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)

41 - 60 of 120 works

2020

Journal Article

Genomes of the dinoflagellate Polarella glacialis encode tandemly repeated single-exon genes with adaptive functions

Stephens, Timothy G., González-Pech, Raúl A., Cheng, Yuanyuan, Mohamed, Amin R., Burt, David W., Bhattacharya, Debashish, Ragan, Mark A. and Chan, Cheong Xin (2020). Genomes of the dinoflagellate Polarella glacialis encode tandemly repeated single-exon genes with adaptive functions. BMC Biology, 18 (1) 56, 56. doi: 10.1186/s12915-020-00782-8

Genomes of the dinoflagellate Polarella glacialis encode tandemly repeated single-exon genes with adaptive functions

2020

Journal Article

Evidence that inconsistent gene prediction can mislead analysis of dinoflagellate genomes

Chen, Yibi, González‐Pech, Raúl A., Stephens, Timothy G., Bhattacharya, Debashish and Chan, Cheong Xin (2020). Evidence that inconsistent gene prediction can mislead analysis of dinoflagellate genomes. Journal of Phycology, 56 (1), 6-10. doi: 10.1111/jpy.12947

Evidence that inconsistent gene prediction can mislead analysis of dinoflagellate genomes

2020

Other Outputs

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

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

2019

Journal Article

A genomic view of the reef-building coral Porites lutea and its microbial symbionts

Robbins, Steven J., Singleton, Caitlin M., Chan, Cheong Xin, Messer, Lauren F., Geers, Aileen U., Ying, Hua, Baker, Alexander, Bell, Sara C., Morrow, Kathleen M., Ragan, Mark A., Miller, David J., Forêt, Sylvain, Voolstra, Christian R., Tyson, Gene W. and Bourne, David G. (2019). A genomic view of the reef-building coral Porites lutea and its microbial symbionts. Nature Microbiology, 4 (12), 2090-2100. doi: 10.1038/s41564-019-0532-4

A genomic view of the reef-building coral Porites lutea and its microbial symbionts

2019

Journal Article

Genome evolution of coral reef symbionts as intracellular residents

González-Pech, Raúl A., Bhattacharya, Debashish, Ragan, Mark A. and Chan, Cheong Xin (2019). Genome evolution of coral reef symbionts as intracellular residents. Trends in Ecology and Evolution, 34 (9), 799-806. doi: 10.1016/j.tree.2019.04.010

Genome evolution of coral reef symbionts as intracellular residents

2019

Journal Article

Commonly misunderstood parameters of NCBI BLAST and important considerations for users

González-Pech, Raúl A., Stephens, Timothy G. and Chan, Cheong Xin (2019). Commonly misunderstood parameters of NCBI BLAST and important considerations for users. Bioinformatics, 35 (15) bty1018, 2697-2698. doi: 10.1093/bioinformatics/bty1018

Commonly misunderstood parameters of NCBI BLAST and important considerations for users

2019

Journal Article

Benchmarking of alignment-free sequence comparison methods

Zielezinski, Andrzej, Girgis, Hani Z., Bernard, Guillaume, Leimeister, Chris-Andre, Tang, Kujin, Dencker, Thomas, Lau, Anna Katharina, Röhling, Sophie, Choi, Jae Jin, Waterman, Michael S., Comin, Matteo, Kim, Sung-Hou, Vinga, Susana, Almeida, Jonas S., Chan, Cheong Xin, James, Benjamin T., Sun, Fengzhu, Morgenstern, Burkhard and Karlowski, Wojciech M. (2019). Benchmarking of alignment-free sequence comparison methods. Genome Biology, 20 (1) 144, 144. doi: 10.1186/s13059-019-1755-7

Benchmarking of alignment-free sequence comparison methods

2019

Journal Article

Analysis of an improved Cyanophora paradoxa genome assembly

Price, Dana C., Goodenough, Ursula W., Roth, Robyn, Lee, Jae-Hyeok, Kariyawasam, Thamali, Mutwil, Marek, Ferrari, Camilla, Facchinelli, Fabio, Ball, Steven G., Cenci, Ugo, Chan, Cheong Xin, Wagner, Nicole E., Yoon, Hwan Su, Weber, Andreas P. M. and Bhattacharya, Debashish (2019). Analysis of an improved Cyanophora paradoxa genome assembly. DNA Research, 26 (4), 287-299. doi: 10.1093/dnares/dsz009

Analysis of an improved Cyanophora paradoxa genome assembly

2019

Journal Article

Resolving structure and function of metaorganisms through a holistic framework combining reductionist and integrative approaches

Jaspers, Cornelia, Fraune, Sebastian, Arnold, A. Elizabeth, Miller, David J., Bosch, Thomas C. G., Voolstra, Christian R., Consortium of Australian Academy of Science Boden Research Conference Participants, Adamska, Maja, Ainsworth, Tracy, Ball, Eldon, Boote, Chloe, Bourne, David, Butterfield, Nicholas J., Chan, Cheong Xin, Cooke, Ira, Cowman, Peter F., Darling, Aaron, Davy, Simon K., Mohamed, Amin, Fabricius, Katharina, Fortunato, Sofia, Hernandez, Alejandra, Hoogenboom, Mia, Moya, Aurelie, Pita, Lucia, Ragan, Mark A., Robbins, Steven J., Andrade, Natalia R., Sakamaki, Kazuhiro ... Ying, Hua (2019). Resolving structure and function of metaorganisms through a holistic framework combining reductionist and integrative approaches. Zoology, 133, 81-87. doi: 10.1016/j.zool.2019.02.007

Resolving structure and function of metaorganisms through a holistic framework combining reductionist and integrative approaches

2019

Journal Article

Alignment-free inference of hierarchical and reticulate phylogenomic relationships

Bernard, Guillaume, Chan, Cheong Xin, Chan, Yao-ban, Chua, Xin-Yi, Cong, Yingnan, Hogan, James M., Maetschke, Stefan R. and Ragan, Mark A. (2019). Alignment-free inference of hierarchical and reticulate phylogenomic relationships. Briefings in Bioinformatics, 20 (2), 426-435. doi: 10.1093/bib/bbx067

Alignment-free inference of hierarchical and reticulate phylogenomic relationships

2019

Other Outputs

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

Revised genome sequences and annotations of six Symbiodiniaceae taxa

2018

Journal Article

Core genes in diverse dinoflagellate lineages include a wealth of conserved dark genes with unknown functions

Stephens, Timothy G., Ragan, Mark A., Bhattacharya, Debashish and Chan, Cheong Xin (2018). Core genes in diverse dinoflagellate lineages include a wealth of conserved dark genes with unknown functions. Scientific Reports, 8 (1) 17175, 17175. doi: 10.1038/s41598-018-35620-z

Core genes in diverse dinoflagellate lineages include a wealth of conserved dark genes with unknown functions

2018

Journal Article

k-mer similarity, networks of microbial genomes, and taxonomic rank

Bernard, Guillaume, Greenfield, Paul, Ragan, Mark A. and Chan, Cheong Xin (2018). k-mer similarity, networks of microbial genomes, and taxonomic rank. mSystems, 3 (6) e00257-18, 1-16. doi: 10.1128/msystems.00257-18

k-mer similarity, networks of microbial genomes, and taxonomic rank

2018

Journal Article

Symbiodinium genomes reveal adaptive evolution of functions related to coral-dinoflagellate symbiosis

Liu, Huanle, Stephens, Timothy G., González-Pech, Raúl A., Beltran, Victor H., Lapeyre, Bruno, Bongaerts, Pim, Cooke, Ira, Aranda, Manuel, Bourne, David G., Forêt, Sylvain, Miller, David J., van Oppen, Madeleine J. H., Voolstra, Christian R., Ragan, Mark A. and Chan, Cheong Xin (2018). Symbiodinium genomes reveal adaptive evolution of functions related to coral-dinoflagellate symbiosis. Communications Biology, 1 (1) 95, 95. doi: 10.1038/s42003-018-0098-3

Symbiodinium genomes reveal adaptive evolution of functions related to coral-dinoflagellate symbiosis

2018

Journal Article

Selection of reference genes for transcript profiling of Sargassum polycystum by quantitative real‐time polymerase chain reaction

Sim, Mei-Chea, Chan, Cheong Xin, Ho, Chai-Ling and Phang, Siew-Moi (2018). Selection of reference genes for transcript profiling of Sargassum polycystum by quantitative real‐time polymerase chain reaction. Phycological Research, 66 (4), 247-252. doi: 10.1111/pre.12328

Selection of reference genes for transcript profiling of Sargassum polycystum by quantitative real‐time polymerase chain reaction

2018

Journal Article

Analysis of the draft genome of the red seaweed Gracilariopsis chorda provides insights into genome size evolution in Rhodophyta

Lee, JunMo, Yang, Eun Chan, Graf, Louis, Yang, Ji Hyun, Qiu, Huan, Zel Zion, Udi, Chan, Cheong Xin, Stephens, Timothy G., Weber, Andreas P. M., Boo, Ga Hun, Boo, Sung Min, Kim, Kyeong Mi, Shin, Younhee, Jung, Myunghee, Lee, Seung Jae, Yim, Hyung-Soon, Lee, Jung-Hyun, Bhattacharya, Debashish and Yoon, Hwan Su (2018). Analysis of the draft genome of the red seaweed Gracilariopsis chorda provides insights into genome size evolution in Rhodophyta. Molecular Biology and Evolution, 35 (8), 1869-1886. doi: 10.1093/molbev/msy081

Analysis of the draft genome of the red seaweed Gracilariopsis chorda provides insights into genome size evolution in Rhodophyta

2018

Journal Article

Active host response to algal symbionts in the sea slug Elysia chlorotica

Chan, Cheong Xin, Vaysberg, Pavel, Price, Dana C, Pelletreau, Karen N, Rumpho, Mary E and Bhattacharya, Debashish (2018). Active host response to algal symbionts in the sea slug Elysia chlorotica. Molecular Biology and Evolution, 35 (7), 1706-1711. doi: 10.1093/molbev/msy061

Active host response to algal symbionts in the sea slug Elysia chlorotica

2018

Journal Article

Plastid phylogenomics with broad taxon sampling further elucidates the distinct evolutionary origins and timing of secondary green plastids

Jackson, Christopher, Knoll, Andrew H, Chan, Cheong Xin and Verbruggen, Heroen (2018). Plastid phylogenomics with broad taxon sampling further elucidates the distinct evolutionary origins and timing of secondary green plastids. Scientific reports, 8 (1) 1523, 1523. doi: 10.1038/s41598-017-18805-w

Plastid phylogenomics with broad taxon sampling further elucidates the distinct evolutionary origins and timing of secondary green plastids

2018

Journal Article

Deciphering the nature of the coral-Chromera association

Mohamed, Amin R., Cumbo, Vivian R., Harii, Saki, Shinzato, Chuya, Chan, Cheong Xin, Ragan, Mark A., Satoh, Nori, Ball, Eldon E. and Miller, David J. (2018). Deciphering the nature of the coral-Chromera association. The ISME Journal, 12 (3), 776-790. doi: 10.1038/s41396-017-0005-9

Deciphering the nature of the coral-Chromera association

2017

Journal Article

Signatures of adaptation and symbiosis in genomes and transcriptomes of Symbiodinium

González-Pech, Raúl A., Ragan, Mark A. and Chan, Cheong Xin (2017). Signatures of adaptation and symbiosis in genomes and transcriptomes of Symbiodinium. Scientific Reports, 7 (15021) 15021, 15021. doi: 10.1038/s41598-017-15029-w

Signatures of adaptation and symbiosis in genomes and transcriptomes of Symbiodinium

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

    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

  • Doctor Philosophy

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

    Associate Advisor

  • 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

    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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