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Unit of study_
PGEN5001: Pathogen Genomics
2025 unit information
Genomics has revolutionised medicine, providing information on a scale not previously available. Pathogen Genomics is part of this revolution and the applications of this technology have provided crucial information on pathogen discovery, new drug development, control of outbreaks, pandemics and antibiotic resistance. This unit of study will introduce students to analysis of bacterial and viral genomes and main applications of genomics for translational research, precision medicine and control of diseases with epidemic potential. Students will learn how DNA or RNA is sequenced in the laboratory and develop analytical skills in microbial genomics, using public databases and the University of Sydney's high performance computing cluster. A combination of lectures delivered by domain experts and interactive practicals will provide detailed understanding of the key concepts of genomics utilized in research and clinical practice. Through targeted assignment, oral presentations and group projects students are encouraged to apply their learnings to critically examine genomic evidence and answer practical questions relevant to outbreak investigations and disease emergence.
Unit details and rules
Managing faculty or University school:
Medicine and Health
| Study level | Postgraduate |
|---|---|
| Academic unit | Department of Medical Sciences |
| Credit points | 6 |
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Prerequisites:
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None |
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Corequisites:
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None |
| Prohibitions:
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None |
| Assumed knowledge:
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Basic understanding of microbiology or medical microbiology and genetics |
At the completion of this unit, you should be able to:
- LO1. Understand sequencing data and relevant quality metrics
- LO2. Taxonomically classify microorganisms using short read sequencing data
- LO3. Identify variation in viral, bacterial and metagenomics data
- LO4. Generate and examine phylogenetic trees based on nucleotide polymorphisms and core genomes
- LO5. Perform genome mapping, assembly and annotation using different resources
- LO6. Interpret genomic data from an outbreak investigation
- LO7. Determine relevant drug resistance genes and mutations
- LO8. Understand main approaches for genome data visualisation
- LO9. Recognise challenges and identify solutions for pathogen genomic data gathering, analysis, governance and reporting
Unit availability
This section lists the session, attendance modes and locations the unit is available in. There is a unit outline for each of the unit availabilities, which gives you information about the unit including assessment details and a schedule of weekly activities.
The outline is published 2 weeks before the first day of teaching. You can look at previous outlines for a guide to the details of a unit.
| Session | MoA ? | Location | Outline ? |
|---|---|---|---|
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Semester 2 2025
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Normal day | Westmead, Sydney |
Outline unavailable
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Modes of attendance (MoA)
This refers to the Mode of attendance (MoA) for the unit as it appears when you’re selecting your units in Sydney Student. Find more information about modes of attendance on our website.
