David Airault

Creation and development of a bioinformatics service activity specializing in applied microbiology and molecular detection.

-Development of a proprietary pipeline for detecting microbial genes on raw reads, without assembly.

-Design of specific PCR/qPCR primers.

Location in Lyon in 2019 and 2020, then remotely in Nantes.

Five years of bioinformatics service missions, primarily at bioMérieux (in vitro diagnostics) and Lesaffre (biotechnology).

At bioMérieux Clinical Studies: Automated retrieval of bacterial sequences from NCBI (e-utilities), integration and quality control into a reference typing database (EpiSeq) with evaluation of incoming sequence divergence and recalibration of classification thresholds.

On internal Soladis assignment: responding to ad-hoc client needs: PCR primer design, protein quantification, custom bioinformatics analyses.

At bioMérieux Augmented Diagnostic (~3.5 years): development of a complete pipeline for bacterial genome assembly and characterization from raw Illumina reads. The pipeline produced variant profiles and pathogenic strain typings (via BioNumerics allele calling) used as input data for a machine learning model aiming to identify minimal molecular markers for PCR detection of pathogenic bacteria (GenUP Tracker project, bioMérieux). Nextflow/Snakemake development, BitBucket management, AWS deployment, code industrialization, and bioinformatics support for other teams.

At Lesaffre: construction of a proprietary yeast pangenome and integration of variant calling for characterization of the core genome vs. accessory genome.

Joined the Bioscience team for the development and maintenance of new features on the SeqOne platform (clinical NGS analysis). Development of Nextflow pipelines, interactions with the platform's API.