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)

81 - 100 of 120 works

2013

Journal Article

Biological intuition in alignment-free methods: response to Posada

Ragan, Mark A. and Chan, Cheong Xin (2013). Biological intuition in alignment-free methods: response to Posada. Journal of Molecular Evolution, 77 (1-2), 1-2. doi: 10.1007/s00239-013-9573-0

Biological intuition in alignment-free methods: response to Posada

2013

Journal Article

Evidence for widespread exonic small RNAs in the glaucophyte alga Cyanophora paradoxa

Gross, Jeferson, Wajid, Sana, Price, Dana C., Zelzion, Ehud, Li, Junyi, Chan, Cheong Xin and Bhattacharya, Debashish (2013). Evidence for widespread exonic small RNAs in the glaucophyte alga Cyanophora paradoxa. PLoS One, 8 (7) e67669, 67669.1-67669.9. doi: 10.1371/journal.pone.0067669

Evidence for widespread exonic small RNAs in the glaucophyte alga Cyanophora paradoxa

2013

Journal Article

Genome of the red alga Porphyridium purpureum

Bhattacharya, Debashish, Price, Dana C., Chan, Cheong Xin, Qiu, Huan, Rose, Nicholas, Ball, Steven, Weber, Andreas P. M., Arias, Maria Cecilia, Henrissat, Bernard, Coutinho, Pedro M., Krishnan, Anagha, Zaeuner, Simone, Morath, Shannon, Hilliou, Frederique, Egizi, Andrea, Perrineau, Marie-Mathilde and Yoon, Hwan Su (2013). Genome of the red alga Porphyridium purpureum. Nature Communications, 4 (1) 2931, 1941.1-1941.10. doi: 10.1038/ncomms2931

Genome of the red alga Porphyridium purpureum

2013

Journal Article

Clustering evolving proteins into homologous families

Chan, Cheong Xin, Mahbob, Maisarah and Ragan, Mark A. (2013). Clustering evolving proteins into homologous families. BMC Bioinformatics, 14 (1) 120, 120.1-120.11. doi: 10.1186/1471-2105-14-120

Clustering evolving proteins into homologous families

2013

Journal Article

Next-generation phylogenomics

Chan, Cheong Xin and Ragan, Mark A. (2013). Next-generation phylogenomics. Biology Direct, 8 (1) 3, 3.1-3.14. doi: 10.1186/1745-6150-8-3

Next-generation phylogenomics

2013

Journal Article

Phylogenomics of marine algae

Chan, C. X. (2013). Phylogenomics of marine algae. Malaysian Journal of Science, 32 (SPEC. ISS.), 11-18. doi: 10.22452/mjs.vol32no3.2

Phylogenomics of marine algae

2013

Conference Publication

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

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

2012

Journal Article

Porphyra (Bangiophyceae) transcriptomes provide insights into red algal development and metabolism

Chan, Cheong Xin, Blouin, Nicolas A., Zhuang, Yunyun, Zaeuner, Simone, Prochnik, Simon E., Lindquist, Erika, Lin, Senjie, Benning, Christoph, Lohr, Martin, Yarish, Charles, Gantt, Elisabeth, Grossman, Arthur R., Lu, Shan, Mueller, Kirsten, Stiller, John W., Brawley, Susan H. and Bhattacharya, Debashish (2012). Porphyra (Bangiophyceae) transcriptomes provide insights into red algal development and metabolism. Journal of Phycology, 48 (6), 1328-1342. doi: 10.1111/j.1529-8817.2012.01229.x

Porphyra (Bangiophyceae) transcriptomes provide insights into red algal development and metabolism

2012

Journal Article

Analysis of Alexandrium tamarense (Dinophyceae) genes reveals the complex evolutionary history of a microbial eukaryote

Chan, Cheong Xin, Soares, Marcelo B., Bonaldo, Maria F., Wisecaver, Jennifer H., Hackett, Jeremiah D., Anderson, Donald M., Erdner, Deana L. and Bhattacharya, Debashish (2012). Analysis of Alexandrium tamarense (Dinophyceae) genes reveals the complex evolutionary history of a microbial eukaryote. Journal of Phycology, 48 (5), 1130-1142. doi: 10.1111/j.1529-8817.2012.01194.x

Analysis of Alexandrium tamarense (Dinophyceae) genes reveals the complex evolutionary history of a microbial eukaryote

2012

Journal Article

Major developmental regulators and their expression in two closely related species of Porphyra (Rhodophyta)

Stiller, John W., Perry, Justin, Rymarquis, Linda A., Accerbi, Monica, Green, Pamela J., Prochnik, Simon, Lindquist, Erika, Chan, Cheong Xin, Yarish, Charles, Lin, Senjie, Zhuang, Yunyun, Blouin, Nicolas A. and Brawley, Susan H. (2012). Major developmental regulators and their expression in two closely related species of Porphyra (Rhodophyta). Journal of Phycology, 48 (4), 883-896. doi: 10.1111/j.1529-8817.2012.01138.x

Major developmental regulators and their expression in two closely related species of Porphyra (Rhodophyta)

2012

Journal Article

Analysis of Porphyra membrane transporters demonstrates gene transfer among photosynthetic eukaryotes and numerous sodium-coupled transport systems

Chan, Cheong Xin, Zauner, Simone, Wheeler, Glen, Grossman, Arthur R., Prochnik, Simon E., Blouin, Nicolas A., Zhuang, Yunyun, Benning, Christoph, Berg, Gry Mine, Yarish, Charles, Eriksen, Renee L., Klein, Anita S., Lin, Senjie, Levine, Ira, Brawley, Susan H. and Bhattacharya, Debashish (2012). Analysis of Porphyra membrane transporters demonstrates gene transfer among photosynthetic eukaryotes and numerous sodium-coupled transport systems. Plant Physiology, 158 (4), 2001-2012. doi: 10.1104/pp.112.193896

Analysis of Porphyra membrane transporters demonstrates gene transfer among photosynthetic eukaryotes and numerous sodium-coupled transport systems

2012

Journal Article

Endosymbiotic and horizontal gene transfer in microbial eukaryotes: impacts on cell evolution and the tree of life

Chan, Cheong Xin, Bhattacharya, Debashish and Reyes-Prieto, Adrian (2012). Endosymbiotic and horizontal gene transfer in microbial eukaryotes: impacts on cell evolution and the tree of life. Mobile Genetic Elements, 2 (2), 101-105. doi: 10.4161/mge.20110

Endosymbiotic and horizontal gene transfer in microbial eukaryotes: impacts on cell evolution and the tree of life

2012

Journal Article

Cyanophora paradoxa genome elucidates origin of photosynthesis in algae and plants

Price, Dana C., Chan, Cheong Xin, Yoon, Hwan Su, Yang, Eun Chan, Qiu, Huan, Weber, Andreas P. M., Schwacke, Rainer, Gross, Jeferson, Blouin, Nicolas A., Lane, Chris, Reyes-Prieto, Adrian, Durnford, Dion G., Neilson, Jonathan A. D., Lang, B. Franz, Burger, Gertraud, Steiner, Jurgen M., Loffelhardt, Wolfgang, Meuser, Jonathan E., Posewitz, Matthew C., Ball, Steven, Arias, Maria Cecilia, Henrissat, Bernard, Coutinho, Pedro M., Rensing, Stefan A., Symeonidi, Aikaterini, Doddapaneni, Harshavardhan, Green, Beverley R., Rajah, Veeran D., Boore, Jeffrey and Bhattacharya, Debashish (2012). Cyanophora paradoxa genome elucidates origin of photosynthesis in algae and plants. Science, 335 (6070), 843-847. doi: 10.1126/science.1213561

Cyanophora paradoxa genome elucidates origin of photosynthesis in algae and plants

2012

Conference Publication

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

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

2012

Conference Publication

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

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

2011

Journal Article

Red and green algal origin of diatom membrane transporters: Insights into environmental adaptation and cell evolution

Chan, Cheong Xin, Reyes-Prieto, Adrian and Bhattacharya, Debashish (2011). Red and green algal origin of diatom membrane transporters: Insights into environmental adaptation and cell evolution. PLoS One, 6 (12) e29138, e29138.1-e29138.11. doi: 10.1371/journal.pone.0029138

Red and green algal origin of diatom membrane transporters: Insights into environmental adaptation and cell evolution

2011

Journal Article

Lateral transfer of genes and gene fragments in Staphylococcus extends beyond mobile elements

Chan, Cheong Xin, Beiko, Robert G. and Ragan, Mark A. (2011). Lateral transfer of genes and gene fragments in Staphylococcus extends beyond mobile elements. Journal of Bacteriology, 193 (15), 3964-3977. doi: 10.1128/JB.01524-10

Lateral transfer of genes and gene fragments in Staphylococcus extends beyond mobile elements

2011

Journal Article

Non-random sharing of plantae genes

Chan, Cheong Xin and Bhattacharya, Debashish (2011). Non-random sharing of plantae genes. Communicative and Integrative Biology, 4 (3), 361-363. doi: 10.4161/cib.4.3.15700

Non-random sharing of plantae genes

2011

Journal Article

Plastid origin and evolution: New models provide insights into old problems

Chan, Cheong Xin, Gross, Jeferson, Yoon, Hwan Su and Bhattacharya, Debashish (2011). Plastid origin and evolution: New models provide insights into old problems. Plant Physiology, 155 (4), 1552-1560. doi: 10.1104/pp.111.173500

Plastid origin and evolution: New models provide insights into old problems

2011

Journal Article

Red and green algal monophyly and extensive gene sharing found in a rich repertoire of red algal genes

Chan, Cheong Xin, Yang, Chan Yang, Banerjee, Titas, Yoon, Hwan Su, Martone, Patrick T., Estevez, Jose M. and Bhattacharya, Debashish (2011). Red and green algal monophyly and extensive gene sharing found in a rich repertoire of red algal genes. Current Biology, 21 (4), 328-333. doi: 10.1016/j.cub.2011.01.037

Red and green algal monophyly and extensive gene sharing found in a rich repertoire of red algal 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

    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

  • 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

Completed supervision

Enquiries

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