Journal articles


Commonly misunderstood parameters of NCBI BLAST and important considerations for users
González-Pech RA, Stephens TG, Chan CX
Bioinformatics • bty1018 • online 12 December 2018 • DOIPDF (accepted manuscript)


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

Video Feature

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


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
2017. Briefings in Bioinformatics • bbx067 • online 30 June 2017 • DOIPubMedPDF


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 • DOIPubMedPDF