Lucien Piat

About Me

I'm a Bioinformatics Engineer currently working at Agroscope (Switzerland) on de novo genome assembly and genetic diversity in grass ecotypes. I recently completed my M.Sc. in Bioinformatics from the University of Rouen, with an 18-month apprenticeship at INRAE.

My work centers on pangenomics, genome assembly, and NGS analysis, where I develop computational tools and workflows for large-scale genomic data. These are topics I'm eager to explore further and at greater depth.

I also served as House Manager at the Bordeaux National Opera for five years, coordinating reception teams during evening performances, a role that taught me rigor, teamwork, and attention to detail.

Main skills

Publications & Reports

Papers

• (preprint) A chromosome-scale genome assembly of the Swiss Lolium multiflorum ecotype Tremona reveals a scalable method to purge spurious duplications L. Piat, G. Herren, C. Grieder, A.C. Roulin bioRxiv, 2026 bioRxiv
• (preprint) Simulating population pangenomes under coalescent demographic models with MSpangenome L. Piat, S. Denni, S. Dubois, B. Linard, L. Duvaux bioRxiv, 2026 bioRxiv
• (preprint) A reference genome assembly for Quercus canariensis Willd F. Couturier, C. Cravero, I. Lesur, J. Confais, E. Belmonte, L. Piat, W. Marande, C. Rellstab, M. Valbuena, E. Saez-Laguna, L. Duvaux bioRxiv, 2026 bioRxiv

Posters & Conference Presentations

• MSpangepop: Simulating complex structural variants under advanced demographic scenarios using the coalescent L. Piat, S. Denni, S. Dubois, F. Couturier, N. Lapalu, B. Linard, C. Lemaitre, L. Duvaux JOBIM 2025, Bordeaux, France HAL

Reports

• De la construction a la simulation des pangenomes : une approche bioinformatique integree via Asm4pg et MSpangepop PDF M.Sc. apprenticeship report, INRAE BIOGECO / Univ. Rouen, 2024-2026 | Supervised by Dr. Ludovic Duvaux
• Single Tree Detection: The Jurassic Bark PDF M. Nurmukhambetov, C. Salzmann, K. Verhaeghe, L. Piat Erasmus+ research project, University of Groningen, March 2024

Projects

Main Projects

ParaLies

Tool using synonymous divergence (Ks) to detect and remove artefactual duplications caused by failed allelic collapse in heterozygous diploid genome assemblies, while preserving genuine ancient paralogues.

Supervised by : Dr Anne C. Roulin

Python Genome Assembly DIAMOND MCScanX Apptainer Conda

GitHub

MSpangepop ⋆

Python library for pangenome simulation under coalescent demographic models. Features clean, object-oriented architecture designed for extensibility and ease of use by biologists.

Supervised by : DSc Ludovic Duvaux

Python Population Genetics Coalescent Theory OOP MSprime / tskit Pangenome Graphs

GitHub GitLab Poster

Asm4gp ⋆

Comprehensive long-read assembly and QC pipeline supporting PacBio, ONT, TRIO, Hi-C, and HiFi data. Developed using Snakemake to automate haplotype-resolved genome assembly inputs for pangenome construction.

Supervised by : DSc Ludovic Duvaux

Snakemake Python SLURM Apptainer Conda Bash

GitHub GitLab Annimated flowchart

Smaller Projects

MycoLasso

MycoLasso is a Shiny GUI app to load, visualize, and interactively explore geospatial data points.

R Shiny Leaflet

GitHub Website

Urban Tree Detection

U-Net Deep learning pipeline for tree detection and counting from satellite imagery.

Supervised by : Pr Jean-Christophe Taveau

Computer Vision Python Deep Learning

Report

FEAther

Shiny GUI for functional enrichment analysis of biological data.

Supervised by : Asst. Prof Hélène Dauchel

R Shiny Functional Enrichment Analysis

GitHub Website

Fruit Proteomics Analysis

Statistical analysis of proteomic data across five fruit species.

Supervised by : Dr Sophie Colombié

R Functional Enrichment Analysis Proteomics

Contact