Select preprint articles


Chromosomal inversions harbour excess mutational load in the coral, Acropora kenti, on the Great Barrier Reef
Zhang J, Schneller NM, Field MA, Chan CX, Miller DJ, Strugnell JM, Riginos C, Bay L, Cooke IR
2024. bioRxiv 2024.02.19.580031. • DOIPDF


Genome-wide transcriptome analysis reveals the diversity and function of long non-coding RNAs in dinoflagellates
Chen Y, Dougan KE, Nguyen Q, Bhattacharya D, Chan CX
2023. bioRxiv 2023.06.27.546665. • DOIPDF


In vivo structure probing of RNA in Archaea: Novel insights into the ribosome structure of Methanosarcina acetivorans
Williams AM, Jolley E, Santiago-Martinez MG, Chan CX, Gutell R, Ferry JG, Bevilacqua PC
2023. bioRxiv 2023.04.14.536875. • DOIPDF


Intraspecies genomic divergence of coral algal symbionts shaped by gene duplication
Shah S, Dougan KE, Chen Y, Bhattacharya D, Chan CX
2023. bioRxiv 2023.03.28.534646. • DOIPDF


Massive genome reduction occurred prior to the origin of coral algal symbionts
Shah S, Dougan KE, Chen Y, Lo R, Laird G, Fortuin MDA, Rai SK, Murigneux V, Bellantuono AJ, Rodriguez-Lanetty M, Bhattacharya D, Chan CX
2023. bioRxiv 2023.03.24.534093. • DOIPDF



Multi-omics analysis reveals the molecular response to heat stress in a “red tide” dinoflagellate
Dougan KE, Deng ZL, Woehlbrand L, Reuse C, Bunk B, Chen Y, Hartlich J, Hiller K, John U, Kalvelage J, Mansky J, Neumann-Schaal M, Overmann J, Petersen J, Sanchez-Garcia S, Schmidt-Hohagen K, Shah S, Sproer C, Sztajer H, Wang H, Bhattacharya D, Rabus R, Jahn D, Chan CX, Wagner-Doebler I
2022. bioRxiv 2022.07.25.501386. • DOIPDF


Improved Cladocopium goreaui genome assembly reveals features of a facultative coral symbiont and the complex evolutionary history of dinoflagellate genes
Chen Y, Shah S, Dougan KE, van Oppen MJH, Bhattacharya D, Chan CX
2022. bioRxiv 2022.07.19.500725. • DOIPDF


Building consensus around the assessment and interpretation of Symbiodiniaceae diversity
Davies S, Gamache MH, Howe-Kerr LI, Kriefall NG, Baker AC, Banaszak AT, Bay LK, Bellantuono AJ, Bhattacharya D, Chan CX, Claar DC, Coffroth MA, Cunning R, Davy SK, del Campo J, Diaz-Almeyda EM, Frommlet JC, Fuess LE, Gonzalez-Pech RA, Goulet TL, Hoadley KD, Howells EJ, Hume BCC, Kemp DW, Kenkel CD, Kitchen SA, LaJeunesse TC, Lin S, McIlroy S, McMinds R, Nitschke MR, Oakley CA, Peixoto RS, Prada C, Putnam HM, Quigley K, Reich HG, Reimer JD, Rodriguez-Lanetty M, Rosalas S, Saad OS, Sampayo EM, Santos S, Shoguchi E, Smith EG, Stat M, Stephens TG, Strader ME, Suggett DJ, Swain TD, Tran C, Traylor-Knowles N, Voolstra CR, Warner ME, Weis VM, Wright R, Xiang T, Yamashita H, Ziegler M, Correa AM, Parkinson JE
2022. Preprints 2022060284. • DOIPDF


Whole-genome duplication in an algal symbiont serendipitously confers thermal tolerance to corals
Dougan KE, Bellantuono AJ, Kahlke T, Abbriano RM, Chen Y, Shah S, Granados-Cifuentes C, van Oppen MJH, Bhattacharya D, Suggett DJ, Chan CX, Rodriguez-Lanetty M
2022. bioRxiv doi:10.1101/2022.04.10.487810 • DOIPDF


Evolutionary responses of a reef-building coral to climate change at the end of the last glacial maximum
Zhang J, Richards ZT, Adam AAS, Chan CX, Shinzato C, Gilmour J, Thomas L, Strugnell JM, Miller DJ, Cooke I
2022. bioRxiv doi:10.1101/2022.04.02.486852 • DOIPDF


Transcriptome of the coralline alga Calliarthron tuberculosum (Corallinales, Rhodophyta) reveals convergent evolution of a partial lignin biosynthesis pathway
Xue JY, Hind K, Lemay MA, Mcminigal A, Jourdain E, Chan CX, Martone PT
2022. bioRxiv doi:10.1101/2022.03.30.486440 • DOIPDF



Tightly constrained genome reduction and relaxation of purifying selection during secondary plastid endosymbiosis
Uthanumallian K, Iha C, Repetti SI, Chan CX, Bhattacharya D, Duchene S, Verbruggen H
2021. bioRxiv doi:10.1101/2021.05.27.446077 • DOIPDF


Nuclear genome of a pedinophyte pinpoints genomic innovation and streamlining in the green algae
Repetti SI, Iha C, Uthanumallian K, Jackson CJ, Chen Y, Chan CX, Verbruggen H
2021. bioRxiv doi:10.1101/2021.10.04.463119 • DOIPDF



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, Chen Y, Basso LC, Frazzon J, Chan CX, Gross J
2020. bioRxiv doi:10.1101/2020.12.15.422965 • DOIPDF


Genomic adaptations to an endolithic lifestyle in the coral-associated alga Ostreobium
Iha C, Varela JA, Avila V, Jackson CJ, Bogaert KA, Chen Y, Judd LM, Wick RR, Holt KE, Pasella MM, Ricci F, Repetti SI, Medina M, Marcelino VR, Chan CX, Verbruggen H
2020. bioRxiv doi:10.1101/2020.07.21.211367 • DOIPDF



Close relationships between coral-associated Chromera strains despite differences within the Symbiodiniaceae
Mohamed AR, Chan CX, Ragan MA, Zhang J, Cooke I, Ball E, Miller DJ
2019. bioRxiv doi:10.1101/825992 • DOIPDF


Genomes of Symbiodiniaceae reveal extensive sequence divergence but conserved functions at family and genus levels
González-Pech RA, Chen Y, Stephens TG, Shah S, Mohamed AR, Lagorce R, Bhattacharya D, Ragan MA, Chan CX
2019. bioRxiv doi:10.1101/800482 • DOIPDF


Structural rearrangements drive extensive genome divergence between symbiotic and free-living Symbiodinium
González-Pech RA, Stephens TG, Chen Y, Mohamed AR, Cheng Y, Burt DW, Bhattacharya D, Ragan MA, Chan CX
2019. bioRxiv doi:10.1101/783902 • DOIPDF


Polarella glacialis genomes encode tandem repeats of single-exon genes with functions critical to adaptation of dinoflagellates
Stephens TG, González-Pech RA, Cheng Y, Mohamed AR, Bhattacharya D, Ragan MA, Chan CX
2019. bioRxiv doi:10.1101/704437 • DOIPDF


Evidence that inconsistent gene prediction can mislead analysis of algal genomes
Chen Y, González-Pech RA, Stephens TG, Bhattacharya D, Chan CX
2019. bioRxiv doi:10.1101/690040 • DOIPDF


Transcriptomic insights into the establishment of coral-algal symbioses from the symbiont perspective
Mohamed AR, Andrade N, Moya A, Chan CX, Negri AP, Bourne DG, Ball EE, Miller DJ
2019. bioRxiv doi:10.1101/652131 • DOIPDF


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. bioRxiv doi:10.1101/611137 • DOIPDFAFproject Website



Symbiodinium genomes reveal adaptive evolution of functions related to symbiosis
Liu H, Stephens TG, González-Pech RA, Beltran VH, Lapeyre B, Bongaerts P, Cooke I, Bourne DG, Forêt S, Miller DJ, van Oppen MJH, Voolstra CR, Ragan MA, Chan CX
2017. bioRxiv doi:10.1101/198762 • DOIPDF


k-mer similarity, networks of microbial genomes and taxonomic rank
Bernard G, Greenfield P, Ragan MA, Chan CX
2017. bioRxiv doi:10.1101/125237 • DOIPDF




PhySortR: a fast, flexible tool for sorting phylogenetic trees in R
Stephens TG, Bhattacharya D, Ragan MA, Chan CX
2015. PeerJ PrePrints 3:e1609v1. • DOIPDF



Full conference papers/abstracts


Genome analysis of two Symbiodinium isolates
Chan CX, Stephens TG, Ling EYS, Forêt S, Morrow K, Bourne DG, Voolstra CR, Leggat W, Miller DJ, Ragan MA
2015. European Journal of Phycology 50 (S1): 57-58
Proceedings of the 6th European Phycological CongressDOIPDF

Scalable phylogenomic approaches to study algal evolution
Chan CX, Bernard G, Chalmers BDB, Ragan MA
2015. European Journal of Phycology 50 (S1): 150
Proceedings of the 6th European Phycological CongressDOIPDF

Analysis of Symbiodinium genomes reveals remarkable divergence
Chan CX, Stephens TG, Forêt S, Morrow K, Bourne DG, Voolstra CR, Leggat W, Miller DJ, Ragan MA
2015. Proceedings of Annual Meeting of Phycological Society of America p57 • Book PDF


The Cyanophora genome: analysis of gene and small RNA content in a pivotal algal lineage
Bhattacharya D, Gross J, Price DC, Chan CX, Zelzion U
2013. Phycologia 52 (sp4): 10-11
Proceedings of the 10th International Phycological CongressDOIIssue PDF


Recent advances in the Calliarthron genome: climate responses and cell wall evolution
Chan CX, Martone PT
2012. Journal of Phycology 48: S1-S2
Proceedings of the Annual Meeting of the Phycological Society of AmericaDOIIssue PDF

sRNAs of Cyanophora paradoxa and Chlamydomonas reinhardtii, a system genomics approach to understand algal evolution
Gross J, Wajid S, Price D, Chan CX, Bhattacharya D
2012. Journal of Phycology 48: S20
Proceedings of the Annual Meeting of the Phycological Society of AmericaDOIIssue PDF


A phylogenomic approach for studying plastid endosymbiosis
Moustafa A*, Chan CX*, Danforth M, Zear D, Ahmed H, Jadhav N, Savage T, Bhattacharya D (*equal contribution)
2008. Genome Informatics 21: 165-176 • PubMedPDF


Large-scale detection of recombination in nucleotide sequences
Chan CX, Beiko RG, Ragan MA
2008. AIP Conference Proceedings 971(1): 101-104
Proceedings of the International Conference on Mathematical BiologyDOIPDF


A two-phase approach for detecting recombination in nucleotide sequences
Chan CX, Beiko RG, Ragan MA
2007. Proceedings of the 1st Southern African Bioinformatics Workshop pp. 9-16. • RepositoryPDF


Other peer-reviewed articles


Plastid origin and evolution
Chan CX, Bhattacharya D
In: Encyclopedia of Life Sciences (eLS)
2011. John Wiley & Sons, Ltd, Chichester DOI:10.1002/9780470015902.a0023639PDF


The origin of plastids
Chan CX, Bhattacharya D
Nature Education 3(9):84. • WebPDF