<b>Professor Mark Ragan</b><br>
Co-Division Head, Genomics of Development and Disease Division<br><p>
P: +61 7 3346 2616<br>
E: m.ragan@imb.uq.edu.au<p>
<b>Keywords</b><br>
- breast cancer<br>
- pancreatic cancer<br>
- prostate cancer<br>
- gastrointestinal disorders<br>
- urohaemolytic disorders<br>
- staphylococcal diseases
Professor Mark Ragan
Co-Division Head, Genomics of Development and Disease Division

P: +61 7 3346 2616
E: m.ragan@imb.uq.edu.au

Keywords
- breast cancer
- pancreatic cancer
- prostate cancer
- gastrointestinal disorders
- urohaemolytic disorders
- staphylococcal diseases

Computational systems biology

The structure, function and fate of living cells are determined by complex networks of interactions among biomolecules. These networks cannot be observed directly, but must be reverse-engineered from genome-scale data. Our research develops and applies approaches based on mathematics, statistics, computer science and bioinformatics to infer and analyse these networks from individual samples or patients.

We are particularly interested in understanding how networks of gene regulation differ between normal and cancerous states. We collaborate with biologists and clinicians on projects investigating breast cancer, ovarian cancer, pancreatic cancer and prostate cancer. Likewise, the spread of drug resistance and virulence among infectious-disease bacteria can be drawn as a graph and studied mathematically. Using high-performance computers, we identify features of these networks that help us understand and predict properties of cells, organisms and communities.

Our research in computational systems biology of mammalian cells will extend the power of genome-scale sequencing, including personal genomics, to help understand normal developmental processes and to design systems-level intervention in chronic disease and cancer.

During the past 12 months, we developed and applied computational approaches to discover the backup systems that cells use to repair damage to their DNA. These backup pathways can differ between cancerous and normal cells, and we are applying these approaches to discover novel ways to target breast cancer cells with minimal risk to normal healthy cells.

The international Sea-Quence Project aims to generate core genetic data from the Great Barrier Reef and coral reefs in the Red Sea. As part of this collaboration, we began to assemble and analyse genomes of Symbiodinium, the algal symbiont in corals. Our goal is to identify the gene systems and mechanisms that underpin and stabilise this symbiosis, to assist in improving coral health and managing reef ecosystems.

Finally, we extended our studies of bacterial genomes to the communities associated with roots of sugarcane. In partnership with fellow UQ scientists, we identified a new soil bacterium, which under controlled conditions, promotes the growth of sugarcane. We then sequenced the genome of this bacterium to investigate its potential to supply nitrogen compounds to sugarcane. 

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Learn more

To learn more about the Sea-Quence Project and the ReFuGe 2020 consortium, please watch this video

Sea-Quence: ReFuGe 2020 Consortium from April Renee Bailey on Vimeo.

Research training opportunities

There are no PhD or MPhil research training opportunities available within Professor Ragan’s group.
Please refer to the IMB Postgraduate website to find another suitable advisor.

However, there are opportunities for students wishing to apply for research training opportunities within the following programs: UQ’s Advanced Study Program in Science (ASPinS), research projects as part of UQ's bioinformatics and biotechnology masters programs, summer/winter research programs, traineeships, and honours.

Key publications

View more publications by Professor Ragan via Pubmed or via UQ Researchers. 

Liu C, Srihari S, Lê Cao K-A, Chenevix-Trench G, Simpson PT, Ragan MA & Khanna KK (2014) A fine-scale dissection of the DNA double-strand break repair machinery and its implications for breast cancer therapy. Nucleic Acids Research 42:6106-6127.

Maetschke SR, Madhamshettiwar PB, Davis MJ & Ragan MA (2013) Supervised, semi-supervised and unsupervised inference of gene regulatory networks. Briefings in Bioinformatics 15:195-211.

Primmer CR, Papakostas S, Leder EH, Davis MJ & Ragan MA (2013) Annotated genes and non-annotated genomes: cross-species use of Gene Ontology in ecology and evolution research. Molecular Ecology 22:3216-3241.

Srihari S & Ragan MA (2013) Systematic tracking of dysregulated modules identifies novel genes in cancer. Bioinformatics 29:1553-1561.

Madhamshettiwar P, Maetschke SR, Davis MJ, Reverter A & Ragan MA (2012) Gene regulatory network inference: evaluation and application to ovarian cancer allows the priorisation of drug targets. Genome Medicine 4:41.

Group contacts

Dr Alison Anderson
Research staff
+61 7 334 62605
a.anderson@imb.uq.edu.au
Mr Chao Liu
Research higher degree student
+61 7 334 62606
chao.liu@imb.uq.edu.au
 
Ms Shelley Barfoot
ASPiNS student
+61 7 334 62606
shelley.barfoot@uq.net.au
Professor Mark Ragan
Group leader
+61 7 334 62616
m.ragan@imb.uq.edu.au 
 
Mr Guillaume Bernard
Research higher degree student
+61 7 334 62606
guillaume.bernard@imb.uq.edu.au
Dr Sriganesh Srihari
Research officer
+61 7 334 62178
s.srihari@imb.uq.edu.au
 
Mr Ben Chalmers 
Honours student
+61 7 334 62036
benjamin.chalmers1@uqconnect.edu.au
Mr Timothy Stephens
Honours student
+61 7 334 62606
timothy.stephens1@uqconnect.edu.au
 
Dr Cheong-Xin Chan
Research officer
+61 7 334 62619
c.chan@imb.uq.edu.au
Mrs Atefeh Taherian Fard
Research higher degree student
+61 7 334 62606
a.taherian@imb.uq.edu.au
 
Mr Yingnan Cong
Research higher degree student
+61 7 334 62606
y.cong@imb.uq.edu.au
Ms Lanna Wong
Executive officer
+61 7 334 62617
l.wong@imb.uq.edu.au 
 

Mr Xavier de Luca
Honours student
+61 7 3346 62606
s4254427@student.uq.edu.au

Mr Yun Kit Yeoh
Research higher degree student
+61 7 334 62623
y.yeoh@imb.uq.edu.au 
 
Dr Edmund Ling
Research visitor
+61 7 334 62606
e.ling1@uq.edu.au
   

 

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