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

119 works between 2002 and 2025
All (119) Journal Article (88) Book Chapter (7) Conference Publication (11) Other Outputs (13)

1 - 20 of 119 works

2025

Journal Article

Insights Into Phylogeny, Diversity and Functional Potential of Poseidoniales Viruses

Prabhu, Apoorva, Zaugg, Julian, Chan, Cheong Xin, McIlroy, Simon J. and Rinke, Chris (2025). Insights Into Phylogeny, Diversity and Functional Potential of Poseidoniales Viruses. Environmental Microbiology, 27 (1) e70017, 1. doi: 10.1111/1462-2920.70017

Insights Into Phylogeny, Diversity and Functional Potential of Poseidoniales Viruses

2024

Journal Article

Progress and future directions for seaweed holobiont research

Saha, Mahasweta, Dittami, Simon M., Chan, Cheong Xin, Raina, Jean‐Baptiste, Stock, Willem, Ghaderiardakani, Fatemeh, Valathuparambil Baby John, Ann Mary, Corr, Shauna, Schleyer, Guy, Todd, Jonathan, Cardini, Ulisse, Bengtsson, Mia M., Prado, Soizic, Skillings, Derek, Sonnenschein, Eva C., Engelen, Aschwin H., Wang, Gaoge, Wichard, Thomas, Brodie, Juliet, Leblanc, Catherine and Egan, Suhelen (2024). Progress and future directions for seaweed holobiont research. New Phytologist, 244 (2), 364-376. doi: 10.1111/nph.20018

Progress and future directions for seaweed holobiont research

2024

Journal Article

Chromosomal inversions harbour excess mutational load in the coral, <i>Acropora kenti</i>, on the Great Barrier Reef

Zhang, Jia, Schneller, Nadja M., Field, Matt A., Chan, Cheong Xin, Miller, David J., Strugnell, Jan M., Riginos, Cynthia, Bay, Line and Cooke, Ira (2024). Chromosomal inversions harbour excess mutational load in the coral, Acropora kenti, on the Great Barrier Reef. Molecular Ecology, 33 (16) e17468, e17468. doi: 10.1111/mec.17468

Chromosomal inversions harbour excess mutational load in the coral, <i>Acropora kenti</i>, on the Great Barrier Reef

2024

Journal Article

Whole-genome duplication in an algal symbiont bolsters coral heat tolerance

Dougan, Katherine E., Bellantuono, Anthony J., Kahlke, Tim, Abbriano, Raffaela M., Chen, Yibi, Shah, Sarah, Granados-Cifuentes, Camila, van Oppen, Madeleine J. H., Bhattacharya, Debashish, Suggett, David J., Rodriguez-Lanetty, Mauricio and Chan, Cheong Xin (2024). Whole-genome duplication in an algal symbiont bolsters coral heat tolerance. Science Advances, 10 (29) eadn2218, eadn2218. doi: 10.1126/sciadv.adn2218

Whole-genome duplication in an algal symbiont bolsters coral heat tolerance

2024

Journal Article

Nuclear genomes of dinoflagellates reveal evolutionarily conserved pattern of RNA editing relative to stress response

Chen, Yibi, Dougan, Katherine E., Bhattacharya, Debashish and Chan, Cheong Xin (2024). Nuclear genomes of dinoflagellates reveal evolutionarily conserved pattern of RNA editing relative to stress response. Frontiers in Protistology, 2. doi: 10.3389/frpro.2024.1320917

Nuclear genomes of dinoflagellates reveal evolutionarily conserved pattern of RNA editing relative to stress response

2024

Journal Article

Contaminant or goldmine? In silico assessment of Symbiodiniaceae community using coral hologenomes

Ishida, Hisatake, Riginos, Cynthia and Chan, Cheong Xin (2024). Contaminant or goldmine? In silico assessment of Symbiodiniaceae community using coral hologenomes. Frontiers in Protistology, 2. doi: 10.3389/frpro.2024.1376877

Contaminant or goldmine? In silico assessment of Symbiodiniaceae community using coral hologenomes

2024

Journal Article

Genome-wide transcriptome analysis reveals the diversity and function of long non-coding RNAs in dinoflagellates

Chen, Yibi, Dougan, Katherine E., Nguyen, Quan, Bhattacharya, Debashish and Chan, Cheong Xin (2024). Genome-wide transcriptome analysis reveals the diversity and function of long non-coding RNAs in dinoflagellates. NAR Genomics and Bioinformatics, 6 (1) lqae016, lqae016. doi: 10.1093/nargab/lqae016

Genome-wide transcriptome analysis reveals the diversity and function of long non-coding RNAs in dinoflagellates

2024

Journal Article

Facultative lifestyle drives diversity of coral algal symbionts

Bhattacharya, Debashish, Stephens, Timothy G., Chille, Erin E., Benites, L. Felipe and Chan, Cheong Xin (2024). Facultative lifestyle drives diversity of coral algal symbionts. Trends in Ecology and Evolution, 39 (3), 239-247. doi: 10.1016/j.tree.2023.10.005

Facultative lifestyle drives diversity of coral algal symbionts

2024

Journal Article

Massive genome reduction predates the divergence of Symbiodiniaceae dinoflagellates

Shah, Sarah, Dougan, Katherine E., Chen, Yibi, Lo, Rosalyn, Laird, Gemma, Fortuin, Michael D. A., Rai, Subash K., Murigneux, Valentine, Bellantuono, Anthony J., Rodriguez-Lanetty, Mauricio, Bhattacharya, Debashish and Chan, Cheong Xin (2024). Massive genome reduction predates the divergence of Symbiodiniaceae dinoflagellates. The ISME Journal, 18 (1) wrae059. doi: 10.1093/ismejo/wrae059

Massive genome reduction predates the divergence of Symbiodiniaceae dinoflagellates

2023

Journal Article

Multi-omics analysis reveals the molecular response to heat stress in a “red tide” dinoflagellate

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, Chan, Cheong Xin and Wagner-Döbler, Irene (2023). Multi-omics analysis reveals the molecular response to heat stress in a “red tide” dinoflagellate. Genome Biology, 24 (1) 265, 1-32. doi: 10.1186/s13059-023-03107-4

Multi-omics analysis reveals the molecular response to heat stress in a “red tide” dinoflagellate

2023

Journal Article

In vivo structure probing of RNA in Archaea: novel insights into the ribosome structure of Methanosarcina acetivorans

Williams, Allison M, Jolley, Elizabeth, Santiago-Martínez, Michel Geovanni, Chan, Cheong Xin, Gutell, Robin, Ferry, James G and Bevilacqua, Philip C (2023). In vivo structure probing of RNA in Archaea: novel insights into the ribosome structure of Methanosarcina acetivorans. RNA, 29 (10), 1610-1620. doi: 10.1261/rna.079687.123

In vivo structure probing of RNA in Archaea: novel insights into the ribosome structure of Methanosarcina acetivorans

2023

Journal Article

Developing model systems for dinoflagellates in the post‐genomic era

Ishida, Hisatake, John, Uwe, Murray, Shauna A., Bhattacharya, Debashish and Chan, Cheong Xin (2023). Developing model systems for dinoflagellates in the post‐genomic era. Journal of Phycology, 59 (5), 799-808. doi: 10.1111/jpy.13386

Developing model systems for dinoflagellates in the post‐genomic era

2023

Journal Article

Gene duplication is the primary driver of intraspecific genomic divergence in coral algal symbionts

Shah, Sarah, Dougan, Katherine E., Chen, Yibi, Bhattacharya, Debashish and Chan, Cheong Xin (2023). Gene duplication is the primary driver of intraspecific genomic divergence in coral algal symbionts. Open Biology, 13 (9) 230182, 1-10. doi: 10.1098/rsob.230182

Gene duplication is the primary driver of intraspecific genomic divergence in coral algal symbionts

2023

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

Long non-coding RNAs of three dinoflagellate species

2023

Other Outputs

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

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

2023

Journal Article

Building consensus around the assessment and interpretation of Symbiodiniaceae diversity

Davies, Sarah W., Gamache, Matthew H., Howe-Kerr, Lauren I., Kriefall, Nicola G., Baker, Andrew C., Banaszak, Anastazia T., Bay, Line Kolind, Bellantuono, Anthony J., Bhattacharya, Debashish, Chan, Cheong Xin, Claar, Danielle C., Coffroth, Mary Alice, Cunning, Ross, Davy, Simon K., del Campo, Javier, Díaz-Almeyda, Erika M., Frommlet, Jörg C., Fuess, Lauren E., González-Pech, Raúl A., Goulet, Tamar L., Hoadley, Kenneth D., Howells, Emily J., Hume, Benjamin C. C., Kemp, Dustin W., Kenkel, Carly D., Kitchen, Sheila A., LaJeunesse, Todd C., Lin, Senjie, McIlroy, Shelby E. ... Parkinson, John Everett (2023). Building consensus around the assessment and interpretation of Symbiodiniaceae diversity. PeerJ, 11 e15023, 1-77. doi: 10.7717/peerj.15023

Building consensus around the assessment and interpretation of Symbiodiniaceae diversity

2023

Other Outputs

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

Effrenium voratum genomes and genes

2023

Journal Article

Micro-analytical and molecular approaches for understanding the distribution, biochemistry, and molecular biology of selenium in (hyperaccumulator) plants

Pinto Irish, Katherine, Harvey, Maggie-Anne, Harris, Hugh H., Aarts, Mark G. M., Chan, Cheong Xin, Erskine, Peter D. and van der Ent, Antony (2023). Micro-analytical and molecular approaches for understanding the distribution, biochemistry, and molecular biology of selenium in (hyperaccumulator) plants. Planta, 257 (1) 2, 1-17. doi: 10.1007/s00425-022-04017-8

Micro-analytical and molecular approaches for understanding the distribution, biochemistry, and molecular biology of selenium in (hyperaccumulator) plants

2022

Journal Article

Evolutionary responses of a reef-building coral to climate change at the end of the last glacial maximum

Zhang, Jia, Richards, Zoe T, Adam, Arne A S, Chan, Cheong Xin, Shinzato, Chuya, Gilmour, James, Thomas, Luke, Strugnell, Jan M, Miller, David J and Cooke, Ira (2022). Evolutionary responses of a reef-building coral to climate change at the end of the last glacial maximum. Molecular Biology and Evolution, 39 (10) msac201, 1-18. doi: 10.1093/molbev/msac201

Evolutionary responses of a reef-building coral to climate change at the end of the last glacial maximum

2022

Journal Article

Improved Cladocopium goreaui genome assembly reveals features of a facultative coral symbiont and the complex evolutionary history of dinoflagellate genes

Chen, Yibi, Shah, Sarah, Dougan, Katherine E., van Oppen, Madeleine J. H., Bhattacharya, Debashish and Chan, Cheong Xin (2022). Improved Cladocopium goreaui genome assembly reveals features of a facultative coral symbiont and the complex evolutionary history of dinoflagellate genes. Microorganisms, 10 (8) 1662, 1-20. doi: 10.3390/microorganisms10081662

Improved Cladocopium goreaui genome assembly reveals features of a facultative coral symbiont and the complex evolutionary history of dinoflagellate genes

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 John Pandolfi, Professor Cynthia Riginos

  • 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

    Diversity and evolution of phytoplasmas infecting banana and coconut in Papua New Guinea

    Associate Advisor

    Other advisors: Dr Lilia Carvalhais, Professor Andre Drenth

Completed supervision

Enquiries

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