Sean P Kennedy, PhD, received his doctorate in microbiology from the University of Massachusetts studying the sequence and genetic structure of Archaea. He then took on a post-doc position at the Massachusetts Institute of Technology (MIT) studying transcription initiation and non-natural amino acids before coming to France in 2005. Sean worked at the CNRS in the domain of cellular division and chromosome replication before taking a position at INRA to head a new NGS sequencing initiative, MetaQuant, studying the intestinal microbiota and its link with obesity. Through his experience in hig-throughput sequencing and data analysis, he served a critical role in the sequence and analysis of metagenomic data for the European projects MetaHIT (obesity, IBS, Crohn’s Disease), EvoTAR (antibiotic resistance in hospitals) and MetaCardis (cardiovascular disease and diabetes) as well as many project with industrial partners involved in allergies and childhood development and disease.
In 2012 the MetaQuant team was a primary founder of the MetaGenoPolis Unit at INRA, financed by the French government’s “Investissements d’Avenir”. By 2015 the platform housed four Life Technologies SOLiD sequencers and a new Life Technologies Ion Proton Sequencer as well as a suite of robotic solutions to fully integrate DNA quantification and NGS library production. Over 100 small to large projects and over 5000 samples were processed during this period.
Sean joined the Pasteur Institute in Paris in 2015 as the Director of the Biomics Pole. Here he oversaw the introduction of long-read technology (PacBio / Nanopore), obtained ISO 9001 certification of DNA/RNA services and developed an active metagenomics research activity with several financed projects. In 2018 Sean moved to the The Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), also at the Pasteur Institute. Sean is currently focused on and machine learning and functional prediction to investigate the role the microbiota plays in health and well-being. Of particular interest is how mother-infant colonization occurs and how this transmission impacts maturation of the immune system and contributes to health and disease later in life.