Publications
2024
33. What has Paulinella taught us about endosymbiont metabolic integration?
Calatrava V.*, Stephens T. G.*, Grossman A. R., and Bhattacharya D. Schwartzbach, S.D., Kroth, P.G., Obornik, M. (eds) Endosymbiotic Organelle Acquisition. Springer, Cham., 2024.
[URL]
32. Gene expression response under thermal stress in two Hawaiian corals is dominated by ploidy and genotype
Chille E. E., Stephens T. G., Misri D., Strand E. L, Putnam H. M., and Bhattacharya D. Ecology and Evolution, 14:e70037, 2024.
[URL]
31. Evidence of a putative CO2 delivery system to the chromatophore in the photosynthetic amoeba Paulinella
Gabr A., Stephens T. G., Reinfelder J. R., Liau P., Calatrava V., Grossman A. R., and Bhattacharya D. Environmental Microbiology Reports, e13304, 2024.
[URL]
30. Diverse fates of ancient horizontal gene transfers in extremophilic red algae
Etten J. V., Stephens T. G., Chille E., Lipzen A., Peterson D., Barry K., Grigoriev I. V., and Bhattacharya D. Environmental Microbiology, 26(5):e16629, 2024.
[URL]
29. Viruses associated with extremophilic red algal mats reveal signatures of early thermal adaptation
Benites L. F., Stephens T. G., Etten J. V., James T., Christian W. C., Barry K., Grigoriev I. V., McDermott T. R. & Bhattacharya D. Communications Biology, 2024.
2023
28. Facultative lifestyle drives diversity of coral algal symbionts
Bhattacharya D., Stephens T. G., Chille E. E., Benites L. F., Chan C. X. Trends in Ecology and Evolution, 39(3):239-247, 2023.
[URL]
27. Peeling back the layers of coral holobiont multi-omics data
*Williams A., *Stephens T. G., Shumaker A., and Bhattacharya D. iScience, 26(9):107623, 2023.
[URL]
26. Ploidy variation and its implications for reproduction and population dynamics in two sympatric Hawaiian coral species
Stephens T. G., Strand E. L., Putnam H. M., and Bhattacharya D. Genome Biology and Evolution, evad149, 2023.
25. A k-mer-based approach for inferring phylogenetic relatedness of environmental genomic data
Etten J. V, Stephens T. G., and Bhattacharya D. Systems Biology, syad037, 2023.
[URL]
Won the Publisher’s Award for Excellence in Systematic Research
24. Algae obscura: The potential of rare species as model systems
Etten J. V., Benites F. L., Stephens T. G., Yoon H. S., and Bhattacharya D. Journal of Phycology, 59(2):293-300, 2023.
[URL]
2022
23. High-quality genome assemblies from key Hawaiian coral species
Stephens T. G., Lee J., Jeong Y., Yoon H. S., Putnam H. M., Majerova E., and Bhattacharya D. GigaScience, 11:giac098, 2022.
[URL]
22. Multiple waves of viral invasions in Symbiodiniaceae algal genomes
Benites L. F., Stephens T. G., and Bhattacharya D. Virus Evolution, 8:veac101, 2022.
21. Endosymbiotic ratchet accelerates divergence after organelle origin
Bhattacharya D., Etten J. V., Benites L. F., and Stephens T. G. BioEssays, e2200165, 2022.
[URL]
20. Loss of key endosymbiont genes may facilitate early host control of the chromatophore in Paulinella
*Gabr A., *Stephens T. G., and Bhattacharya D. iScience, 25:104974, 2022.
[URL]
*Co-first authorship
19. Development of a portable toolkit to diagnose coral thermal stress
Meng Z., Williams A., Liau P., Stephens T. G., Drury C., Chiles E. N., Su X., Javanmard M., and Bhattacharya D. Scientific Reports, 12:14398, 2022.
[URL]
18. Life on the edge: Hawaiian model for coral evolution
Bhattacharya D., Stephens T. G., Tinoco A., Richmond R., and Cleves P. A. Limnology and Oceanography, 67:1976-1985, 2022.
[URL]
17. Retrotransposition facilitated the establishment of a primary plastid in the thecate amoeba Paulinella
*Calatreva V., *Stephens T. G., Gabr A., Grossman A. R., and Bhattacharya D. PNAS, 119:e2121241119, 2022.
[URL]
*Co-first authorship
16. Hypothesis: Trans-splicing generates evolutionary novelty in the photosynthetic amoeba Paulinella
*Gabr A., *Stephens T. G., and Bhattacharya D. Journal of Phycology, 58:392-405, 2022.
[URL]
*Co-first authorship
15. Genome-powered classification of microbial eukaryotes: focus on coral algal symbionts
Dougan K. E., Gonzalez-Pech R. A., Stephens T. G., Shah S., Chen Y., Ragan M. A., Bhattacharya D., and Chan C. X. Trends in Microbiology, 30:831-840, 2022.
[URL]
14. Evidence for a robust photosystem II in the photosynthetic amoeba Paulinella
Gabr A., Zournas A., Stephens T. G., Dismukes G., and Bhattacharya D. New Phytologist, 234:934-945, 2022.
[URL]
2021
13. Multi-omic characterization of the thermal stress phenome in the stony coral Montipora capitata
Williams A., Pathmanathan J. S., Stephens T. G., Su X., Chiles E. N., Conetta D., Putnam H. M., and Bhattacharya D. PeerJ, 9:e12335, 2021.
[URL] [Preprint]
Featured by PeerJ Expert Curations: Molecular Ecology: PeerJ Expert Curations, PeerJ Blog
12. Why is primary endosymbiosis so rare?
Stephens T. G., Gabr A., Calatreva V., Grossman A. R., and Bhattacharya D. New Phytologist, 231:1693-1699, 2021.
[URL]
11. Inferring phylogenomic relationship of microbes using scalable alignment-free methods
Bernard G., Stephens T. G., Gonzalez-Pech R. A., and Chan C. X. Methods in Molecular Biology, 2242:69-76, 2021.
[URL]
10. Comparative genomics supports that Brazilian bioethanol Saccharomyces cerevisiae comprise a unified group of domesticated strains related to cachaca spirit yeasts
Jacobus A. P., Stephens T. G., Youssef P., Gonzalez-Pech R., Ciccotosto-Camp M. M., Dougan K. E., Chen Y., Basso L. C., Frazzon J., Chan C. X., and Gross J. Frontiers in Microbiology, 12:644089, 2021.
9. Comparison of 15 dinoflagellate genomes reveals extensive sequence and structural divergence in family Symbiodiniaceae and genus Symbiodinium
Gonzalez-Pech, R. A., Stephens T. G., Chen Y., Mohamed A. R., Cheng Y., Shah S., Dougan K. E., Fortuin M. D. A., Lagorce R., Burt D. W., Bhattacharya D., Ragan M. A., and Chan C. X. BMC Biology, 0.842361111, 2021.
2020
8. Amoeba genome reveals dominant host contribution to plastid endosymbiosis
Lhee D., Lee J., Ettahi K., Cho C. H., Ha J., Chan Y., Zelzion U., Stephens T. G., Price D. C., Gabr A., Nowack E. C. M., Bhattacharya D., and Yoon H. S. Molecular Biology and Evolution, 38:344-357, 2020.
[URL]
7. Genomes of the dinoflagellate Polarella glacialis encode tandemly repeated single-exon genes with adaptive functions
Stephens T. G., Gonzalez-Pech R. A., Cheng Y., Mohamed A. R., Burt D. W., Bhattacharya D., Ragan M. A., and Chan C. X. BMC Biology, 18:56, 2020.
[URL] [Preprint]
Featured in: IMB News: Algae use distinct method when swapping DNA during sex
2019
6. Evidence that inconsistent gene prediction can mislead analysis of dinoflagellate genomes
Chen Y., Gonzalez-Pech R. A., Stephens T. G., Bhattacharya D., and Chan C. X. Journal of Phycology, 56:6-10, 2019.
2018
5. Commonly misunderstood parameters of NCBI BLAST and important considerations for users
*Gonzalez-Pech R. A., *Stephens T. G., and Chan C. X. Bioinformatics, 35:2697-6998, 2018.
[URL]
*Co-first authorship [F1000 recommended]
4. Core genes in diverse dinoflagellate lineages include a wealth of conserved dark genes with unknown functions
Stephens T. G., Ragan M. A., Bhattacharya D., and Chan C. X. Scientific Reports, 8:17175, 2018.
[URL]
3. Symbiodinium genomes reveal adaptive evolution of functions related to coral-dinoflagellate symbiosis
Liu H., Stephens T. G., Gonzalez-Pech R. A., Beltran V. H., Lapeyre B., Bongaerts P., Cooke I., Aranda M., Bourne D. G., Foret S., Miller D. J., van Oppen M. J. H., Voolstra C. R., Ragan M.A., and Chan C.X. Communications Biology, 0.107638889, 2018.
[URL] [Preprint]
Featured in:
- IMB News: Unlocking genetic secrets to help save the Great Barrier Reef
- GBRF: Decoding the Reef leads to world first. Unlocking genetic secrets of coral symbiosis to preserve iconic Great Barrier Reef
- Video Feature
- Featured in IMB 2018 year in review
2. Analysis of the draft genome of the red seaweed Gracilariopsis chorda provides insights into genome size evolution in Rhodophyta
Lee J, Yang E. C., Graf L., Yang J. H., Qiu H., Zelzion U., Chan C. X., Stephens T. G., Weber A. P. M., Boo G. H., Boo S. M., Kim K. M., Shin Y., Jung M., Lee S. J., Yim H. S., Lee J. Y., Bhattacharya D., and Yoon H. S. Molecular Biology and Evolution, 35:1869-1886, 2018.
[URL]
2016
1. PhySortR: a fast, flexible tool for sorting phylogenetic trees in R
Stephens T. G., Bhattacharya D., Ragan M. A., and Chan C. X. PeerJ, 4:e2038, 2016.