paul de bakker

Paul de Bakker is an Assistant Professor of Medicine in the Division of Genetics at the Brigham and Women's Hospital and Harvard Medical School, and is Associate Member of the Broad Institute of MIT and Harvard. Paul is also Director of the Genomics Program of the Harvard University Center for AIDS Research (HU CFAR).


Before joining the BWH faculty, he was a postdoctoral fellow in the Department of Molecular Biology and the Center for Human Genetic Research at the Massachusetts General Hospital, and the Broad Institute of Harvard and MIT, where he trained with David Altshuler and Mark Daly.

He has concentrated on the characterization of haplotype structure in human genomic data (specifically for the International HapMap Project) and understanding how linkage disequilibrium and haplotype structure can be exploited to perform powerful genetic association studies. He has developed the widely-used Tagger tool for selecting tag SNPs, for evaluating whole-genome SNP genotyping platforms, and for deriving haplotype tests to improve coverage and power. He was actively involved in candidate gene association studies of type 2 diabetes, and contributed to the statistical analysis of genome-wide association studies of type 2 diabetes and related metabolic traits (by the Diabetes Genetics Initiative) and multiple sclerosis (by the International Multiple Sclerosis Genetics Consortium).

a long, long time ago...

Paul has degrees in biochemistry (B.Sc. Hons.) from the University of Bristol, UK, and pharmacy (M.Sc.) from Utrecht University, The Netherlands. He was a visiting student in the group of J. Andrew McCammon at the University of California, San Diego, where he studied protein dynamics and molecular simulations. Before starting graduate work in Cambridge, he worked briefly with Andrej Sali on ModBase, a database of three-dimensional protein models based on genomic sequences.

In 2003 he received a Ph.D. from the University of Cambridge, UK, working with Sir Tom Blundell in the Crystallography and Bioinformatics Group in the Department of Biochemistry. His Ph.D. thesis is titled "Ab initio sampling of polypeptide conformations and the prediction of protein structure", which describes a computational approach for modelling ensembles of protein conformers at atomic resolution by satisfaction of spatial restraints. This method (called RAPPER) is now part of the widely used CCP4 package for semi-automated model building in X-ray crystallography. Prior to completing his Ph.D., Paul was a visiting student in Ken Dill's group at the University of California, San Francisco.