![Associate Professor Cheong Xin Chan](/sites/default/files/profiles/1283.jpeg)
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
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. doi: 10.1111/nph.20018
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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)
Funding
Current 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
Genetics of climate-change adaptation in Great Barrier Reef corals
Associate Advisor
Other advisors: Professor John Pandolfi, Professor Cynthia Riginos
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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
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
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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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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