Preprints+



Select preprint articles

2022

18
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

 

17
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

 

16
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

 

15
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

 


2021

14
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

 

13
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

 

2020

12
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

 

11
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

 

2019

10
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

 

9
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

 

8
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

 

7
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

 

6
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


 

5
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


 

4
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


 

2017

3
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

 

2
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

 

 

2015

1
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

2015

9
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

8
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

7
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

2013

6
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

2012

5
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

4
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

2008

3
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

 

2
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

2007

1
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

2011

2
Plastid origin and evolution
Chan CX, Bhattacharya D
In: Encyclopedia of Life Sciences (eLS)
2011. John Wiley & Sons, Ltd, Chichester http://www.els.net/ DOI:10.1002/9780470015902.a0023639PDF

2010

1
The origin of plastids
Chan CX, Bhattacharya D
Nature Education 3(9):84. • WebPDF