Journal articles

2019

55
Evidence that inconsistent gene prediction can mislead analysis of dinoflagellate genomes
Chen Y, González-Pech RA, Stephens TG, Bhattacharya D, Chan CX
Journal of Phycology, online 12 November 2019. DOIPubMedPDFData Site

 

54
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, online 23 September 2019. • DOIPubMedPDFData Site

    Featured in:
  • 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

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    53
    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

     

    52
    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

     

    51
    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)

      Featured in:
    • UQ News: Understanding relationship break-ups to protect the reef
    • IMB News: Genomic data helping unlock secrets behind coral 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
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      50
      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)

       

       

      49
      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

       

       

      2018

      48
      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

       

       

      47
      k-mer similarity, networks of microbial genomes and taxonomic rank
      Bernard G, Greenfield P, Ragan MA, Chan CX
      mSystems • 3: e00257-18. • DOIPubMedPDFSupplemental Site

       

       

      46
      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

       

      Video Feature

      Featured in IMB 2018 year in review

       

      45
      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

       

       

      44
      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

       

       

      43
      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

       

       

      42
      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

       

       

      41
      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
       


      2017

      40
      Signatures of adaptation and symbiosis in genomes and transcriptomes of Symbiodinium
      González-Pech RA, Ragan MA, Chan CX
      2017. Scientific Reports • 7: 15021. • DOIPubMedPDF

       

       

      39
      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

       

       

      38
      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

       

       

      37
      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

       

       


      2016

      36
      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

       

       

      35
      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

       

       

      34
      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

       

       

      33
      PhySortR: a fast, flexible tool for sorting phylogenetic trees in R
      Stephens TG, Bhattacharya D, Ragan MA, Chan CX
      2016. PeerJ 4: e2038. • DOIPubMedPDFSoftware

       

       


      2015

      32
      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

       

       


      2014

      31
      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

       

       

      30
      Molecular phylogenetics before sequences: oligonucleotide catalogs as k-mer spectra
      Ragan MA, Bernard G, Chan CX
      2014. RNA Biology 11(3): 176-185. • DOIPubMedPDF

       

       

      29
      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

       

       


      2013

      28
      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

       

       

      27
      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

       

       

      26
      Biological intuition in alignment-free methods: response to Posada
      Ragan MA, Chan CX
      2013. Journal of Molecular Evolution 77(1-2): 1-2 • DOIPubMedPDF

       

      25
      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

       

       

      24
      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

       

       

      23
      Clustering evolving proteins into homologous families
      Chan CX, Mahbob M, Ragan MA
      2013. BMC Bioinformatics 14: 120 • DOIPubMedPDF

       

       

      22
      Next-generation phylogenomics
      Chan CX, Ragan MA
      2013. Biology Direct 8: 3. • DOIPubMedPDF

       

       

      21
      Phylogenomics of marine algae
      Chan CX
      2013. Malaysian Journal of Science 32 (SCS Special Issue): 11-18. • wwwPDF
       


      2012

      20
      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

       

       

      19
      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

       

       

      18
      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

       

      17
      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

       

       

      16
      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

       

      15
      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

       

       


      2011

      14
      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

       

      13
      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

       

       

      12
      Non-random sharing of Plantae genes
      Chan CX, Bhattacharya D
      2011. Communicative and Integrative Biology 4(3): 361-363 • DOIPubMedPDF
       

      11
      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

       

       

      10
      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

       

       


      2009

      9
      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

       

      8
      Are protein domains modules of lateral genetic transfer?
      Chan CX, Darling AE, Beiko RG, Ragan MA
      2009. PLoS ONE 4(2): e4524. • DOIPubMedPDF

       


      2007

      7
      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
       


      2006

      6
      Detecting recombination in evolving nucleotide sequences
      Chan CX, Beiko RG, Ragan MA
      2006. BMC Bioinformatics 7:412 • DOIPubMedPDF

       

      5
      Trends in seaweed research
      Chan CX, Ho CL, Phang SM
      2006. Trends in Plant Science 11(4): 165-166 • DOIPubMedPDF

       


      2005

      4
      A word-oriented approach to alignment validation
      Beiko RG, Chan CX, Ragan MA
      2005. Bioinformatics 21(10): 2230-2239 • DOIPubMedPDFSoftware

       

      3
      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
       


      2004

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

      1
      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