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Otago School of Medical Sciences

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Current and recent research projects in this area at the University of Otago

Academic Staff currently involved in this area with links to their individual pages:

Dr. Chris M. Brown (Coordinator)
Prof. Warren Tate
Dr. Peter Stockwell
Dr. Craig Marshall
Assoc. Prof. John Cutfield
Dr. Russell Poulter
Dr Judy Broom
Prof David Green
Dr Jo-Ann Stanton
Dr Mik Black
Dr Lubica Benuskova

Dr. Grant Jacobs (now at Bioinfotools Inc, Dunedin)
Dr Andrew Firth (now at Biosciences Centre, Cork)
Dr Nattanan Panjaworayan (now at Biochemistry Dept, Kasedsart University, Bangkok)

Current research projects with a significant Bioinformatics component

Development of genomic databases and analysis of genomic gene expression data

Dr. M Black, Sarah Song

Analysis of data from gene expression microarray experiments, Bayesian statistical methods, and statistical computing. Bioconductor development, for example PCOT2.

Programming and Systems Management to support Bioinformatics at Otago

Dr. P. Stockwell

Development of general purpose sequence manipulation and analysis tools. Development of tools for managing repetitious sequences in homology searching. The application of novel encryption methods to homology comparison and searching algorithms. Automated parsing of sequence database entries for features of interest. Application of relational database systems to biological data. Maintenance of UNIX/Xserve systems and applications.

A database of mRNA sequences and motifs -Transterm.

Dr. C. Brown, Prof. W. Tate, Dr. P. Stockwell, Dr Grant Jacobs

We have established the first database of translation signals in the world (Transterm). These signals control the process by which proteins are made translation (initiation, elongation, termination). Transterm was developed using our own database analysis tools.

Integrated Genomics Resources for Health and Disease

S Stevens, J Panjaworyan, S Roessner, A Das, Dr M Black, Dr. C. Brown

Website for these services http://bioanalysis.otago.ac.nz/

Detection of Hidden Signals in Genes, Regulatory Genomics of Human and virus genes

S Stevens, J Panjaworyan, S Roessner, A Das, Dr M Black, Dr. C. Brown

We are using computer tools to detect hidden signals in new genomic sequences particularly the human genome. For this project the Transterm database is being extended to include 3' and 5' Untranslated sequences (UTRs). Key findings are being tested experimentally.

Selenium Incorporation at Translational Stop Signals

Prof W. Tate, Dr P Stockwell

This research is focusing on a recoding event that permits incorporation of Selenocysteine at UGA codons that would normally decoded as stops. We are identifying features that distinguish the sites of selenocysteine incorporation from bone fide UGA stop codons .

Structural Biology

Dr. J. Cutfield and Dr. S. Cutfield

Inhibition of enzymes secreted by the pathogenic fungi Candida albicans (the cause of thrush and more serious infections in humans) and Glomerella cingulata (the cause of bitter rot in pip-fruit).These studies involve cloning and over-expression of the relevant genes, protein purification, enzyme kinetics and inhibition, site-directed mutagenesis, and when the protein structures have been determined computer modeling for inhibitor design.  

Phylogenetic Analysis of Molecular Data

Dr. Craig Marshall

Phylogenetic analysis of DNA and protein sequence to understand the relationship of the gene of interest to similar genes from other species. An understanding of the phylogenetic relationship of the species from which the genes were derived may be also be determined. This work is important and helpful in understanding how small changes in gene sequence are correlated with differences in function.

Phylogenetic Analysis of Molecular Data from Seaweed

Dr. Judy Broom, Dr W. Nelson

Molecular phylogenetic analysis of seaweed

Analysis of Microarray data

Prof. N Kasabov (Pacific Edge Biotechnology)

Creating new algorithms to analyse microaaray data. These algorithms are based on Connectionist Information Systems.

Analysis of molecular sequence, structure and function

Dr. G. Jacobs (BioinfoTools)

Computational studies to understand the structural basis of protein-DNA interactions and developing methods to predict structural and functional information about proteins from their sequences. Computational studies to understand the structural basis of protein-DNA interactions.

Visualisation of RNA structures

J. Todz, Dr C. Brown

Bacterial promoter and ribosome binding site analysis

P. Laws, Dr I lamont, Dr C. Brown, M Schreiber

Logopaint software available

Mammalian promoter analysis, analysis of gene expression data.

A. Zadissa, J McEwan (AgResearch) C. Brown

Software and analysis available

Analysis of mammalian gene expression

Dr J Stanton, Prof D. Green

Molecular embryology group

Green egg database

Tagsorter software

Genome Sequencing

Analysis of crystallographic and structural data.

Dr S. Wilbanks, Assoc Prof J Cutfield, K Krause

Imprinted Genes

Dr I Morison

Imprinted Genes database

Visualisation of Genomes

Dr Lubica Benuskova

Iterated function system for visualisation of genomes

Discovery of new genes and structures within genomes

Dr A. Firth, Dr C. Brown

MLOGD website

Viral genomes, Virology Research Theme

Updated 14/6/10

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