עקוב אחר
Rayan Chikhi
Rayan Chikhi
Institut Pasteur & CNRS
כתובת אימייל מאומתת בדומיין ens-cachan.org - דף הבית
כותרת
צוטט על ידי
צוטט על ידי
שנה
Informed and automated k-mer size selection for genome assembly‏
R Chikhi, P Medvedev‏
Bioinformatics 30 (1), 31-37, 2014‏
8432014
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
8202017
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
8112013
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
6332011
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
5322013
DSK: k-mer counting with very low memory usage‏
G Rizk, D Lavenier, R Chikhi‏
Bioinformatics 29 (5), 652-653, 2013‏
3902013
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
3892022
Computational pan-genomics: status, promises and challenges‏
Briefings in bioinformatics 19 (1), 118-135, 2018‏
3712018
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
2742022
Compacting de Bruijn graphs from sequencing data quickly and in low memory‏
R Chikhi, A Limasset, P Medvedev‏
Bioinformatics 32 (12), i201-i208, 2016‏
2572016
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
2142014
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
1342012
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
1232015
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
1192021
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
1152011
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
1112016
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
109*2021
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
1082017
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
1032021
GATB: genome assembly & analysis tool box‏
E Drezen, G Rizk, R Chikhi, C Deltel, C Lemaitre, P Peterlongo, ...‏
Bioinformatics 30 (20), 2959-2961, 2014‏
982014
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מאמרים 1–20