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Bioinformatics Student Exchange Program (BSEP) 2024 CSIRO

The Bioinformatics Student Exchange Program (BSEP) is aimed at giving overseas students
the opportunity to contribute to world-class research and gain experience in an
international research environment. Master and Honours students are invited to conduct original research as part of their University Thesis. This is an exciting opportunity to forge new collaboration and build up a strong international network.

How to apply

Please choose the project you are interested in and get in touch with your contact person listed above. Your first step will be to organize funding by applying (see below). After a successful interview, CSIRO will issue a contract with a visa sponsorship number in January. It is crucial to apply for the Australian Visa quickly as it can take up to 3 months to be approved. CSIRO will guide you through the process but

please have a look at:
Funding

Students are encouraged to apply for funding. Unless stated otherwise, the projects will not provide funding.

PROMOS

German funding through PROMOS (Deadline Early October to early November), which will
cover from 300 to 500 EUR per month or traveling costs up to 1950 EUR
Note, PROMOS is not explicitly paying a health insurance, this hence needs to be covered by the student.

DAAD

The DAAD offers Study Scholarships, such as Master Studies for All Academic Disciplines
https://www2.daad.de/deutschland/stipendium/datenbank/en/21148-scholarshipdatabase/?detail=50026200 with funding between 10 and 24 months.
There are also other funding sources available such as http://www.ranke-heinemann.de.

Project

Projects can be altered to fit the students interests and skills. The Transformational Bioinformatics group at CSIRO has a very broad spectrum of activities, ranging from human health to biosecurity; from basic science to real-world applications. We highly encourage you to check our webpage (https://bioinformatics.csiro.au/) for our activities and approach us with your own project ideas.

Project Title BSEP03 Programming CRISPR scoring methods

Brief description of the project
highlighting expected outcomes

The student will learn how to 1) utilise existing CRISPR scoring algorithms
(MIT, Tuscan); and 2) perform research into emerging CRISPR scoring
methods (e.g. Cas-13) to develop reusable high-performance computing
software libraries within a cloud-computing development environment. The
resulting score-function will be included into the GT-Scan web service.

Duties/Tasks The student will perform
• Programming Python/C++/AWS
• Translation of biological/genome-editing research into cloud software
Relevant field/s of
study

• Bioinformatics

• Software Programming

• Cloud computing

Supervisor Tracey Wright

Contact Details [email protected]
Location Remote or in person in Brisbane

Project Title BSEP05 Identification of epistatic biomarkers in a cancer dataset

Brief description of the project

highlighting expected outcomes

Metastatic cancer, cancer that has spread from its primary site, poses significant challenges in terms of treatment and often carries a high risk of
mortality. For this project, we propose conducting a comprehensive analysis of cancer data from a systems perspective. By incorporating multiple variables (i.e., whole genomic sequencing, metadata) and their interactions, we can potentially uncover novel insights that could contribute to improved diagnostics and treatment strategies for metastatic
cancer. The work will be based on publicly available data
https://www.nature.com/articles/s41586-023-06054-z

Duties/Tasks The student will perform

• VariantSpark analysis (random forest)
• Epistasis detection tools
• AWS + python
• Interpret and summarise results
Relevant field/s of
study

• Bioinformatics

Supervisor Roc Reguant
Mitchell O’Brien Letitia Sng
Contact Details [email protected]
mitchell.o’[email protected]
[email protected]

Location Remote or in person in Sydney

Key dates

Date

June CSIRO calls for project proposals 31st July Program Booklet sent to the Universities

Early August to early November

Students choose proposals and get in contact with CSIRO

Early August to early November

Deadline for PROMOS or equivalent funding application

Dec Thesis committee assesses suitability of projects and identifies appropriate
co-supervisor amongst the faculty.
Jan CSIRO starts recruitment process (visa)
May* Students commence research in Australia
Oct* Students return home

Nov* Students finalise reports and write master thesis with input from CSIRO
researchers

Bioinformatics Student Exchange Program

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