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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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