Journal articles


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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  • Cosmos Magazine: Corals need a lot of help from their friends
  • United Press International: DNA analysis details relationships between coral, algae and bacteria
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    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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    • 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 D, 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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      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