JCVI: About / Bios / Granger G. Sutton
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Granger G. Sutton III, Ph.D.

Research Interests and Accomplishments

Dr. Granger Sutton, Ph.D., is a Professor of Informatics at JCVI and as the Prokaryotic Informatics Coordinator is responsible for all aspects of prokaryotic bioinformatics and software engineering for JCVI’s sequencing and sequence-related informatics, including assembly and annotation. Dr. Sutton has been employed with JCVI and its predecessor organizations for over 14 years, and has authored or co-authored more than 70 publications. Dr. Sutton was a Director in the Informatics Research Department at Celera Genomics for six years where he developed and managed research programs in gene finding, comparative genomics, and shotgun fragment assembly including the development of the Celera Assembler used for assembling the fruit fly, human, and mouse genomes and many others. Dr. Sutton worked on whole genome alignment, detection of population and haplotype variation such as SNPs, and comparative mammalian genomics. He pioneered whole genome shotgun assembly while working at TIGR, developing the assembler used to assemble the first prokaryotic genome, H. influenza, as well as many others. He co-authored many of the initial whole genome sequencing projects in the early days of the genome revolution. After the merger of JCVI and TIGR in 2006, Dr. Sutton became Senior Director of Informatics at JCVI and oversaw the assembly and annotation pipelines for the Moore marine prokaryotic reference genome project and helped design the protein clustering approach used for the largest metagenomic sequencing project to date, the Global Ocean Survey (GOS). Dr. Sutton was also Principal Investigator for a NIH grant to enhance the open source Celera Assembler, Principal Investigator for the NIAID Pathema Bioinformatics Resource Center, and a Co-Investigator on the NIH Roadmap to sequence the Human Microbiome. Within that project which is still ongoing he has played a major role in overseeing the sequencing and analysis of the close to 600 reference bacterial genomes which are being generated for that project.

JCVI is one of three NIAID Genome Sequencing Centers (GSC) providing genome sequencing and genotyping in response to infectious diseases community white papers. Dr. Sutton co-coordinates the informatics technology core for this center which comprises groups for viral, eukaryotic, prokaryotic, and data management. His group supports the annotation and analysis for prokaryotic projects under this contract. The group continually enhances the prokaryotic annotation pipeline and has recently ported it to the cloud. The nature of the GSC prokaryotic projects, where dozens or hundreds of strains or closely related species were to be sequenced, necessitated the development of pan-genome analysis tools. Dr. Sutton’s group has developed a pan-genome analysis pipeline using PanOCT for pan-genome ortholog clustering. Dr. Sutton chaired the working group for pan-genome standards at the most recent NCBI Genome Submission and Annotation Workshop and gave a talk on pan-genome standards at the latest Genome Standards Consortium meeting.

In addition to his roles at the JCVI, Dr. Sutton has been a reviewer for a number of scientific journals including Genome Research, Genome Biology, Bioinformatics, BMC Bioinformatics, Journal of Bioinformatics and Computational Biology, Nature Methods, PLoS Computational Biology, and PLoS ONE. Dr. Sutton serves on the Scientific Advisory Boards of the Genome Reference Consortium and Archon Genomics Xprize. Dr. Sutton earned his Ph.D. in Computer Science and B.S. in Electrical Engineering from University of Maryland, College Park, and M.S. in computer engineering from Stanford University.

Select Publications

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

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

Yooseph, S., Nealson, K. H., et al.
Genomic and Functional Adaptation In Surface Ocean Planktonic Prokaryotes

Nature. 2010 Nov 04; 468(7320): 60-6.[more]

Miller, J. R., Koren, S., et al.
Assembly Algorithms for Next-generation Sequencing Data

Genomics. 2010 Mar 06; 95(6). : 315-27.[more]

Davidsen, T., Beck, E., et al.
The Comprehensive Microbial Resource

Nucleic Acids Res. 2010 Jan 01; 38(0): D340-5.[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]

Chain, P. S., Grafham, D. V., et al.
Genomics. Genome Project Standards In a New Era of Sequencing

Science. 2009 Oct 09; 326(5950): 236-7.[more]

Warren, R. L., Sutton, G. G., et al.
Assembling Millions of Short DNA Sequences Using SSAKE

Bioinformatics. 2007 Feb 15; 23(4): 500-1.[more]

Goldberg, S. M., Johnson, J., et al.
A Sanger/pyrosequencing Hybrid Approach for the Generation of High-quality Draft Assemblies of Marine Microbial Genomes

Proc Natl Acad Sci U S A. 2006 Jul 13; 103(30): 11240-5.[more]

Sutton G, Dew I
Shotgun Fragment Assembly

2006 Jan 01; 1: Chapter 3:79-117.[more]

Florea, L., Di Francesco, V., et al.
Gene and Alternative Splicing Annotation With AIR

Genome Res. 2005 Jan 01; 15(1). : 54-66.[more]

Istrail, S., Sutton, G. G., et al.
Whole-genome Shotgun Assembly and Comparison of Human Genome Assemblies

Proc Natl Acad Sci U S A. 2004 Feb 17; 101(7). : 1916-21.[more]

Myers, E. W., Sutton, G. G., et al.
A Whole-genome Assembly of Drosophila

Science. 2000 Mar 24; 287(5461): 2196-204.[more]

Sutton, G. G., White, O., et al.
TIGR Assembler: A New Tool for Assembling Large Shotgun Sequencing Projects

Genome Science and Technology. 1995 Jan 01; 1(1): 9-19.[more]