Associate Professor Cheong Xin Chan
Research Visitor & Affiliate Research Fellow
Institute for Molecular Bioscience
Researcher biography
Dr Chan has a PhD in Genomics and Computational Biology from UQ. He underwent postdoctoral training at Rutgers University (USA) in algal genomics and evolution. He returmed to UQ in late 2011 as one of the inaugural Great Barrier Reef Foundation Bioinformatics Fellows.
Dr Chan joined the School of Chemistry and Molecular Biosciences in 2020 as a group leader at the Australian Centre for Ecogenomics (ACE). His group uses advanced computational approaches to study genome evolution and develop scalable approaches for comparative genomics.
| Featured projects | Duration |
|---|---|
| Microbial Genomics |
Publications
Book Chapters
Shah, Sarah, Dougan, Katherine E., Bhattacharya, Debashish and Chan, Cheong Xin (2022). Coral conservation from the genomic perspective on symbiodiniaceae diversity and function in the holobiont. Coral reefs of the world. (pp. 85-96) edited by Madeleine J. H. van Oppen and Manuel Aranda Lastra. Cham, Switzerland: Springer Cham. doi: 10.1007/978-3-031-07055-6_6
Bernard, 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
Chan, Cheong Xin, Beiko, Robert G. and Ragan, Mark A. (2017). Scaling up the phylogenetic detection of lateral gene transfer events. In Keith, JM (Ed.), Bioinformatics (pp. 421-432) New York, United States: Humana Press. doi:10.1007/978-1-4939-6622-6_16
Chan, 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
Bhattacharya, 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
Chan, Cheong Xin and Bhattacharya, Debashish (2011). Plastid origin and evolution. eLS. (pp. 1-8) Chichester, United Kingdom: John Wiley & Sons. doi: 10.1002/9780470015902.a0023639
Gantt, Elisabeth, Berg, G. Mine, Bhattacharya, Debashish, Blouin, Nicolas A., Brodie, Juliet A., Chan, Cheong Xin, Collen, Jonas, Cunningham, Francis X., Gross, Jeferson, Grossman, Arthur R., Karpowicz, Steven, Kitade, Yukihiro, Klein, Anita S., Levine, Ira A., Lin, Senjie, Lu, Shan, Lynch, Michael, Minocha, Subhash C., Muller, Kirsten, Neefus, Christopher D., De Oliveira, Mariana Cabral, Rymarquis, Linda, Smith, Alison, Stiller, John W., Wu, Wen-Kai, Yarish, Charles, Zhuang, Yun and Brawley, Susan H. (2010). Porphyra: Complex life histories in a harsh environment. Red algae in the genomic age. (pp. 129-148) edited by Joseph Seckbach and David J. Chapman. New York , NY, U.S.A.: Springer. doi: 10.1007/978-90-481-3795-4_7
Journal Articles
Chen, 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
Bhattacharya, 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
Dougan, 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, 265. doi: 10.1186/s13059-023-03107-4
Williams, 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
Ishida, 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
Shah, 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
Davies, 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
Pinto 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
Zhang, 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
Chen, 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
Xue, 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
Shah, 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
Lo, 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
Dougan, 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
Repetti, Sonja I., Iha, Cintia, Uthanumallian, Kavitha, Jackson, Christopher J., Chen, Yibi, Chan, Cheong Xin and Verbruggen, Heroen (2022). Nuclear genome of a pedinophyte pinpoints genomic innovation and streamlining in the green algae. New Phytologist, 233 (5), 2144-2154. doi: 10.1111/nph.17926
Uthanumallian, Kavitha, Iha, Cintia, Repetti, Sonja I, Chan, Cheong Xin, Bhattacharya, Debashish, Duchene, Sebastian and Verbruggen, Heroen (2022). Tightly constrained genome reduction and relaxation of purifying selection during secondary plastid endosymbiosis. Molecular Biology and Evolution, 39 (1) msab295. doi: 10.1093/molbev/msab295
Voolstra, Christian R., Quigley, Kate M., Davies, Sarah W., Parkinson, John Everett, Peixoto, Raquel S., Aranda, Manuel, Baker, Andrew C., Barno, Adam R., Barshis, Daniel J., Benzoni, Francesca, Bonito, Victor, Bourne, David G., Buitrago-López, Carol, Bridge, Tom C. L., Chan, Cheong Xin, Combosch, David J., Craggs, Jamie, Frommlet, Jörg C., Herrera, Santiago, Quattrini, Andrea M., Röthig, Till, Reimer, James D., Rubio-Portillo, Esther, Suggett, David J., Villela, Helena, Ziegler, Maren and Sweet, Michael (2021). Consensus guidelines for advancing coral holobiont genome and specimen voucher deposition. Frontiers in Marine Science, 8 701784, 1-12. doi: 10.3389/fmars.2021.701784
Jacobus, Ana Paula, Stephens, Timothy G., Youssef, Pierre, González-Pech, Raul, Ciccotosto-Camp, Michael M., Dougan, Katherine E., Chen, Yibi, Basso, Luiz Carlos, Frazzon, Jeverson, Chan, Cheong Xin and Gross, Jeferson (2021). Comparative genomics supports that Brazilian bioethanol Saccharomyces cerevisiae comprise a unified group of domesticated strains related to Cachaça spirit yeasts. Frontiers in Microbiology, 12 644089, 644089. doi: 10.3389/fmicb.2021.644089
Gonzalez-Pech, Raul A., Stephens, Timothy G., Chen, Yibi, Mohamed, Amin R., Cheng, Yuanyuan, Shah, Sarah, Dougan, Katherine E., Fortuin, Michael D. A., Lagorce, Remi, Burt, David W., Bhattacharya, Debashish, Ragan, Mark A. and Chan, Cheong Xin (2021). Comparison of 15 dinoflagellate genomes reveals extensive sequence and structural divergence in family Symbiodiniaceae and genus Symbiodinium. BMC Biology, 19 (1) 73, 73. doi: 10.1186/s12915-021-00994-6
Iha, Cintia, Dougan, Katherine E., Varela, Javier A., Avila, Viridiana, Jackson, Christopher J., Bogaert, Kenny A., Chen, Yibi, Judd, Louise M., Wick, Ryan, Holt, Kathryn E., Pasella, Marisa M., Ricci, Francesco, Repetti, Sonja I., Medina, Mónica, Marcelino, Vanessa R., Chan, Cheong Xin and Verbruggen, Heroen (2021). Genomic adaptations to an endolithic lifestyle in the coral-associated alga Ostreobium. Current Biology, 31 (7), 1-10.e1–e5. doi: 10.1016/j.cub.2021.01.018
Shah, 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
Mohamed, 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
Mohamed, 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
Stephens, 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
Chen, 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
Robbins, 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
González-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
González-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
Zielezinski, 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
Price, 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
Jaspers, 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
Bernard, 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
Stephens, 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
Bernard, 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
Liu, 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
Sim, 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
Lee, 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
Chan, 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
Jackson, 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
Mohamed, 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
González-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
Brodie, 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
Brodie, 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
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
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
Mohamed, 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
Bernard, 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
Stephens, 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
ReFuGe 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
Chan, 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
Paungfoo-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
Ragan, 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
Chan, 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
Chan, 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
Ragan, 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
Gross, 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
Bhattacharya, 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
Chan, 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
Chan, 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
Chan, C. X. (2013). Phylogenomics of marine algae. Malaysian Journal of Science, 32 (SPEC. ISS.), 11-18. doi: 10.22452/mjs.vol32no3.2
Chan, 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
Chan, 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
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
Chan, 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
Chan, Cheong Xin, Bhattacharya, Debashish and Reyes-Prieto, Adrian (2012). Endosymbiotic and horizontal gene transfer in microbial eukaryotes: impacts on cell evolution and the tree of life. Mobile Genetic Elements, 2 (2), 101-105. doi: 10.4161/mge.20110
Price, Dana C., Chan, Cheong Xin, Yoon, Hwan Su, Yang, Eun Chan, Qiu, Huan, Weber, Andreas P. M., Schwacke, Rainer, Gross, Jeferson, Blouin, Nicolas A., Lane, Chris, Reyes-Prieto, Adrian, Durnford, Dion G., Neilson, Jonathan A. D., Lang, B. Franz, Burger, Gertraud, Steiner, Jurgen M., Loffelhardt, Wolfgang, Meuser, Jonathan E., Posewitz, Matthew C., Ball, Steven, Arias, Maria Cecilia, Henrissat, Bernard, Coutinho, Pedro M., Rensing, Stefan A., Symeonidi, Aikaterini, Doddapaneni, Harshavardhan, Green, Beverley R., Rajah, Veeran D., Boore, Jeffrey and Bhattacharya, Debashish (2012). Cyanophora paradoxa genome elucidates origin of photosynthesis in algae and plants. Science, 335 (6070), 843-847. doi: 10.1126/science.1213561
Chan, Cheong Xin, Reyes-Prieto, Adrian and Bhattacharya, Debashish (2011). Red and green algal origin of diatom membrane transporters: Insights into environmental adaptation and cell evolution. PLoS One, 6 (12) e29138, e29138.1-e29138.11. doi: 10.1371/journal.pone.0029138
Chan, Cheong Xin, Beiko, Robert G. and Ragan, Mark A. (2011). Lateral transfer of genes and gene fragments in Staphylococcus extends beyond mobile elements. Journal of Bacteriology, 193 (15), 3964-3977. doi: 10.1128/JB.01524-10
Chan, Cheong Xin and Bhattacharya, Debashish (2011). Non-random sharing of plantae genes. Communicative and Integrative Biology, 4 (3), 361-363. doi: 10.4161/cib.4.3.15700
Chan, Cheong Xin, Gross, Jeferson, Yoon, Hwan Su and Bhattacharya, Debashish (2011). Plastid origin and evolution: New models provide insights into old problems. Plant Physiology, 155 (4), 1552-1560. doi: 10.1104/pp.111.173500
Chan, Cheong Xin, Yang, Chan Yang, Banerjee, Titas, Yoon, Hwan Su, Martone, Patrick T., Estevez, Jose M. and Bhattacharya, Debashish (2011). Red and green algal monophyly and extensive gene sharing found in a rich repertoire of red algal genes. Current Biology, 21 (4), 328-333. doi: 10.1016/j.cub.2011.01.037
Chan, Cheong Xin and Bhattacharya, Debashish (2010). The origin of plastids. Nature Education, 3 (9), 84-1-84-5.
Chan, Cheong Xin, Beiko, Robert G., Darling, Aaron E. and Ragan, Mark A. (2009). Lateral transfer of genes and gene fragments in prokaryotes. Genome Biology and Evolution, 1, 429-438. doi: 10.1093/gbe/evp044
Chan, Cheong Xin, Darling, Aaron E., Beiko, Robert G. and Ragan, Mark A. (2009). Are protein domains modules of lateral genetic transfer?. PLoS One, 4 (2) e4524, e4524.1-e4524.8. doi: 10.1371/journal.pone.0004524
Moustafa, Ahmed, Chan, Cheong Xin, Danforth, Megan, Zear, David, Ahmed, Hiba, Jadhav, Nagnath, Savage, Trevor and Bhattacharya, Debashish (2008). A phylogenomic approach for studying plastid endosymbiosis. Genome informatics. International Conference on Genome Informatics, 21, 165-176.
Chan, Cheong Xin, Beiko, Robert G. and Ragan, Mark A. (2006). Detecting Recombination in Evolving Nucleotide Sequences. BMC Bioinformatics, 7 (Article 412) 412, 1-15. doi: 10.1186/1471-2105-7-412
Chan, Cheong-Xin, Ho, Chai-Ling and Phang, Siew-Moi (2006). Trends in Seaweed Research. Trends in Plant Science, 11 (4), 165-166. doi: 10.1016/j.tplants.2006.02.003
Beiko, Robert G., Chan, Cheong Xin and Ragan, Mark A. (2005). A Word-Oriented Approach to Alignment Validation. Bioinformatics, 21 (10), 2230-2239. doi: 10.1093/bioinformatics/bti335
Phang, Siew-Moi, Wong, Ching-Lee, Lim, Phaik-Eem, Yeong, Hui-Yin and Chan, Cheong Xin (2005). Seaweed diversity of Langkawi with emphasis on Northeast Langkawi. Malaysian Journal of Science, 24, 77-94.
Chan, Cheong Xin (2004). Comparing Different Approaches in Large-Scale Seaweed Gene Discovery. Bioinformatics India, 2 (3), 106-111.
Chan, Cheong Xin, Teo, Swee-Sen, Ho, Chai-Ling, Othman, Rofina Yasmin and Phang, Siew-Moi (2004). Optimisation of RNA Extraction from Gracilaria changii (Gracilariales, Rhodophyta). Journal of Applied Phycology, 16 (4), 297-301. doi: 10.1023/B:JAPH.0000047782.20940.de
Conference Papers
Chan, 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
Chan, 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
Bhattacharya, 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
Gross, J., Wajid, S., Price, D., Chan, C. X. and Bhattacharya, D. (2012). Srnas of cyanophora paradoxa and chlamydomonas reinhardtii, a system genomics approach to understand algal evolution. Annual Meeting of the Phycological Society of America (PSA) 2012, Charleston SC, United States, 20-23 June 2012. Hoboken, NJ., United States: Wiley-Blackwell Publishing. doi: 10.1111/j.1529-8817.2012.01206.x
Chan, C. X. and Martone, P. T. (2012). Recent advances in the calliarthron genome: climate Responses and cell wall evolution. Annual Meeting of the Phycological Society of America (PSA) 2012, Charleston SC, United States, 20-23 June 2012. Hoboken, NJ., United States: Wiley-Blackwell Publishing. doi: 10.1111/j.1529-8817.2012.01206.x
Moustafa, Ahmed, Chan, Cheong Xin, Danforth, Megan, Zear, David, Ahmed, Hiba, Jadhav, Nagnath, Savage, Trevor and Bhattacharya, Debashish (2008). A phylogenomic approach for studying plastid endosymbiosis. 19th International Conference on Genome Informatics (GIW 2008), Gold Coast , Qld., Australia, 1 - 3 December 2008. London, United Kingdom: Imperial College Press.
Chan, Cheong Xin, Beiko, Robert G. and Ragan, Mark A. (2008). Large-scale detection of recombination in nucleotide sequences. International Conference on Mathematical Biology 2007, Putrajaya, Malaysia, 4-6 September 2007. Melville, NY, USA: American Institute of Physics. doi: 10.1063/1.2883829
Chan, Cheong Xin, Beiko, Robert G. and Ragan, Mark A. (2007). A two-phase approach for detecting recombination in nucleotide sequences. The First Southern African Bioinformatics Workshop, Johannesburg, South Africa, 28-30 January 2007. Johannesburg, South Africa: University of the Witwatersrand.
Chan, Cheong Xin, Beiko, Robert G. and Ragan, Mark A. (2004). Benchmarking the Detection and Analysis of Recombination. 12th International Conference Intelligent Systems for Molecular Biology (ISMB) and 3rd European Conference in Computational Biology (ECCB), Glasgow, UK, 31 July - 4 August 2004.
Chan, Cheong Xin, Beiko, Robert G. and Ragan, Mark A. (2004). Oh Father Where Art Thou? Comparing Different Ways of Finding Recombination Events. First ARC Centre in Bioinformatics Annual All Hands Meeting, The University of Queensland, 10-11 May, 2004.
Chan, Cheong Xin, Ho, Chai-Ling, Othman, Rofina Yasmin and Phang, Siew-Moi (2002). Total RNA Extraction for the Red Seaweed Gracilaria changii (Gracilariales, Rhodophyta). Asia-Pacific Conference in Marine Science and Technology, Kuala Lumpur, Malaysia, 12-16 May, 2002.
Thesis
Chan, Cheong Xin (2007). Units of genetic transfer in prokaryotes. PhD Thesis, Institute For Molecular Bioscience, The University of Queensland. doi: 10.14264/132182
Preprint
Data Collections
Chen, Yibi, Dougan, Katherine E., Nguyen, Quen, Bhattacharya, Debashish and Chan, Cheong Xin (2023). Long non-coding RNAs of three dinoflagellate species. The University of Queensland. (Dataset) doi: 10.48610/2692e99
Dougan, 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, Wagner-Döbler, Irene and Chan, Cheong Xin (2023). Genome and transcriptome data for bloom-forming dinoflagellate Prorocentrum cordatum CCMP1329. The University of Queensland. (Dataset) doi: 10.48610/bc851b7
Shah, Sarah and Chan, Cheong Xin (2023). Effrenium voratum genomes and genes. The University of Queensland. (Dataset) doi: 10.48610/1f0377a
Chen, Yibi, Shah, Sarah, Dougan, Katherine E., van Oppen, Madeleine, J. H., Bhattacharya, Debashish and Chan, Cheong Xin (2022). Improved assembled genome of Cladocopium goreaui SCF055. The University of Queensland. (Dataset)
Shah, 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). Genomic resources of seven Australian weed species of national significance. The University of Queensland. (Dataset) doi: 10.48610/c22c10c
Katherine E. Dougan, Anthony J. Bellantuono, Tim Kahlke, Raffaela M. Abbriano, Yibi Chen, Sarah Shah, Camila Granados-Cifuentes, Madeleine J. H. van Oppen, Debashish Bhattacharya, David J. Suggett, Mauricio Rodriguez-Lanetty and Cheong Xin Chan (2022). Genome data for Durusdinium trenchii CCMP2556 and SCF082. The University of Queensland. (Dataset) doi: 10.48610/27da3e7
González-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
Stephens, 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
Chen, 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
Bernard, 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
Bernard, Guillaume, Chan, Cheong Xin and Ragan, Mark A. (2016). 143 Prokaryote genomes. The University of Queensland. (Dataset) doi: 10.14264/uql.2016.908