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2021 Book Chapter Inferring phylogenomic relationship of microbes using scalable alignment-free methodsBernard, Guillaume, Stephens, Timothy G., González-Pech, Raúl A. and Chan, Cheong Xin (2021). Inferring phylogenomic relationship of microbes using scalable alignment-free methods. Bacterial pangenomics: methods and protocols. (pp. 69-76) New York, United States: Humana Press. doi: 10.1007/978-1-0716-1099-2_5 |
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2021 Other Outputs Genome assemblies and the associated annotations for seven Symbiodinium isolatesGonzález-Pech, Raúl A., Ragan, Mark A., Bhattacharya, Debashish and Chan, Cheong Xin (2021). Genome assemblies and the associated annotations for seven Symbiodinium isolates. The University of Queensland. (Dataset) doi: 10.14264/f1b3a11 |
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2020 Journal Article Sex in Symbiodiniaceae dinoflagellates: genomic evidence for independent loss of the canonical synaptonemal complexShah, Sarah, Chen, Yibi, Bhattacharya, Debashish and Chan, Cheong Xin (2020). Sex in Symbiodiniaceae dinoflagellates: genomic evidence for independent loss of the canonical synaptonemal complex. Scientific Reports, 10 (1) 9792, 9792. doi: 10.1038/s41598-020-66429-4 |
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2020 Journal Article Dual RNA‐seq analyses of a coral and its native symbiont during the establishment of symbiosisMohamed, Amin R., Andrade, Natalia, Moya, Aurelie, Xin Chan, Cheong, Negri, Andrew P., Bourne, David G., Ying, Hua, Ball, Eldon E. and Miller, David J. (2020). Dual RNA‐seq analyses of a coral and its native symbiont during the establishment of symbiosis. Molecular Ecology, 29 (20), 3921-3937. doi: 10.1111/mec.15612 |
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2020 Journal Article Comparative transcriptomic analyses of Chromera and SymbiodiniaceaeMohamed, Amin R., Chan, Cheong Xin, Ragan, Mark A., Zhang, Jia, Cooke, Ira, Ball, Eldon E. and Miller, David J. (2020). Comparative transcriptomic analyses of Chromera and Symbiodiniaceae. Environmental Microbiology Reports, 12 (4), 435-443. doi: 10.1111/1758-2229.12859 |
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2020 Journal Article Genomes of the dinoflagellate Polarella glacialis encode tandemly repeated single-exon genes with adaptive functionsStephens, Timothy G., González-Pech, Raúl A., Cheng, Yuanyuan, Mohamed, Amin R., Burt, David W., Bhattacharya, Debashish, Ragan, Mark A. and Chan, Cheong Xin (2020). Genomes of the dinoflagellate Polarella glacialis encode tandemly repeated single-exon genes with adaptive functions. BMC Biology, 18 (1) 56, 56. doi: 10.1186/s12915-020-00782-8 |
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2020 Journal Article Evidence that inconsistent gene prediction can mislead analysis of dinoflagellate genomesChen, Yibi, González‐Pech, Raúl A., Stephens, Timothy G., Bhattacharya, Debashish and Chan, Cheong Xin (2020). Evidence that inconsistent gene prediction can mislead analysis of dinoflagellate genomes. Journal of Phycology, 56 (1), 6-10. doi: 10.1111/jpy.12947 |
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2020 Other Outputs Genome assemblies and the associated annotations for Polarella glacialis CCMP1383 and CCMP2088Stephens, Timothy, Ragan, Mark A., Bhattacharya, Debashish and Chan, Cheong Xin (2020). Genome assemblies and the associated annotations for Polarella glacialis CCMP1383 and CCMP2088. The University of Queensland. (Dataset) doi: 10.14264/uql.2020.222 |
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2019 Journal Article Molecular techniques and their limitations shape our view of the holobiontCooke, Ira, Mead, Oliver, Whalen, Casey, Boote, Chloë, Moya, Aurelie, Ying, Hua, Robbins, Steven, Strugnell, Jan M., Darling, Aaron, Miller, David, Voolstra, Christian R., Adamska, Maja, Consortium of Australian Academy of Science Boden Research Conference Participants, Esmail, Amin and Chan, Cheong Xin (2019). Molecular techniques and their limitations shape our view of the holobiont. Zoology, 137 125695, 1-8. doi: 10.1016/j.zool.2019.125695 |
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2019 Journal Article A genomic view of the reef-building coral Porites lutea and its microbial symbiontsRobbins, Steven J., Singleton, Caitlin M., Chan, Cheong Xin, Messer, Lauren F., Geers, Aileen U., Ying, Hua, Baker, Alexander, Bell, Sara C., Morrow, Kathleen M., Ragan, Mark A., Miller, David J., Forêt, Sylvain, Voolstra, Christian R., Tyson, Gene W. and Bourne, David G. (2019). A genomic view of the reef-building coral Porites lutea and its microbial symbionts. Nature Microbiology, 4 (12), 2090-2100. doi: 10.1038/s41564-019-0532-4 |
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2019 Journal Article Genome evolution of coral reef symbionts as intracellular residentsGonzález-Pech, Raúl A., Bhattacharya, Debashish, Ragan, Mark A. and Chan, Cheong Xin (2019). Genome evolution of coral reef symbionts as intracellular residents. Trends in Ecology and Evolution, 34 (9), 799-806. doi: 10.1016/j.tree.2019.04.010 |
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2019 Journal Article Commonly misunderstood parameters of NCBI BLAST and important considerations for usersGonzález-Pech, Raúl A., Stephens, Timothy G. and Chan, Cheong Xin (2019). Commonly misunderstood parameters of NCBI BLAST and important considerations for users. Bioinformatics, 35 (15) bty1018, 2697-2698. doi: 10.1093/bioinformatics/bty1018 |
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2019 Journal Article Benchmarking of alignment-free sequence comparison methodsZielezinski, Andrzej, Girgis, Hani Z., Bernard, Guillaume, Leimeister, Chris-Andre, Tang, Kujin, Dencker, Thomas, Lau, Anna Katharina, Röhling, Sophie, Choi, Jae Jin, Waterman, Michael S., Comin, Matteo, Kim, Sung-Hou, Vinga, Susana, Almeida, Jonas S., Chan, Cheong Xin, James, Benjamin T., Sun, Fengzhu, Morgenstern, Burkhard and Karlowski, Wojciech M. (2019). Benchmarking of alignment-free sequence comparison methods. Genome Biology, 20 (1) 144, 144. doi: 10.1186/s13059-019-1755-7 |
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2019 Journal Article Analysis of an improved Cyanophora paradoxa genome assemblyPrice, Dana C., Goodenough, Ursula W., Roth, Robyn, Lee, Jae-Hyeok, Kariyawasam, Thamali, Mutwil, Marek, Ferrari, Camilla, Facchinelli, Fabio, Ball, Steven G., Cenci, Ugo, Chan, Cheong Xin, Wagner, Nicole E., Yoon, Hwan Su, Weber, Andreas P. M. and Bhattacharya, Debashish (2019). Analysis of an improved Cyanophora paradoxa genome assembly. DNA Research, 26 (4), 287-299. doi: 10.1093/dnares/dsz009 |
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2019 Journal Article Resolving structure and function of metaorganisms through a holistic framework combining reductionist and integrative approachesJaspers, Cornelia, Fraune, Sebastian, Arnold, A. Elizabeth, Miller, David J., Bosch, Thomas C. G., Voolstra, Christian R., Consortium of Australian Academy of Science Boden Research Conference Participants, Adamska, Maja, Ainsworth, Tracy, Ball, Eldon, Boote, Chloe, Bourne, David, Butterfield, Nicholas J., Chan, Cheong Xin, Cooke, Ira, Cowman, Peter F., Darling, Aaron, Davy, Simon K., Mohamed, Amin, Fabricius, Katharina, Fortunato, Sofia, Hernandez, Alejandra, Hoogenboom, Mia, Moya, Aurelie, Pita, Lucia, Ragan, Mark A., Robbins, Steven J., Andrade, Natalia R., Sakamaki, Kazuhiro ... Ying, Hua (2019). Resolving structure and function of metaorganisms through a holistic framework combining reductionist and integrative approaches. Zoology, 133, 81-87. doi: 10.1016/j.zool.2019.02.007 |
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2019 Journal Article Alignment-free inference of hierarchical and reticulate phylogenomic relationshipsBernard, Guillaume, Chan, Cheong Xin, Chan, Yao-ban, Chua, Xin-Yi, Cong, Yingnan, Hogan, James M., Maetschke, Stefan R. and Ragan, Mark A. (2019). Alignment-free inference of hierarchical and reticulate phylogenomic relationships. Briefings in Bioinformatics, 20 (2), 426-435. doi: 10.1093/bib/bbx067 |
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2019 Other Outputs Revised genome sequences and annotations of six Symbiodiniaceae taxaChen, Yibi, González-Pech, Raúl A., Stephens, Timothy G., Bhattacharya, Debashish and Chan, Cheong Xin (2019). Revised genome sequences and annotations of six Symbiodiniaceae taxa. The University of Queensland. (Dataset) doi: 10.14264/uql.2019.745 |
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2018 Journal Article Core genes in diverse dinoflagellate lineages include a wealth of conserved dark genes with unknown functionsStephens, Timothy G., Ragan, Mark A., Bhattacharya, Debashish and Chan, Cheong Xin (2018). Core genes in diverse dinoflagellate lineages include a wealth of conserved dark genes with unknown functions. Scientific Reports, 8 (1) 17175, 17175. doi: 10.1038/s41598-018-35620-z |
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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 |
