Journal articles

In Press

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
Nature Microbiology, accepted 5 July 2019.



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
DNA Research • online 16 May 2019 • 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 • DOIPubMedFull Text Access

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    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
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    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