Center for Applied and Experimental Genomics

Mission

The goal of the Center for Applied and Experimental Genomics is to promote collaborative, multidisciplinary research focused on the use of genomic, bioinformatic, and proteomic approaches to solve biological problems. Participants include faculty and students from multiple Colleges at SDSU. The experimental approaches combine comparative genomics, bioinfomatic analyses, and computational biology with traditional genetics, molecular biology, cell biology, biochemistry, and structural biology to address problems in systems that include bacteria, viruses, animal and human physiology, epidemiology and public health, chemistry, and engineering. The Center will facilitate the acquisition of new equipment and technologies required for genome research, research seminars, workshops, and courses in the field of genome science.

Announcements

Two CAEG participants, Rob Edwards and Stanley Maloy, have been appointed to the Scientific Working Group for the Enteropathogen Resource Integration Center (ERIC), an NIAID sponsored genomics/bioinformatics resource. For more information, see: http://www.ericbrc.org/
Several CAEG Seed Grants to stimulate genomics research supported in Spring, 2004.
Suggestions for CAEG sponsored seminars are welcomed from any CAEG members.
If you would like to participate in the CAEG, please send an email message to smaloy@sciences.sdsu.edu.

Recent CAEG Sponsored Seminars

Brandon Gaut, UC Irvine - 4/19/04.
Mark Goulian Biophysics, Univ. Pennsylvania - 3/11/04
Gary Stormo, Washington Univ. Medical School - 12/2/03
Gary Olsen, Univ. Illinois, Urbana - 12/4/03
James Hu, Texas A&M University - 3/27/03
Elizabeth Waters, SDSU - 3/13/03

Recent genomics publications by CAEG scientists

Waters E, Hohn MJ, Ahel I, Graham DE, Adams MD, Barnstead M, Beeson KY, Bibbs L, Bolanos R, Keller M, Kretz K, Lin X, Mathur E, Ni J, Podar M, Richardson T, Sutton GG, Simon M, Soll D, Stetter KO, Short JM, Noordewier M. . 2003. The genome of Nanoarchaeum equitans: Insights into early archaeal evolution and derived parasitism. Proc Natl Acad Sci USA
Seguritan V, Feng IW, Rohwer F, Swift M, Segall AM. 2003. Genome sequences of two closely related Vibrio parahaemolyticus phages, VP16T and VP16C. J Bacteriol. 185(21):6434-6447.
Breitbart M, Hewson I, Felts B, Mahaffy JM, Nulton J, Salamon P, Rohwer F. 2003. Metagenomic analyses of an uncultured viral community from human feces. J Bacteriol. 185(20):6220-6223.
Rohwer F. 2003. Global phage diversity. Cell 113(2):141.
Harris JK, Kelley ST, Spiegelman GB, Pace NR. 2003. The genetic core of the universal ancestor. Genome Res. 13(3):407-412.
Reeder TW. 2003. A phylogeny of the Australian Sphenomorphus group (Scincidae: Squamata) and the phylogenetic placement of the crocodile skinks (Tribolonotus): Bayesian approaches to assessing congruence and obtaining confidence in maximum likelihood inferred relationships. Mol Phylogenet Evol. 27: 384-397.
Paul JH, Sullivan MB, Segall AM, Rohwer F. 2002. Marine phage genomics. Comp Biochem Physiol B Biochem Mol Biol. 133(4):463-476.
Breitbart M, Salamon P, Andresen B, Mahaffy JM, Segall AM, Mead D, Azam F, Rohwer F. 2002. Genomic analysis of uncultured marine viral communities. Proc Natl Acad Sci USA 99(22):14250-14255.
Rohwer F, Edwards R. 2002. The Phage Proteomic Tree: a genome-based taxonomy for phage. J Bacteriol. 184(16):4529-4535.
Hagstrom A, Pommier T, Rohwer F, Simu K, Stolte W, Svensson D, Zweifel UL. 2002. Use of 16S ribosomal DNA for delineation of marine bacterioplankton species. Appl Environ Microbiol. 68(7):3628-33.
Valafar F. 2002. Pattern recognition techniques in microarray data analysis: a survey. Ann NY Acad Sci. 980: 41-64.
Valafar H, Prestegard JH, Valafar F. 2002. Datamining protein structure databanks for crystallization patterns of proteins. Ann NY Acad Sci. 980: 13-22.
Leache AD, Reeder TW. 2002. Molecular systematics of the Eastern Fence Lizard (Sceloporus undulatus): a comparison of Parsimony, Likelihood, and Bayesian approaches. Syst Biol. 51(1): 44-68.
Forsyth RA, Haselbeck R, Ohlsen K, Yamamoto R, Xu H, Trawick J, Wall D, Wang L, Brown-Driver V, Froelich J, King P, McCarthy M, Malone C, Misiner B, Robbins D, Tan Z, Zhu Z, Carr G, Mosc, D, Zamudio C, Foulkes J, and Zyskind JW 2002. A genome-wide strategy for the identification of essential genes inStaphylococcus aureus. Mol. Microbiol. 43: 1387-1400.
Edwards RA, Olsen GJ, Maloy SR. 2002. Comparative genomics of closely related salmonellae. Trends Microbiol. 10(2):94-99.

CAEG Participants

Useful Links

Genomics tutorials:

A guide to molecular sequence analysis
Homology modeling for beginners
Microbial genomics primer
Tutorial on finding promoters and regulatory sequences

Genome analysis resources:

Bioinformatics

NCBI bioinformatics resources
European Bioinformatics Institute
EnteriX: Bacterial genome alignments
Whole genome PCR on completed bacterial genomes
ERGO light (genome analysis software)
KEGG (pathways, enzymes, other databases)

Protein structure

Cn3D (3D structure viewer)
PEDANT: Protein extraction, description, and analysis tool
RasMol (molecular visualization)

Statistics

Statistics resources

Genome centers, sequences, and databases

Baylor Human Genome Sequencing Center
DOE Genome Center
Sanger Genome Sequencing Centre
Saccharomyces Genome Database
TIGR
WUSTL Genome Sequencing Center

Protocols

Molecular biology protocols (via NWFSC)

Educational resources:

Future needs for bioinformatics (Department of Commerce)
Microbial genomics primer

Local Centers and Research Facilities:

SDSU Microchemical Core Facility
San Diego Supercomputer Center
CSUPERB (Program for Education and Research in Biotechnology)
SDSU College of Sciences - Departments and Programs
Center for Microbial Sciences
Center for Research in Mathematics and Science Education
Educational Center on Computational Science and Engineering

Please send questions or comments to smaloy@sciences.sdsu.edu

Last modified on December 12, 2004

This page has been viewed times since April 7, 2003.

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