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Centre for Bioinformatics and Computational Genetics

For the past three years at Texas A&M University I have been primarily working in beef cattle genomics, with collaborative ventures into equine gene mapping and ovine reproductive functional genomics.  In addition to my participation in the international consortium to physically map the bovine genome and as part of the bovine genome project technical committee, I have two major ongoing commitments of effort in the area of beef cattle research, one is to generate novel bioinformatics tools to fully take advantage of the bovine genome sequence in the context of the developmental regulation of carcass traits such as adiposity. In addition, we have developed a database of public domain bovine Quantitative Trait Loci (QTL) and have coupled this to an easily navigated web interface that allows researchers to compare QTL locations for varied QTL within the bovine genome.  We have recently linked this to a genome browser (Gbrowse) in order to allow researchers to be able to transition directly from QTL data to SNP locations, gene locations and annotations.  For the future, I anticipate contributing to an integrated web based resource for the bovine genome.  In addition to working on cattle, I work on equine genomics.  As part of a consortium between TAMU, U Kentucky and Cornell, I have performed the clustering and selection of ~8000 Expressed Sequence Tags (EST) out of 45,000 equine ESTs for use on an equine spotted cDNA microarray.  I am extending this work to include an equine genomics database covering the functional annotation of the microarray ESTs, mapping data and homology to cattle and human genes.  I have also pioneered the establishment of bioinformatics resources at TAMU aimed at making high throughput bioinformatics analysis available to researchers using a simple web interface.  We were the first to couple Apple Xserve cluster technology with a job queue and web based user interface.  This original concept, implemented by the BioTeam as part of a contract with TAMU has become a commercial bioinformatics solution now known as iNquiry.  iNquiry is now used by growing number of universities and pharmaceutical companies to provide a low cost, powerful bioinformatic resource for researchers. 

Here in Adelaide, research in my lab has two foci: one aimed at creating new software tools for biologists to analyse genomic data, the other aimed at analysing genome data using computational methods. 

The first aim is currently served by improving our bovine Quantitative Trait Locus database, and implementing a Java based object oriented framework for genomic data. 

The second aim currently involves analysing the bovine and equine genome sequence assemblies for repeated sequence elements using a de novo repeat identification tool developed by and in collaboration with Bob Edgar that has only been used for dipteran repeat analysis to date.

Honours projects in either area, or related to these areas are available in my lab.  It would be helpful (but not required) if students already had some familiarity with either Unix/Linux or Perl or Java.  All that is really required is curiosity and an interest in Bioinformatics.