Dr Cheong Xin Chan

Senior Research Fellow

School of Chemistry and Molecular Biosciences
Faculty of Science

Affiliate Research Fellow

Institute for Molecular Bioscience
+61 7 336 53829


Dr Chan has a PhD in Genomics and Computational Biology from UQ. Upon graduation, he underwent postdoctoral training with Professor Debashish Bhattacharya at Rutgers University (New Brunswick, New Jersey), focusing on algal genomics and evolution (phylogenomics), and the origin of plastids. His research routinely involves de novo assembly and analysis of high-throughput sequencing data.

Since his return to UQ in November 2011, Chan has been using advanced computational and database approaches to explore and develop highly scalable phylogenomic approaches, and to study genome evolution of microbes, including bacteria, algae and protists.

Research Interests

  • Genomics of coral symbionts and their relatives
    Reef-building corals are critically sustained by the symbiosis between the coral animal and the symbiotic dinoflagellate algae. Breakdown of this symbiosis leads to coral bleaching, and if not soon re-established, coral death. The coral symbionts (in family Symbiodiniaceae) and their close relatives (i.e. the other dinoflagellates) are highly diverse, and are key primary producers in the oceans. Working with our collaborators nationally and internationally, we are generating de novo core genome data from coral symbionts and their relatives, including symbionts isolated from the Great Barrier Reef. We are interested in genome evolution of these ecologically important species, specifically related to their evolutionary transition from free-living to symbiotic lifestyles, and its functional implications on the coral holobiont and the health of the coral reefs (e.g. via hologenomics approach).
  • 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. Some of the questions we are interested in include genome features unique to the coral symbionts, stress tolerance, and antibiotic resistance in bacteria. Through UQ Genomics Initiative and UQ Genome Innovation Hub, we adopt cutting-edge genomic technologies to generate high-quality genome-scale data for addressing these questions. Working with our collaborators, we adopt an experimental approach to assess microbial genome evolution in real-time, i.e. decoding the genomes across multiple generations of the microbes grown under a controlled, stress condition.
  • Scalable phylogenomics using alignment-free methods
    Highly scalable phylogenomic approaches are needed to make evolutionary sense of the ongoing deluge of sequence data. The current standard phylogenetic/phylogenomic approach using multiple sequence alignment is based on the implicit assumption that all homologous sequences are contiguous, and can be computational expensive. We are exploring the use of alignment-free methods (specifically the use of k-mers) in large-scale phylogenomic analysis, and their sensitivity to key aspects in molecular evolution. We are expanding this approach to infer phylogenomic relationships beyond the conventional tree-like structure (i.e. as networks).

Research Impacts

Chan has published over 60 scholarly publications in the areas of microbial genomics, evolutionary biology, and bioinformatics. His research work since 2003 has been continuously challenging the working hypotheses in evolutionary biology. His PhD thesis work overthrew the plausible but incorrect assumption that whole genes are the units of lateral transfer, and revealed a bigger footprint of genetic transfer in the evolution of bacterial genomes. His research of algal genomics demonstrates a single origin of primary plastids, and the remarkably complicated evolutionary histories of algae due to genetic transfer and endosymbiosis. This body of work establishes a single origin of Plantae, the foundational lineage that gave rise to all plants and algae. His current research on the coral reef symbionts aims to elucidate the roles that algae play in the adaptability of coral reefs. His recent research on scalable phylogenomics demonstrates the use of alignment-free methods to accurately and quickly infer phylogenomic relationships from thousands of microbial genomes.


  • Doctor of Philosophy, The University of Queensland
  • Master of Philosophy, University of Malaya
  • Bachelor of Science (Industrial Biology) Honours, Universiti Teknologi Malaysia


View all Publications


  • Doctor Philosophy

  • Doctor Philosophy

  • (2020) Doctor Philosophy

View all Supervision


Book Chapter

  • Chan, Cheong Xin, Beiko, Robert G. and Ragan, Mark A. (2017). Scaling up the phylogenetic detection of lateral gene transfer events. In Keith, JM (Ed.), Bioinformatics (pp. 421-432) New York, United States: Humana Press. doi:10.1007/978-1-4939-6622-6_16

  • Chan, Cheong Xin (2015). Phylogenomics in algal research: current trends and future perspectives. The Algae World. (pp. 501-517) edited by Dinabandhu Sahoo and Joseph Seckbach. Dordrecht, Netherlands: Springer. doi: 10.1007/978-94-017-7321-8_20

  • Bhattacharya, Debashish, Price, Dana C., Chan, Cheong Xin, Gross, Jeferson, Steiner, Jürgen M. and Löffelhardt, Wolfgang (2014). Analysis of the genome of Cyanophora paradoxa: an algal model for understanding primary endosymbiosis. Endosymbiosis. (pp. 135-148) edited by Wolfgang Löffelhardt. Wien, Austria: Springer. doi: 10.1007/978-3-7091-1303-5_7

  • 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

  • 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

Journal Article

Conference Publication

  • Chan, Cheong Xin, Stephens, Timothy G., Ling, Edmund Y. S., Foret, Sylvain, Morrow, Kathleen, Bourne, David G., Voolstra, Christian R., Leggat, William, Miller, David J. and Ragan, Mark A. (2015). Genome Analysis of Two Symbiodinium Isolates. 6th European Phycological Congress, London, United Kingdom, 23-28 August 2015. Abingdon, Oxfordshire, United Kingdom: Taylor and Francis. doi: 10.1080/09670262.2015.1069489

  • Chan, Cheong Xin, Bernard, Guillaume, Chalmers, Benjamin D. B. and Ragan, Mark A. (2015). Scalable phylogenomic approaches to study algal evolution. 6th European Phycological Congress, London, United Kingdom, 23-28 August 2015. Abingdon, Oxfordshire, United Kingdom: Taylor and Francis. doi: 10.1080/09670262.2015.1069493

  • Bhattacharya, D., Gross, J., Price, D. C., Chan, C. X. and Zelzion, U. (2013). The Cyanophora genome: analysis of gene and small RNA content in a pivotal algal lineage. 10th International Phycological Congress, Orlando, FL, United States, 4-10 August 2013. Lawrence, KS, United States: International Phycological Society. doi: 10.2216/0031-8884-52.sp4.1

  • Chan, C. X. and Martone, P. T. (2012). Recent advances in the calliarthron genome: climate Responses and cell wall evolution. Annual Meeting of the Phycological Society of America (PSA) 2012, Charleston SC, United States, 20-23 June 2012. Hoboken, NJ., United States: Wiley-Blackwell Publishing. doi: 10.1111/j.1529-8817.2012.01206.x

  • Gross, J., Wajid, S., Price, D., Chan, C. X. and Bhattacharya, D. (2012). Srnas of cyanophora paradoxa and chlamydomonas reinhardtii, a system genomics approach to understand algal evolution. Annual Meeting of the Phycological Society of America (PSA) 2012, Charleston SC, United States, 20-23 June 2012. Hoboken, NJ., United States: Wiley-Blackwell Publishing. doi: 10.1111/j.1529-8817.2012.01206.x

  • 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.

  • 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

  • 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.

  • 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.

  • 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.

  • 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.

Other Outputs

PhD and MPhil Supervision

Note for students: Dr Cheong Xin Chan is not currently available to take on new students.

Current Supervision

  • Doctor Philosophy — Principal Advisor

    Other advisors:

  • Doctor Philosophy — Principal Advisor

    Other advisors:

  • Doctor Philosophy — Associate Advisor

  • Doctor Philosophy — Associate Advisor

    Other advisors:

Completed Supervision