Sean Kennedy

Director of the Bio-Omics Pole - Institut Pasteur Paris

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 high-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 five latest generation NGS Sequencers 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 is currently the Director of the Biomics Unit at the Pasteur Institute in Paris. Biomics is part of Pasteur’s new Center of Innovation and Technology (CITECH). The Biomics Unit is a principal partner in government’s “Investissements d'Avenir – Infrastructures” program, in the France Genomique Consortium. The Unit, equipped with several high throughput Illumina instruments as well as a PacBio SEQUEL, offers collaboration and services for genomics, transcriptomics, metagenomics and genotyping project. In addition to offering sequencing of both DNA and RNA samples, the group also develops and provides access to a number of analysis pipelines for data analysis. The primary research activity of the group continues to focus on the microbiota and specifically the colonization of the intestine and its relationship with health and disease as mediated by the immune system and the environment.