Paul Medvedev
Disk Compression of k-mer Sets. WABI (2020)
Pierre Marijon, Rayan Chikhi, Jean-Stéphane Varré
yacrd and fpa: upstream tools for long-read genome assembly. Bioinform. 36 (12) (2020)
Rayan Chikhi, Vladan Jovicic, Stefan Kratsch, Paul Medvedev, Martin Milanic, Sofya Raskhodnikova, Nithin Varma
Bipartite graphs of small readability. Theor. Comput. Sci. 806 (2020)
Pierre Marijon, Rayan Chikhi, Jean-Stéphane Varré
Graph analysis of fragmented long-read bacterial genome assemblies. Bioinform. 35 (21) (2019)
Maël Kerbiriou, Rayan Chikhi
Parallel decompression of gzip-compressed files and random access to DNA sequences. CoRR (2019)
Rayan Chikhi, Jan Holub, Paul Medvedev
Data structures to represent sets of k-long DNA sequences. CoRR (2019)
Veli Mäkinen, Alexandru I. Tomescu, Anna Kuosmanen, Topi Paavilainen, Travis Gagie, Rayan Chikhi
Sparse Dynamic Programming on DAGs with Small Width. ACM Trans. Algorithms 15 (2) (2019)
Maël Kerbiriou, Rayan Chikhi
Parallel Decompression of Gzip-Compressed Files and Random Access to DNA Sequences. IPDPS Workshops (2019)
Anna Kuosmanen, Topi Paavilainen, Travis Gagie, Rayan Chikhi, Alexandru I. Tomescu, Veli Mäkinen
Using Minimum Path Cover to Boost Dynamic Programming on DAGs: Co-linear Chaining Extended. RECOMB (2018)
Samarth Rangavittal, Robert S. Harris, Monika Cechova, Marta Tomaszkiewicz, Rayan Chikhi, Kateryna D. Makova, Paul Medvedev
RecoverY: k-mer-based read classification for Y-chromosome-specific sequencing and assembly. Bioinform. 34 (7) (2018)
Victoria G. Crawford, Alan Kuhnle, Christina Boucher, Rayan Chikhi, Travis Gagie
Practical dynamic de Bruijn graphs. Bioinform. 34 (24) (2018)
Rayan Chikhi, Alexander Schönhuth
Dualities in Tree Representations. CoRR (2018)
Rayan Chikhi, Alexander Schönhuth
Dualities in Tree Representations. CPM (2018)
Chen Sun, Robert S. Harris, Rayan Chikhi, Paul Medvedev
AllSome Sequence Bloom Trees. J. Comput. Biol. 25 (5) (2018)
Rayan Chikhi, Vladan Jovicic, Stefan Kratsch, Paul Medvedev, Martin Milanic, Sofya Raskhodnikova, Nithin Varma
Bipartite Graphs of Small Readability. COCOON (2018)
Rayan Chikhi, Vladan Jovicic, Stefan Kratsch, Paul Medvedev, Martin Milanic, Sofya Raskhodnikova, Nithin Varma
Bipartite Graphs of Small Readability. CoRR (2018)
Chen Sun, Robert S. Harris, Rayan Chikhi, Paul Medvedev
AllSome Sequence Bloom Trees. RECOMB (2017)
Anna Kuosmanen, Topi Paavilainen, Travis Gagie, Rayan Chikhi, Alexandru I. Tomescu, Veli Mäkinen
Speeding up Dynamic Programming on DAGs through a Fast Approximation of Path Cover. CoRR (2017)
Antoine Limasset, Guillaume Rizk, Rayan Chikhi, Pierre Peterlongo
Fast and scalable minimal perfect hashing for massive key sets. CoRR (2017)
Antoine Limasset, Guillaume Rizk, Rayan Chikhi, Pierre Peterlongo
Fast and Scalable Minimal Perfect Hashing for Massive Key Sets. SEA (2017)
Rayan Chikhi, Antoine Limasset, Paul Medvedev
Compacting de Bruijn graphs from sequencing data quickly and in low memory. Bioinform. 32 (12) (2016)
Kristoffer Sahlin, Rayan Chikhi, Lars Arvestad
Assembly scaffolding with PE-contaminated mate-pair libraries. Bioinform. 32 (13) (2016)
Rayan Chikhi, Paul Medvedev, Martin Milanic, Sofya Raskhodnikova
On the readability of overlap digraphs. Discret. Appl. Math. 205 (2016)
Rayan Chikhi, Paul Medvedev, Martin Milanic, Sofya Raskhodnikova
On the readability of overlap digraphs. CoRR (2015)
Rayan Chikhi, Paul Medvedev, Martin Milanic, Sofya Raskhodnikova
On the Readability of Overlap Digraphs. CPM (2015)
Rayan Chikhi, Antoine Limasset, Shaun Jackman, Jared T. Simpson, Paul Medvedev
On the Representation of De Bruijn Graphs. J. Comput. Biol. 22 (5) (2015)
Guillaume Rizk, Anaïs Gouin, Rayan Chikhi, Claire Lemaitre
MindTheGap: integrated detection and assembly of short and long insertions. Bioinform. 30 (24) (2014)
Rayan Chikhi, Paul Medvedev
-mer size selection for genome assembly. Bioinform. 30 (1) (2014)
Rayan Chikhi, Antoine Limasset, Shaun Jackman, Jared T. Simpson, Paul Medvedev
On the representation of de Bruijn graphs. CoRR (2014)
Erwan Drezen, Guillaume Rizk, Rayan Chikhi, Charles Deltel, Claire Lemaitre, Pierre Peterlongo, Dominique Lavenier
GATB: Genome Assembly & Analysis Tool Box. Bioinform. 30 (20) (2014)
Rayan Chikhi, Antoine Limasset, Shaun Jackman, Jared T. Simpson, Paul Medvedev
On the Representation of de Bruijn Graphs. RECOMB (2014)
Rayan Chikhi, Guillaume Rizk
Space-efficient and exact de Bruijn graph representation based on a Bloom filter. Algorithms Mol. Biol. 8 (2013)
Guillaume Rizk, Dominique Lavenier, Rayan Chikhi
-mer counting with very low memory usage. Bioinform. 29 (5) (2013)
Pierre Peterlongo, Rayan Chikhi
Mapsembler, targeted and micro assembly of large NGS datasets on a desktop computer. BMC Bioinform. 13 (2012)
Rayan Chikhi, Guillaume Rizk
Space-Efficient and Exact de Bruijn Graph Representation Based on a Bloom Filter. WABI (2012)
Nicolas Maillet, Claire Lemaitre, Rayan Chikhi, Dominique Lavenier, Pierre Peterlongo
Compareads: comparing huge metagenomic experiments. BMC Bioinform. 13 (S-19) (2012)
Gustavo Akio Tominaga 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 Bioinform. 13 (S-6) (2012)
Rayan Chikhi, Dominique Lavenier
Localized Genome Assembly from Reads to Scaffolds: Practical Traversal of the Paired String Graph. WABI (2011)
Guillaume Chapuis, Rayan Chikhi, Dominique Lavenier
Parallel and Memory-Efficient Reads Indexing for Genome Assembly. PPAM (2) (2011)
Rayan Chikhi, Dominique Lavenier
Paired-end read length lower bounds for genome re-sequencing. BMC Bioinform. 10 (S-13) (2009)
Rayan Chikhi, Steven Derrien, Auguste Noumsi, Patrice Quinton
Combining Flash Memory and FPGAs to Efficiently Implement a Massively Parallel Algorithm for Content-Based Image Retrieval. ARC (2007)

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Publication Activity (10 Years)

Top Topics

Top Venues

Rayan Chikhi