Rayan Chikhi
Rayan Chikhi
Institut Pasteur & CNRS
Verified email at ens-cachan.org - Homepage
Cited by
Cited by
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
Informed and automated k-mer size selection for genome assembly
R Chikhi, P Medvedev
Bioinformatics 30 (1), 31-37, 2014
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
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
Space-efficient and exact de Bruijn graph representation based on a Bloom filter
R Chikhi, G Rizk
Algorithms for Molecular Biology 8 (1), 1-9, 2013
DSK: k-mer counting with very low memory usage
G Rizk, D Lavenier, R Chikhi
Bioinformatics 29 (5), 652-653, 2013
Computational pan-genomics: status, promises and challenges
Briefings in bioinformatics 19 (1), 118-135, 2018
On the representation of de Bruijn graphs
R Chikhi, A Limasset, S Jackman, JT Simpson, P Medvedev
International conference on Research in computational molecular biology, 35-55, 2014
Compacting de Bruijn graphs from sequencing data quickly and in low memory
R Chikhi, A Limasset, P Medvedev
Bioinformatics 32 (12), i201-i208, 2016
K is s plice: 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 (6), 1-12, 2012
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
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
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
GATB: genome assembly & analysis tool box
E Drezen, G Rizk, R Chikhi, C Deltel, C Lemaitre, P Peterlongo, ...
Bioinformatics 30 (20), 2959-2961, 2014
Real‐time ligand binding pocket database search using local surface descriptors
R Chikhi, L Sael, D Kihara
Proteins: Structure, Function, and Bioinformatics 78 (9), 2007-2028, 2010
Compareads: comparing huge metagenomic experiments
N Maillet, C Lemaitre, R Chikhi, D Lavenier, P Peterlongo
BMC bioinformatics 13 (19), 1-10, 2012
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
MindTheGap: integrated detection and assembly of short and long insertions
G Rizk, A Gouin, R Chikhi, C Lemaitre
Bioinformatics 30 (24), 3451-3457, 2014
Mapsembler, targeted and micro assembly of large NGS datasets on a desktop computer
P Peterlongo, R Chikhi
BMC bioinformatics 13 (1), 1-14, 2012
Allsome sequence bloom trees
C Sun, RS Harris, R Chikhi, P Medvedev
International Conference on Research in Computational Molecular Biology, 272-286, 2017
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