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2024 Journal Article Progress and future directions for seaweed holobiont researchSaha, 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 |
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2024 Journal Article Chromosomal inversions harbour excess mutational load in the coral, <i>Acropora kenti</i>, on the Great Barrier ReefZhang, 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 |
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2024 Journal Article Whole-genome duplication in an algal symbiont bolsters coral heat toleranceDougan, 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 |
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2024 Journal Article Nuclear genomes of dinoflagellates reveal evolutionarily conserved pattern of RNA editing relative to stress responseChen, 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 |
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2024 Journal Article Contaminant or goldmine? In silico assessment of Symbiodiniaceae community using coral hologenomesIshida, 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 |
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2024 Journal Article Genome-wide transcriptome analysis reveals the diversity and function of long non-coding RNAs in dinoflagellatesChen, 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 |
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2024 Journal Article Facultative lifestyle drives diversity of coral algal symbiontsBhattacharya, 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 |
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2024 Journal Article Massive genome reduction predates the divergence of Symbiodiniaceae dinoflagellatesShah, 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 |
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2023 Journal Article Multi-omics analysis reveals the molecular response to heat stress in a “red tide” dinoflagellateDougan, 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 |
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2023 Journal Article In vivo structure probing of RNA in Archaea: novel insights into the ribosome structure of Methanosarcina acetivoransWilliams, 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 |
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2023 Journal Article Developing model systems for dinoflagellates in the post‐genomic eraIshida, 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 |
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2023 Journal Article Gene duplication is the primary driver of intraspecific genomic divergence in coral algal symbiontsShah, 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 |
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2023 Journal Article Building consensus around the assessment and interpretation of Symbiodiniaceae diversityDavies, 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 |
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2023 Journal Article Micro-analytical and molecular approaches for understanding the distribution, biochemistry, and molecular biology of selenium in (hyperaccumulator) plantsPinto 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 |
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2022 Journal Article Evolutionary responses of a reef-building coral to climate change at the end of the last glacial maximumZhang, 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 |
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2022 Journal Article Improved Cladocopium goreaui genome assembly reveals features of a facultative coral symbiont and the complex evolutionary history of dinoflagellate genesChen, 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 |
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2022 Journal Article Transcriptome of the coralline alga Calliarthron tuberculosum (Corallinales, Rhodophyta) reveals convergent evolution of a partial lignin biosynthesis pathwayXue, 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 |
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2022 Journal Article Genome-guided analysis of seven weed species reveals conserved sequence and structural features of key gene targets for herbicide developmentShah, 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 |
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2022 Journal Article Alignment-free analysis of whole-genome sequences from Symbiodiniaceae reveals different phylogenetic signals in distinct regionsLo, 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 |
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2022 Journal Article Genome-powered classification of microbial eukaryotes: focus on coral algal symbiontsDougan, 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 |
