| Informed and automated k-mer size selection for genome assembly R Chikhi, P Medvedev Bioinformatics 30 (1), 31-37, 2014 | 829 | 2014 |
| 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 | 817 | 2013 |
| 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 | 812 | 2017 |
| 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 | 637 | 2011 |
| 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 | 533 | 2013 |
| DSK: k-mer counting with very low memory usage G Rizk, D Lavenier, R Chikhi Bioinformatics 29 (5), 652-653, 2013 | 386 | 2013 |
| 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 | 370 | 2022 |
| Computational pan-genomics: status, promises and challenges Briefings in bioinformatics 19 (1), 118-135, 2018 | 363 | 2018 |
| 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 | 265 | 2022 |
| Compacting de Bruijn graphs from sequencing data quickly and in low memory R Chikhi, A Limasset, P Medvedev Bioinformatics 32 (12), i201-i208, 2016 | 247 | 2016 |
| 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 | 209 | 2014 |
| 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 | 129 | 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 | 120 | 2015 |
| 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 | 114 | 2011 |
| 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 | 113 | 2021 |
| 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 | 110 | 2016 |
| 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 | 108 | 2017 |
| 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 | 104 | 2021 |
| 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 | 97 | 2021 |
| GATB: genome assembly & analysis tool box E Drezen, G Rizk, R Chikhi, C Deltel, C Lemaitre, P Peterlongo, ... Bioinformatics 30 (20), 2959-2961, 2014 | 97 | 2014 |
Paul MedvedevPenn StateVerified email at cse.psu.edu
