Journal articles


Comparative genomics supports that Brazilian bioethanol Saccharomyces cerevisiae comprise a unified group of domesticated strains related to cachaça spirit yeasts
Jacobus AP, Stephens TG, Youssef P, González-Pech RA, Ciccotosto-Camp MM, Dougan KE, Chen Y, Basso LC, Frazzon J, Chan CX, Gross J
2021 Frontiers in Microbiology • 12: 644089. • DOIPDF


Comparison of 15 dinoflagellate genomes reveals extensive sequence and structural divergence in family Symbiodiniaceae and genus Symbiodinium
González-Pech RA, Stephens TG, Chen Y, Mohamed AR, Cheng Y, Shah S, Dougan KE, Fortuin MDA, Lagorce R, Burt DW, Bhattacharya D, Ragan MA, Chan CX
2021. BMC Biology • 19: 73. • DOIPubMedPDF


Genomic adaptations to an endolithic lifestyle in the coral-associated alga Ostreobium
Iha C, Dougan KE, Varela JA, Avila V, Jackson CJ, Bogaert KA, Chen Y, Judd LM, Wick R, Holt KE, Pasella MM, Ricci F, Repetti SI, Medina M, Marcelino VR, Chan CX, Verbruggen H
2021. Current Biology • 31(7): 1393-1402 • DOIPubMed



Dual RNA-seq analyses of a coral and its native symbiont during the establishment of symbiosis
Mohamed AR, Andrade N, Moya A, Chan CX, Negri A, Bourne DG, Ying H, Ball EE, Miller DJ
2020. Molecular Ecology • 29: 3921-3937. • DOIPubMed


Comparative transcriptomic analyses of Chromera and Symbiodiniaceae
Mohamed AR, Chan CX, Ragan MA, Zhang J, Cooke I, Ball EE, Miller DJ
2020. Environmental Microbiology Reports • 12: 435-443. • DOIPubMedPDF


Sex in Symbiodiniaceae dinoflagellates: genomic evidence for independent loss of the canonical synaptonemal complex
Shah S, Chen Y, Bhattacharya D, Chan CX
2020. Scientific Reports • 10: 9792. DOIPubMedPDF

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  • IMB News: Algae use distinct method when swapping DNA during sex

      Genomes of the dinoflagellate Polarella glacialis encode tandemly repeated single-exon genes with adaptive functions
      Stephens TG, González-Pech RA, Cheng Y, Mohamed AR, Burt DW, Bhattacharya D, Ragan MA, Chan CX
      2020. BMC Biology • 18: 56. DOIPubMedPDF

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      • IMB News: Algae use distinct method when swapping DNA during sex

          Evidence that inconsistent gene prediction can mislead analysis of dinoflagellate genomes
          Chen Y, González-Pech RA, Stephens TG, Bhattacharya D, Chan CX
          2020. Journal of Phycology • 56: 6-10. DOIPubMedPDFData Site



          A genomic view of the reef-building coral Porites lutea and its microbial symbionts
          Robbins SJ, Singleton CM, Chan CX, Messer LF, Geers AU, Ying H, Baker A, Bell SC, Morrow KM, Ragan MA, Miller DJ, Forêt S, ReFuGe2020 Consortium, Voolstra CR, Tyson GW, Bourne DG
          2019. Nature Microbiology • 4: 2090-2100. • DOIPubMedPDFData Site

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          • UQ News: Scientists decode DNA of coral and all its microscopic supporters
          • IMB News: Genetics of coral a key to saving reefs from climate change
          • Nature Microbiology Community – Behind the Paper: A genomic view of a coral holobiont
          • Cosmos Magazine: Corals need a lot of help from their friends
          • United Press International: DNA analysis details relationships between coral, algae and bacteria
          • Sci-News: Researchers sequence genomes of reef-building coral and its microbial symbionts


            Benchmarking of alignment-free sequence comparison methods
            Zielezinski A, Girgis HZ, Bernard G, Leimeister CA, Tang K, Dencker T, Lau AK, Röhling S, Choi J, Waterman MS, Comin M, Kim SH, Vinga S, Almeida JS, Chan CX, James BT, Sun F, Morgenstern B, Karlowski WM
            2019. Genome Biology • 20: 144. • DOIPubMedPDFAFproject site


            Analysis of an improved Cyanophora paradoxa genome assembly
            Price DC, Goodenough UW, Roth R, Lee JH, Kariyawasam T, Mutwil M, Ferrari C, Facchinelli F, Ball SG, Cenci U, Chan CX, Wagner NE, Yoon HS, Weber APM, Bhattacharya D
            2019. DNA Research • 26: 287-299. • DOIPubMedPDF


            Genome evolution of coral reef symbionts as intracellular residents
            González-Pech RA, Bhattacharya D, Ragan MA, ChanCX
            2019. Trends in Ecology & Evolution • 34: 799-806 • DOIPubMedPublisherPDF (accepted manuscript)

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            • UQ News: Understanding relationship break-ups to protect the reef
            • IMB News: Coral and algae relationship the key to understanding bleaching
            • United Press: Better understanding of coral-algae relationship could help prevent bleaching
            • Brisbane Times: Good relationships under the sea could hold key to coral bleaching
            • Sydney Morning Herald: Good relationships under the sea could hold key to coral bleaching
            • Space Daily: Better understanding of coral-algae relationship could help prevent bleaching

              Molecular techniques and their limitations shape our view of the holobiont
              Cooke I, Mead O, Whalen C, Boote C, Moya A, Ying H, Robbins S, Strugnell JM, Darling A, Miller DJ, Voolstra CR, Adamska M, Consortium of Australian Academy of Science Boden Research Conference Participants
              2019. Zoology • 137: 125695 • DOIPubMedPDF



              Resolving structure and function of metaorganisms through a holistic framework combining reductionist and integrative approaches
              Jaspers C, Fraune S, Arnold AE, Miller DJ, Bosch TCG, Voolstra CR, Consortium of Australian Academy of Science Boden Research Conference Participants
              2019. Zoology • 133: 81-87 • DOIPubMedPDF



              Commonly misunderstood parameters of NCBI BLAST and important considerations for users
              González-Pech RA, Stephens TG, Chan CX
              2019. Bioinformatics • 35: 2697-2698. DOIPubMedPDF (accepted manuscript)



              Alignment-free inference of hierarchical and reticulate phylogenomic relationships
              Bernard G, Chan CX, Chan YB, Chua XY, Cong Y, Hogan JM, Maetschke SR, Ragan MA
              2019. Briefings in Bioinformatics • 20: 426-435. • DOIPubMedPDF




              Core genes in diverse dinoflagellate lineages include a wealth of conserved dark genes with unknown functions
              Stephens TG, Ragan MA, Bhattacharya D, Chan CX
              Scientific Reports • 8: 17175. • DOIPubMedPDF



              k-mer similarity, networks of microbial genomes and taxonomic rank
              Bernard G, Greenfield P, Ragan MA, Chan CX
              mSystems • 3: e00257-18. • DOIPubMedPDFSupplemental Site



              Symbiodinium genomes reveal adaptive evolution of functions related to coral-dinoflagellate symbiosis
              Liu H, Stephens TG, González-Pech RA, Beltran VH, Lapeyre B, Bongaerts P, Cooke I, Aranda M, Bourne DG, Forêt S, Miller DJ, van Oppen MJH, Voolstra CR, Ragan MA, Chan CX
              2018. Communications Biology • 1: 95. • DOIPubMedPDFBehind-the-Paper


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              Featured in IMB 2018 year in review


              Analysis of the draft genome of the red seaweed Gracilariopsis chorda provides insights into genome size evolution in Rhodophyta
              Lee J, Yang EC, Graf L, Yang JH, Qiu H, Zelzion U, Chan CX, Stephens TG, Weber APM, Boo GH, Boo SM, Kim KM, Shin Y, Jung M, Lee SJ, Yim HS, Lee JY, Bhattacharya D, Yoon HS
              2018. Molecular Biology and Evolution • 35: 1869-1886. • DOIPubMedPDF



              Active host response to algal symbionts in the sea slug Elysia chlorotica
              Chan CX, Vaysberg P, Price DC, Pelletreau KN, Rumpho ME, Bhattacharya D
              2018. Molecular Biology and Evolution • 35: 1706-1711. • DOIPubMedFull textPDFNational Geographic FeatureVideo Feature



              Plastid phylogenomics with broad taxon sampling further elucidates the distinct evolutionary origins and timing of secondary green plastids
              Jackson C, Knoll AH, Chan CX, Verbruggen H
              2018. Scientific Reports • 8: 1523. • DOIPubMedPDF



              Deciphering the nature of the coral-Chromera association
              Mohamed AR, Cumbo V, Harii S, Shinzato C, Chan CX, Ragan MA, Satoh N, Ball EE, Miller DJ
              2018. ISME Journal • 12: 776–790. • DOIPubMedPDFFeature



              Selection of reference genes for transcript profiling of Sargassum polycystum by quantitative Real-Time Polymerase Chain Reaction
              Sim MC, Chan CX, Ho CL, Phang SM
              2018. Phycological Research • 66: 247–252. • DOIPDF


              Signatures of adaptation and symbiosis in genomes and transcriptomes of Symbiodinium
              González-Pech RA, Ragan MA, Chan CX
              2017. Scientific Reports • 7: 15021. • DOIPubMedPDF



              Biotic interactions as drivers of algal origin and evolution
              Brodie J, Ball SG, Bouget FY, Chan CX, De Clerck O, Cock JM, Gachon C, Grossman AR, Mock T, Raven JA, Saha M, Smith AG, Vardi A, Yoon HS, Bhattacharya D
              2017. New Phytologist • 216(3): 670-681 • DOIPubMedPDF



              Insights into the red algae and eukaryotic evolution from the genome of Porphyra umbilicalis (Bangiophyceae, Rhodophyta)
              Brawley SH, Blouin NA, Ficko-Blean E, Wheeler GL, Lohr M, Goodson HV, Jenkins JW, Blaby-Haas CE, Helliwell KE, Chan CX, Marriage TN, Bhattacharya D, Klein AS, Badis Y, Brodie J, Cao Y, Collén J, Dittami SM, Gachon CMM, Green BR, Karpowicz SJ, Kim JW, Kudahl UJ, Lin S, Michel G, Mittag M, Olson BJSC, Pangilinan JL, Peng Y, Qiu H, Shu S, Singer JT, Smith AG, Sprecher BN, Wagner V, Wang W, Wang ZY, Yan J, Yarish C, Zäuner-Riek S, Zhuang Y, Zou Y, Lindquist EA, Grimwood J, Barry KW, Rokhsar DS, Schmutz J, Stiller JW, Grossman AR, Prochnik SE
              2017. Proceedings of the National Academy of Sciences USA • 114(31): E6361-E6370. • DOIPubMedPDFFeature



              The algal revolution
              Brodie J, Chan CX, De Clerck O, Cock JM, Coelho SM, Gachon C, Grossman AR, Mock T, Raven JA, Smith AG, Yoon HS, Bhattacharya D
              2017. Trends in Plant Science • 22(8): 726-738. • DOIPubMedPublisherPDF




              Recapitulating phylogenies using k-mers: from trees to networks [version 2; referees: 2 approved]
              Bernard G, Ragan MA, Chan CX
              2016. F1000Research • 5: 2789. • DOIPDFNetwork



              The transcriptomic response of the coral Acropora digitifera to a competent Symbiodinium strain: the symbiosome as an arrested early phagosome
              Mohamed AR, Cumbo V, Harii S, Shinzato C, Chan CX, Ragan MA, Bourne DG, Willis BL, Ball EE, Satoh N, Miller DJ
              2016. Molecular Ecology • 25(13): 3127–3141. • DOIPubMedPDF



              Alignment-free microbial phylogenomics under scenarios of sequence divergence, genome rearrangement and lateral genetic transfer
              Bernard G, Chan CX, Ragan MA
              2016. Scientific Reports 6: 28970. • DOIPubMed • PDF



              PhySortR: a fast, flexible tool for sorting phylogenetic trees in R
              Stephens TG, Bhattacharya D, Ragan MA, Chan CX
              2016. PeerJ 4: e2038. • DOIPubMedPDFSoftware




              The ReFuGe 2020 consortium – using ‘omics’ approaches to explore the adaptability and resilience of coral holobionts to environmental change
              Voolstra CR, Miller DJ, Ragan MA, Hoffmann A, Hoegh-Guldberg O, Bourne D, Ball E, Ying H, Forêt S, Takahashi S, Weynberg KD, van Oppen MJ, Morrow K, Chan CX, Rosic N, Leggat W, Sprungala S, Imelfort M, Tyson GW, Kassahn K, Lundgren P, Beeden R, Ravasi T, Berumen M, Abel E, Fyffe T
              2015. Frontiers in Marine Science 2: 68. • DOIPDF




              Inferring phylogenies of evolving sequences without multiple sequence alignment
              Chan CX, Bernard G, Poirion O, Hogan JM, Ragan MA
              2014. Scientific Reports 4: 6504. • DOIPubMedPDFSoftware



              Molecular phylogenetics before sequences: oligonucleotide catalogs as k-mer spectra
              Ragan MA, Bernard G, Chan CX
              2014. RNA Biology 11(3): 176-185. • DOIPubMedPDF



              A new species of Burkholderia isolated from sugarcane roots promotes plant growth
              Paungfoo-Lonhienne C, Lonhienne T, Yeoh YK, Webb RI, Lakshmanan P, Chan CX, Lim PE, Ragan MA, Schmidt S, Hugenholtz P
              2014. Microbial Biotechnology 7(2): 142-154. • DOIPubMedPDF




              Analysis of horizontal genetic transfer in red algae in the post-genomics age
              Chan CX, Bhattacharya D
              2013. Mobile Genetic Elements 3(6): e27669 • DOIPubMedPDF
              Online 2 Jan 2014



              Foreign gene recruitment to the fatty acid biosynthesis pathway in diatoms
              Chan CX, Baglivi FL, Jenkins CE, Bhattacharya D
              2013. Mobile Genetic Elements 3(5): e27313 • DOIPubMedPDF
              Online 10 Dec 2013



              Biological intuition in alignment-free methods: response to Posada
              Ragan MA, Chan CX
              2013. Journal of Molecular Evolution 77(1-2): 1-2 • DOIPubMedPDF


              Evidence for widespread exonic small RNAs in the glaucophyte alga Cyanophora paradoxa
              Gross J, Wajid S, Price DC, Zelzion E, Li J, Chan CX, Bhattacharya D
              2013. PLoS ONE 8(7): e67669 • DOIPubMedPDF



              Genome of the red alga Porphyridium purpureum
              Bhattacharya D, Price DC, Chan CX, Qiu H, Rose N, Ball S, Weber APM, Arias MC, Henrissat B, Coutinho PM, Krishnan A, Zäuner S, Morath S, Hilliou F, Egizi A, Perrineau MM, Yoon HS
              2013. Nature Communications 4: 1941 • DOIPubMedPDF
              ISI Highly Cited



              Clustering evolving proteins into homologous families
              Chan CX, Mahbob M, Ragan MA
              2013. BMC Bioinformatics 14: 120 • DOIPubMedPDF



              Next-generation phylogenomics
              Chan CX, Ragan MA
              2013. Biology Direct 8: 3. • DOIPubMedPDF



              Phylogenomics of marine algae
              Chan CX
              2013. Malaysian Journal of Science 32 (SCS Special Issue): 11-18. • wwwPDF


              Porphyra (Bangiophyceae) transcriptomes provide insights into red algal development and metabolism
              Chan CX, Blouin NA, Zhuang Y, Zäuner S, Prochnik SE, Lindquist E, Lin S, Benning C, Lohr M, Yarish C, Gantt E, Grossman AR, Lu S, Müller K, Stiller J, Brawley SH, Bhattacharya D
              2012. Journal of Phycology 48(6): 1328-1342 • DOIPDFData Site



              Analysis of Alexandrium tamarense (Dinophyceae) genes reveals the complex evolutionary history of a microbial eukaryote
              Chan CX, Soares MB, Bonaldo MF, Wisecaver JH, Hackett JD, Anderson DM, Erdner DL, Bhattacharya D
              2012. Journal of Phycology 48(5): 1130-1142 • DOIPubMedPDFSupp Info



              Major developmental regulators and their expression in two closely related species of Porphyra (Rhodophyta)
              Stiller JW, Perry J, Rymarquis LA, Accerbi M, Green PJ, Prochnik S, Lindquist E, Chan CX, Yarish C, Lin S, Zhuang Y, Blouin NA, Brawley SH
              2012. Journal of Phycology 48(4): 883-896 • DOIPubMedPDF


              Endosymbiotic and horizontal gene transfer in microbial eukaryotes: impacts on cell evolution and the tree of life
              Chan CX, Bhattacharya D, Reyes-Prieto A
              2012. Mobile Genetic Elements 2(2): 101-105 • DOIPubMedPDF



              Analysis of Porphyra membrane transporters demonstrates gene transfer among photosynthetic eukaryotes and numerous sodium-coupled transport systems
              Chan CX, Zäuner S, Wheeler GL, Grossman AR, Prochnik SE, Blouin NA, Zhuang Y, Benning C, Berg GM, Yarish C, Eriksen RL, Klein AS, Lin S, Levine I, Brawley SH, Bhattacharya D
              2012. Plant Physiology 158(4): 2001-2012 • DOIPubMedPDFSupp Info


              Cyanophora paradoxa genome elucidates origin of photosynthesis in algae and plants
              Price DC, Chan CX, Yoon HS, Yang EC, Qiu H, Weber AP, Schwacke R, Gross J, Blouin NA, Lane C, Reyes-Prieto A, Durnford DG, Neilson JAD, Lang BF, Burger G, Steiner JM, Löffelhardt W, Meuser JE, Posewitz MC, Ball S, Arias MC, Henrissat B, Coutinho PM, Rensing SA, Symeonidi A, Doddapaneni H, Green BR, Rajah VD, Boore J, Bhattacharya D
              2012. Science 335(6070): 843-847 • DOIPubMedPDFData Site




              Red and green algal origin of diatom membrane transporters: insights into environmental adaptation and cell evolution
              Chan CX, Reyes-Prieto A, Bhattacharya D
              2011. PLoS ONE 6(12): e29138 • DOIPubMedPDFSupp Info


              Lateral transfer of genes and gene fragments in Staphylococcus extends beyond mobile elements
              Chan CX, Beiko RG, Ragan MA
              2011. Journal of Bacteriology 193(15): 3964-3977 • DOIPubMedPDFData Site



              Non-random sharing of Plantae genes
              Chan CX, Bhattacharya D
              2011. Communicative and Integrative Biology 4(3): 361-363 • DOIPubMedPDF

              Plastid origin and evolution: new models provide insights into old problems
              Chan CX, Gross J, Yoon HS, Bhattacharya D
              2011. Plant Physiology 155(4): 1552-1560 • DOIPubMedPDF



              Red and green algal monophyly and extensive gene sharing found in a rich repertoire of red algal genes
              Chan CX, Yang EC, Banerjee T, Yoon HS, Martone PT, Estevez JM, Bhattacharya D
              2011. Current Biology 21(4): 328-333 • DOIPubMedPDFSupp Info




              Lateral transfer of genes and gene fragments in prokaryotes
              Chan CX, Beiko RG, Darling AE, Ragan MA
              2009. Genome Biology and Evolution 1:429-438 • DOIPubMedPDF


              Are protein domains modules of lateral genetic transfer?
              Chan CX, Darling AE, Beiko RG, Ragan MA
              2009. PLoS ONE 4(2): e4524. • DOIPubMedPDF



              A two-phase strategy for detecting recombination in nucleotide sequences
              Chan CX, Beiko RG, Ragan MA
              2007. South African Computer Journal 38: 20-27 • linkPDF


              Detecting recombination in evolving nucleotide sequences
              Chan CX, Beiko RG, Ragan MA
              2006. BMC Bioinformatics 7:412 • DOIPubMedPDF


              Trends in seaweed research
              Chan CX, Ho CL, Phang SM
              2006. Trends in Plant Science 11(4): 165-166 • DOIPubMedPDF



              A word-oriented approach to alignment validation
              Beiko RG, Chan CX, Ragan MA
              2005. Bioinformatics 21(10): 2230-2239 • DOIPubMedPDFSoftware


              Seaweed diversity of the Langkawi Islands with emphasis on the northeastern region
              Phang SM, Wong CL, Lim PE, Yeong HY, Chan CX
              2005. Malaysian Journal of Science 24 (Langkawi Special Issue): 77-94 • linkPDF


              Comparing different approaches in large-scale seaweed gene discovery
              Chan CX
              2004. Bioinformatics India 2(3): 106-111 • PDF

              Optimisation of RNA extraction from Gracilaria changii (Gracilariales, Rhodophyta)
              Chan CX, Teo SS, Ho CL, Othman RY, Phang SM
              2004. Journal of Applied Phycology 16(4): 297-301 • DOIPDF