Our laboratory specializes in developing and evaluating new bioinformatics approaches to facilitate biomedical research. We often collaborate with experimental and clinical laboratories to apply the approaches we develop, in combination with approaches developed in the broader bioinformatics community, to address specific biomedical questions. Current method development and collaborative projects are described in more detail below. For a list of previous projects, see the Publications and Software pages.
We are currently developing:
- Scalable approaches to manage next-generation sequencing data, see the Goby framework and its web analysis front-end GobyWeb.
- Reliable protocols for biomarker discovery and biomarker candidate model selection (in collaboration with the MAQC-II consortium). New protocols are implemented in the BDVal suite of programs.
The laboratory participates to the following projects:
- Risk factors for late onset Alzheimer’s disease (with Dr. Philippe Marambaud‘s laboratory), including the role of the CALHM1 gene in Alzheimer’s.
- Clinical subtype discovery in DLBCL patients from DNA methylation data (collaboration with Dr. Rita Shaknovich and Dr. Ari Melnick‘s laboratory).
- Analysis of samples from kidney transplant recipient and donors to develop non invasive diagnostic tests of acute rejection and other significant clinical endpoints (in collaboration with Drs. Manikkam Suthanthiran and Muthukumar Thangamani, Dept of Medicine, Nephrology).
- Integration of gene expression and epigenetic data to study non genetic inheritance of behavioral traits (in collaboration with Dr. Miklos Toth, Dept of Pharmacology).
- Microarray Quality Control Project (MAQC-II)