RC
Rayan Chikhi
bioinformaticsSoftwareAlgorithmscs.DSHigh-Throughput Nucleotide SequencingGenome, BacterialMetagenomeq-bio.GNComputational BiologyGenomics
On Valency
published · living versionsW_26xzgw86·v1 · currentpublished
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
with Keith R. Bradnam, Joseph N. Fass, Anton Alexandrov, Paul Baranay +86
1 version
Preprints & journals
95 papers in the corpus · 2010–2026Sketching the SRA: experiment-wide similarity search across 4.8 million metagenomes.42926794 · Faure, Roland, Nakshi, Adrita Hossain, Abrar, Md Hasin et al.2026 · 0 citationsbioRxiv : the preprint server for biology. 2026
Shuttling, swapping, and mixing: the rapid modular evolution of antiviral repertoires in temperate phages and their satellites.42755366 · de Sousa, Jorge Moura, Depardieu, Florence, Touchon, Marie et al.2026 · 0 citationsNucleic acids research. 2026;54(17)
A versatile multi-components mixed model for bacterial-Genome Wide association studies.42098097 · Frouin, Arthur, Laporte, Fabien, Hafner, Lukas et al.2026 · 0 citationsNature communications. 2026;17(1)
Petabase-scale Papillomavirus Discovery10.64898/2026.04.21.719858v1 · Shen, J., Chikhi, R., Korobeynikov, A. et al.2026 · 0 citationsbioRxiv
High-quality metagenome assembly from nanopore reads with nanoMDBG.41792155 · Benoit, Gaëtan, James, Robert, Raguideau, Sébastien et al.2026 · 16 citationsNature communications. 2026;17(1)
Taxonomic-free metagenome GWAS to identify gut microbiome functions influencing host phenotypes10.64898/2026.01.15.699651v1 · Malak, R., Frouin, A., Henches, L. et al.2026 · 0 citationsbioRxiv
Inverted colored de Bruijn Graph for practical kmer sets storage10.64898/2025.12.08.692073v1 · Rouze, T., Chikhi, R., Limasset, A.2025 · 0 citationsbioRxiv
Anyone can be the best: Impact of diverse methodologies on the evaluation of structural variant callers10.1101/2025.08.28.672546v1 · Denti, L., Krannich, T., Vinar, T. et al.2025 · 0 citationsbioRxiv
Logan: Planetary-Scale Genome Assembly Surveys Life's Diversity.40950083 · Chikhi, Rayan, Lemane, Téo, Loll-Krippleber, Raphaël et al.2025 · 74 citationsbioRxiv : the preprint server for biology. 2025
Processing-in-memory for genomics workloads2506.00597v2 · William Andrew Simon, Leonid Yavits, Konstantina Koliogeorgi et al.2025 · 2 citationsIEEE Micro, 46 (2): 70-80, 2026
Statistical signature of subtle behavioral changes in large-scale assays.40258220 · Blanc, Alexandre, Laurent, François, Barbier-Chebbah, Alex et al.2025 · 2 citationsPLoS computational biology. 2025;21(4):e1012990
MUSET: set of utilities for constructing abundance unitig matrices from sequencing data.39898792 · Vicedomini, Riccardo, Andreace, Francesco, Dufresne, Yoann et al.2025 · 4 citationsBioinformatics (Oxford, England). 2025;41(3)
Pangenome graph augmentation from unassembled long reads10.1101/2025.02.07.637057v2 · Denti, L., Bonizzoni, P., Brejova, B. et al.2025 · 3 citationsbioRxiv
BFVD-a large repository of predicted viral protein structures.39574394 · Kim, Rachel Seongeun, Levy Karin, Eli, Mirdita, Milot et al.2025 · 86 citationsNucleic acids research. 2025;53(D1):D340-D347
Analysis of metagenomic data.40688383 · Liu, Shaopeng, Rodriguez, Judith S, Munteanu, Viorel et al.2025 · 89 citationsNature reviews. Methods primers. 2025;5
Differential stress responsiveness determines intraspecies virulence heterogeneity and host adaptation in Listeria monocytogenes.39578578 · Hafner, Lukas, Gadin, Enzo, Huang, Lei et al.2024 · 15 citationsNature microbiology. 2024;9(12):3345-3361
Constructing and personalizing population pangenome graphs.39433877 · Chikhi, Rayan, Dufresne, Yoann, Medvedev, Paul2025 · 2 citationsNature methods. 2024;21(11):1980-1981
Transipedia.org: k-mer-based exploration of large RNA sequencing datasets and application to cancer data.39390592 · Bessière, Chloé, Xue, Haoliang, Guibert, Benoit et al.2024 · 8 citationsGenome biology. 2024;25(1):266
Efficient and Robust Search of Microbial Genomes via Phylogenetic Compression.37131636 · Břinda, Karel, Lima, Leandro, Pignotti, Simone et al.2025 · 28 citationsbioRxiv : the preprint server for biology. 2024
Statistical signature of subtle behavioural changes inlarge-scale behavioural assays10.1101/2024.05.03.591825v1 · Blanc, A., Laurent, F., Barbier--Chebbah, A. et al.2024 · 1 citationbioRxiv
Exploring a large cancer cell line RNA-sequencing dataset with k-mers10.1101/2024.02.27.581927v1 · Bessiere, C., Xue, H., Guibert, B. et al.2024 · 4 citationsbioRxiv
Petabase-Scale Homology Search for Structure Prediction.38316555 · Lee, Sewon, Kim, Gyuri, Karin, Eli Levy et al.2024 · 7 citationsCold Spring Harbor perspectives in biology. 2024;16(5)
Indexing and real-time user-friendly queries in terabyte-sized complex genomic datasets with kmindex and ORA.38413777 · Lemane, Téo, Lezzoche, Nolan, Lecubin, Julien et al.2024 · 18 citationsNature computational science. 2024;4(2):104-109
Reference-free Structural Variant Detection in Microbiomes via Long-read Coassembly Graphs.38352454 · Curry, Kristen D, Yu, Feiqiao Brian, Vance, Summer E et al.2024 · 10 citationsbioRxiv : the preprint server for biology. 2024
High-quality metagenome assembly from long accurate reads with metaMDBG.38168989 · Benoit, Gaëtan, Raguideau, Sébastien, James, Robert et al.2024 · 197 citationsNature biotechnology. 2024;42(9):1378-1383
Comparing methods for constructing and representing human pangenome graphs.38037131 · Andreace, Francesco, Lechat, Pierre, Dufresne, Yoann et al.2023 · 56 citationsGenome biology. 2023;24(1):274
The genomics and evolution of inter-sexual mimicry and female-limited polymorphisms in damselflies.37932383 · Willink, Beatriz, Tunström, Kalle, Nilén, Sofie et al.2024 · 22 citationsNature ecology & evolution. 2024;8(1):83-97
aKmerBroom: Ancient oral DNA decontamination using Bloom filters on k-mer sets.37876815 · Duitama González, Camila, Rangavittal, Samarth, Vicedomini, Riccardo et al.2024 · 7 citationsiScience. 2023;26(11):108057
Seedability: optimizing alignment parameters for sensitive sequence comparison.37621456 · Ayad, Lorraine A K, Chikhi, Rayan, Pissis, Solon P2023 · 2 citationsBioinformatics advances. 2023;3(1):vbad108
Petascale Homology Search for Structure Prediction.37503235 · Lee, Sewon, Kim, Gyuri, Karin, Eli Levy et al.2024 · 16 citationsbioRxiv : the preprint server for biology. 2023
Efficient High-Quality Metagenome Assembly from Long Accurate Reads using Minimizer-space de Bruijn Graphs.37786716 · Benoit, Gaëtan, Raguideau, Sébastien, James, Robert et al.2024 · 12 citationsbioRxiv : the preprint server for biology. 2023
Efficient mapping of accurate long reads in minimizer space with mapquik.37399256 · Ekim, Bariş, Sahlin, Kristoffer, Medvedev, Paul et al.2023 · 16 citationsGenome research. 2023;33(7):1188-1197
kmindex and ORA: indexing and real-time user-friendly queries in terabytes-sized complex genomic datasets10.1101/2023.05.31.543043v4 · Lemane, T., Lezzoche, N., Lecubin, J. et al.2023 · 2 citationsbioRxiv
Construction and representation of human pangenome graphs10.1101/2023.06.02.542089v1 · Andreace, F., Lechat, P., Dufresne, Y. et al.2023 · 4 citationsbioRxiv
Hybrids of RNA viruses and viroid-like elements replicate in fungi.37147358 · Forgia, Marco, Navarro, Beatriz, Daghino, Stefania et al.2023 · 83 citationsNature communications. 2023;14(1):2591
ChoruMM: a versatile multi-components mixed model for bacterial-GWAS10.1101/2023.03.28.534531v1 · Frouin, A., Laporte, F., Hafner, L. et al.2023 · 2 citationsbioRxiv
decOM: Similarity-based microbial source tracking of ancient oral samples using k-mer-based methods10.1101/2023.01.26.525439v1 · Duitama Gonzalez, C., Vicedomini, R., Lemane, T. et al.2023 · 15 citationsbioRxiv
mapquik: Efficient low-divergence mapping of long reads in minimizer space10.1101/2022.12.23.521809v2 · Ekim, B., Sahlin, K., Medvedev, P. et al.2022 · 3 citationsbioRxiv
SVDSS: structural variation discovery in hard-to-call genomic regions using sample-specific strings from accurate long reads.36550274 · Denti, Luca, Khorsand, Parsoa, Bonizzoni, Paola et al.2023 · 36 citationsNature methods. 2023;20(4):550-558
k mdiff, large-scale and user-friendly differential k-mer analyses.36315078 · Lemane, Téo, Chikhi, Rayan, Peterlongo, Pierre2022 · 15 citationsBioinformatics (Oxford, England). 2022;38(24):5443-5445
Draft genome of the lowland anoa (Bubalus depressicornis) and comparison with buffalo genome assemblies (Bovidae, Bubalina).36111873 · Porrelli, Stefano, Gerbault-Seureau, Michèle, Rozzi, Roberto et al.2022 · 3 citationsG3 (Bethesda, Md.). 2022;12(11)
Mapping-friendly sequence reductions: Going beyond homopolymer compression.36339268 · Blassel, Luc, Medvedev, Paul, Chikhi, Rayan2024 · 9 citationsiScience. 2022;25(11):105305
The K-mer File Format: a standardized and compact disk representation of sets of k-mers.35904548 · Dufresne, Yoann, Lemane, Teo, Marijon, Pierre et al.2022 · 17 citationsBioinformatics (Oxford, England). 2022;38(18):4423-4425
kmtricks: efficient and flexible construction of Bloom filters for large sequencing data collections.36699393 · Lemane, Téo, Medvedev, Paul, Chikhi, Rayan et al.2024 · 51 citationsBioinformatics advances. 2022;2(1):vbac029
Unlocking the microblogging potential for science and medicine10.1101/2022.04.22.488804v2 · Sarkar, A., Giros, A., Mockly, L. et al.2022 · 1 citationbioRxiv
Critical Assessment of Metagenome Interpretation: the second round of challenges.35396482 · Meyer, Fernando, Fritz, Adrian, Deng, Zhi-Luo et al.2022 · 384 citationsNature methods. 2022;19(4):429-440
Improved structural variant discovery in hard-to-call regions using sample-specific string detection from accurate long reads10.1101/2022.02.12.480198v1 · Denti, L., Khorsand, P., Bonizzoni, P. et al.2022 · 4 citationsbioRxiv
Petabase-scale sequence alignment catalyses viral discovery.35082445 · Edgar, Robert C, Taylor, Brie, Lin, Victor et al.2022 · 498 citationsNature. 2022;602(7895):142-147
Recombination Marks the Evolutionary Dynamics of a Recently Endogenized Retrovirus.34480565 · Yang, Lei, Malhotra, Raunaq, Chikhi, Rayan et al.2022 · 6 citationsMolecular biology and evolution. 2021;38(12):5423-5436
Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer.34525345 · Ekim, Barış, Berger, Bonnie, Chikhi, Rayan2022 · 114 citationsCell systems. 2021;12(10):958-968.e6
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