Senjie Lin

University of Connecticut Department of Marine Sciences
1080 Shennecossett Road Groton, CT 06340
Phone: (860) 405-9168
Fax: (860) 405-9153

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) transcriptomics and genomics of dinoflagellates to understand gene regulation in dinoflagellates; 2) molecular markers for studying phytoplankton nutrient (especially P) metabolism and growth rate in situ; 3) relationships and evolutionary trends of dinoflagellates and their important traits; 3) harmful algae; and 4) interactions between microalgae and other microbes.

The second focus of my research is microalgae for biofuel. We search for most promising candidate species (robust, fast growing, high lipid content) and cheap ways (e.g. wastewater) to grow for feedstock, investigate genetic regulatory network of lipid synthesis, and explore the potential of genetic manipulation to enhance lipid production in algae. 

In addition, we study the interaction between grazer and phytoplankton (and macroalgae). In particular, we are studying  zooplankton diet diversity in the natural environment.


Research Projects

EAGER-Investigate a novel way of light harvesting by marine phytoplankton: proton-pump rhodopsin in dinoflagellates. - National Science Foundation

Collaborative Research: Costs and Advantages of a novel sodium channel mutation in copepods” (PI: Hans G. Dam) - National Science Foundation

AToL (Assemling the Tree of Life): An integrated approach to phylogeny of dinoflagellates - National Science Foundation

Analysis of Phytoplankton in Long Island Sound - CT DEP

Oceanography Alumni

Timothy Feinstein - M.Sc. 2007
Christina Haska - M.Sc. 2008
Yubo Hou - Ph.D. 2008
Chiu-Yen (Rita) Kuo - Ph.D. 2012
Lilibeth Miranda - Ph.D. 2009
Yunyun Zhuang - Ph.D. 2013

Courses Taught

MARN4010/5010 Biological Oceanography (Spring)

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

MARN5014 Marine Phytoplankton Ecology and Physiology (Fall in even number years)

MARN5898 Special Topics-Marine Genomics (Spring in even number years)

MARN4001 Measurement and Analysis in Coastal Ecosystems (Fall)


Honors Received

1. Elected member of Connecticut Academy of Science and Engineering (2010-).

2. Qualified nominee for the Cronin ‘Early in Career Estuarine Scientist’ Award of Estuarine Research Federation (1997).

3. Don Pritchard Best Dissertation Award, MSRC, SUNY Stony Brook (1996).



Representative peer-reviewed publications in the last five years


Lin, X., Zhang, H., Cui, Y. and Lin, S. 2012. High sequence variability, diverse subcellular localizations, and ecological implications of alkaline phosphatase in dinoflagellates and other eukaryotic phytoplankton. Frontiers Aquat. Micorbiol. (in press).


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


Lin, X., Zhang, H., Huang, B. and Lin, S. 2011. Alkaline phosphatase gene sequence and transcriptional regulation by phosphate limitation in Amphidinium carterae (dinophyceae). J. Phycol. 47: 1110-1120.


Zhang, H., Dungan, C. F. and Lin, S. 2011. Introns, alternative splicing, spliced leader trans-splicing and differential expression of pcna and cyclin in Perkinsus marinus. Protist 162: 154-167.


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.


Hou, Y., Zhang, H., Miranda, L. and Lin, S. 2010. Serious overestimation in quantitative PCR by circular (supercoiled) plasmid standard: microalgal pcna as the model gene. PLoS ONE 5(3): e9545. 


Hou, Y. and Lin, S. 2009. Distinct gene number-genome size relationships for eukaryotes and non-eukaryotes: gene content estimation for dinoflagellate genomes. PLoS ONE 4(9): e6978. doi 10.1371/journal.pone.0006978.


Lin, S., Zhang, H., Hou, Y., Zhuang, Y. and Miranda, L. 2009. High-level diversity of dinoflagellates in the natural environment, revealed by assessment of mitochondrial cox1 and cob for dinoflagellate DNA barcoding. Appl. Environ. Microbiol. 75: 1279-1290.


Lin, S., Zhang, H. and Gray, M. W. 2008. RNA editing in dinoflagellates and its implications for the evolutionary history of the editing machinery. In: H. Smith (ed.), RNA and DNA editing: Molecular Mechanisms and Their Integration into Biological Systems. John Wiley & Sons, Inc. p280-309.


Zhang, H., Litaker, W., Vandersea, M. W., Tester, P. and Lin, S. 2008. Geographic distribution of Karlodinium veneficum in the US east coast as detected by dual-gene Real-Time PCR assay. J. Plankton Res. 30: 905-922.


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.

Zhang, H., Bhattacharya, D. and Lin, S. 2007.
A three-gene dinoflagellate phylogeny suggests monophyly of Prorocentrales and a basal position for Amphidinium and Heterocapsa  J. Mol. Evol. 65: 463-474.