Conference proceedings+



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


 

Select preprint articles

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
bioRxiv 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
bioRxiv 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
bioRxiv 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
bioRxiv 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
bioRxiv 690040. (version 2, 22 July 2019)• 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
bioRxiv 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
bioRxiv 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
bioRxiv 198762. • DOIPDF

 

2
k-mer similarity, networks of microbial genomes and taxonomic rank
Bernard G, Greenfield P, Ragan MA, Chan CX
bioRxiv 125237. • DOIPDF

 

 

2015

1
PhySortR: a fast, flexible tool for sorting phylogenetic trees in R
Stephens TG, Bhattacharya D, Ragan MA, Chan CX
PeerJ PrePrints 3:e1609v1. • DOIPDF