Timothy Stephens

I am a computational biologist working on understanding the forces that govern the interactions between organisms in ecologically critical environments, such as coral reefs, and the forces that drive major evolutionary transitions, such as the one that gave rise to the first photosynthetic Eukaryotas. I am also CTO of OceanOmics, a company dedicated to developing salable tools for environmental health monitoring.

Undergraduate

• 11:115:423 | Fundamentals of Microbial Genomics (313k PDF)

Graduate

• 16:682:534 | Fundamentals of Genomics (311k PDF)

• Van Etten J., Stephens T. G., and Bhattacharya D. Genetic transfer in action: uncovering DNA flow in an extremophilic microbial community. Environmental Microbiology, 2025. 10.1111/1462-2920.70048
• Stephens T. G., Van Etten J., McDermott T., Christian W., Chaverra M., Gurney J., Lee Y., Kim H., Hyun Cho C., Chovancek E., Westhoff P., Otte A., Northen T. R., Bowen B. P., Louie K. B., Barry K., Grigoriev I. V., Mock T., Liu S., Miyagishima S., Yoshinaga M, Weber A. P.M., Yoon H. S., and Bhattacharya D. Temporal dynamics in a red alga dominated geothermal feature in Yellowstone National Park. ISME Communications, 4:1, 2024. 10.1093/ismeco/ycae151
• Boyd J. M, Kaler K. R., Esquilin-Lebron K., Pall A., Campbell C. J., Foley M. E., Rios- Delgado G., Mustor E. M., Stephens T. G., Bovermann H., Greco T. M., Cristea I. M., Carabetta V. J., Beavers W. N., Bhattacharya D., Skaar E. P., Shaw L. N., Stemmler T. L. Fpa (YlaN) is an iron(II) binding protein that functions to relieve Fur-mediated repression of gene expression in Staphylococcus aureus. mBio, 2024. 10.1128/mbio.02310-24
• Calatrava V.*, Stephens T. G.*, Grossman A. R., and Bhattacharya D. What has Paulinella taught us about endosymbiont metabolic integration?. Schwartzbach, S.D., Kroth, P.G., Obornik, M. (eds) Endosymbiotic Organelle Acquisition. Springer, Cham., 2024. *Co-first authorship 10.1007/978-3-031-57446-7_12
• Chille E. E., Stephens T. G., Misri D., Strand E. L, Putnam H. M., and Bhattacharya D. Gene expression response under thermal stress in two Hawaiian corals is dominated by ploidy and genotype. Ecology and Evolution, 14:e70037, 2024. 10.1002/ece3.70037
• Gabr A., Stephens T. G., Reinfelder J. R., Liau P., Calatrava V., Grossman A. R., and Bhattacharya D. Evidence of a putative CO2 delivery system to the chromatophore in the photosynthetic amoeba Paulinella. Environmental Microbiology Reports, e13304, 2024. 10.1111/1758-2229.13304
• Etten J. V., Stephens T. G., Chille E., Lipzen A., Peterson D., Barry K., Grigoriev I. V., and Bhattacharya D. Diverse fates of ancient horizontal gene transfers in extremophilic red algae. Environmental Microbiology, 26(5):e16629, 2024. 10.1111/1462-2920.16629
• Benites L. F., Stephens T. G., Etten J. V., James T., Christian W. C., Barry K., Grigoriev I. V., McDermott T. R. & Bhattacharya D. Viruses associated with extremophilic red algal mats reveal signatures of early thermal adaptation. Communications Biology, 2024. 10.1038/s42003-024-05931-1
• Bhattacharya D., Stephens T. G., Chille E. E., Benites L. F., Chan C. X. Facultative lifestyle drives diversity of coral algal symbionts. Trends in Ecology and Evolution, 39(3):239-247, 2023. 10.1016/j.tree.2023.10.005
• *Williams A., *Stephens T. G., Shumaker A., and Bhattacharya D. Peeling back the layers of coral holobiont multi-omics data. iScience, 26(9):107623, 2023. *Co-first authorship 10.1016/j.isci.2023.107623
• Stephens T. G., Strand E. L., Putnam H. M., and Bhattacharya D. Ploidy variation and its implications for reproduction and population dynamics in two sympatric Hawaiian coral species. Genome Biology and Evolution, evad149, 2023. 10.1093/gbe/evad149
• Etten J. V, Stephens T. G., and Bhattacharya D. A k-mer-based approach for inferring phylogenetic relatedness of environmental genomic data. Systems Biology, syad037, 2023. 10.1093/sysbio/syad037
• Etten J. V., Benites F. L., Stephens T. G., Yoon H. S., and Bhattacharya D. Algae obscura: The potential of rare species as model systems. Journal of Phycology, 59(2):293-300, 2023. 10.1111/jpy.13321
• Stephens T. G., Lee J., Jeong Y., Yoon H. S., Putnam H. M., Majerova E., and Bhattacharya D. High-quality genome assemblies from key Hawaiian coral species. GigaScience, 11:giac098, 2022. 10.1093/gigascience/giac098
• Benites L. F., Stephens T. G., and Bhattacharya D. Multiple waves of viral invasions in Symbiodiniaceae algal genomes. Virus Evolution, 8:veac101, 2022. 10.1093/ve/veac101
• Bhattacharya D., Etten J. V., Benites L. F., and Stephens T. G. Endosymbiotic ratchet accelerates divergence after organelle origin. BioEssays, e2200165, 2022. 10.1002/bies.202200165
• *Gabr A., *Stephens T. G., and Bhattacharya D. Loss of key endosymbiont genes may facilitate early host control of the chromatophore in Paulinella. iScience, 25:104974, 2022. *Co-first authorship 10.1016/j.isci.2022.104974
• Meng Z., Williams A., Liau P., Stephens T. G., Drury C., Chiles E. N., Su X., Javanmard M., and Bhattacharya D. Development of a portable toolkit to diagnose coral thermal stress. Scientific Reports, 12:14398, 2022. 10.1038/s41598-022-18653-3
• Bhattacharya D., Stephens T. G., Tinoco A., Richmond R., and Cleves P. A. Life on the edge: Hawaiian model for coral evolution. Limnology and Oceanography, 67:1976-1985, 2022. 10.1002/lno.1218
• *Calatreva V., *Stephens T. G., Gabr A., Grossman A. R., and Bhattacharya D. Retrotransposition facilitated the establishment of a primary plastid in the thecate amoeba Paulinella. PNAS, 119:e2121241119, 2022. *Co-first authorship 10.1073/pnas.2121241119
• *Gabr A., *Stephens T. G., and Bhattacharya D. Hypothesis: Trans-splicing generates evolutionary novelty in the photosynthetic amoeba Paulinella. Journal of Phycology, 58:392- 405, 2022. *Co-first authorship 10.1111/jpy.13247
• Dougan K. E., Gonzalez-Pech R. A., Stephens T. G., Shah S., Chen Y., Ragan M. A., Bhattacharya D., and Chan C. X. Genome-powered classification of microbial eukaryotes: focus on coral algal symbionts. Trends in Microbiology, 30:831-840, 2022. 10.1016/j.tim.2022.02.001
• Gabr A., Zournas A., Stephens T. G., Dismukes G., and Bhattacharya D. Evidence for a robust photosystem II in the photosynthetic amoeba Paulinella. New Phytologist, 234:934-945, 2022. 10.1111/nph.18052
• Williams A., Pathmanathan J. S., Stephens T. G., Su X., Chiles E. N., Conetta D., Putnam H. M., and Bhattacharya D. Multi-omic characterization of the thermal stress phenome in the stony coral Montipora capitata. PeerJ, 9:e12335, 2021. 10.7717/peerj.12335
• Stephens T. G., Gabr A., Calatreva V., Grossman A. R., and Bhattacharya D. Why is primary endosymbiosis so rare?. New Phytologist, 231:1693-1699, 2021. 10.1111/nph.17478
• Bernard G., Stephens T. G., Gonzalez-Pech R. A., and Chan C. X. Inferring phylogenomic relationship of microbes using scalable alignment-free methods. Methods in Molecular Biology, 2242:69-76, 2021. 10.1007/978-1-0716-1099-2_5
• 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. Comparative genomics supports that Brazilian bioethanol Saccharomyces cerevisiae comprise a unified group of domesticated strains related to cachaca spirit yeasts. Frontiers in Microbiology, 12:644089, 2021. 10.3389/fmicb.2021.644089
• 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. Comparison of 15 dinoflagellate genomes reveals extensive sequence and structural divergence in family Symbiodiniaceae and genus Symbiodinium. BMC Biology, 0.842361111, 2021. 10.1186/s12915-021-00994-6
• 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. Amoeba genome reveals dominant host contribution to plastid endosymbiosis. Molecular Biology and Evolution, 38:344-357, 2020. 10.1093/molbev/msaa206
• Stephens T. G., Gonzalez-Pech R. A., Cheng Y., Mohamed A. R., Burt D. W., Bhattacharya D., Ragan M. A., and Chan C. X. Genomes of the dinoflagellate Polarella glacialis encode tandemly repeated single-exon genes with adaptive functions. BMC Biology, 18:56, 2020. 10.1186/s12915-020-00782-8
• Chen Y., Gonzalez-Pech R. A., Stephens T. G., Bhattacharya D., and Chan C. X. Evidence that inconsistent gene prediction can mislead analysis of dinoflagellate genomes. Journal of Phycology, 56:6-10, 2019. 10.1111/jpy.12947
• *Gonzalez-Pech R. A., *Stephens T. G., and Chan C. X. Commonly misunderstood parameters of NCBI BLAST and important considerations for users. Bioinformatics, 35:2697- 6998, 2018. *Co-first authorship 10.1093/bioinformatics/bty1018
• Stephens T. G., Ragan M. A., Bhattacharya D., and Chan C. X. Core genes in diverse dinoflagellate lineages include a wealth of conserved dark genes with unknown functions. Scientific Reports, 8:17175, 2018. 10.1038/s41598-018-35620-z
• 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. Symbiodinium genomes reveal adaptive evolution of functions related to coral-dinoflagellate symbiosis. Communications Biology, 0.107638889, 2018. 10.1038/s42003-018-0098-3
• 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. Analysis of the draft genome of the red seaweed Gracilariopsis chorda provides insights into genome size evolution in Rhodophyta. Molecular Biology and Evolution, 35:1869-1886, 2018. 10.1093/molbev/msy081
• Stephens T. G., Bhattacharya D., Ragan M. A., and Chan C. X. PhySortR: a fast, flexible tool for sorting phylogenetic trees in R. PeerJ, 4:e2038, 2016. 10.7717/peerj.2038