Roland Faure

Roland Faure

My research lies at the intersection of biology and computer science, with a focus on developing algorithms for large-scale (meta)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 and strain separation under the joint supervision of Dominique Lavenier (Inria Rennes) and Jean-François Flot (Université Libre de Bruxelles).

// PUBLICATIONS, PROCEEDINGS & PREPRINTS

    First author

  • R. Faure et al. SNooPy: a statistical framework for long-read metagenomic variant calling, Preprint (2025), [PDF] [link]
  • 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, Proceedings of BIOSTEC/BIOINFORMATICS 2024, [PDF] [link]
  • R. Faure et al. GraphUnzip: Untangling assembly graphs to finish assemblies, [Proceedings of JOBIM 2023] [Ph.D. chapter (2024)]
  • R. Faure et al. QuickDeconvolution: fast and scalable deconvolution of linked-read sequencing data, Bioinformatics advances (2022), [PDF] [link]

    • Ph.D. thesis

  • R. Faure Haplotype assembly from long reads, (2024), [PDF]

    • Contributing author

  • 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]

// CONFERENCE TALKS & PRESENTATIONS

Logan project

MSR sketching & Alice assembler

HairSplitter: distinguishing errors and variants in long reads

GraphUnzip: combining Hi-C with assembly graphs

  • SeqBIM 2021 [slides]
  • JOBIM 2021

Ph.D. defenses

  • Rennes 2024 (official defense) [slides]
  • Brussels 2024 (unofficial defense) [slides]

// INVITED SEMINARS

Searching through the SRA: The Logan Project

December 2025 Institute for Bioinformatics in Brussels, Vrije Universiteit Brussel, invited by Wim Vranken [slides]

Genome Assembly with MSR sketching

September 2025 The Huck Institute, Pennsylvania State University, invited by Paul Medvedev [slides]

// SOFTWARE

Alice

[GitHub]
HiFi metagenomic assembler. Its originality is to introduce and use MSR sketching, which allows the assembler to assembler reduced sketches rather than original reads while distinguishing strains

SNooPy

[GitHub]
Long read metagenomic variant caller. Implements a novel statistical framework tailored for metagenomic, with no assumptions on coverage, strain evolutionnary history or number of haplotypes.

HairSplitter

[GitHub]
Maps long reads to an assembly, detects regions where haplotypes are collapsed, groups reads by haplotype, and reassembles each group separately. Yields an assembly where all haplotypes are separated.

Strainminer

[GitHub]
Same software as HairSplitter, with the core algorithm reformulated as an ILP problem solved with Gurobi (experimental).

GenomeTailor

[GitHub]
Correct an assembly graph by realigning long reads on it.

GraphUnzip

[GitHub]
Uses long reads and/or Hi-C to improve the contiguity of assembly graphs.

QuickDeconvolution

[GitHub]
Scalable solution for barcode deconvolution of 10x reads.

// CAREER

Postdoc

2025-?

Browsing the SRA - Institut Pasteur

Working with Rayan Chikhi on searching efficiently through the Logan database, both for nucleotide sequences and for proteins.

Ph.D.

2021-2024

Haplotype assembly from long reads - INRIA Rennes and Université Libre de Bruxelles (ULB)

Developed HairSplitter and Alice assembler. Two years in Rennes and one year in Brussels, co-supervised by Dominique Lavenier and Jean-François Flot.

// RESEARCH EXCHANGES

Research exchange at Penn State University

September-October 2025

Comparing all metagenomes of Logan

Five week exchange in Paul Medvedev's group in Penn State University. Worked on comparing the five million metagenomes of Logan.

// STUDENTS SUPERVISED

Tam Minh Khac Truong

2022-2023

StrainMiner: ILP for strain separation in metagenomes

Two master internships (4+6 months). Best student paper award at BIOSTEC 2024.

Olivier De Thier

2023

Improving ascidian genome assemblies with long reads

6-month master thesis producing high-quality genomes for Botryllus schlosseri and Polyandrocarpa zorritensis.

Baptiste Hilaire

2023

Sequence reduction for bioinformatic tools

6-week bachelor internship exploring Mapping-friendly Sequence Reductions (MSRs).

// REVIEW ACTIVITIES

Conference Reviews

ISMB/ECCB 2024, Recomb-SEQ 2024

Journal Reviews

NAR Genomics and Bioinformatics (2022), Bioinformatics advances (2024), PCI Mathematical and Computational biology (2025)

// TEACHING EXPERIENCE

Java Programming

2021-2022 20h×2 practical sessions for 1st year bachelor computer science students, University of Rennes.

Python Object-Oriented Programming

2022-2023 34h×2 practical sessions for 1st year master bioinformatics students, University of Rennes.

Bioinformatics Crash Course

2022,2023,2024 6-hour crash course for high-school students selected for the International Biology Olympiad, Brussels.

// EDUCATION

Master in Bioinformatics & Modeling

2020-2021

Sorbonne Universités, Paris

Engineering Degree

2017-2020

École Polytechnique, Saclay

// CONTACT INFORMATION

Email roland.faure@pasteur.fr
GitHub RolandFaure
Bluesky @rfaure
ORCID 0000-0003-2245-4284