Dr Cheong Xin Chan

Senior Research Officer

Institute for Molecular Bioscience
c.chan@imb.uq.edu.au
+61 7 334 62619

Overview

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. Chan is an Associate Faculty Member of F1000Prime in Bioinformatics, Biomedical Informatics & Computational Biology, and currently an Affiliate Lecturer at UQ's School of Chemistry and Molecular Biosciences.

Research Interests

  • Genome sequencing of Symbiodinium from the Great Barrier Reef
    The dinoflagellates, Symbiodinium grow symbiotically with corals. They play critical roles as the primary producers in the oceans, and contribute to the survival of coral reefs. In collaboration with partners in the Reef Future Genomics (ReFuGe) 2020 consortium led by the Great Barrier Reef Foundation (GBRF), we are assembling the genomes of Symbiodinium isolated from the Reef. We are interested in genome evolution of these dinoflagellates, specifically related to their evolutionary transition from free-living to symbiotic lifestyles, and its functional implications on the coral host and the health of the coral reefs, particularly in light of global climate change. Our group is also sequencing the genomes of the closely related dinoflagellate species from the polar regions, Polarella glacialis.
  • Environmental genomics and adaptation of microbes
    We are interested in the innovation of microbial genomes due to adaptation, both in short-term e.g. development of antibiotic-resistance in bacteria, and in long term e.g. microbial adaptation to extreme environments. Chan is involved in a number of algal genome projects, including the biotechnologically important red seaweed Porphyra (an US NSF-funded research collaborative network), and the calcifying coralline alga, Calliarthron, which could provide us clues about how these genomes evolve and adapt to the environment as induced by global climate change.
  • 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 e.g. the use of k-mer (or n-gram) in large-scale phylogenomic analysis, and their sensitivity to key aspects in molecular evolution.

Research Impacts

Chan has published over 50 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, and how we can sustain the ecosystem in light of global climate change.

Qualifications

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

Publications

  • Brodie, Juliet, Ball, Steven G., Bouget, François-Yves, Chan, Cheong Xin, De Clerck, Olivier, Cock, J. Mark, Gachon, Claire, Grossman, Arthur R., Mock, Thomas, Raven, John A., Saha, Mahasweta, Smith, Alison G., Vardi, Assaf, Yoon, Hwan Su and Bhattacharya, Debashish (2017) Biotic interactions as drivers of algal origin and evolution. New Phytologist, . doi:10.1111/nph.14760

  • Brawley, Susan H., Blouin, Nicolas A., Ficko-Blean, Elizabeth, Wheeler, Glen L., Lohr, Martin, Goodson, Holly V., Jenkins, Jerry W., Blaby-Haas, Crysten E., Helliwell, Katherine E., Chan, Cheong Xin, Marriage, Tara N., Bhattacharya, Debashish, Klein, Anita S., Badis, Yacine, Brodie, Juliet, Cao, Yuanyu, Collén, Jonas, Dittami, Simon M., Gachon, Claire M. M., Green, Beverley R., Karpowicz, Steven J., Kim, Jay W., Kudahl, Ulrich Johan, Lin, Senjie, Michel, Gurvan, Mittag, Maria, Olson, Bradley J. S. C., Pangilinan, Jasmyn L., Peng, Yi, Qiu, Huan, Shu, Shenqiang, Singer, John T., Smith, Alison G., Sprecher, Brittany N., Wagner, Volker, Wang, Wenfei, Wang, Zhi-Yong, Yan, Juying, Yarish, Charles, Zäuner-Riek, Simone, Zhuang, Yunyun, Zou, Yong, Lindquist, Erika A., Grimwood, Jane, Barry, Kerrie W., Rokhsar, Daniel S., Schmutz, Jeremy, Stiller, John W., Grossman, Arthur R. and Prochnik, Simon E. (2017) Insights into the red algae and eukaryotic evolution from the genome of Porphyra umbilicalis (Bangiophyceae, Rhodophyta). Proceedings of the National Academy of Sciences, 114 31: E6361-E6370. doi:10.1073/pnas.1703088114

  • Brodie, Juliet, Chan, Cheong Xin, De Clerck, Olivier, Cock, J. Mark, Coelho, Susana M., Gachon, Claire, Grossman, Arthur R., Mock, Thomas, Raven, John A., Smith, Alison S., Yoon, Hwan Su and Bhattacharya, Debashish (2017) The algal revolution. Trends in Plant Science, 22 8: 726-738. doi:10.1016/j.tplants.2017.05.005

View all Publications

Supervision

  • Doctor Philosophy

  • Doctor Philosophy

  • Doctor Philosophy

View all Supervision

Publications

Book Chapter

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

  • Chan, Cheong Xin (2015). Phylogenomics in algal research: current trends and future perspectives. In The Algae World (pp. 501-517) 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. In Wolfgang Löffelhardt (Ed.), Endosymbiosis (pp. 135-148) Wien, Austria: Springer. doi:10.1007/978-3-7091-1303-5_7

  • Chan, Cheong Xin and Bhattacharya, Debashish (2011). Plastid origin and evolution. In 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. In Joseph Seckbach and David J. Chapman (Ed.), Red algae in the genomic age (pp. 129-148) 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. In: Programme and Abstracts of the Sixth European Phycological Congress. 6th European Phycological Congress, London, United Kingdom, (57-58). 23-28 August 2015. 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. In: Programme and Abstracts of the Sixth European Phycological Congress. 6th European Phycological Congress, London, United Kingdom, (150-150). 23-28 August 2015. 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. In: Phycologia. 10th International Phycological Congress, Orlando, FL, United States, (10-11). 4-10 August 2013. 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. In: PSA 2012 Abstracts. Annual Meeting of the Phycological Society of America (PSA) 2012, Charleston SC, United States, (S1-S2). 20-23 June 2012. doi:10.1111/j.1529-8817.2012.01206.x

  • Chan, C. X. and Martone, P. T. (2012). Recent advances in the calliarthron genome: climate Responses and cell wall evolution. In: PSA 2012 Abstracts. Annual Meeting of the Phycological Society of America (PSA) 2012, Charleston SC, United States, (S1-S2). 20-23 June 2012. 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. In: PSA 2012 Abstracts. Annual Meeting of the Phycological Society of America (PSA) 2012, Charleston SC, United States, (S20-S20). 20-23 June 2012. 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. In: Jonathan Arthur and See-Kiong Ng, Genome Informatics 2008: Proceedings of the 19th International Conference. 19th International Conference on Genome Informatics (GIW 2008), Gold Coast , Qld., Australia, (165-176). 1 - 3 December 2008.

  • Chan, Cheong Xin, Beiko, Robert G. and Ragan, Mark A. (2008). Large-scale detection of recombination in nucleotide sequences. In: Atan, Mohd. K. A. and Krishnarajan, I. S., AIP Conference Proceedings: International Conference on Mathematical Biology 2007. International Conference on Mathematical Biology 2007, Putrajaya, Malaysia, (101-104). 4-6 September 2007. 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. In: Proceedings of the First Southern African Bioinformatics Workshop (SABioinf 2007). The First Southern African Bioinformatics Workshop, Johannesburg, South Africa, (9-16). 28-30 January 2007.

  • Chan, Cheong Xin, Beiko, Robert G. and Ragan, Mark A. (2004). Benchmarking the Detection and Analysis of Recombination. In: Proceedings of the 12th International Conference Intelligent Systems for Molecular Biology (ISMB) and 3rd European Conference in Computational Biology (ECCB). 12th International Conference Intelligent Systems for Molecular Biology (ISMB) and 3rd European Conference in Computational Biology (ECCB), Glasgow, UK, (160-160). 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. In: 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). In: Asia-Pacific Conference in Marine Science and Technology, Kuala Lumpur, Malaysia, (). 12-16 May, 2002.

Other Outputs

Grants (Administered at UQ)

PhD and MPhil Supervision

Current Supervision

  • Doctor Philosophy — Associate Advisor

    Other advisors:

  • Doctor Philosophy — Associate Advisor

    Other advisors:

  • Doctor Philosophy — Associate Advisor

    Other advisors: