David Jaffe, Ph.D.
David Jaffe is the Director of Computational Research and Development (CRD) in the Genome Sequencing and Analysis Program. The CRD group works on analytical and computational aspects of genome sequencing, from getting the most out of the laboratory process, to getting the data into a form that can answer biological questions. The group works on data from a wide range of cutting-edge DNA sequencing technologies.
Applications worked on by the group include detection of differences, for genomes for which there is a similar reference, and de novo assembly, for genomes for which there is not. For example, the group has used tiny reads to detect differences between TB strains isolated from patients and a reference strain. The group has been developing assembly algorithms for seven years and has applied them to about a hundred genomes, including many mammals, fungi, and disease vectors. The dramatically lower cost of data from new technologies has enabled a whole host of other biological applications, that the group is actively supporting, including ChIP-Seq, bisulfite sequencing, directed evolution, and sequencing of exons.
David's background is in mathematics: algebraic geometry and error-correcting codes. He received his PhD from the University of California (Berkeley) in 1987 and was Professor at the University of Nebraska (Lincoln) before coming here in 2000. He was initially funded by an NHGRI K01 "retraining" grant and is currently principal investigator of an NHGRI R01 grant in genome assembly.