Seminar 10.8.14, noon, Barker 101: "From Fasta to Function: Leveraging Genomic Data to Advance Crop Science"
By Karyn Houston
Plant & Microbial Biology
Former PMB grad student Devin Coleman-Derr has joined the Plant Gene Expression Center (PGEC) as a new Principal Investigator.
"Devin is perfectly suited for the combined computational/plant biology position," said Sarah Hake, PMB professor and director of the PGEC.
Coleman-Derr's research focus will be on improving crop development and advancing crop science, specifically using statistical methods and computational tools to research drought response in sorghum, a crop with both feedstock and biofuels potential.
"Maximizing the utility of genomic data available for crop species is essential if crop production is to continue to keep pace with the increasing world population and rate of climate change," Coleman-Derr said.
"In recent years, crop science has reached the point where the real challenge is no longer the generation of genomic sequence data, but instead careful bioinformatic analysis and effective dissemination of results," Coleman-Derr said. "In my future research, I wish to address the question, “How best can current sequencing technologies and genomic analysis tools be brought to bear on improving crop development?”
Extensive Work with PMB Scientists
While completing his Ph.D. in the Department of Plant & Microbial Biology, Coleman-Derr worked extensively with PMB scientists Daniel Zilberman and Robert Fischer, both professors in the department.
"He has experience with large plant genomes from his work in the Genomics and Gene Discovery group at the USDA's Western Regional Research Center (WRRC), prior to his PhD with Daniel Zilberman, where he studied epigenetic marks on a genomic scale in Arabidopsis," Hake said. "He has spent the last two years working at the Joint Genome Institute (JGI) examining the microbiome of the Agave plant and the effects of genotype and environment on microbial community composition."
Work at Joint Genome Institute
After graduation from PMB, Coleman-Derr worked as a postdoctoral scholar at the Joint Genome Institute, a U.S. Department of Energy facility in Walnut Creek, dedicated to bioenergy research.
"The research done at JGI represented the first deep-sequence-based investigation of fungal and prokaryotic communities across both aerial and below-ground communities associated with a plant host," Coleman-Derr said. "The study uncovered significant differences in the primary drivers of fungal and bacterial community composition, as well as a startling loss of microbial diversity in the epispheres of the cultivated agave, due in part to the overabundance of a few potentially pathogenic bacterial lineages. In the course of this research, I also developed a suite of statistical tools in R for use with tag-based metagenomic datasets that enables a variety of comparative analyses of microbial alpha and betadiversity."
Important Links
PGEC Website: pgec.berkeley.edu/
JGI Website: jgi.doe.gov/
Zilberman Lab: dzlab.pmb.berkeley.edu/
Western Regional Research Center: www.ars.usda.gov