Overview
Background
Dr Chan has a PhD in Genomics and Computational Biology from UQ. He underwent postdoctoral training at Rutgers University (USA) in algal genomics and evolution. He returmed to UQ in late 2011 as one of the inaugural Great Barrier Reef Foundation Bioinformatics Fellows.
Dr Chan joined the School of Chemistry and Molecular Biosciences in 2020 as a group leader at the Australian Centre for Ecogenomics (ACE). His group uses advanced computational approaches to study genome evolution and develop scalable approaches for comparative genomics.
Availability
- Associate Professor Cheong Xin Chan is:
- Available for supervision
Fields of research
Qualifications
- Bachelor (Honours) of Science (Advanced), Universiti Teknologi Malaysia
- Masters (Research) of Molecular Biotechnology, University of Malaya
- Doctor of Philosophy, The University of Queensland
Research interests
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Genome evolution and innovation
We are interested in the evolution of genomes in response to the organism's adaptation to changing environments. Using comparative genomics, we aim to identify genome features, gene content, functions, and/or pathways that are specific to distinct ecological niches. We work with our collaborators on a range of microbes, algae, drought-resistant plants, weeds, corals and jellyfish.
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Hologenomics of symbiosis
We aim to understand the genetic capacity of symbiotic partners in sustaining a functional ecological unit. Central to our research are the reef-building corals, critically sustained by symbiosis between the coral animal and the symbiotic dinoflagellate algae. Breakdown of this symbiosis leads to coral bleaching. Working with our collaborators nationally and internationally, we are generating de novo core genome data from coral symbionts and their relatives.
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Scalable phylogenomics using alignment-free methods
Highly scalable phylogenomic approaches are needed to make evolutionary sense of the ongoing deluge of sequence data. Working with our international collaborators, we are developing and exploring the use of alignment-free methods in large-scale inference of genome evolution as networks, beyond the conventional tree-like assumption of evolutionary history.
Research impacts
Chan has published 100 scholarly publications in the areas of microbial genomics, evolutionary biology, and bioinformatics. His research work continuously challenges the working hypotheses in evolutionary biology. This body of work demonstrates a single origin of Archaeplastida (Plantae), the foundational lineage that gave rise to all plants and algae. His recent research reveals molecular functions that underpin coral-alga symbiosis, and demonstrates the scalability of alignment-free methods to accurately and quickly infer phylogenetic relationships from thousands of microbial genomes.
Works
Search Professor Cheong Xin Chan’s works on UQ eSpace
2011
Book Chapter
Plastid origin and evolution
Chan, Cheong Xin and Bhattacharya, Debashish (2011). Plastid origin and evolution. eLS. (pp. 1-8) Chichester, United Kingdom: John Wiley & Sons. doi: 10.1002/9780470015902.a0023639
2010
Journal Article
The origin of plastids
Chan, Cheong Xin and Bhattacharya, Debashish (2010). The origin of plastids. Nature Education, 3 (9), 84-1-84-5.
2010
Book Chapter
Porphyra: Complex life histories in a harsh environment
Gantt, Elisabeth, Berg, G. Mine, Bhattacharya, Debashish, Blouin, Nicolas A., Brodie, Juliet A., Chan, Cheong Xin, Collen, Jonas, Cunningham, Francis X., Gross, Jeferson, Grossman, Arthur R., Karpowicz, Steven, Kitade, Yukihiro, Klein, Anita S., Levine, Ira A., Lin, Senjie, Lu, Shan, Lynch, Michael, Minocha, Subhash C., Muller, Kirsten, Neefus, Christopher D., De Oliveira, Mariana Cabral, Rymarquis, Linda, Smith, Alison, Stiller, John W., Wu, Wen-Kai, Yarish, Charles, Zhuang, Yun and Brawley, Susan H. (2010). Porphyra: Complex life histories in a harsh environment. Red algae in the genomic age. (pp. 129-148) edited by Joseph Seckbach and David J. Chapman. New York , NY, U.S.A.: Springer. doi: 10.1007/978-90-481-3795-4_7
2009
Journal Article
Lateral transfer of genes and gene fragments in prokaryotes
Chan, Cheong Xin, Beiko, Robert G., Darling, Aaron E. and Ragan, Mark A. (2009). Lateral transfer of genes and gene fragments in prokaryotes. Genome Biology and Evolution, 1, 429-438. doi: 10.1093/gbe/evp044
2009
Journal Article
Are protein domains modules of lateral genetic transfer?
Chan, Cheong Xin, Darling, Aaron E., Beiko, Robert G. and Ragan, Mark A. (2009). Are protein domains modules of lateral genetic transfer?. PLoS One, 4 (2) e4524, e4524.1-e4524.8. doi: 10.1371/journal.pone.0004524
2008
Conference Publication
Large-scale detection of recombination in nucleotide sequences
Chan, Cheong Xin, Beiko, Robert G. and Ragan, Mark A. (2008). Large-scale detection of recombination in nucleotide sequences. International Conference on Mathematical Biology 2007, Putrajaya, Malaysia, 4-6 September 2007. Melville, NY, USA: American Institute of Physics. doi: 10.1063/1.2883829
2008
Journal Article
A phylogenomic approach for studying plastid endosymbiosis
Moustafa, Ahmed, Chan, Cheong Xin, Danforth, Megan, Zear, David, Ahmed, Hiba, Jadhav, Nagnath, Savage, Trevor and Bhattacharya, Debashish (2008). A phylogenomic approach for studying plastid endosymbiosis. Genome informatics. International Conference on Genome Informatics, 21, 165-176.
2008
Conference Publication
A phylogenomic approach for studying plastid endosymbiosis
Moustafa, Ahmed, Chan, Cheong Xin, Danforth, Megan, Zear, David, Ahmed, Hiba, Jadhav, Nagnath, Savage, Trevor and Bhattacharya, Debashish (2008). A phylogenomic approach for studying plastid endosymbiosis. 19th International Conference on Genome Informatics (GIW 2008), Gold Coast , Qld., Australia, 1 - 3 December 2008. London, United Kingdom: Imperial College Press.
2007
Other Outputs
Units of genetic transfer in prokaryotes
Chan, Cheong Xin (2007). Units of genetic transfer in prokaryotes. PhD Thesis, Institute For Molecular Bioscience, The University of Queensland. doi: 10.14264/132182
2007
Other Outputs
A two-phase strategy for detecting recombination in nucleotide sequences
Chan, Cheong Xin, Beiko, Robert G. and Ragan, Mark A. (2007). A two-phase strategy for detecting recombination in nucleotide sequences.
2007
Conference Publication
A two-phase approach for detecting recombination in nucleotide sequences
Chan, Cheong Xin, Beiko, Robert G. and Ragan, Mark A. (2007). A two-phase approach for detecting recombination in nucleotide sequences. The First Southern African Bioinformatics Workshop, Johannesburg, South Africa, 28-30 January 2007. Johannesburg, South Africa: University of the Witwatersrand.
2006
Journal Article
Detecting Recombination in Evolving Nucleotide Sequences
Chan, Cheong Xin, Beiko, Robert G. and Ragan, Mark A. (2006). Detecting Recombination in Evolving Nucleotide Sequences. BMC Bioinformatics, 7 (Article 412) 412, 1-15. doi: 10.1186/1471-2105-7-412
2006
Journal Article
Trends in Seaweed Research
Chan, Cheong-Xin, Ho, Chai-Ling and Phang, Siew-Moi (2006). Trends in Seaweed Research. Trends in Plant Science, 11 (4), 165-166. doi: 10.1016/j.tplants.2006.02.003
2005
Journal Article
A Word-Oriented Approach to Alignment Validation
Beiko, Robert G., Chan, Cheong Xin and Ragan, Mark A. (2005). A Word-Oriented Approach to Alignment Validation. Bioinformatics, 21 (10), 2230-2239. doi: 10.1093/bioinformatics/bti335
2005
Journal Article
Seaweed diversity of Langkawi with emphasis on Northeast Langkawi
Phang, Siew-Moi, Wong, Ching-Lee, Lim, Phaik-Eem, Yeong, Hui-Yin and Chan, Cheong Xin (2005). Seaweed diversity of Langkawi with emphasis on Northeast Langkawi. Malaysian Journal of Science, 24, 77-94.
2004
Journal Article
Comparing Different Approaches in Large-Scale Seaweed Gene Discovery
Chan, Cheong Xin (2004). Comparing Different Approaches in Large-Scale Seaweed Gene Discovery. Bioinformatics India, 2 (3), 106-111.
2004
Journal Article
Optimisation of RNA Extraction from Gracilaria changii (Gracilariales, Rhodophyta)
Chan, Cheong Xin, Teo, Swee-Sen, Ho, Chai-Ling, Othman, Rofina Yasmin and Phang, Siew-Moi (2004). Optimisation of RNA Extraction from Gracilaria changii (Gracilariales, Rhodophyta). Journal of Applied Phycology, 16 (4), 297-301. doi: 10.1023/B:JAPH.0000047782.20940.de
2004
Conference Publication
Oh Father Where Art Thou? Comparing Different Ways of Finding Recombination Events
Chan, Cheong Xin, Beiko, Robert G. and Ragan, Mark A. (2004). Oh Father Where Art Thou? Comparing Different Ways of Finding Recombination Events. First ARC Centre in Bioinformatics Annual All Hands Meeting, The University of Queensland, 10-11 May, 2004.
2004
Conference Publication
Benchmarking the Detection and Analysis of Recombination
Chan, Cheong Xin, Beiko, Robert G. and Ragan, Mark A. (2004). Benchmarking the Detection and Analysis of Recombination. 12th International Conference Intelligent Systems for Molecular Biology (ISMB) and 3rd European Conference in Computational Biology (ECCB), Glasgow, UK, 31 July - 4 August 2004.
2002
Conference Publication
Total RNA Extraction for the Red Seaweed Gracilaria changii (Gracilariales, Rhodophyta)
Chan, Cheong Xin, Ho, Chai-Ling, Othman, Rofina Yasmin and Phang, Siew-Moi (2002). Total RNA Extraction for the Red Seaweed Gracilaria changii (Gracilariales, Rhodophyta). Asia-Pacific Conference in Marine Science and Technology, Kuala Lumpur, Malaysia, 12-16 May, 2002.
Funding
Past funding
Supervision
Availability
- Associate Professor Cheong Xin Chan is:
- Available for supervision
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Supervision history
Current supervision
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Doctor Philosophy
Hologenomic variation in the reef-building coral Acropora hyacinthus across the Great Barrier Reef
Principal Advisor
Other advisors: Professor Cynthia Riginos
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Doctor Philosophy
Diversity and evolution of phytoplasmas infecting banana and coconut in Papua New Guinea
Associate Advisor
Other advisors: Dr Lilia Carvalhais, Professor Andre Drenth
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Doctor Philosophy
Ecophysiology and molecular genetics of selenium tolerance and accumulation in the selenium hyperaccumulator Neptunia amplexicaulis
Associate Advisor
Other advisors: Professor Peter Erskine
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Doctor Philosophy
Genetics of climate-change adaptation in Great Barrier Reef corals
Associate Advisor
Other advisors: Professor Cynthia Riginos
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Doctor Philosophy
Ecophysiology and molecular genetics of selenium tolerance and accumulation in the selenium hyperaccumulator Neptunia amplexicaulis
Associate Advisor
Other advisors: Professor Peter Erskine
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Doctor Philosophy
Understanding the metabolic capabilities and evolutionary relatiosnhips of novel microorganisms from hot springs
Associate Advisor
Other advisors: Professor Phil Hugenholtz, Dr Paul Evans
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Doctor Philosophy
Towards understanding microbial community dynamics in a subtropical estuary: a multi-omics approach
Associate Advisor
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Doctor Philosophy
Ecophysiology and molecular genetics of selenium tolerance and accumulation in the selenium hyperaccumulator Neptunia amplexicaulis
Associate Advisor
Other advisors: Professor Peter Erskine
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Doctor Philosophy
Towards understanding microbial community dynamics in a subtropical estuary: a multi-omics approach
Associate Advisor
Completed supervision
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2024
Doctor Philosophy
Assessing complex gene and genome features of dinoflagellates
Principal Advisor
Other advisors: Dr Quan Nguyen
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2023
Doctor Philosophy
Evolution and adaptation of non-symbiotic Symbiodiniaceae
Principal Advisor
Other advisors: Dr Quan Nguyen
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2019
Doctor Philosophy
Polarella genomics: understanding the evolutionary transition to algal symbiosis and cold adaptation
Principal Advisor
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2025
Doctor Philosophy
Towards understanding microbial community dynamics in a subtropical estuary: a multi-omics approach
Associate Advisor
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2024
Doctor Philosophy
Genomic, Genetic, and Mass Spectrometry Glycoproteomic Investigations of the Roles of Oligosaccharyltransferase Subunits in N-Glycosylation in Yeast
Associate Advisor
Other advisors: Associate Professor Michael Landsberg, Professor Benjamin Schulz
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2023
Doctor Philosophy
Developing novel spatio-temporal inference methods using single cell, spatial omics and imaging data for studying neuroinflammation and cancer progression
Associate Advisor
Other advisors: Professor Marc Ruitenberg, Dr Quan Nguyen
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2017
Doctor Philosophy
Scalable alignment-free approaches in microbial phylogenomics
Associate Advisor
Media
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