Patrick Nitschké

The fondation Imagine, as a partner of the Paris-Descartes University and of the Faculty of Medicine, benefits from the support of the Paris-Descartes Bioinformatics Platform to come-along with the scientists throughout their Imagine labeled projects (support for the experimental design planning, data handling and analysis, biological tools for data integration and interpretation).

The bioinformatics Platform collaborated with the Imagine scientists and genomic platform to develop an original pipeline for genetic linkage studies (from raw SNP microarray data to visualisation and annotation of the candidate genomic regions via an interactive web interface). This pipeline allowed the analysis of 50 linkage projects by year.

Since 2009, the Fondation Imagine followed the “next” generation sequencer evolution and acquired severall machines more and more powerful. The increasing amount of data generated by these technologies created new challenging issues to store, analyze, integrate and visualize pertinent information. To reach this goal, we have developed a new original pipeline to analyze resequencing projects. Our pipeline, Polypipeline is based on public tools (alignment, variation finding) as well as an original database design PolyDB (storage and minning data) and finally a new graphical interface Polyweb (interpretation and visualization). Our tool is completely generic and is independant from the sequencing technology used.

Our team participates also to various projects, either relating to sequencing like chip/seq, rna/seq… or more broadly to biostatistics like transcriptomic, pathway analysis… We can also help the researcher during the design step of her/his experiment to optimize the odds of positive findings.