معرفی
Rayan Chikhi is a Researcher and Structure Manager Responsible at the Institut Pasteur, affiliated with the UMR3569 – Virology unit and the Advanced Molecular Virology department. His work lies at the intersection of bioinformatics, algorithmics, and computational biology, with a strong focus on developing efficient data structures and analytical tools for genome and metagenome analysis.
His research interests include:
- Bioinformatics and algorithm development for biological sequences
- Pangenomics and variation graph construction
- k-mer and minimizer-based data structures
- Genome and metagenome assembly
- Ancient DNA analysis and decontamination
- Microbial source tracking
Rayan Chikhi’s recent publications demonstrate a consistent trend toward creating scalable, efficient, and open-source computational tools that address bottlenecks in genomic data analysis. His work on unitig matrices (MUSET), quotient filters, and pangenome graphs reflects a focus on reducing computational resource demands while preserving biological accuracy. These tools are widely applicable in metagenomics, ancient DNA studies, and large-scale genomic association studies.
Scientific contributions and software developments include:
- MUSET: for constructing abundance-preserving unitig matrices
- Backpack Quotient Filter: a dynamic, space-efficient k-mer index
- decOM: for microbial source tracking in ancient samples
- aKmerBroom: for decontaminating ancient oral DNA
- Contributions to K-mer File Format standardization
He actively mentors and collaborates with junior researchers, including PhD students Francesco Andreace and Timothé Rouzé, and postdoctoral fellows such as Camila Duitama González and Kristen Curry. He is involved in major institutional initiatives such as the INCEPTION Convergence Institute and the Artificial Intelligence at the Pasteur Institute cross-functional project, highlighting his role in interdisciplinary research. His work is supported by collaborative grants and contributes to advancing open science in computational genomics.
Rayan Chikhi is a key member of the bioinformatics team at the Institut Pasteur, contributing to both methodological innovation and practical applications in virology and microbial genomics. His lab and team focus on building robust, open-source software tools that empower large-scale biological discovery.
