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 (ARC, 2007)

Paired-end read length lower bounds for genome re-sequencing. - Rayan Chikhi; Dominique Lavenier (BMC Bioinform., 2009)

Parallel and Memory-Efficient Reads Indexing for Genome Assembly. - Guillaume Chapuis; Rayan Chikhi; Dominique Lavenier (PPAM (2), 2011)

Localized Genome Assembly from Reads to Scaffolds: Practical Traversal of the Paired String Graph. - Rayan Chikhi; Dominique Lavenier (WABI, 2011)

Compareads: comparing huge metagenomic experiments. - Nicolas Maillet; Claire Lemaitre; Rayan Chikhi; Dominique Lavenier; Pierre Peterlongo (BMC Bioinform., 2012)

Mapsembler, targeted and micro assembly of large NGS datasets on a desktop computer. - Pierre Peterlongo; Rayan Chikhi (BMC Bioinform., 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)

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 (2012)

Space-efficient and exact de Bruijn graph representation based on a Bloom filter. - Rayan Chikhi; Guillaume Rizk (Algorithms Mol. Biol., 2013)

DSK: k-mer counting with very low memory usage. - Guillaume Rizk; Dominique Lavenier; Rayan Chikhi (Bioinform., 2013)

Informed and automated k-mer size selection for genome assembly. - Rayan Chikhi; Paul Medvedev (Bioinform., 2014)

GATB: Genome Assembly & Analysis Tool Box. - Erwan Drezen; Guillaume Rizk; Rayan Chikhi; Charles Deltel; Claire Lemaitre; Pierre Peterlongo; Dominique Lavenier (Bioinform., 2014)

MindTheGap: integrated detection and assembly of short and long insertions. - Guillaume Rizk; Anaïs Gouin; Rayan Chikhi; Claire Lemaitre (Bioinform., 2014)

On the Representation of De Bruijn Graphs. - Rayan Chikhi; Antoine Limasset; Shaun Jackman; Jared T. Simpson; Paul Medvedev (J. Comput. Biol., 2015)

Compacting de Bruijn graphs from sequencing data quickly and in low memory. - Rayan Chikhi; Antoine Limasset; Paul Medvedev (Bioinform., 2016)

Assembly scaffolding with PE-contaminated mate-pair libraries. - Kristoffer Sahlin; Rayan Chikhi; Lars Arvestad (Bioinform., 2016)

On the readability of overlap digraphs. - Rayan Chikhi; Paul Medvedev; Martin Milanic; Sofya Raskhodnikova (Discret. Appl. Math., 2016)

Fast and Scalable Minimal Perfect Hashing for Massive Key Sets. - Antoine Limasset; Guillaume Rizk; Rayan Chikhi; Pierre Peterlongo (SEA, 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)

Dualities in Tree Representations. - Rayan Chikhi; Alexander Schönhuth (CPM, 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 (RECOMB, 2018)

Practical dynamic de Bruijn graphs. - Victoria G. Crawford; Alan Kuhnle; Christina Boucher 001; Rayan Chikhi; Travis Gagie (Bioinform., 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)

AllSome Sequence Bloom Trees. - Chen Sun 014; Robert S. Harris; Rayan Chikhi; Paul Medvedev (J. Comput. Biol., 2018)

Parallel Decompression of Gzip-Compressed Files and Random Access to DNA Sequences. - Maël Kerbiriou; Rayan Chikhi (IPDPS Workshops, 2019)

Graph analysis of fragmented long-read bacterial genome assemblies. - Pierre Marijon; Rayan Chikhi; Jean-Stéphane Varré (Bioinform., 2019)

Data structures to represent sets of k-long DNA sequences. - Rayan Chikhi; Jan Holub 001; Paul Medvedev (CoRR, 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)

A Graph-Theoretic Barcode Ordering Model for Linked-Reads. - Yoann Dufresne; Chen Sun 014; Pierre Marijon; Dominique Lavenier; Cédric Chauve; Rayan Chikhi (WABI, 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)

REINDEER: efficient indexing of k-mer presence and abundance in sequencing datasets. - Camille Marchet; Zamin Iqbal; Daniel Gautheret; Mikaël Salson; Rayan Chikhi (Bioinform., 2020)

yacrd and fpa: upstream tools for long-read genome assembly. - Pierre Marijon; Rayan Chikhi; Jean-Stéphane Varré (Bioinform., 2020)

Bipartite graphs of small readability. - Rayan Chikhi; Vladan Jovicic; Stefan Kratsch; Paul Medvedev; Martin Milanic; Sofya Raskhodnikova; Nithin Varma 001 (Theor. Comput. Sci., 2020)

A Tale of Optimizing the Space Taken by de Bruijn Graphs. - Rayan Chikhi (CiE, 2021)

Disk compression of k-mer sets. - Amatur Rahman; Rayan Chikhi; Paul Medvedev (Algorithms Mol. Biol., 2021)

The K-mer File Format: a standardized and compact disk representation of sets of k-mers. - Yoann Dufresne; Téo Lemane; Pierre Marijon; Pierre Peterlongo; Amatur Rahman; Marek Kokot; Paul Medvedev; Sebastian Deorowicz; Rayan Chikhi (Bioinform., 2022)

Data Structures to Represent a Set of k-long DNA Sequences. - Rayan Chikhi; Jan Holub 001; Paul Medvedev (ACM Comput. Surv., 2022)

k mdiff, large-scale and user-friendly differential k-mer analyses. - Téo Lemane; Rayan Chikhi; Pierre Peterlongo (Bioinform., 2022)

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)

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)

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; et al. (PLoS Comput. Biol., 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; et al. (CoRR, 2025)