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

Projects

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

MycoLasso

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

R Shiny Leaflet

GitHub Website

Urban Tree Detection

Deep learning pipeline for automated tree detection and counting from satellite imagery using U-Net architecture. Developed during Erasmus+ exchange at University of Groningen.

Supervised by : Pr Jean-Christophe Taveau

Computer Vision Python Deep Learning

Report

FEAther

Shiny application designed for functional enrichment analysis of biological data. It allows users to upload CSV files, select various analysis options, and visualize results through interactive plots and tables.

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 to identify differential protein expression patterns during development. Utilized R for data processing, visualization, and interpretation.

Supervised by : Dr Sophie Colombié

R Functional Enrichment Analysis Proteomics

Publications & Reports

Papers

• 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
• The pangenome of European white oaks: A new approach to identify potential barriers to gene flow F. Couturier, L. Piat, A. Mergez, F. Graziani, S. Denni, G. Magris, A. Szukala, M. Valbuena, S. Pinosio, C. Klopp, C. Rellstab, C. Plomion, E. Saez-Laguna, L. Duvaux EVOLTREE & Forgenius Final Conference, Nov 2025, Madrid, Spain HAL
• The pangenome of European white oaks: A new approach to assess genetic diversity F. Couturier, L. Piat, S. Denni, A. Mergez, G. Magris, A. Szukala, M. Valbuena, C. Plomion, S. Pinosio, E. Saez-Laguna, C. Klopp, L. Duvaux Doctorales de la foret, Feb 2025, Poitiers, 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

Contact