Rayan Chikhi

Institut Pasteur — France

Biochemistry, Genetics and Molecular Biology · Life Sciences

41h-index8.0kcitations162works14.52yr avg
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Research Topics

Genomics and Phylogenetic Studies(103), Algorithms and Data Compression(38), RNA and protein synthesis mechanisms(29), Chromosomal and Genetic Variations(27), Microbial Community Ecology and Physiology(16)

Publications162 total

asl/BandageNG: Continuous build
Zenodo (CERN European Organization for Nuclear Research)·2025Open Access
Inverted colored de Bruijn Graph for practical kmer sets storage
2025Open Access
Anyone can be the best: Impact of diverse methodologies on the evaluation of structural variant callers
2025Open Access
Processing-in-memory for genomics workloads
2025Open Access
High-quality metagenome assembly from nanopore reads with nanoMDBG
2025· 6 citedOpen Access
Statistical signature of subtle behavioral changes in large-scale assays
PLoS Computational Biology·2025· 2 citedOpen Access
Efficient and robust search of microbial genomes via phylogenetic compression
Nature Methods·2025· 11 citedOpen Access
Pangenome graph augmentation from unassembled long reads
2025Open Access
MUSET: set of utilities for constructing abundance unitig matrices from sequencing data
Bioinformatics·2025· 1 citedOpen Access
Analysis of metagenomic data
Nature Reviews Methods Primers·2025· 33 citedOpen Access
MUSET: Set of utilities for the construction of abundance unitig matrices from sequencing data
SPIRE - Sciences Po Institutional REpository·2024Open Access
Differential stress responsiveness determines intraspecies virulence heterogeneity and host adaptation in Listeria monocytogenes
Nature Microbiology·2024· 10 cited
BFVD—a large repository of predicted viral protein structures
Nucleic Acids Research·2024· 62 citedOpen Access
Constructing and personalizing population pangenome graphs
Nature Methods·2024· 1 citedOpen Access
Transipedia.org: k-mer-based exploration of large RNA sequencing datasets and application to cancer data
Genome biology·2024· 7 citedOpen Access
Logan: Planetary-Scale Genome Assembly Surveys Life’s Diversity
2024· 47 citedOpen Access
Reference-free structural variant detection in microbiomes via long-read co-assembly graphs
Bioinformatics·2024· 5 citedOpen Access
Statistical signature of subtle behavioural changes in large-scale behavioural assays
2024· 1 citedOpen Access
Exploring a large cancer cell line RNA-sequencing dataset with k-mers
2024· 4 citedOpen Access
Indexing and real-time user-friendly queries in terabyte-sized complex genomic datasets with kmindex and ORA
Nature Computational Science·2024· 12 citedOpen Access
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Frequent Co-authors

Paul Medvedev(13), Pierre Peterlongo(12), Guillaume Rizk(9), Claire Lemaitre(8), Dominique Lavenier(7), Aaron E. Darling(7), Antoine Limasset(7), David Koslicki(5), Christopher Quince(5), Riccardo Vicedomini(5), Anton Korobeynikov(5), Camille Marchet(5), Adrian Fritz(4), Rubén Garrido‐Oter(4), Tue Sparholt Jørgensen(4), Alexey Gurevich(4), Niranjan Nagarajan(4), Fernando Meyer(4), Lars Hestbjerg Hansen(4), Søren J. Sørensen(4)