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ORCIDRayan Chikhi
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2020 – today
- 2024
[j27]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): 104-109 (2024)- 2022
- [j26]Yoann Dufresne, Téo Lemane, Pierre Marijon, Pierre Peterlongo, Amatur Rahman, Marek Kokot, Paul Medvedev, Sebastian Deorowicz, Rayan Chikhi:
The K-mer File Format: a standardized and compact disk representation of sets of k-mers. Bioinform. 38(18): 4423-4425 (2022) - [j25]Téo Lemane, Rayan Chikhi, Pierre Peterlongo:
k mdiff, large-scale and user-friendly differential k-mer analyses. Bioinform. 38(24): 5443-5445 (2022) - [j24]Rayan Chikhi, Jan Holub, Paul Medvedev:
Data Structures to Represent a Set of k-long DNA Sequences. ACM Comput. Surv. 54(1): 17:1-17:22 (2022) - 2021
- [j23]Amatur Rahman, Rayan Chikhi, Paul Medvedev:
Disk compression of k-mer sets. Algorithms Mol. Biol. 16(1): 10 (2021) - [c15]Rayan Chikhi:
A Tale of Optimizing the Space Taken by de Bruijn Graphs. CiE 2021: 120-134 - 2020
- [j22]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): 1164-1181 (2020) - [j21]Pierre Marijon, Rayan Chikhi, Jean-Stéphane Varré:
yacrd and fpa: upstream tools for long-read genome assembly. Bioinform. 36(12): 3894-3896 (2020) - [j20]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): i177-i185 (2020) - [j19]Rayan Chikhi, Vladan Jovicic, Stefan Kratsch, Paul Medvedev, Martin Milanic, Sofya Raskhodnikova, Nithin Varma:
Bipartite graphs of small readability. Theor. Comput. Sci. 806: 402-415 (2020) - [c14]Yoann Dufresne, Chen Sun, Pierre Marijon, Dominique Lavenier, Cédric Chauve, Rayan Chikhi:
A Graph-Theoretic Barcode Ordering Model for Linked-Reads. WABI 2020: 11:1-11:17 - [c13]Amatur Rahman, Rayan Chikhi, Paul Medvedev:
Disk Compression of k-mer Sets. WABI 2020: 16:1-16:18
2010 – 2019
- 2019
- [j18]Pierre Marijon, Rayan Chikhi, Jean-Stéphane Varré:
Graph analysis of fragmented long-read bacterial genome assemblies. Bioinform. 35(21): 4239-4246 (2019) - [j17]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): 29:1-29:21 (2019) - [c12]Maël Kerbiriou, Rayan Chikhi:
Parallel Decompression of Gzip-Compressed Files and Random Access to DNA Sequences. IPDPS Workshops 2019: 209-217 - [i8]Rayan Chikhi, Jan Holub, Paul Medvedev:
Data structures to represent sets of k-long DNA sequences. CoRR abs/1903.12312 (2019) - [i7]Maël Kerbiriou, Rayan Chikhi:
Parallel decompression of gzip-compressed files and random access to DNA sequences. CoRR abs/1905.07224 (2019) - 2018
- [j16]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): 1125-1131 (2018) - [j15]Victoria G. Crawford, Alan Kuhnle, Christina Boucher, Rayan Chikhi, Travis Gagie:
Practical dynamic de Bruijn graphs. Bioinform. 34(24): 4189-4195 (2018) - [j14]Chen Sun, Robert S. Harris, Rayan Chikhi, Paul Medvedev:
AllSome Sequence Bloom Trees. J. Comput. Biol. 25(5): 467-479 (2018) - [c11]Rayan Chikhi, Vladan Jovicic, Stefan Kratsch, Paul Medvedev, Martin Milanic, Sofya Raskhodnikova, Nithin Varma:
Bipartite Graphs of Small Readability. COCOON 2018: 467-479 - [c10]Rayan Chikhi, Alexander Schönhuth:
Dualities in Tree Representations. CPM 2018: 18:1-18:12 - [c9]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: 105-121 - [i6]Rayan Chikhi, Alexander Schönhuth:
Dualities in Tree Representations. CoRR abs/1804.04263 (2018) - [i5]Rayan Chikhi, Vladan Jovicic, Stefan Kratsch, Paul Medvedev, Martin Milanic, Sofya Raskhodnikova, Nithin Varma:
Bipartite Graphs of Small Readability. CoRR abs/1805.04765 (2018) - 2017
- [c8]Chen Sun, Robert S. Harris, Rayan Chikhi, Paul Medvedev:
AllSome Sequence Bloom Trees. RECOMB 2017: 272-286 - [c7]Antoine Limasset, Guillaume Rizk, Rayan Chikhi, Pierre Peterlongo:
Fast and Scalable Minimal Perfect Hashing for Massive Key Sets. SEA 2017: 25:1-25:16 - [i4]Antoine Limasset, Guillaume Rizk, Rayan Chikhi, Pierre Peterlongo:
Fast and scalable minimal perfect hashing for massive key sets. CoRR abs/1702.03154 (2017) - [i3]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 abs/1705.08754 (2017) - 2016
- [j13]Rayan Chikhi, Antoine Limasset, Paul Medvedev:
Compacting de Bruijn graphs from sequencing data quickly and in low memory. Bioinform. 32(12): 201-208 (2016) - [j12]Kristoffer Sahlin, Rayan Chikhi, Lars Arvestad:
Assembly scaffolding with PE-contaminated mate-pair libraries. Bioinform. 32(13): 1925-1932 (2016) - [j11]Rayan Chikhi, Paul Medvedev, Martin Milanic, Sofya Raskhodnikova:
On the readability of overlap digraphs. Discret. Appl. Math. 205: 35-44 (2016) - 2015
- [j10]Rayan Chikhi, Antoine Limasset, Shaun Jackman, Jared T. Simpson, Paul Medvedev:
On the Representation of De Bruijn Graphs. J. Comput. Biol. 22(5): 336-352 (2015) - [c6]Rayan Chikhi, Paul Medvedev, Martin Milanic, Sofya Raskhodnikova:
On the Readability of Overlap Digraphs. CPM 2015: 124-137 - [i2]Rayan Chikhi, Paul Medvedev, Martin Milanic, Sofya Raskhodnikova:
On the readability of overlap digraphs. CoRR abs/1504.04616 (2015) - 2014
- [j9]Rayan Chikhi, Paul Medvedev:
Informed and automated k-mer size selection for genome assembly. Bioinform. 30(1): 31-37 (2014) - [j8]Erwan Drezen, Guillaume Rizk, Rayan Chikhi, Charles Deltel, Claire Lemaitre, Pierre Peterlongo, Dominique Lavenier:
GATB: Genome Assembly & Analysis Tool Box. Bioinform. 30(20): 2959-2961 (2014) - [j7]Guillaume Rizk, Anaïs Gouin, Rayan Chikhi, Claire Lemaitre:
MindTheGap: integrated detection and assembly of short and long insertions. Bioinform. 30(24): 3451-3457 (2014) - [c5]Rayan Chikhi, Antoine Limasset, Shaun Jackman, Jared T. Simpson, Paul Medvedev:
On the Representation of de Bruijn Graphs. RECOMB 2014: 35-55 - [i1]Rayan Chikhi, Antoine Limasset, Shaun Jackman, Jared T. Simpson, Paul Medvedev:
On the representation of de Bruijn graphs. CoRR abs/1401.5383 (2014) - 2013
- [j6]Rayan Chikhi, Guillaume Rizk:
Space-efficient and exact de Bruijn graph representation based on a Bloom filter. Algorithms Mol. Biol. 8: 22 (2013) - [j5]Guillaume Rizk, Dominique Lavenier, Rayan Chikhi:
DSK: k-mer counting with very low memory usage. Bioinform. 29(5): 652-653 (2013) - 2012
- [b1]Rayan Chikhi:
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). École normale supérieure de Cachan, France, 2012 - [j4]Pierre Peterlongo, Rayan Chikhi:
Mapsembler, targeted and micro assembly of large NGS datasets on a desktop computer. BMC Bioinform. 13: 48 (2012) - [j3]Nicolas Maillet, Claire Lemaitre, Rayan Chikhi, Dominique Lavenier, Pierre Peterlongo:
Compareads: comparing huge metagenomic experiments. BMC Bioinform. 13(S-19): S10 (2012) - [j2]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): S5 (2012) - [c4]Rayan Chikhi, Guillaume Rizk:
Space-Efficient and Exact de Bruijn Graph Representation Based on a Bloom Filter. WABI 2012: 236-248 - 2011
- [c3]Guillaume Chapuis, Rayan Chikhi, Dominique Lavenier:
Parallel and Memory-Efficient Reads Indexing for Genome Assembly. PPAM (2) 2011: 272-280 - [c2]Rayan Chikhi, Dominique Lavenier:
Localized Genome Assembly from Reads to Scaffolds: Practical Traversal of the Paired String Graph. WABI 2011: 39-48
2000 – 2009
- 2009
- [j1]Rayan Chikhi, Dominique Lavenier:
Paired-end read length lower bounds for genome re-sequencing. BMC Bioinform. 10(S-13): 0 (2009) - 2007
- [c1]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: 247-258
Coauthor Index
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