Associate Professor Cheong Xin Chan
Associate Professor

Cheong Xin Chan

Email: 
Phone: 
+61 7 336 53829

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

Bacteriology Bioinformatics and computational biology Biological Sciences Biological adaptation Evolutionary impacts of climate change Genetics Genomics Microbial ecology Microbial genetics Microbiology Molecular evolution Phycology (incl. marine grasses) Phylogeny and comparative analysis Plant biology

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

  • 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 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.

Search Professor Cheong Xin Chan’s works on UQ eSpace

120 works between 2002 and 2025
All (120) Journal Article (88) Book Chapter (7) Conference Publication (11) Other Outputs (14)

61 - 80 of 120 works

2017

Journal Article

Biotic interactions as drivers of algal origin and evolution

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, 216 (3), 670-681. doi: 10.1111/nph.14760

Biotic interactions as drivers of algal origin and evolution

2017

Journal Article

Insights into the red algae and eukaryotic evolution from the genome of Porphyra umbilicalis (Bangiophyceae, Rhodophyta)

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 ... 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

Insights into the red algae and eukaryotic evolution from the genome of Porphyra umbilicalis (Bangiophyceae, Rhodophyta)

2017

Journal Article

The algal revolution

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

The algal revolution

2017

Book Chapter

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

Scaling up the phylogenetic detection of lateral gene transfer events

2016

Journal Article

Recapitulating phylogenies using k-mers: from trees to networks [version 2; referees: 2 approved]

Bernard, Guillaume, Ragan, Mark A. and Chan, Cheong Xin (2016). Recapitulating phylogenies using k-mers: from trees to networks [version 2; referees: 2 approved]. F1000Research, 5 (2789) 2789, 2789. doi: 10.12688/f1000research.10225.2

Recapitulating phylogenies using k-mers: from trees to networks [version 2; referees: 2 approved]

2016

Journal Article

The transcriptomic response of the coral Acropora digitifera to a competent Symbiodinium strain: the symbiosome as an arrested early phagosome

Mohamed, A. R., Cumbo, V., Harii, S., Shinzato,C., Chan, C. X., Ragan, M. A., Bourne, D. G., Willis, B. L., Ball, E. E., Satoh, N. and Miller, D. J. (2016). The transcriptomic response of the coral Acropora digitifera to a competent Symbiodinium strain: the symbiosome as an arrested early phagosome. Molecular Ecology, 25 (13), 3127-3141. doi: 10.1111/mec.13659

The transcriptomic response of the coral Acropora digitifera to a competent Symbiodinium strain: the symbiosome as an arrested early phagosome

2016

Journal Article

Alignment-free microbial phylogenomics under scenarios of sequence divergence, genome rearrangement and lateral genetic transfer

Bernard, Guillaume, Chan, Cheong Xin and Ragan, Mark A. (2016). Alignment-free microbial phylogenomics under scenarios of sequence divergence, genome rearrangement and lateral genetic transfer. Scientific Reports, 6 (1) 28970, 28970.1-28970.12. doi: 10.1038/srep28970

Alignment-free microbial phylogenomics under scenarios of sequence divergence, genome rearrangement and lateral genetic transfer

2016

Journal Article

PhySortR: a fast, flexible tool for sorting phylogenetic trees in R

Stephens, Timothy, Bhattacharya, Debashish, Ragan, Mark A. and Chan, Cheong Xin (2016). PhySortR: a fast, flexible tool for sorting phylogenetic trees in R. PeerJ, 4 (5) e2038, e2038.1-e2038.13. doi: 10.7717/peerj.2038

PhySortR: a fast, flexible tool for sorting phylogenetic trees in R

2016

Other Outputs

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

Alignment-free network of 143 Prokaryote genomes

2016

Other Outputs

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

143 Prokaryote genomes

2015

Journal Article

The ReFuGe 2020 Consortium—using “omics” approaches to explore the adaptability and resilience of coral holobionts to environmental change

ReFuGe 2020 Consortium, Voolstra, Christian R, Miller, David J., Ragan, Mark A., Hoffmann, Ary A., Hoegh-Guldberg, Ove, Bourne, David G., Ball, Eldon E., Ying, Hua, Forêt, Sylvain, Takahashi, Shunichi, Weynberg, Karen D., van Oppen, Madeleine J. H., Morrow, Kathleen, Chan, Cheong Xin, Rosic, Nedeljka, Leggat, William, Sprungala, Susanne, Imelfort, Michael, Tyson, Gene W., Kassahn, Karin S., Lundgren, Petra B., Beeden, Roger J., Ravasi, Timothy, Berumen, Michael L., Abal, Eva and Fyffe, Theresa (2015). The ReFuGe 2020 Consortium—using “omics” approaches to explore the adaptability and resilience of coral holobionts to environmental change. Frontiers in Marine Science, 2 (Art No.: 68) 68. doi: 10.3389/fmars.2015.00068

The ReFuGe 2020 Consortium—using “omics” approaches to explore the adaptability and resilience of coral holobionts to environmental change

2015

Conference Publication

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

Scalable phylogenomic approaches to study algal evolution

2015

Book Chapter

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

Phylogenomics in algal research: current trends and future perspectives

2015

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

Genome Analysis of Two Symbiodinium Isolates

2014

Journal Article

Inferring phylogenies of evolving sequences without multiple sequence alignment

Chan, Cheong Xin, Bernard, Guillaume, Poirion, Olivier, Hogan, James M. and Ragan, Mark A. (2014). Inferring phylogenies of evolving sequences without multiple sequence alignment. Scientific Reports, 4 (3) 6504, e6504.1-e6504.9. doi: 10.1038/srep06504

Inferring phylogenies of evolving sequences without multiple sequence alignment

2014

Journal Article

Molecular phylogenetics before sequences : oligonucleotide catalogs as k-mer spectra

Ragan, Mark A., Bernard, Guillaume and Chan, Cheong Xin (2014). Molecular phylogenetics before sequences : oligonucleotide catalogs as k-mer spectra. RNA Biology, 11 (3), 176-185. doi: 10.4161/rna.27505

Molecular phylogenetics before sequences : oligonucleotide catalogs as k-mer spectra

2014

Journal Article

A new species of Burkholderia isolated from sugarcane roots promotes plant growth

Paungfoo-Lonhienne, Chanyarat, Lonhienne, Thierry G. A., Yeoh, Yun Kit, Webb, Richard I., Lakshmanan, Prakash, Chan, Cheong Xin, Lim, Phaik-Eem, Ragan, Mark A., Schmidt, Susanne and Hugenholtz, Philip (2014). A new species of Burkholderia isolated from sugarcane roots promotes plant growth. Microbial Biotechnology, 7 (2), 142-154. doi: 10.1111/1751-7915.12105

A new species of Burkholderia isolated from sugarcane roots promotes plant growth

2014

Book Chapter

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

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

2013

Journal Article

Analysis of horizontal genetic transfer in red algae in the post-genomics age

Chan, Cheong Xin and Bhattacharya, Debashish (2013). Analysis of horizontal genetic transfer in red algae in the post-genomics age. Mobile Genetic Elements, 3 (6), e27669.1-e27669.5. doi: 10.4161/mge.27669

Analysis of horizontal genetic transfer in red algae in the post-genomics age

2013

Journal Article

Foreign gene recruitment to the fatty acid biosynthesis pathway in diatoms

Chan, Cheong Xin, Baglivi, Francesca L., Jenkins, Christina E. and Bhattacharya, Debashish (2013). Foreign gene recruitment to the fatty acid biosynthesis pathway in diatoms. Mobile Genetic Elements, 3 (5), e27313.1-e27313.7. doi: 10.4161/mge.27313

Foreign gene recruitment to the fatty acid biosynthesis pathway in diatoms

Past funding

  • 2023 - 2024
    Deciphering the molecular regulations of heat tolerance in a coral algal symbiont
    Australian Academy of Science
    Open grant
  • 2019 - 2022
    Genomics and evolution of symbiont transmission in coral reefs
    ARC Discovery Projects
    Open grant
  • 2018 - 2019
    Integrated genomic approaches to understand stress tolerance in bioethanol-producing yeasts and coral reef symbionts
    UQ-FAPESP Strategic Research Fund SPRINT
    Open grant
  • 2015 - 2018
    Genome dynamics following plastid endosymbiosis (ARC Discovery Project administered by The University of Melbourne)
    University of Melbourne
    Open grant
  • 2015 - 2017
    Symbiodinium: the evolutionary transition to coral reef symbiont
    ARC Discovery Projects
    Open grant
  • 2014
    Host-specific adaptive evolution of the coral reef symbiont Symbiodinium
    UQ Early Career Researcher
    Open grant
  • 2013
    ResTeach 2013 0.1 FTE School of Chemsitry and Molecular Biosciences
    UQ ResTeach
    Open grant

Availability

Associate Professor Cheong Xin Chan is:
Available for supervision

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Supervision history

Current supervision

  • Doctor Philosophy

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

    Principal Advisor

    Other advisors: Professor Cynthia Riginos

  • Doctor Philosophy

    Towards understanding microbial community dynamics in a subtropical estuary: a multi-omics approach

    Associate Advisor

  • Doctor Philosophy

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

    Associate Advisor

    Other advisors: Professor Peter Erskine

  • 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

  • Doctor Philosophy

    Genetics of climate-change adaptation in Great Barrier Reef corals

    Associate Advisor

    Other advisors: Professor Cynthia Riginos

  • Doctor Philosophy

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

    Associate Advisor

    Other advisors: Professor Peter Erskine

  • 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

  • Doctor Philosophy

    Towards understanding microbial community dynamics in a subtropical estuary: a multi-omics approach

    Associate Advisor

  • Doctor Philosophy

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

    Associate Advisor

    Other advisors: Professor Peter Erskine

Completed supervision

Enquiries

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