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Indiana University Bloomington

Department of Biology

Faculty & Research

Faculty Profile

Don Gilbert

Photo of Don Gilbert
Research Images
Research photo by Don Gilbert

Research photo by Don Gilbert

Senior Scientist
Contact Information
By telephone: unlisted phone
JH 336A

Genome Informatics Lab

Research Area
Genomics and Bioinformatics
Education

Ph.D., Indiana University, 1981
Postdoctoral, Syracuse University, 1981-1983
Postdoctoral, University of Chicago, 1983-1984

Research Description

Bioscientists are assembling the genomes of thousands of organisms, comprising millions of genes, proteins and related bio-information, now part of biology's digital library distributed on computers around the world. Coping with this wealth of genomes requires cost-effective, shared database tools, such as those built under the umbrella of the collaborative Generic Model Organism Database ( GMOD ) project. Software tools to fully assembly, analyze and compare these genomes are available, but the ability to employ them is limited to those with extensive computational resources and engineering talent.

In this genome informatics laboratory, methods are developed for use by existing and emerging model organism databases that address genome database access needs and middleware for comparative analyses. Effective use of shared cyberinfrastructure, such as the NSF-sponsored TeraGrid and other Grid systems, is a problem today for bioinformatics, that our research addresses with data grid methods for large genome databases.

Daphnia and Drosophila genome databases

Genome informatics methods developed here are applied to the needs research communities for the waterflea Daphnia and several fruitfly Drosophila genomes as useful cases. These include finding Daphnia's genome is rich in tandem gene duplications, with direct implications on how this organism uses duplicate genes as part of rapid genetic adaptations to stressful ecological and environmental conditions.

A stunning example is with Daphnia's well known hemoglobin genes. These are called into play as these aquatic creatures rapidly turn blood-red to cope when the oxygen is depleted in their ponds. Four Hb genes have been described prior to whole genome analysis. We find now a tandem cluster of 8 hemoglobin genes, as part of a genetic adaptation to environmental stresses.

Biology news and data dissemination

BIOSCI/Bionet, a network of biology news and discussion, is approaching its third decade of service to the life sciences community. These popular and widely used discussion groups are a venue for several model organism communities, and areas of molecular methods, bio-software, microbiology, proteins, plant biology. The Bio-mirror project for distribution of large genomic and biology databanks provides infrastructure for effective experimental work in the biosciences.

This work is part of an international collaboration for improving research and public access to biology and bioinformatics information, in the US and with partnerships with Asian-Pacific, African, European and western hemisphere nations. BIOSCI/Bionet news, IUBio Archive and Bio-Mirror projects have a multi-decade record of serving the world community.

Current bioinformatics public services

BIOSCI/Bionet, long-term Biology news and discussion groups, http://www.bio.net/

DroSpeGe, Comparative Drosophila Species Genomes, http://eugenes.org/drospege/

wFleaBase, Daphnia Genome Database, http://wfleabase.org/

Bio-Mirror for world distribution of large bioinformatics data sets, http://www.bio-mirror.net/

IUBio Archive of Biology software and data, http://iubio.bio.indiana.edu/

 

Select Publications
Gilbert, D.G., 2007. DroSpeGe: Rapid access Drosophila species genomes database. Nucleic Acids Res. (Database issue): D480ÐD485 doi:10.1093/nar/gkl997
Colbourne, J.K., Singan, V.R., Gilbert, D.G. 2005. wFleaBase: the Daphnia genome database, BMC Bioinformatics, 6:45 doi:10.1186/1471-2105-6-45
Gilbert, D.G., Y Ugawa, M Buchhorn, T Tan Wee, A Mizushima, H Kim, K Chon, S Weon, J Ma, Y Ichiyanagi, D Liou, S Keretho, and S Napis, 2004. Bio-Mirror project for public bio-data distribution. Bioinformatics, 20:3238-3240. doi:10.1093/bioinformatics/bth219
Gilbert, D.G., 2004. Bioinformatics software resources. Briefings in Bioinformatics, 5(3): 300-304. doi:10.1093/bib/5.3.300
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