JCVI: About / Bios / Derek M. Harkins
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Derek M. Harkins
Sr. Bioinformatics Analyst

Research Interests and Accomplishments

Derek Harkins is a Senior Bioinformatics Analyst in the Informatics group at the J. Craig Venter Institute. He originally joined TIGR in 2006 and stayed on with the Institute during the merger with the Venter Institute.

Mr. Harkins' primary interests are in functional and structural annotation, automated annotation, microbial genome sequencing and comparative genomics. He has been and is responsible for overseeing the annotation and submission of over 200 genomes to the public databases. He has contributed extensively to development and improvement of the JCVI automated annotation pipeline and the autoAnnotate tool. He has also contributed extensively to the curation and improvement of JCVI's annotation tools and resources such as the Characterized Protein Database (CharProtDB), Protein Naming Utility (PNU), TIGRfams, MGAT and Manatee. He has also provided support to faculty in individual projects.

Mr. Harkins is currently providing informatics support to several projects at JCVI including the "Human Microbiome Project" (HMP), and the "Vaccinobacter" project —a collaboration between the Synthetic Biology & Bioenergy Group and Novartis. He also serves as the principal bioinformatics analyst for two of the Genomic Sequencing Center for Infectious Diseases (GSCID) projects at JCVI: the "Leptospira Genomics and Human Health" project and the "Genome Sequencing of Diverse US Military Acinetobacter baumannii-calcoaceticus Complex Isolates" project.

During the Bioinformatics Resource Center (BRC) contract, he was the principal curator for over 35 genomes in the Burkholderia clade of the Pathema resource and served as an instructor for the Burkholderia Annotation Jamboree.

Prior to joining JCVI, Mr. Harkins served as consultant for a contract with the Genetics Research Group of International Paper Company doing marker-aided selection. Previously he was a Biologist with the USDA-Forest Service and led a team working on genetic mapping of white pine blister rust resistance genes in white pines. Before that he was a Biologist with the USDA-Agricultural Research Service doing population genetics and disease resistance research.

Mr. Harkins received his M.S. in Forestry and Genetics from North Carolina State University, and earned a B.S. in Biology from the University of Miami. 

Select Publications

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

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

Madupu R, Richter A, et al.
CharProtDB: a Database of Experimentally Characterized Protein Annotations.

Nucleic acids research. 2012 Jan 01; 40: D237-41.[more]

Cuív PÓ, Klaassens ES, et al.
Draft Genome Sequence of Bacteroides vulgatus PC510, a Strain Isolated from Human Feces.

Journal of bacteriology. 2011 Aug 01; 193: 4025-6.[more]

Cuív PÓ, Klaassens, E. S., et al.
Draft Genome Sequence of Turicibacter sanguinis PC909 Isolated from Human Faeces

J Bacteriol. 2010 Dec 23;[more]

Goll, J., Montgomery, R., et al.
The Protein Naming Utility: a Rules Database for Protein Nomenclature

Nucleic Acids Res. 2010 Jan 01; 38(0): D336-9.[more]

Brinkac, L. M., Davidsen, T., et al.
Pathema: a Clade-specific Bioinformatics Resource Center for Pathogen Research

Nucleic Acids Res. 2009 Oct 20;[more]