Roland Faure
I am a recently graduated PhD student working on sequence bioinformatics. I like imagining and implementing algorithmic solutions for biological problems. During my Ph.D., I focused on genome assembly, more specifically the problems of haplotyping and metagenome assembly. For my postdoc, I am implementing efficient methods to browse through the Logan dataset.
// ABOUT ME
My research lies at the intersection of biology and computer science, with a focus on developing algorithms for large-scale genomic data analysis. Since February 2025, I am a postdoctoral researcher in Rayan Chikhi's group at Institut Pasteur, Paris, working on efficient indexing and exploration of the Logan dataset. Previously, I completed my Ph.D. (2021–2024) on metagenome assembly under the joint supervision of Dominique Lavenier (Inria Rennes) and Jean-François Flot (Université Libre de Bruxelles).// PUBLICATIONS & PREPRINTS
- R. Faure et al. Alice: fast and haplotype-aware assembly of high-fidelity reads based on MSR sketching, Preprint (2025), [PDF] [link]
- R. Faure et al. Hairsplitter: Separating noisy long reads into an unknown number of haplotypes, Peer Community Journal (2024), [PDF] [link]
- R. Faure et al. strainMiner: Combining Integer Programming and Data Mining Techniques for Strain-level Metagenome Assembly, BIOSTEC/BIOINFORMATICS 2024, [PDF]
- R. Faure et al. QuickDeconvolution: fast and scalable deconvolution of linked-read sequencing data, Bioinformatics advances (2022), [PDF] [link]
- R. Faure et al. GraphUnzip: Untangling assembly graphs to finish assemblies, [JOBIM 2023] [Ph.D. chapter (2024)]
- R. Faure Haplotype assembly from long reads, (2024), [PDF]
- R. Chikhi et al. Logan: Planetary-Scale Genome Assembly Surveys Life’s Diversity, Preprint (2025), [PDF] [link]
- O. De Thier et al. First chromosome-level genome assembly of the colonial chordate model Botryllus schlosseri (Tunicata), GigaScience (2025), [PDF] [link]
- A. Choudhury et al. Deep mutational scanning reveals the molecular determinants of RNA polymerase-mediated adaptation and tradeoffs, Nature Communications (2023), [PDF] [link]