Senjie Lin

(Ph.D., SUNY Stony Brook) Professor of Marine Sciences

The primary focus of my research is molecular ecology/functional genomics of dinoflagellates and other marine phytoplankton (microalgae). Current research can be summarized as: 1) genomics and functional genetics in dinoflagellates; 2) nutrient (especially P) physiology in phytoplankton; 3) proton-pump rhodopsin in dinoflagellates as potential solar energy harnessing mechanism; 4) phylogeny and evolution of dinoflagellates; 5) ecology of harmful algae; and 6) DNA barcoding and phytoplankton biodiversity.

The second focus of my research is symbioses (e.g. coral-dinoflagellate, Noctiluca-green alga, protist-alga). We take genomic approach to study how host/symbiont specificity (or plasticity) and symbiosis is regulated, and to provide insights into how coral bleaching is triggered and how bleached corals may be restored.

In addition, we use DNA barcoding technology to study biodiversity in the ocean and in animals (diet) or on organisms (epibiotic). For instance, we have developed PCR-based techniques for analyses of diets of wild-caught copepods, which have revealed surprising diet compositions.

Open Resources developed

To facilitate updates and further analyses of genomic and environmental omics data, we have developed Symbiodiniaceae and Algae Genomic Resource (SAGER) platform that houses updated genomic data and analysis tools allowing download, BLAST, keyword search, and genome browsing.

Research Projects

Screening strains to establish a transformation system for dinoflagellates-The Gordon and Betty Moore Foundation

Moving from transformation to CRISPR/Cas9 gene knockout for dinoflagellates

Analysis of Phytoplankton in Long Island Sound – CT DEEP

Dinoflagellate bloom mechanism by genomic approach

Oceanography Student

Lingjie Zhou – Ph.D. Student

Felipe Porto– Ph. D. student

Oceanography Alumni

Batta Lona – M.Sc. 2005

Timothy Feinstein – M.Sc. 2002

Christina Haska – M.Sc. 2008

Yubo Hou – Ph.D. 2008

Lilibeth Miranda – Ph.D. 2009

Chiu-Yen (Rita) Kuo – Ph.D. 2012

Yunyun Zhuang – Ph.D. 2013

Brittany Sprecher – Ph.D. 2020

Many visiting Ph. D. students and scholars

Courses Taught

MARN4010/5010 Biological Oceanography (Spring)

MARN5015/3015 Molecular Approaches to Biological Oceanography (Fall in odd number years)

MARN5014 Algae and the Environment (formerly Marine Phytoplankton Ecology and Physiology; Fall in even number years)

MARN5830 Seminar in (Molecular) Oceanography (Spring in odd years)

MARN6010 Advanced Biological Oceanography-Pelagic Processes (Fall in even number years)

MARN6012 Marine Genomics (Spring in even number years)

MARN4001 Measurement and Analysis in Coastal Ecosystems (Fall)

MARN1002 Introduction to Oceanography (Spring)


Representative peer-reviewed publications (out of 210; for the full list or more information about his research check Google Scholar, ResearchGate, or

Lin, S. 2023. Phosphate limitation and ocean acidification co-shape phytoplankton physiology and community structure. Nature Communications 14: 2699.

You, Y., Sun, X., Ma, M., He, J., Li, L., Porto, F. and Lin, S. 2022. Trypsin is a coordinate regulator of N and P nutrients in marine phytoplankton. Nature Communications 13: 4022. Doi: 10.1038/s41467-022-31802-6

Zhang, K., Wang, J., Li, Jia, Lin, X., Li, L., Wu, X., You, Y. and Lin, S. 2022. Functional differentiation and complementation of alkaline phosphatases and choreography of DOP scavenging in a marine diatom. Molecular Ecology 31: 3389-3399. Doi: 10.1111.mec.16475.

Saad, O. S., Lin, X., Ng, T. Y., Li, L., Ang, P. and Lin, S. 2021. Underappreciated species richness and generalists-specialists mosaicism of symbiodiniacean symbionts in Hong Kong marginal coral community. Coral Reefs doi: 10.1007/s00338-021-02196-6.

Faktorova, D., Nisbet, R. E., Robledo, J. A. F,….Lin, S.,…, Sprecher, B., Wang, L. Zhang, H.….2020. Genetic tool development in marine protists: Emerging model organisms for experimental cell biology. Nature Methods

Sprecher, B. N., Zhang, H. and Lin, S. 2020. Nuclear gene transformation in a dinoflagellate. Microorganisms 18(1):126. Preprint published in BioRxiv,

Li, T., Chen, X. and Lin, S. 2020. Physiological and transcriptomic responses to N-deficiency and ammonium: nitrate shift in Fugacium kawagutii (Symbiodiniaceae). Science of the Total Environment 753: 141906.

Liu, C., Cheng, B. H. and Lin, S. 2020. Illuminating the dark depths inside coral. Cellular Microbiology 22(1):e13122. doi: 10.1111/cmi.13122. (Cover article)

Zhang, Y., Lin, X., Shi, X., Lin, L.-X., Luo, H., Li, L. and Lin, S. 2019. Metatranscriptomic signatures associated with regime shift from diatom dominance to a dinoflagellate bloom. Frontiers in Microbiology 10: 590. doi:10.3389/fmicb.2019.00590

Tang, J., Ni, X., Zhou Z., Wang, L. and Lin, S. 2018. Acute microplastic exposure raises stress response and suppresses detoxification and immune capabilities in the scleractinian coral Pocillopora damicornis. Environmental Pollution 243: 66-74.

Mendoza, A., Bonnet, A., Vargas-Landin, D. B., Ji, N., Li, H., Yang, F., Li, L., Hori, K., Pflueger, J., Buckberry, S., Ohta, H., Rosic, N., Lesage, P., Lin, S. and Lister, R. 2018. Recurrent acquisition of cytosine methyltransferases into eukaryotic retrotransposons. Nature Communications 9: 1342. doi: 10.1038/s41467-018-03724-9.

Brawley, S., Blouin, N. A., Ficko-Blean, E. … Lin, S., …Sprecher, B. N.,…, Prochnid, S. E.  2017. Insights into the red algae and eukaryotic evolution from the genome of Porphyra umbilicalis (Bangiophyceae, Rhodophyta). Proc. Natl. Acad. Sci. USA 114: E6361-6370. doi/10.1073/pnas.1703088114

Shi, X., Lin, X., Li, L., Li, M., Palenik, B. and Lin, S. 2017. Transcriptomic and microRNAomic profiling reveals multi-faceted mechanisms to cope with phosphate stress in a dinoflagellate. ISME J. 11: 2209-2218. doi:10.1038/ismej.2017.81

Qiu, D., Huang, L. and Lin, S. 2016. Crytophyte farming by symbiotic ciliate host detected in situ. Proc. Natl. Acad. Sci. USA 113: 12208-12213. Doi: 10.1073/pnas.1612483113.

Lin, S., Cheng, S., Song, B., Zhong, X., Lin, X. et al. 2015. The genome of Symbiodinium kawagutii illuminates dinoflagellate gene expression and coral symbiosis. Science 359: 691-694. [PDF][Abstract][Full Text]

Dierssen, H. M., McManus, G., Chlus, A., Qiu, D., Gao, B.-C. and Lin, S. 2015. Space station image captures a red tide ciliate bloom at high spectral and spatial resolution. Proc. Natl. Acad. Sci. USA 48: 14783-14787.

Lin, S., Litaker, R. W. and Sunda, W. 2015. Phosphorus physiological ecology and molecular mechanisms in marine phytoplankton. (Invited Review). J. Phycol. doi: 10.111/jpy.12365.

Shi, X. Li, L., Guo, C., Lin, X., Li, M. and Lin, S. 2015. Rhodopsin gene expression regulated by light dark cycle, light spectrum and light intensity in the dinoflagellate Prorocentrum. Front. Microbiol. 6: article 555. doi: 10.3389/fmicb.2015.00555

Wang, L., Zhuang, Y., Zhang, H., Lin, X. and Lin, S. 2014. DNA barcoding species in Alexandrium tamarense complex using ITS and proposing designation of five species. Harmful Algae 31: 100-113.

Lin, S. 2011. Genomic understanding of dinoflagellates. Res. Microbiol. (invited review). 165: 551-569.

Lin, S., Zhang, H., Zhuang, Y., Bao, T. and Gill, J. 2010. Spliced leader-based metatranscriptomic analyses lead to recognition of hidden genomic features in dinoflagellates. Proc. Natl. Acad. Sci. USA 107: 20033-20038.

Zhang, H., Hou, Y., Miranda, L., Campbell, D. A., Sturm, N. R., Gaasterland, T. and Lin, S. 2007. Spliced leader RNA trans-splicing in dinoflagellates. Proc. Natl. Acad. Sci. USA 104: 4618-4623.

Bio10-Senjie Lin
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