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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 |
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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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2014 Book Chapter Analysis of the genome of Cyanophora paradoxa: an algal model for understanding primary endosymbiosisBhattacharya, Debashish, Price, Dana C., Chan, Cheong Xin, Gross, Jeferson, Steiner, Jürgen M. and Löffelhardt, Wolfgang (2014). Analysis of the genome of Cyanophora paradoxa: an algal model for understanding primary endosymbiosis. Endosymbiosis. (pp. 135-148) edited by Wolfgang Löffelhardt. Wien, Austria: Springer. doi: 10.1007/978-3-7091-1303-5_7 |
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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 |
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2013 Journal Article Foreign gene recruitment to the fatty acid biosynthesis pathway in diatomsChan, Cheong Xin, Baglivi, Francesca L., Jenkins, Christina E. and Bhattacharya, Debashish (2013). Foreign gene recruitment to the fatty acid biosynthesis pathway in diatoms. Mobile Genetic Elements, 3 (5), e27313.1-e27313.7. doi: 10.4161/mge.27313 |
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2013 Journal Article Biological intuition in alignment-free methods: response to PosadaRagan, Mark A. and Chan, Cheong Xin (2013). Biological intuition in alignment-free methods: response to Posada. Journal of Molecular Evolution, 77 (1-2), 1-2. doi: 10.1007/s00239-013-9573-0 |
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2013 Journal Article Evidence for widespread exonic small RNAs in the glaucophyte alga Cyanophora paradoxaGross, Jeferson, Wajid, Sana, Price, Dana C., Zelzion, Ehud, Li, Junyi, Chan, Cheong Xin and Bhattacharya, Debashish (2013). Evidence for widespread exonic small RNAs in the glaucophyte alga Cyanophora paradoxa. PLoS One, 8 (7) e67669, 67669.1-67669.9. doi: 10.1371/journal.pone.0067669 |
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2013 Journal Article Genome of the red alga Porphyridium purpureumBhattacharya, Debashish, Price, Dana C., Chan, Cheong Xin, Qiu, Huan, Rose, Nicholas, Ball, Steven, Weber, Andreas P. M., Arias, Maria Cecilia, Henrissat, Bernard, Coutinho, Pedro M., Krishnan, Anagha, Zaeuner, Simone, Morath, Shannon, Hilliou, Frederique, Egizi, Andrea, Perrineau, Marie-Mathilde and Yoon, Hwan Su (2013). Genome of the red alga Porphyridium purpureum. Nature Communications, 4 (1) 2931, 1941.1-1941.10. doi: 10.1038/ncomms2931 |
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2013 Journal Article Clustering evolving proteins into homologous familiesChan, Cheong Xin, Mahbob, Maisarah and Ragan, Mark A. (2013). Clustering evolving proteins into homologous families. BMC Bioinformatics, 14 (1) 120, 120.1-120.11. doi: 10.1186/1471-2105-14-120 |
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2013 Journal Article Next-generation phylogenomicsChan, Cheong Xin and Ragan, Mark A. (2013). Next-generation phylogenomics. Biology Direct, 8 (1) 3, 3.1-3.14. doi: 10.1186/1745-6150-8-3 |
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2013 Journal Article Phylogenomics of marine algaeChan, C. X. (2013). Phylogenomics of marine algae. Malaysian Journal of Science, 32 (SPEC. ISS.), 11-18. doi: 10.22452/mjs.vol32no3.2 |
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2013 Conference Publication The Cyanophora genome: analysis of gene and small RNA content in a pivotal algal lineageBhattacharya, D., Gross, J., Price, D. C., Chan, C. X. and Zelzion, U. (2013). The Cyanophora genome: analysis of gene and small RNA content in a pivotal algal lineage. 10th International Phycological Congress, Orlando, FL, United States, 4-10 August 2013. Lawrence, KS, United States: International Phycological Society. doi: 10.2216/0031-8884-52.sp4.1 |
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2012 Journal Article Porphyra (Bangiophyceae) transcriptomes provide insights into red algal development and metabolismChan, Cheong Xin, Blouin, Nicolas A., Zhuang, Yunyun, Zaeuner, Simone, Prochnik, Simon E., Lindquist, Erika, Lin, Senjie, Benning, Christoph, Lohr, Martin, Yarish, Charles, Gantt, Elisabeth, Grossman, Arthur R., Lu, Shan, Mueller, Kirsten, Stiller, John W., Brawley, Susan H. and Bhattacharya, Debashish (2012). Porphyra (Bangiophyceae) transcriptomes provide insights into red algal development and metabolism. Journal of Phycology, 48 (6), 1328-1342. doi: 10.1111/j.1529-8817.2012.01229.x |
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2012 Journal Article Analysis of Alexandrium tamarense (Dinophyceae) genes reveals the complex evolutionary history of a microbial eukaryoteChan, Cheong Xin, Soares, Marcelo B., Bonaldo, Maria F., Wisecaver, Jennifer H., Hackett, Jeremiah D., Anderson, Donald M., Erdner, Deana L. and Bhattacharya, Debashish (2012). Analysis of Alexandrium tamarense (Dinophyceae) genes reveals the complex evolutionary history of a microbial eukaryote. Journal of Phycology, 48 (5), 1130-1142. doi: 10.1111/j.1529-8817.2012.01194.x |
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2012 Journal Article Major developmental regulators and their expression in two closely related species of Porphyra (Rhodophyta)Stiller, John W., Perry, Justin, Rymarquis, Linda A., Accerbi, Monica, Green, Pamela J., Prochnik, Simon, Lindquist, Erika, Chan, Cheong Xin, Yarish, Charles, Lin, Senjie, Zhuang, Yunyun, Blouin, Nicolas A. and Brawley, Susan H. (2012). Major developmental regulators and their expression in two closely related species of Porphyra (Rhodophyta). Journal of Phycology, 48 (4), 883-896. doi: 10.1111/j.1529-8817.2012.01138.x |
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2012 Journal Article Analysis of Porphyra membrane transporters demonstrates gene transfer among photosynthetic eukaryotes and numerous sodium-coupled transport systemsChan, Cheong Xin, Zauner, Simone, Wheeler, Glen, Grossman, Arthur R., Prochnik, Simon E., Blouin, Nicolas A., Zhuang, Yunyun, Benning, Christoph, Berg, Gry Mine, Yarish, Charles, Eriksen, Renee L., Klein, Anita S., Lin, Senjie, Levine, Ira, Brawley, Susan H. and Bhattacharya, Debashish (2012). Analysis of Porphyra membrane transporters demonstrates gene transfer among photosynthetic eukaryotes and numerous sodium-coupled transport systems. Plant Physiology, 158 (4), 2001-2012. doi: 10.1104/pp.112.193896 |
