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Dr Cheong Xin Chan

Senior Lecturer

School of Chemistry and Molecular Biosciences
Faculty of Science
c.chan1@uq.edu.au
+61 7 336 53829

Overview

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.

Research Interests

  • 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.
  • 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.
  • 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 over 70 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.

Qualifications

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

Publications

View all Publications

Grants

View all Grants

Supervision

  • Assessing complex gene and genome features of dinoflagellates

    Doctor Philosophy

  • Hologenomic variation in the reef-building coral Acropora hyacinthus across the Great Barrier Reef

    Doctor Philosophy

  • Evolution and adaptation of non-symbiotic Symbiodiniaceae

    Doctor Philosophy

View all Supervision

Publications

Book Chapter

  • Coral conservation from the genomic perspective on symbiodiniaceae diversity and function in the holobiont

    Shah, Sarah, Dougan, Katherine E., Bhattacharya, Debashish and Chan, Cheong Xin (2022). Coral conservation from the genomic perspective on symbiodiniaceae diversity and function in the holobiont. Coral reefs of the world. (pp. 85-96) edited by Madeleine J. H. van Oppen and Manuel Aranda Lastra. Cham, Switzerland: Springer Cham. doi: 10.1007/978-3-031-07055-6_6

  • Inferring phylogenomic relationship of microbes using scalable alignment-free methods

    Bernard, Guillaume, Stephens, Timothy G., González-Pech, Raúl A. and Chan, Cheong Xin (2021). Inferring phylogenomic relationship of microbes using scalable alignment-free methods. Bacterial pangenomics: methods and protocols. (pp. 69-76) New York, United States: Humana Press. doi: 10.1007/978-1-0716-1099-2_5

  • Scaling up the phylogenetic detection of lateral gene transfer events

    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

  • Phylogenomics in algal research: current trends and future perspectives

    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

  • Analysis of the genome of Cyanophora paradoxa: an algal model for understanding primary endosymbiosis

    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

  • 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

  • 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

Journal Article

Conference Publication

  • Genome Analysis of Two Symbiodinium Isolates

    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

  • Scalable phylogenomic approaches to study algal evolution

    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

  • The Cyanophora genome: analysis of gene and small RNA content in a pivotal algal lineage

    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

  • Recent advances in the calliarthron genome: climate Responses and cell wall evolution

    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

  • Srnas of cyanophora paradoxa and chlamydomonas reinhardtii, a system genomics approach to understand algal evolution

    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

  • 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.

  • 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

  • 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.

  • 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.

  • 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.

  • 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.

Other Outputs

  • Long non-coding RNAs of three dinoflagellate species

    Chen, Yibi, Dougan, Katherine E., Nguyen, Quen, Bhattacharya, Debashish and Chan, Cheong Xin (2023). Long non-coding RNAs of three dinoflagellate species. The University of Queensland. (Dataset) doi: 10.48610/2692e99

  • Genome and transcriptome data for bloom-forming dinoflagellate Prorocentrum cordatum CCMP1329

    Dougan, Katherine E., Deng, Zhi-Luo, Wöhlbrand, Lars, Reuse, Carsten, Bunk, Boyke, Chen, Yibi, Hartlich, Juliane, Hiller, Karsten, John, Uwe, Kalvelage, Jana, Mansky, Johannes, Neumann-Schaal, Meina, Overmann, Jörg, Petersen, Jörn, Sanchez-Garcia, Selene, Schmidt-Hohagen, Kerstin, Shah, Sarah, Spröer, Cathrin, Sztajer, Helena, Wang, Hui, Bhattacharya, Debashish, Rabus, Ralf, Jahn, Dieter, Wagner-Döbler, Irene and Chan, Cheong Xin (2023). Genome and transcriptome data for bloom-forming dinoflagellate Prorocentrum cordatum CCMP1329. The University of Queensland. (Dataset) doi: 10.48610/bc851b7

  • Effrenium voratum genomes and genes

    Shah, Sarah and Chan, Cheong Xin (2023). Effrenium voratum genomes and genes. The University of Queensland. (Dataset) doi: 10.48610/1f0377a

  • Improved assembled genome of Cladocopium goreaui SCF055

    Chen, Yibi, Shah, Sarah, Dougan, Katherine E., van Oppen, Madeleine, J. H., Bhattacharya, Debashish and Chan, Cheong Xin (2022). Improved assembled genome of Cladocopium goreaui SCF055. The University of Queensland. (Dataset)

  • Genomic resources of seven Australian weed species of national significance

    Shah, Sarah, Lonhienne, Thierry, Murray, Cody-Ellen, Chen, Yibi, Dougan, Katherine E., Low, Yu Shang, Williams, Craig M., Schenk, Gerhard, Walter, Gimme H., Guddat, Luke W. and Chan, Cheong Xin (2022). Genomic resources of seven Australian weed species of national significance. The University of Queensland. (Dataset) doi: 10.48610/c22c10c

  • Genome data for Durusdinium trenchii CCMP2556 and SCF082

    Katherine E. Dougan, Anthony J. Bellantuono, Tim Kahlke, Raffaela M. Abbriano, Yibi Chen, Sarah Shah, Camila Granados-Cifuentes, Madeleine J. H. van Oppen, Debashish Bhattacharya, David J. Suggett, Mauricio Rodriguez-Lanetty and Cheong Xin Chan (2022). Genome data for Durusdinium trenchii CCMP2556 and SCF082. The University of Queensland. (Dataset) doi: 10.48610/27da3e7

  • Genome assemblies and the associated annotations for seven Symbiodinium isolates

    González-Pech, Raúl A., Ragan, Mark A., Bhattacharya, Debashish and Chan, Cheong Xin (2021). Genome assemblies and the associated annotations for seven Symbiodinium isolates. The University of Queensland. (Dataset) doi: 10.14264/f1b3a11

  • Genome assemblies and the associated annotations for Polarella glacialis CCMP1383 and CCMP2088

    Stephens, Timothy, Ragan, Mark A., Bhattacharya, Debashish and Chan, Cheong Xin (2020). Genome assemblies and the associated annotations for Polarella glacialis CCMP1383 and CCMP2088. The University of Queensland. (Dataset) doi: 10.14264/uql.2020.222

  • Revised genome sequences and annotations of six Symbiodiniaceae taxa

    Chen, Yibi, González-Pech, Raúl A., Stephens, Timothy G., Bhattacharya, Debashish and Chan, Cheong Xin (2019). Revised genome sequences and annotations of six Symbiodiniaceae taxa. The University of Queensland. (Dataset) doi: 10.14264/uql.2019.745

  • 143 Prokaryote genomes

    Bernard, Guillaume, Chan, Cheong Xin and Ragan, Mark A. (2016). 143 Prokaryote genomes. The University of Queensland. (Dataset) doi: 10.14264/uql.2016.908

  • Alignment-free network of 143 Prokaryote genomes

    Bernard, Guillaume , Chan, Cheong Xin and Ragan, Mark A. (2016). Alignment-free network of 143 Prokaryote genomes. The University of Queensland. (Dataset) doi: 10.14264/uql.2016.952

  • 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.

  • 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.

PhD and MPhil Supervision

Current Supervision

  • Assessing complex gene and genome features of dinoflagellates

    Doctor Philosophy — Principal Advisor

    Other advisors:

  • Hologenomic variation in the reef-building coral Acropora hyacinthus across the Great Barrier Reef

    Doctor Philosophy — Principal Advisor

    Other advisors:

  • Evolution and adaptation of non-symbiotic Symbiodiniaceae

    Doctor Philosophy — Principal Advisor

    Other advisors:

  • Ecophysiology and molecular genetics of selenium tolerance and accumulation in the selenium hyperaccumulator Neptunia amplexicaulis

    Doctor Philosophy — Associate Advisor

    Other advisors:

  • Developing novel spatio-temporal inference methods using single cell, spatial omics and imaging data for studying neuroinflammation and cancer progression

    Doctor Philosophy — Associate Advisor

    Other advisors:

  • Genomic, Genetic, and Mass Spectrometry Glycoproteomic Investigations of the Roles of Oligosaccharyltransferase Subunits in N-Glycosylation in Yeast

    Doctor Philosophy — Associate Advisor

    Other advisors:

  • Understanding the metabolic capabilities and evolutionary relatiosnhips of novel microorganisms from hot springs

    Doctor Philosophy — Associate Advisor

    Other advisors:

  • Genetics of climate-change adaptation in Great Barrier Reef corals

    Doctor Philosophy — Associate Advisor

    Other advisors:

Completed Supervision

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ResearcherID: A-7005-2008

ORCID: 0000-0002-3729-8176

Scopus ID: 8639801400

Google Scholar ID: jmP0excAAAAJ

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