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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, 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 1320917, 1-12. 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

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

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

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

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

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

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