We proposose end-to-end bioinformatics pipelines for Next Generation Sequencing data (NGS): amplicon sequencing (16S/18S/ITS), shotgun metagenomics (short and long reads), metatranscriptomics, metabolomics and metaproteomics. We analyze these data using biostatistics, expertise and, if needed, Artificial Intelligence algorithms (e.g. machine learning). We start from raw data (e.g. fasta/fastq files) up to a complete analysis report.

We create and use pipelines and models for the development of probiotics / prebiotics / synbiotics and live biotherapeutics targeting the human microbiome, as well as to engineer bacteria strains or consortia targeting the animal, environmental and artificial microbiome(s), or to design new metabolic pathways for the production of new metabolites.

We have developed several models of complex microbial communities (e.g. the human gut microbiome) and use them for the development of therapeutics or microbiome-related compounds (e.g. skincare products targeting the human skin microbiome). These models can be applied to various microbiomes such as the animal, the environmental and the industrial microbiomes.

We propose made-to-measure R & D projects related to the development of mathematical models or bioinformatics pipelines. For example, these projects can be the development of pharmacokinetics/pharmacodynamics models for drugs targeting the human microbiome.

To share our expertise in bioinformatics and Systems Biology, we propose made-to-measure trainings related to the development of R, python, Matlab, AWS and bash/unix pipelines.