Research Interests and Accomplishments

Dr. Daniel Haft is a Staff Scientist III at the J. Craig Venter Institute (JCVI). He specializes in database and algorithm development for microbial annotation. He leads TIGRFAMs, a database of hidden Markov model (HMM)-based protein family definitions for use in automated annotation systems. He also created Genome Properties, through which a collection of rules based largely on HMMs determines the presence or absence of a wide variety of metabolic pathways, molecular complexes, transport and secretion systems, selfish genetic elements, regulatory circuits, and so on.

Systems described in Genome Properties include both extractions from the scientific literature and extensions or new results from comparative genomics, such as definition of the multiple subtypes for CRISPR systems. Dr. Haft co-developed the Partial Phylogenetic Profiling algorithm with Dr. Jeremy Selengut, and has used it in the discovery of the PEP-CTERM/exosortase protein sorting system and a selenium insertion system for labile selenoenzymes.

Dr. Haft majored in physics as an undergraduate at Harvard University, and earned a doctorate from the Johns Hopkins University School of Medicine, Immunology Training Program, for work on modeling the B-cell response in mice. He worked for some time at the National Biomedical Research Foundation on the PIR Protein Sequence Database (which is now part of the UniProt Knowledgebase with European collaborators EBI and the Swiss Institute of Bioinformatics) before coming to the J. Craig Venter Institute in 1998 to work in microbial genomics. He has contributed to over two dozen genome analysis papers.

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