Léo d'Agata - Bioinformatician

Transforming biological data into actionable insights

Based in Aix-en-Provence, France • NGS • Microbiome Analysis • Oncology Variant Research

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About Me

Currently based in Aix-en-Provence, France, I am a bioinformatics engineer with strong technical expertise and significant experience in biostatistics, genomics, and bioinformatics across various settings from academic research to the pharmaceutical and cosmetic industry.

My career has included key roles at Life & Soft, INRA, and collaborations with prestigious institutions like GSK, CEA and L'Oréal, where I developed a deep understanding of next-generation sequencing (NGS) data, microbiome analysis, and oncology variant research.

Passionate about using bioinformatics to solve complex problems and drive innovation in health and biology, my team collaboration, communication, and project management skills, combined with my technical expertise, enable me to successfully lead significant projects and work effectively in multidisciplinary teams.

I am open to exploring new opportunities and collaborating on projects that could benefit from my expertise. Feel free to contact me if you wish to discuss how I can contribute to your project.

Skills & Technologies

Programming Languages

Python R Perl SQL Bash

Bioinformatics Tools

BioConductor BLAST Kraken2 Snakemake BWA/Bowtie

Oncology & Variants

GATK/Dragen Mutect2 HaplotypeCaller VarDict Manta/Delly CNVkit

Data Analysis

Genomics RNA-Seq Machine Learning Statistical Analysis Data Visualization

Tools & Platforms

Docker Git AWS SLURM/HPC Linux Conda

Education

Master's Degree in Bioinformatics and Biostatistics

Université de Nantes

2012 - 2014

Bachelor's Degree in Biology

Université de Nantes

2009 - 2012

Professional Experience

NGS Data Scientist (Through Amaris Consulting)

GSK

September 2023 - Present
  • Facilitate the analysis of massive high-throughput sequencing data for Vaccines QC on several projects
  • Perform adventitious virus detection in upstream samples and final containers
  • Viral stability analysis, investigate QC material integrity, bacterial assembly
  • Maintained reproducible, version-controlled tools scalable on HPC clusters and adapted for cloud-based (AWS) environments

Bioinformatics/Biostatistics Engineer

Life & Soft

October 2018 - August 2023
  • Bioinformatics & biostatistics analyses (16S, WGS, RNA-seq) for L'Oréal, CEA and Cerba HealthCare
  • Pipeline development for microbiome and oncology (Illumina/Nanopore)
  • Client interactions, project scoping, and results presentation
  • Agile collaboration with developers for web-based result visualization

Bioinformatics Engineer

INRAE – Genoscope

October 2014 - September 2018
  • Management of the single-cell genome assembly (SAGs) project with oral communication of results
  • Co-developed a published tool (MaGuS) to assess genome assembly quality using physical/genetic maps
  • Genome assembly and decontamination (Pisum sativum, Saccharomyces cerevisiae S288C, TARA Oceans marine protists) from Illumina and Nanopore data
  • Delivered scientific reports and gave oral internal and external presentations

Scientific Publications

Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean

Cell Genomics, 2022

Analysis of eukaryotic plankton functional convergence in ocean ecosystems.

Local Innate Markers and Vaginal Microbiota Composition Are Influenced by Hormonal Cycle Phases

Frontiers in Immunology, 2022

Collaboration with CEA on microbiome and RNAseq data analysis.

A reference genome for pea provides insight into legume genome evolution

Nature Genetics, 2019

Contribution to the pea genome sequencing project at Genoscope.

De novo assembly and annotation of three Leptosphaeria genomes using Oxford Nanopore MinION sequencing

Scientific Data (Nature), 2018

Genome assembly using long-read Nanopore technology.

De novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer

bioRxiv, 2016

Assembly of Saccharomyces cerevisiae S288C strain genomes from Nanopore data.

MaGuS: a tool for quality assessment and scaffolding of genome assemblies with Whole Genome Profiling™ Data

BMC Bioinformatics, 2016

Co-developed tool to assess and improve genome assembly quality using physical/genetic maps.

Get In Touch

Interested in collaboration or have a project in mind? Feel free to reach out!