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2018 Journal Article k-mer similarity, networks of microbial genomes, and taxonomic rankBernard, Guillaume, Greenfield, Paul, Ragan, Mark A. and Chan, Cheong Xin (2018). k-mer similarity, networks of microbial genomes, and taxonomic rank. mSystems, 3 (6) e00257-18, 1-16. doi: 10.1128/msystems.00257-18 |
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2018 Journal Article Symbiodinium genomes reveal adaptive evolution of functions related to coral-dinoflagellate symbiosisLiu, Huanle, Stephens, Timothy G., González-Pech, Raúl A., Beltran, Victor H., Lapeyre, Bruno, Bongaerts, Pim, Cooke, Ira, Aranda, Manuel, Bourne, David G., Forêt, Sylvain, Miller, David J., van Oppen, Madeleine J. H., Voolstra, Christian R., Ragan, Mark A. and Chan, Cheong Xin (2018). Symbiodinium genomes reveal adaptive evolution of functions related to coral-dinoflagellate symbiosis. Communications Biology, 1 (1) 95, 95. doi: 10.1038/s42003-018-0098-3 |
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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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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 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 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 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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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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2014 Journal Article Inferring phylogenies of evolving sequences without multiple sequence alignmentChan, Cheong Xin, Bernard, Guillaume, Poirion, Olivier, Hogan, James M. and Ragan, Mark A. (2014). Inferring phylogenies of evolving sequences without multiple sequence alignment. Scientific Reports, 4 (3) 6504, e6504.1-e6504.9. doi: 10.1038/srep06504 |
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2014 Journal Article Molecular phylogenetics before sequences : oligonucleotide catalogs as k-mer spectraRagan, Mark A., Bernard, Guillaume and Chan, Cheong Xin (2014). Molecular phylogenetics before sequences : oligonucleotide catalogs as k-mer spectra. RNA Biology, 11 (3), 176-185. doi: 10.4161/rna.27505 |
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2014 Journal Article A new species of Burkholderia isolated from sugarcane roots promotes plant growthPaungfoo-Lonhienne, Chanyarat, Lonhienne, Thierry G. A., Yeoh, Yun Kit, Webb, Richard I., Lakshmanan, Prakash, Chan, Cheong Xin, Lim, Phaik-Eem, Ragan, Mark A., Schmidt, Susanne and Hugenholtz, Philip (2014). A new species of Burkholderia isolated from sugarcane roots promotes plant growth. Microbial Biotechnology, 7 (2), 142-154. doi: 10.1111/1751-7915.12105 |
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2013 Journal Article Analysis of horizontal genetic transfer in red algae in the post-genomics ageChan, Cheong Xin and Bhattacharya, Debashish (2013). Analysis of horizontal genetic transfer in red algae in the post-genomics age. Mobile Genetic Elements, 3 (6), e27669.1-e27669.5. doi: 10.4161/mge.27669 |
