Overview
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
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
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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.
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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.
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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.
Works
Search Professor Cheong Xin Chan’s works on UQ eSpace
2022
Other Outputs
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)
2022
Journal Article
Transcriptome of the coralline alga Calliarthron tuberculosum (Corallinales, Rhodophyta) reveals convergent evolution of a partial lignin biosynthesis pathway
Xue, Jan Y., Hind, Katharine R., Lemay, Matthew A., Mcminigal, Andrea, Jourdain, Emma, Chan, Cheong Xin and Martone, Patrick T. (2022). Transcriptome of the coralline alga Calliarthron tuberculosum (Corallinales, Rhodophyta) reveals convergent evolution of a partial lignin biosynthesis pathway. PLoS One, 17 (7) e0266892, 1-20. doi: 10.1371/journal.pone.0266892
2022
Journal Article
Genome-guided analysis of seven weed species reveals conserved sequence and structural features of key gene targets for herbicide development
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). Genome-guided analysis of seven weed species reveals conserved sequence and structural features of key gene targets for herbicide development. Frontiers in Plant Science, 13 909073. doi: 10.3389/fpls.2022.909073
2022
Other Outputs
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
2022
Journal Article
Alignment-free analysis of whole-genome sequences from Symbiodiniaceae reveals different phylogenetic signals in distinct regions
Lo, Rosalyn, Dougan, Katherine E., Chen, Yibi, Shah, Sarah, Bhattacharya, Debashish and Chan, Cheong Xin (2022). Alignment-free analysis of whole-genome sequences from Symbiodiniaceae reveals different phylogenetic signals in distinct regions. Frontiers in Plant Science, 13 815714, 1-13. doi: 10.3389/fpls.2022.815714
2022
Other Outputs
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
2022
Journal Article
Genome-powered classification of microbial eukaryotes: focus on coral algal symbionts
Dougan, Katherine E., González-Pech, Raúl A., Stephens, Timothy G., Shah, Sarah, Chen, Yibi, Ragan, Mark A., Bhattacharya, Debashish and Chan, Cheong Xin (2022). Genome-powered classification of microbial eukaryotes: focus on coral algal symbionts. Trends in Microbiology, 30 (9), 831-840. doi: 10.1016/j.tim.2022.02.001
2022
Journal Article
Nuclear genome of a pedinophyte pinpoints genomic innovation and streamlining in the green algae
Repetti, Sonja I., Iha, Cintia, Uthanumallian, Kavitha, Jackson, Christopher J., Chen, Yibi, Chan, Cheong Xin and Verbruggen, Heroen (2022). Nuclear genome of a pedinophyte pinpoints genomic innovation and streamlining in the green algae. New Phytologist, 233 (5), 2144-2154. doi: 10.1111/nph.17926
2022
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
2022
Journal Article
Tightly constrained genome reduction and relaxation of purifying selection during secondary plastid endosymbiosis
Uthanumallian, Kavitha, Iha, Cintia, Repetti, Sonja I, Chan, Cheong Xin, Bhattacharya, Debashish, Duchene, Sebastian and Verbruggen, Heroen (2022). Tightly constrained genome reduction and relaxation of purifying selection during secondary plastid endosymbiosis. Molecular Biology and Evolution, 39 (1) msab295. doi: 10.1093/molbev/msab295
2021
Journal Article
Consensus guidelines for advancing coral holobiont genome and specimen voucher deposition
Voolstra, Christian R., Quigley, Kate M., Davies, Sarah W., Parkinson, John Everett, Peixoto, Raquel S., Aranda, Manuel, Baker, Andrew C., Barno, Adam R., Barshis, Daniel J., Benzoni, Francesca, Bonito, Victor, Bourne, David G., Buitrago-López, Carol, Bridge, Tom C. L., Chan, Cheong Xin, Combosch, David J., Craggs, Jamie, Frommlet, Jörg C., Herrera, Santiago, Quattrini, Andrea M., Röthig, Till, Reimer, James D., Rubio-Portillo, Esther, Suggett, David J., Villela, Helena, Ziegler, Maren and Sweet, Michael (2021). Consensus guidelines for advancing coral holobiont genome and specimen voucher deposition. Frontiers in Marine Science, 8 701784, 1-12. doi: 10.3389/fmars.2021.701784
2021
Journal Article
Comparative genomics supports that Brazilian bioethanol Saccharomyces cerevisiae comprise a unified group of domesticated strains related to Cachaça spirit yeasts
Jacobus, Ana Paula, Stephens, Timothy G., Youssef, Pierre, González-Pech, Raul, Ciccotosto-Camp, Michael M., Dougan, Katherine E., Chen, Yibi, Basso, Luiz Carlos, Frazzon, Jeverson, Chan, Cheong Xin and Gross, Jeferson (2021). Comparative genomics supports that Brazilian bioethanol Saccharomyces cerevisiae comprise a unified group of domesticated strains related to Cachaça spirit yeasts. Frontiers in Microbiology, 12 644089, 644089. doi: 10.3389/fmicb.2021.644089
2021
Journal Article
Comparison of 15 dinoflagellate genomes reveals extensive sequence and structural divergence in family Symbiodiniaceae and genus Symbiodinium
Gonzalez-Pech, Raul A., Stephens, Timothy G., Chen, Yibi, Mohamed, Amin R., Cheng, Yuanyuan, Shah, Sarah, Dougan, Katherine E., Fortuin, Michael D. A., Lagorce, Remi, Burt, David W., Bhattacharya, Debashish, Ragan, Mark A. and Chan, Cheong Xin (2021). Comparison of 15 dinoflagellate genomes reveals extensive sequence and structural divergence in family Symbiodiniaceae and genus Symbiodinium. BMC Biology, 19 (1) 73, 73. doi: 10.1186/s12915-021-00994-6
2021
Journal Article
Genomic adaptations to an endolithic lifestyle in the coral-associated alga Ostreobium
Iha, Cintia, Dougan, Katherine E., Varela, Javier A., Avila, Viridiana, Jackson, Christopher J., Bogaert, Kenny A., Chen, Yibi, Judd, Louise M., Wick, Ryan, Holt, Kathryn E., Pasella, Marisa M., Ricci, Francesco, Repetti, Sonja I., Medina, Mónica, Marcelino, Vanessa R., Chan, Cheong Xin and Verbruggen, Heroen (2021). Genomic adaptations to an endolithic lifestyle in the coral-associated alga Ostreobium. Current Biology, 31 (7), 1-10.e1–e5. doi: 10.1016/j.cub.2021.01.018
2021
Book Chapter
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
2021
Other Outputs
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
2020
Journal Article
Sex in Symbiodiniaceae dinoflagellates: genomic evidence for independent loss of the canonical synaptonemal complex
Shah, Sarah, Chen, Yibi, Bhattacharya, Debashish and Chan, Cheong Xin (2020). Sex in Symbiodiniaceae dinoflagellates: genomic evidence for independent loss of the canonical synaptonemal complex. Scientific Reports, 10 (1) 9792, 9792. doi: 10.1038/s41598-020-66429-4
2020
Journal Article
Dual RNA‐seq analyses of a coral and its native symbiont during the establishment of symbiosis
Mohamed, Amin R., Andrade, Natalia, Moya, Aurelie, Xin Chan, Cheong, Negri, Andrew P., Bourne, David G., Ying, Hua, Ball, Eldon E. and Miller, David J. (2020). Dual RNA‐seq analyses of a coral and its native symbiont during the establishment of symbiosis. Molecular Ecology, 29 (20), 3921-3937. doi: 10.1111/mec.15612
2020
Journal Article
Comparative transcriptomic analyses of Chromera and Symbiodiniaceae
Mohamed, Amin R., Chan, Cheong Xin, Ragan, Mark A., Zhang, Jia, Cooke, Ira, Ball, Eldon E. and Miller, David J. (2020). Comparative transcriptomic analyses of Chromera and Symbiodiniaceae. Environmental Microbiology Reports, 12 (4), 435-443. doi: 10.1111/1758-2229.12859
2020
Other Outputs
Genomic adaptations to an endolithic lifestyle in the coral-associated alga Ostreobium
Iha, Cintia, Dougan, Katherine E., Varela, Javier A., Avila, Viridiana, Jackson, Christopher J., Bogaert, Kenny A., Chen, Yibi, Judd, Louise M., Wick, Ryan, Holt, Kathryn E., Pasella, Marisa M., Ricci, Francesco, Repetti, Sonja I., Medina, Mónica, Marcelino, Vanessa R., Chan, Cheong Xin and Verbruggen, Heroen (2020). Genomic adaptations to an endolithic lifestyle in the coral-associated alga Ostreobium. doi: 10.1101/2020.07.21.211367
Funding
Past funding
Supervision
Availability
- Associate Professor Cheong Xin Chan is:
- Available for supervision
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Supervision history
Current supervision
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Doctor Philosophy
Hologenomic variation in the reef-building coral Acropora hyacinthus across the Great Barrier Reef
Principal Advisor
Other advisors: Professor Cynthia Riginos
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Doctor Philosophy
Towards understanding microbial community dynamics in a subtropical estuary: a multi-omics approach
Associate Advisor
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Doctor Philosophy
Ecophysiology and molecular genetics of selenium tolerance and accumulation in the selenium hyperaccumulator Neptunia amplexicaulis
Associate Advisor
Other advisors: Professor Peter Erskine
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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
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Doctor Philosophy
Genetics of climate-change adaptation in Great Barrier Reef corals
Associate Advisor
Other advisors: Professor Cynthia Riginos
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Doctor Philosophy
Ecophysiology and molecular genetics of selenium tolerance and accumulation in the selenium hyperaccumulator Neptunia amplexicaulis
Associate Advisor
Other advisors: Professor Peter Erskine
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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
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Doctor Philosophy
Towards understanding microbial community dynamics in a subtropical estuary: a multi-omics approach
Associate Advisor
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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
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2024
Doctor Philosophy
Assessing complex gene and genome features of dinoflagellates
Principal Advisor
Other advisors: Dr Quan Nguyen
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2023
Doctor Philosophy
Evolution and adaptation of non-symbiotic Symbiodiniaceae
Principal Advisor
Other advisors: Dr Quan Nguyen
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2019
Doctor Philosophy
Polarella genomics: understanding the evolutionary transition to algal symbiosis and cold adaptation
Principal Advisor
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2025
Doctor Philosophy
Towards understanding microbial community dynamics in a subtropical estuary: a multi-omics approach
Associate Advisor
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2024
Doctor Philosophy
Genomic, Genetic, and Mass Spectrometry Glycoproteomic Investigations of the Roles of Oligosaccharyltransferase Subunits in N-Glycosylation in Yeast
Associate Advisor
Other advisors: Associate Professor Michael Landsberg, Professor Benjamin Schulz
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2023
Doctor Philosophy
Developing novel spatio-temporal inference methods using single cell, spatial omics and imaging data for studying neuroinflammation and cancer progression
Associate Advisor
Other advisors: Professor Marc Ruitenberg, Dr Quan Nguyen
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2017
Doctor Philosophy
Scalable alignment-free approaches in microbial phylogenomics
Associate Advisor
Media
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