Student Projects
Projects are available for post graduate students through our affiliation with the University of Melbourne. Projects are usually arranged via the departments of Medicine, Genetics or Pathology. Usually joint supervision will be sought.
Students who have their own post graduate award are welcome to apply at any time. We are willing to provide support (in terms of a letter of recommendation) for students' applications to APA where their training is closely allied to our requirements.
Students for BSc Hons should apply via their relevant departments or direct. There will be space for 2-3 laboratory bench students and 2 bioinformatics students. Administration and the laboratories are located at St. Vincent's hospital.
We are also able to offer top up amounts for PhD studentships.
Honours, Masters and PhD projects are available in three areas and detailed below:
Human Variome Project & Mutation Databases
4 projects on offer. These projects relate to the Human Variome Project (www.humanvariomeproject.org). More specifically, to colon cancer databases where possible, as this is a major pilot project for the Human Variome Project.
Contact: Prof. Richard Cotton
cotton@unimelb.edu.au
Project 1
Creating a set of standards and forms for describing phenotypes
(PhD/BSc (Hons))
Project 2
Intelligent prediction of mutation effects
(PhD)
Given a mutation, predict a priori its effect such as protein misfolding and missplicing. The effect of a mutation depends on where it occurs, which could be in an exon (in which case the effect depends on the conservation of the affected residues or whether the mutation is a frameshift), or in a splice site of an intron, elsewhere in an intron, or in a promoter sequence etc.
Project 3
Homology searching to determine conservation
(Masters/PhD)
Given a Gene or Protein identify the homologous Proteins across and within all Species and align them using existing alignment tools (such as BLAST) and possibly existing databases of Multiple Sequence Alignments. For each mutation on the given Gene/Protein a measure of the conservation of the affected residue(s) can then be determined from the alignment.
Project 4
Automated Matching of Mutation Descriptions
(Masters/ V. Good Honours)
Given a Variant Name (mutation description) e.g. BRCA1 c.1225_1227delGAT and a Reference Sequence for the affected Gene (BRCA1 in the example), find all biologically equivalent variants among the known variants in the given gene. This needs to provide for: "Differing formats between the various general mutation and locus (Gene) specific databases (LSDBs)" and "Differing nucleotide numbering conventions used on the various databases".