Rayan Chikhi

According to our database, Rayan Chikhi authored at least 42 papers between 2007 and 2025.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2025

Processing-in-memory for genomics workloads.

William Andrew Simon, Leonid Yavits, Konstantina Koliogeorgi, Yann Falevoz, Yoshihiro Shibuya, Dominique Lavenier, Irem Boybat, Klea Zambaku, Berkan Sahin, Mohammad Sadrosadati, Onur Mutlu, Abu Sebastian, Rayan Chikhi, The BioPIM Consortium, Can Alkan

CoRR, June, 2025

Statistical signature of subtle behavioral changes in large-scale assays.

Alexandre Blanc, François Laurent, Alex Barbier-Chebbah, Hugues Van Assel, Benjamin T. Cocanougher, Benjamin M. W. Jones, Peter Hague, Marta Zlatic, Rayan Chikhi, Christian L. Vestergaard, Tihana Jovanic, Jean-Baptiste Masson, Chloé Barré

PLoS Comput. Biol., 2025

2024

Indexing and real-time user-friendly queries in terabyte-sized complex genomic datasets with kmindex and ORA.

Téo Lemane, Nolan Lezzoche, Julien Lecubin, Eric Pelletier, Magali Lescot, Rayan Chikhi, Pierre Peterlongo

Nat. Comput. Sci., 2024

Reference-free structural variant detection in microbiomes via long-read co-assembly graphs.

Kristen D. Curry, Feiqiao Brian Yu, Summer E. Vance, Santiago Segarra, Devaki Bhaya, Rayan Chikhi, Eduardo P. C. Rocha, Todd J. Treangen

Bioinform., 2024

2022

<tt>k</tt> <tt>mdiff</tt>, large-scale and user-friendly differential <i>k</i>-mer analyses.

Téo Lemane, Rayan Chikhi, Pierre Peterlongo

Bioinform., December, 2022

Data Structures to Represent a Set of <i>k</i>-long DNA Sequences.

Rayan Chikhi, Jan Holub, Paul Medvedev

ACM Comput. Surv., 2022

The K-mer File Format: a standardized and compact disk representation of sets of <i>k</i>-mers.

Yoann Dufresne, Téo Lemane, Pierre Marijon, Pierre Peterlongo, Amatur Rahman, Marek Kokot, Paul Medvedev, Sebastian Deorowicz, Rayan Chikhi

Bioinform., 2022

2021

A Tale of Optimizing the Space Taken by de Bruijn Graphs.

Rayan Chikhi

Proceedings of the Connecting with Computability, 2021

2020

yacrd and fpa: upstream tools for long-read genome assembly.

Pierre Marijon, Rayan Chikhi, Jean-Stéphane Varré

Bioinform., 2020

REINDEER: efficient indexing of k-mer presence and abundance in sequencing datasets.

Camille Marchet, Zamin Iqbal, Daniel Gautheret, Mikaël Salson, Rayan Chikhi

Bioinform., 2020

Comparative assessment of long-read error correction software applied to Nanopore RNA-sequencing data.

Leandro Lima, Camille Marchet, Ségolène Caboche, Corinne Da Silva, Benjamin Istace, Jean-Marc Aury, Hélène Touzet, Rayan Chikhi

Briefings Bioinform., 2020

Disk Compression of k-mer Sets.

Amatur Rahman, Rayan Chikhi, Paul Medvedev

Proceedings of the 20th International Workshop on Algorithms in Bioinformatics, 2020

A Graph-Theoretic Barcode Ordering Model for Linked-Reads.

Yoann Dufresne, Chen Sun, Pierre Marijon, Dominique Lavenier, Cédric Chauve, Rayan Chikhi

Proceedings of the 20th International Workshop on Algorithms in Bioinformatics, 2020

2019

Sparse Dynamic Programming on DAGs with Small Width.

Veli Mäkinen, Alexandru I. Tomescu, Anna Kuosmanen, Topi Paavilainen, Travis Gagie, Rayan Chikhi

ACM Trans. Algorithms, 2019

Data structures to represent sets of k-long DNA sequences.

Rayan Chikhi, Jan Holub, Paul Medvedev

CoRR, 2019

Graph analysis of fragmented long-read bacterial genome assemblies.

Pierre Marijon, Rayan Chikhi, Jean-Stéphane Varré

Bioinform., 2019

Parallel Decompression of Gzip-Compressed Files and Random Access to DNA Sequences.

Maël Kerbiriou, Rayan Chikhi

Proceedings of the IEEE International Parallel and Distributed Processing Symposium Workshops, 2019

2018

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

Samarth Rangavittal, Robert S. Harris, Monika Cechova, Marta Tomaszkiewicz, Rayan Chikhi, Kateryna D. Makova, Paul Medvedev

Bioinform., 2018

Practical dynamic de Bruijn graphs.

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

Bioinform., 2018

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

Anna Kuosmanen, Topi Paavilainen, Travis Gagie, Rayan Chikhi, Alexandru I. Tomescu, Veli Mäkinen

Proceedings of the Research in Computational Molecular Biology, 2018

Dualities in Tree Representations.

Rayan Chikhi, Alexander Schönhuth

Proceedings of the Annual Symposium on Combinatorial Pattern Matching, 2018

Bipartite Graphs of Small Readability.

Rayan Chikhi, Vladan Jovicic, Stefan Kratsch, Paul Medvedev, Martin Milanic, Sofya Raskhodnikova, Nithin Varma

Proceedings of the Computing and Combinatorics - 24th International Conference, 2018

2017

Speeding up Dynamic Programming on DAGs through a Fast Approximation of Path Cover.

Anna Kuosmanen, Topi Paavilainen, Travis Gagie, Rayan Chikhi, Alexandru I. Tomescu, Veli Mäkinen

CoRR, 2017

Fast and Scalable Minimal Perfect Hashing for Massive Key Sets.

Antoine Limasset, Guillaume Rizk, Rayan Chikhi, Pierre Peterlongo

Proceedings of the 16th International Symposium on Experimental Algorithms, 2017

AllSome Sequence Bloom Trees.

Chen Sun, Robert S. Harris, Rayan Chikhi, Paul Medvedev

Proceedings of the Research in Computational Molecular Biology, 2017

2016

Assembly scaffolding with PE-contaminated mate-pair libraries.

Kristoffer Sahlin, Rayan Chikhi, Lars Arvestad

Bioinform., 2016

Compacting de Bruijn graphs from sequencing data quickly and in low memory.

Rayan Chikhi, Antoine Limasset, Paul Medvedev

Bioinform., 2016

2015

On the Readability of Overlap Digraphs.

Rayan Chikhi, Paul Medvedev, Martin Milanic, Sofya Raskhodnikova

Proceedings of the Combinatorial Pattern Matching - 26th Annual Symposium, 2015

2014

MindTheGap: integrated detection and assembly of short and long insertions.

Guillaume Rizk, Anaïs Gouin, Rayan Chikhi, Claire Lemaitre

Bioinform., 2014

GATB: Genome Assembly & Analysis Tool Box.

Erwan Drezen, Guillaume Rizk, Rayan Chikhi, Charles Deltel, Claire Lemaitre, Pierre Peterlongo, Dominique Lavenier

Bioinform., 2014

Informed and automated <i>k</i>-mer size selection for genome assembly.

Rayan Chikhi, Paul Medvedev

Bioinform., 2014

On the Representation of de Bruijn Graphs.

Rayan Chikhi, Antoine Limasset, Shaun Jackman, Jared T. Simpson, Paul Medvedev

Proceedings of the Research in Computational Molecular Biology, 2014

2013

DSK: <i>k</i>-mer counting with very low memory usage.

Guillaume Rizk, Dominique Lavenier, Rayan Chikhi

Bioinform., 2013

2012

Computational methods for de novo assembly of next-generation genome sequencing data. (Méthodes de calcul pour assemblage de novo de nouvelle génération des techniques de séquençage du génome).

Rayan Chikhi

PhD thesis, 2012

KISSPLICE: de-novo calling alternative splicing events from RNA-seq data.

Gustavo Akio Tominaga Sacomoto, Janice Kielbassa, Rayan Chikhi, Raluca Uricaru, Pavlos Antoniou, Marie-France Sagot, Pierre Peterlongo, Vincent Lacroix

BMC Bioinform., 2012

Mapsembler, targeted and micro assembly of large NGS datasets on a desktop computer.

Pierre Peterlongo, Rayan Chikhi

BMC Bioinform., 2012

Compareads: comparing huge metagenomic experiments.

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

BMC Bioinform., 2012

Space-Efficient and Exact de Bruijn Graph Representation Based on a Bloom Filter.

Rayan Chikhi, Guillaume Rizk

Proceedings of the Algorithms in Bioinformatics - 12th International Workshop, 2012

2011

Localized Genome Assembly from Reads to Scaffolds: Practical Traversal of the Paired String Graph.

Rayan Chikhi, Dominique Lavenier

Proceedings of the Algorithms in Bioinformatics - 11th International Workshop, 2011

Parallel and Memory-Efficient Reads Indexing for Genome Assembly.

Guillaume Chapuis, Rayan Chikhi, Dominique Lavenier

Proceedings of the Parallel Processing and Applied Mathematics, 2011

2009

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

Rayan Chikhi, Dominique Lavenier

BMC Bioinform., 2009

2007

Combining Flash Memory and FPGAs to Efficiently Implement a Massively Parallel Algorithm for Content-Based Image Retrieval.

Rayan Chikhi, Steven Derrien, Auguste Noumsi, Patrice Quinton

Proceedings of the Reconfigurable Computing: Architectures, 2007