About this role
Applications are invited for a funded PhD scholarship position at Monash University, Australia. The successful candidate will perform research in the junction of information visualisation, bioinformatics, and the Semantic Web. The candidate will work under the supervision of Prof. Falk Schreiber and Dr. Yuan-Fang Li at the Faculty of Information Technology, Monash University.
The Gene Ontology (GO) [1] is one of the most widely used biomedical ontologies. It comprehensively describes different aspects of genes and gene products under three broad categories, (1) biological process, (2) cellular components and (3) molecular functions. GO is currently being actively extended in the LEGO project to create a new annotation system to provide more extensible and expressive annotations.
This project aims to investigating novel visualisation techniques for GO-LEGO and its integration with the Systems Biology Graphical Notation (SBGN) [2]. The information can be seen as networks, and although there are some solutions for network layout, none is particularly tailered towards this application. Specifically we will investigate how domain knowledge captured in ontologies can assist in creating high-quality layouts.
[1] Ashburner, Michael, et al. “Gene Ontology: tool for the unification of biology.”Nature Genetics 25.1 (2000): 25-29.
[2] Le Nov??re et al. “The Systems Biology Graphical Notation” Nature Biotechnology 27 (2009): 735-741.
Company:
Monash University
Qualifications:
The successful student will have an excellent academic track record in computer science, bioinformatics or a related discipline. Applicants are expected to possess very good programming and analytical skills, be able to work independently as well as cooperatively with others. Research experiences in ontologies, knowledge representation, bioinformatics or information visualisation would be highly advantageous.
Candidates will be required to meet Monash entry requirements which include English-language skills. Details of eligibility requirements to undertake a PhD are available at http://www.monash.edu/migr/apply/eligibility/phd/ and http://infotech.monash.edu/research/degrees/prospective-students/entry-requirements.html.
Specific requirements:
The scholarship is tenable for three years, and extendable for up four years, dependent on satisfactory progress and availability of funding.