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2018 Journal Article Selection of reference genes for transcript profiling of Sargassum polycystum by quantitative real‐time polymerase chain reactionSim, Mei-Chea, Chan, Cheong Xin, Ho, Chai-Ling and Phang, Siew-Moi (2018). Selection of reference genes for transcript profiling of Sargassum polycystum by quantitative real‐time polymerase chain reaction. Phycological Research, 66 (4), 247-252. doi: 10.1111/pre.12328 |
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2018 Journal Article Analysis of the draft genome of the red seaweed Gracilariopsis chorda provides insights into genome size evolution in RhodophytaLee, JunMo, Yang, Eun Chan, Graf, Louis, Yang, Ji Hyun, Qiu, Huan, Zel Zion, Udi, Chan, Cheong Xin, Stephens, Timothy G., Weber, Andreas P. M., Boo, Ga Hun, Boo, Sung Min, Kim, Kyeong Mi, Shin, Younhee, Jung, Myunghee, Lee, Seung Jae, Yim, Hyung-Soon, Lee, Jung-Hyun, Bhattacharya, Debashish and Yoon, Hwan Su (2018). Analysis of the draft genome of the red seaweed Gracilariopsis chorda provides insights into genome size evolution in Rhodophyta. Molecular Biology and Evolution, 35 (8), 1869-1886. doi: 10.1093/molbev/msy081 |
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2018 Journal Article Active host response to algal symbionts in the sea slug Elysia chloroticaChan, Cheong Xin, Vaysberg, Pavel, Price, Dana C, Pelletreau, Karen N, Rumpho, Mary E and Bhattacharya, Debashish (2018). Active host response to algal symbionts in the sea slug Elysia chlorotica. Molecular Biology and Evolution, 35 (7), 1706-1711. doi: 10.1093/molbev/msy061 |
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2018 Journal Article Plastid phylogenomics with broad taxon sampling further elucidates the distinct evolutionary origins and timing of secondary green plastidsJackson, Christopher, Knoll, Andrew H, Chan, Cheong Xin and Verbruggen, Heroen (2018). Plastid phylogenomics with broad taxon sampling further elucidates the distinct evolutionary origins and timing of secondary green plastids. Scientific reports, 8 (1) 1523, 1523. doi: 10.1038/s41598-017-18805-w |
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2018 Journal Article Deciphering the nature of the coral-Chromera associationMohamed, Amin R., Cumbo, Vivian R., Harii, Saki, Shinzato, Chuya, Chan, Cheong Xin, Ragan, Mark A., Satoh, Nori, Ball, Eldon E. and Miller, David J. (2018). Deciphering the nature of the coral-Chromera association. The ISME Journal, 12 (3), 776-790. doi: 10.1038/s41396-017-0005-9 |
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2017 Journal Article Signatures of adaptation and symbiosis in genomes and transcriptomes of SymbiodiniumGonzález-Pech, Raúl A., Ragan, Mark A. and Chan, Cheong Xin (2017). Signatures of adaptation and symbiosis in genomes and transcriptomes of Symbiodinium. Scientific Reports, 7 (15021) 15021, 15021. doi: 10.1038/s41598-017-15029-w |
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2017 Journal Article Biotic interactions as drivers of algal origin and evolutionBrodie, Juliet, Ball, Steven G., Bouget, François-Yves, Chan, Cheong Xin, De Clerck, Olivier, Cock, J. Mark, Gachon, Claire, Grossman, Arthur R., Mock, Thomas, Raven, John A., Saha, Mahasweta, Smith, Alison G., Vardi, Assaf, Yoon, Hwan Su and Bhattacharya, Debashish (2017). Biotic interactions as drivers of algal origin and evolution. New Phytologist, 216 (3), 670-681. doi: 10.1111/nph.14760 |
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2017 Journal Article The algal revolutionBrodie, Juliet, Chan, Cheong Xin, De Clerck, Olivier, Cock, J. Mark, Coelho, Susana M., Gachon, Claire, Grossman, Arthur R., Mock, Thomas, Raven, John A., Smith, Alison S., Yoon, Hwan Su and Bhattacharya, Debashish (2017). The algal revolution. Trends in Plant Science, 22 (8), 726-738. doi: 10.1016/j.tplants.2017.05.005 |
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2017 Journal Article Insights into the red algae and eukaryotic evolution from the genome of Porphyra umbilicalis (Bangiophyceae, Rhodophyta)Brawley, Susan H., Blouin, Nicolas A., Ficko-Blean, Elizabeth, Wheeler, Glen L., Lohr, Martin, Goodson, Holly V., Jenkins, Jerry W., Blaby-Haas, Crysten E., Helliwell, Katherine E., Chan, Cheong Xin, Marriage, Tara N., Bhattacharya, Debashish, Klein, Anita S., Badis, Yacine, Brodie, Juliet, Cao, Yuanyu, Collén, Jonas, Dittami, Simon M., Gachon, Claire M. M., Green, Beverley R., Karpowicz, Steven J., Kim, Jay W., Kudahl, Ulrich Johan, Lin, Senjie, Michel, Gurvan, Mittag, Maria, Olson, Bradley J. S. C., Pangilinan, Jasmyn L., Peng, Yi ... Prochnik, Simon E. (2017). Insights into the red algae and eukaryotic evolution from the genome of Porphyra umbilicalis (Bangiophyceae, Rhodophyta). Proceedings of the National Academy of Sciences, 114 (31), E6361-E6370. doi: 10.1073/pnas.1703088114 |
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2017 Book Chapter Scaling up the phylogenetic detection of lateral gene transfer eventsChan, Cheong Xin, Beiko, Robert G. and Ragan, Mark A. (2017). Scaling up the phylogenetic detection of lateral gene transfer events. Bioinformatics. (pp. 421-432) edited by Keith, JM. New York, United States: Humana Press. doi: 10.1007/978-1-4939-6622-6_16 |
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2016 Journal Article Recapitulating phylogenies using k-mers: from trees to networks [version 2; referees: 2 approved]Bernard, Guillaume, Ragan, Mark A. and Chan, Cheong Xin (2016). Recapitulating phylogenies using k-mers: from trees to networks [version 2; referees: 2 approved]. F1000Research, 5 (2789) 2789, 2789. doi: 10.12688/f1000research.10225.2 |
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2016 Journal Article Alignment-free microbial phylogenomics under scenarios of sequence divergence, genome rearrangement and lateral genetic transferBernard, Guillaume, Chan, Cheong Xin and Ragan, Mark A. (2016). Alignment-free microbial phylogenomics under scenarios of sequence divergence, genome rearrangement and lateral genetic transfer. Scientific Reports, 6 (1) 28970, 28970.1-28970.12. doi: 10.1038/srep28970 |
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2016 Journal Article The transcriptomic response of the coral Acropora digitifera to a competent Symbiodinium strain: the symbiosome as an arrested early phagosomeMohamed, A. R., Cumbo, V., Harii, S., Shinzato,C., Chan, C. X., Ragan, M. A., Bourne, D. G., Willis, B. L., Ball, E. E., Satoh, N. and Miller, D. J. (2016). The transcriptomic response of the coral Acropora digitifera to a competent Symbiodinium strain: the symbiosome as an arrested early phagosome. Molecular Ecology, 25 (13), 3127-3141. doi: 10.1111/mec.13659 |
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2016 Journal Article PhySortR: a fast, flexible tool for sorting phylogenetic trees in RStephens, Timothy, Bhattacharya, Debashish, Ragan, Mark A. and Chan, Cheong Xin (2016). PhySortR: a fast, flexible tool for sorting phylogenetic trees in R. PeerJ, 4 (5) e2038, e2038.1-e2038.13. doi: 10.7717/peerj.2038 |
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2016 Other Outputs Alignment-free network of 143 Prokaryote genomesBernard, Guillaume , Chan, Cheong Xin and Ragan, Mark A. (2016). Alignment-free network of 143 Prokaryote genomes. The University of Queensland. (Dataset) doi: 10.14264/uql.2016.952 |
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2016 Other Outputs 143 Prokaryote genomesBernard, Guillaume, Chan, Cheong Xin and Ragan, Mark A. (2016). 143 Prokaryote genomes. The University of Queensland. (Dataset) doi: 10.14264/uql.2016.908 |
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2015 Journal Article The ReFuGe 2020 Consortium—using “omics” approaches to explore the adaptability and resilience of coral holobionts to environmental changeReFuGe 2020 Consortium, Voolstra, Christian R, Miller, David J., Ragan, Mark A., Hoffmann, Ary A., Hoegh-Guldberg, Ove, Bourne, David G., Ball, Eldon E., Ying, Hua, Forêt, Sylvain, Takahashi, Shunichi, Weynberg, Karen D., van Oppen, Madeleine J. H., Morrow, Kathleen, Chan, Cheong Xin, Rosic, Nedeljka, Leggat, William, Sprungala, Susanne, Imelfort, Michael, Tyson, Gene W., Kassahn, Karin S., Lundgren, Petra B., Beeden, Roger J., Ravasi, Timothy, Berumen, Michael L., Abal, Eva and Fyffe, Theresa (2015). The ReFuGe 2020 Consortium—using “omics” approaches to explore the adaptability and resilience of coral holobionts to environmental change. Frontiers in Marine Science, 2 (Art No.: 68) 68. doi: 10.3389/fmars.2015.00068 |
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2015 Conference Publication Scalable phylogenomic approaches to study algal evolutionChan, Cheong Xin, Bernard, Guillaume, Chalmers, Benjamin D. B. and Ragan, Mark A. (2015). Scalable phylogenomic approaches to study algal evolution. 6th European Phycological Congress, London, United Kingdom, 23-28 August 2015. Abingdon, Oxfordshire, United Kingdom: Taylor and Francis. doi: 10.1080/09670262.2015.1069493 |
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2015 Book Chapter Phylogenomics in algal research: current trends and future perspectivesChan, Cheong Xin (2015). Phylogenomics in algal research: current trends and future perspectives. The Algae World. (pp. 501-517) edited by Dinabandhu Sahoo and Joseph Seckbach. Dordrecht, Netherlands: Springer. doi: 10.1007/978-94-017-7321-8_20 |
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2015 Conference Publication Genome Analysis of Two Symbiodinium IsolatesChan, Cheong Xin, Stephens, Timothy G., Ling, Edmund Y. S., Foret, Sylvain, Morrow, Kathleen, Bourne, David G., Voolstra, Christian R., Leggat, William, Miller, David J. and Ragan, Mark A. (2015). Genome Analysis of Two Symbiodinium Isolates. 6th European Phycological Congress, London, United Kingdom, 23-28 August 2015. Abingdon, Oxfordshire, United Kingdom: Taylor and Francis. doi: 10.1080/09670262.2015.1069489 |
