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Rayan Chikhi
Rayan Chikhi
Institut Pasteur & CNRS
Verified email at ens-cachan.org - Homepage
Title
Cited by
Cited by
Year
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
KR Bradnam, JN Fass, A Alexandrov, P Baranay, M Bechner, I Birol, ...
Gigascience 2 (1), 2047-217X-2-10, 2013
7982013
Informed and automated k-mer size selection for genome assembly
R Chikhi, P Medvedev
Bioinformatics 30 (1), 31-37, 2014
7762014
Critical Assessment of Metagenome Interpretation - a benchmark of metagenomics software
A Sczyrba, P Hofmann, P Belmann, D Koslicki, S Janssen, J Dröge, ...
Nature methods 14 (11), 1063-1071, 2017
7422017
Assemblathon 1: a competitive assessment of de novo short read assembly methods
D Earl, K Bradnam, JS John, A Darling, D Lin, J Fass, HOK Yu, V Buffalo, ...
Genome research 21 (12), 2224-2241, 2011
6352011
Space-efficient and exact de Bruijn graph representation based on a Bloom filter
R Chikhi, G Rizk
Algorithms for Molecular Biology 8, 1-9, 2013
5032013
DSK: k-mer counting with very low memory usage
G Rizk, D Lavenier, R Chikhi
Bioinformatics 29 (5), 652-653, 2013
3702013
Computational pan-genomics: status, promises and challenges
Briefings in bioinformatics 19 (1), 118-135, 2018
3312018
Petabase-scale sequence alignment catalyses viral discovery
RC Edgar, B Taylor, V Lin, T Altman, P Barbera, D Meleshko, D Lohr, ...
Nature 602 (7895), 142-147, 2022
2902022
Compacting de Bruijn graphs from sequencing data quickly and in low memory
R Chikhi, A Limasset, P Medvedev
Bioinformatics 32 (12), i201-i208, 2016
2242016
Critical assessment of metagenome interpretation: the second round of challenges
F Meyer, A Fritz, ZL Deng, D Koslicki, TR Lesker, A Gurevich, G Robertson, ...
Nature methods 19 (4), 429-440, 2022
1992022
On the representation of de Bruijn graphs
R Chikhi, A Limasset, S Jackman, JT Simpson, P Medvedev
Research in Computational Molecular Biology: 18th Annual International …, 2014
1962014
KIS SPLICE: de-novo calling alternative splicing events from RNA-seq data
GAT Sacomoto, J Kielbassa, R Chikhi, R Uricaru, P Antoniou, MF Sagot, ...
BMC bioinformatics 13, 1-12, 2012
1292012
Reference-free detection of isolated SNPs
R Uricaru, G Rizk, V Lacroix, E Quillery, O Plantard, R Chikhi, C Lemaitre, ...
Nucleic acids research 43 (2), e11-e11, 2015
1142015
A time-and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y
M Tomaszkiewicz, S Rangavittal, M Cechova, RC Sanchez, ...
Genome Research 26 (4), 530-540, 2016
1082016
Molecular surface representation using 3D Zernike descriptors for protein shape comparison and docking
D Kihara, L Sael, R Chikhi, J Esquivel-Rodriguez
Current Protein and Peptide Science 12 (6), 520-530, 2011
1072011
Data structures based on k-mers for querying large collections of sequencing data sets
C Marchet, C Boucher, SJ Puglisi, P Medvedev, M Salson, R Chikhi
Genome research 31 (1), 1-12, 2021
982021
Fast and scalable minimal perfect hashing for massive key sets
A Limasset, G Rizk, R Chikhi, P Peterlongo
16th International Symposium on Experimental Algorithms (SEA 2017) 75, 25:1 …, 2017
982017
GATB: genome assembly & analysis tool box
E Drezen, G Rizk, R Chikhi, C Deltel, C Lemaitre, P Peterlongo, ...
Bioinformatics 30 (20), 2959-2961, 2014
942014
STRONG: metagenomics strain resolution on assembly graphs
C Quince, S Nurk, S Raguideau, R James, OS Soyer, JK Summers, ...
Genome biology 22, 1-34, 2021
872021
Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer
B Ekim, B Berger, R Chikhi
Cell systems 12 (10), 958-968. e6, 2021
802021
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Articles 1–20