Rayan Chikhi

55 papers B 6C 5Misc 1Journal 39Unranked 3
YearRankTypeTitle / Venue / Authors
2025 J jnl
MUSET: set of utilities for constructing abundance unitig matrices from sequencing data.
Bioinform.
Riccardo Vicedomini, Francesco Andreace, Yoann Dufresne, Rayan Chikhi, Camila Duitama González
2025 J jnl
Processing-in-memory for genomics workloads.
CoRR
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
2025 J jnl
Statistical signature of subtle behavioral changes in large-scale assays.
PLoS Comput. Biol.
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
2024 J jnl
Indexing and real-time user-friendly queries in terabyte-sized complex genomic datasets with kmindex and ORA.
Nat. Comput. Sci.
Téo Lemane, Nolan Lezzoche, Julien Lecubin, Eric Pelletier, Magali Lescot, Rayan Chikhi, Pierre Peterlongo
2024 J jnl
Reference-free structural variant detection in microbiomes via long-read co-assembly graphs.
Bioinform.
Kristen D. Curry, Feiqiao Brian Yu, Summer E. Vance, Santiago Segarra, Devaki Bhaya, Rayan Chikhi, Eduardo P. C. Rocha, Todd J. Treangen
2022 J jnl
<tt>k</tt> <tt>mdiff</tt>, large-scale and user-friendly differential
Bioinform.
Téo Lemane, Rayan Chikhi, Pierre Peterlongo
2022 J jnl
Data Structures to Represent a Set of
ACM Comput. Surv.
Rayan Chikhi, Jan Holub, Paul Medvedev
2022 J jnl
The K-mer File Format: a standardized and compact disk representation of sets of
Bioinform.
Yoann Dufresne, Téo Lemane, Pierre Marijon, Pierre Peterlongo, Amatur Rahman, Marek Kokot, Paul Medvedev, Sebastian Deorowicz, Rayan Chikhi
2021 C conf
A Tale of Optimizing the Space Taken by de Bruijn Graphs.
CiE
Rayan Chikhi
2021 J jnl
Disk compression of k-mer sets.
Algorithms Mol. Biol.
Amatur Rahman, Rayan Chikhi, Paul Medvedev
2020 C conf
A Graph-Theoretic Barcode Ordering Model for Linked-Reads.
WABI
Yoann Dufresne, Chen Sun, Pierre Marijon, Dominique Lavenier, Cédric Chauve, Rayan Chikhi
2020 J jnl
Bipartite graphs of small readability.
Theor. Comput. Sci.
Rayan Chikhi, Vladan Jovicic, Stefan Kratsch, Paul Medvedev, Martin Milanic, Sofya Raskhodnikova, Nithin Varma
2020 J jnl
Comparative assessment of long-read error correction software applied to Nanopore RNA-sequencing data.
Briefings Bioinform.
Leandro Lima, Camille Marchet, Ségolène Caboche, Corinne Da Silva, Benjamin Istace, Jean-Marc Aury, Hélène Touzet, Rayan Chikhi
2020 C conf
Disk Compression of k-mer Sets.
WABI
Amatur Rahman, Rayan Chikhi, Paul Medvedev
2020 J jnl
REINDEER: efficient indexing of k-mer presence and abundance in sequencing datasets.
Bioinform.
Camille Marchet, Zamin Iqbal, Daniel Gautheret, Mikaël Salson, Rayan Chikhi
2020 J jnl
yacrd and fpa: upstream tools for long-read genome assembly.
Bioinform.
Pierre Marijon, Rayan Chikhi, Jean-Stéphane Varré
2019 J jnl
Data structures to represent sets of k-long DNA sequences.
CoRR
Rayan Chikhi, Jan Holub, Paul Medvedev
2019 J jnl
Graph analysis of fragmented long-read bacterial genome assemblies.
Bioinform.
Pierre Marijon, Rayan Chikhi, Jean-Stéphane Varré
2019 — conf
Parallel Decompression of Gzip-Compressed Files and Random Access to DNA Sequences.
IPDPS Workshops
Maël Kerbiriou, Rayan Chikhi
2019 J jnl
Parallel decompression of gzip-compressed files and random access to DNA sequences.
CoRR
Maël Kerbiriou, Rayan Chikhi
2019 J jnl
Sparse Dynamic Programming on DAGs with Small Width.
ACM Trans. Algorithms
Veli Mäkinen, Alexandru I. Tomescu, Anna Kuosmanen, Topi Paavilainen, Travis Gagie, Rayan Chikhi
2018 J jnl
AllSome Sequence Bloom Trees.
J. Comput. Biol.
Chen Sun, Robert S. Harris, Rayan Chikhi, Paul Medvedev
2018 Misc conf
Bipartite Graphs of Small Readability.
COCOON
Rayan Chikhi, Vladan Jovicic, Stefan Kratsch, Paul Medvedev, Martin Milanic, Sofya Raskhodnikova, Nithin Varma
2018 J jnl
Bipartite Graphs of Small Readability.
CoRR
Rayan Chikhi, Vladan Jovicic, Stefan Kratsch, Paul Medvedev, Martin Milanic, Sofya Raskhodnikova, Nithin Varma
2018 B conf
Dualities in Tree Representations.
CPM
Rayan Chikhi, Alexander Schönhuth
2018 J jnl
Dualities in Tree Representations.
CoRR
Rayan Chikhi, Alexander Schönhuth
2018 J jnl
Practical dynamic de Bruijn graphs.
Bioinform.
Victoria G. Crawford, Alan Kuhnle, Christina Boucher, Rayan Chikhi, Travis Gagie
2018 J jnl
RecoverY: k-mer-based read classification for Y-chromosome-specific sequencing and assembly.
Bioinform.
Samarth Rangavittal, Robert S. Harris, Monika Cechova, Marta Tomaszkiewicz, Rayan Chikhi, Kateryna D. Makova, Paul Medvedev
2018 B conf
Using Minimum Path Cover to Boost Dynamic Programming on DAGs: Co-linear Chaining Extended.
RECOMB
Anna Kuosmanen, Topi Paavilainen, Travis Gagie, Rayan Chikhi, Alexandru I. Tomescu, Veli Mäkinen
2017 B conf
AllSome Sequence Bloom Trees.
RECOMB
Chen Sun, Robert S. Harris, Rayan Chikhi, Paul Medvedev
2017 B conf
Fast and Scalable Minimal Perfect Hashing for Massive Key Sets.
SEA
Antoine Limasset, Guillaume Rizk, Rayan Chikhi, Pierre Peterlongo
2017 J jnl
Fast and scalable minimal perfect hashing for massive key sets.
CoRR
Antoine Limasset, Guillaume Rizk, Rayan Chikhi, Pierre Peterlongo
2017 J jnl
Speeding up Dynamic Programming on DAGs through a Fast Approximation of Path Cover.
CoRR
Anna Kuosmanen, Topi Paavilainen, Travis Gagie, Rayan Chikhi, Alexandru I. Tomescu, Veli Mäkinen
2016 J jnl
Assembly scaffolding with PE-contaminated mate-pair libraries.
Bioinform.
Kristoffer Sahlin, Rayan Chikhi, Lars Arvestad
2016 J jnl
Compacting de Bruijn graphs from sequencing data quickly and in low memory.
Bioinform.
Rayan Chikhi, Antoine Limasset, Paul Medvedev
2016 J jnl
On the readability of overlap digraphs.
Discret. Appl. Math.
Rayan Chikhi, Paul Medvedev, Martin Milanic, Sofya Raskhodnikova
2015 B conf
On the Readability of Overlap Digraphs.
CPM
Rayan Chikhi, Paul Medvedev, Martin Milanic, Sofya Raskhodnikova
2015 J jnl
On the Representation of De Bruijn Graphs.
J. Comput. Biol.
Rayan Chikhi, Antoine Limasset, Shaun Jackman, Jared T. Simpson, Paul Medvedev
2015 J jnl
On the readability of overlap digraphs.
CoRR
Rayan Chikhi, Paul Medvedev, Martin Milanic, Sofya Raskhodnikova
2014 J jnl
GATB: Genome Assembly & Analysis Tool Box.
Bioinform.
Erwan Drezen, Guillaume Rizk, Rayan Chikhi, Charles Deltel, Claire Lemaitre, Pierre Peterlongo, Dominique Lavenier
2014 J jnl
Informed and automated
Bioinform.
Rayan Chikhi, Paul Medvedev
2014 J jnl
MindTheGap: integrated detection and assembly of short and long insertions.
Bioinform.
Guillaume Rizk, Anaïs Gouin, Rayan Chikhi, Claire Lemaitre
2014 B conf
On the Representation of de Bruijn Graphs.
RECOMB
Rayan Chikhi, Antoine Limasset, Shaun Jackman, Jared T. Simpson, Paul Medvedev
2014 J jnl
On the representation of de Bruijn graphs.
CoRR
Rayan Chikhi, Antoine Limasset, Shaun Jackman, Jared T. Simpson, Paul Medvedev
2013 J jnl
DSK:
Bioinform.
Guillaume Rizk, Dominique Lavenier, Rayan Chikhi
2013 J jnl
Space-efficient and exact de Bruijn graph representation based on a Bloom filter.
Algorithms Mol. Biol.
Rayan Chikhi, Guillaume Rizk
2012 J jnl
Compareads: comparing huge metagenomic experiments.
BMC Bioinform.
Nicolas Maillet, Claire Lemaitre, Rayan Chikhi, Dominique Lavenier, Pierre Peterlongo
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 J jnl
KISSPLICE: de-novo calling alternative splicing events from RNA-seq data.
BMC Bioinform.
Gustavo Akio Tominaga Sacomoto, Janice Kielbassa, Rayan Chikhi, Raluca Uricaru, Pavlos Antoniou, Marie-France Sagot, Pierre Peterlongo, Vincent Lacroix
2012 J jnl
Mapsembler, targeted and micro assembly of large NGS datasets on a desktop computer.
BMC Bioinform.
Pierre Peterlongo, Rayan Chikhi
2012 C conf
Space-Efficient and Exact de Bruijn Graph Representation Based on a Bloom Filter.
WABI
Rayan Chikhi, Guillaume Rizk
2011 C conf
Localized Genome Assembly from Reads to Scaffolds: Practical Traversal of the Paired String Graph.
WABI
Rayan Chikhi, Dominique Lavenier
2011 — conf
Parallel and Memory-Efficient Reads Indexing for Genome Assembly.
PPAM (2)
Guillaume Chapuis, Rayan Chikhi, Dominique Lavenier
2009 J jnl
Paired-end read length lower bounds for genome re-sequencing.
BMC Bioinform.
Rayan Chikhi, Dominique Lavenier
2007 — conf
Combining Flash Memory and FPGAs to Efficiently Implement a Massively Parallel Algorithm for Content-Based Image Retrieval.
ARC
Rayan Chikhi, Steven Derrien, Auguste Noumsi, Patrice Quinton