JCVI: About / Bios / Daniel H. Haft
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Daniel H. Haft, Ph.D.
Assistant Professor

Research Interests and Accomplishments

Dr. Daniel Haft is an Assistant Professor at the J. Craig Venter Institute (JCVI). He specializes in the development of databases, algorithms, and reasoning methods 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 and the SIMBAL algorithm (Sites Inferred by Metabolic Background Assertion Labeling) with Dr. Jeremy Selengut. He has used these tools in the discovery of the PEP-CTERM/exosortase protein sorting system, a selenium insertion system for labile selenoenzymes, new families of F420-dependent enzymes in Mycobacterium, a predicted novel redox carrier called mycofactocin, and several new classes of peptide modification system.

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.

Select Publications

Lehmann JS, Fouts DE, et al.
Pathogenomic Inference of Virulence-Associated Genes in Leptospira Interrogans.

PLoS Neglected Tropical Diseases. 2013 Oct 01; 7: e2468.[more]

Ansong C, Ortega C, et al.
Identification of Widespread Adenosine Nucleotide Binding in Mycobacterium Tuberculosis.

Chemistry & Biology. 2013 Jan 24; 20: 123-33.[more]

Haft DH, Selengut JD, et al.
TIGRFAMs and Genome Properties in 2013.

Nucleic Acids Research. 2013 Jan 01; 41: D387-95.[more]

Basu, M. K., Selengut, J. D., et al.
ProPhylo: Partial Phylogenetic Profiling to Guide Protein Family Construction and Assignment of Biological Process

BMC Bioinformatics. 2011 Dec 01; 12: 434.[more]

Haft, D. H., Varghese, N., et al.
GlyGly-CTERM and Rhombosortase: a C-terminal Protein Processing Signal In a Many-to-one Pairing With a Rhomboid Family Intramembrane Serine Protease.

PloS one. 2011 Aug 01; 6(12): e28886.[more]

Haft, D. H.
Bioinformatic Evidence for a Widely Distributed, Ribosomally Produced Electron Carrier Precursor, Its Maturation Proteins, and Its Nicotinoprotein Redox Partners

BMC Genomics. 2011 Feb 01; 12: 21.[more]

Selengut, J. D., Haft, D. H.
Unexpected Abundance of Coenzyme F420-dependent Enzymes In the Genomes of Mycobacterium tuberculosis and Other Actinobacteria

J Bacteriol. 2010 Jul 30;[more]

Haft, D. H., Basu, M. K., et al.
Expansion of Ribosomally Produced Natural Products: a Nitrile Hydratase- and Nif11-related Precursor Family

BMC Biol. 2010 May 25; 8(1): 70.[more]

Selengut, J. D., Rusch, D. B., et al.
Sites Inferred by Metabolic Background Assertion Labeling (SIMBAL): Adapting the Partial Phylogenetic Profiling Algorithm to Scan Sequences for Signatures That Predict Protein Function

BMC Bioinformatics. 2010 Jan 26; 11(1): 52.[more]

Haft, D. H., Self, W. T.
Orphan SelD Proteins and Selenium-dependent Molybdenum Hydroxylases

Biol Direct. 2008 Feb 20; 3(1): 4.[more]

Selengut, J. D., Haft, D. H., et al.
TIGRFAMs and Genome Properties: Tools for the Assignment of Molecular Function and Biological Process In Prokaryotic Genomes

Nucleic Acids Res. 2006 Dec 06; 35: D260-D264.[more]

Haft, D. H., Paulsen, I. T., et al.
Exopolysaccharide-associated Protein Sorting In Environmental Organisms: the PEP-CTERM/EpsH System. Application of a Novel Phylogenetic Profiling Heuristic

BMC Biol. 2006 Aug 24; 4(1): 29.[more]

Haft, D. H., Selengut, J., et al.
A Guild of 45 CRISPR-Associated (Cas) Protein Families and Multiple CRISPR/Cas Subtypes Exist In Prokaryotic Genomes

PLoS Comput Biol. 2005 Nov 11; 1(6): e60.[more]

Haft, D. H., Selengut, J. D., et al.
Genome Properties: a System for the Investigation of Prokaryotic Genetic Content for Microbiology, Genome Annotation and Comparative Genomics

Bioinformatics. 2005 Feb 01; 21(3): 293-306.[more]

Haft, D. H., Selengut, J. D., et al.
The TIGRFAMs Database of Protein Families

Nucleic Acids Res. 2003 Jan 01; 31(1): 371-3.[more]

Nelson, K. E., Clayton, R. A., et al.
Evidence for Lateral Gene Transfer Between Archaea and Bacteria from Genome Sequence of Thermotoga maritima

Nature. 1999 May 27; 399(6734): 323-9.[more]