Senjie Lin

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) gene regulation 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, 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 molecular techniques to study trophic relationships (food web structure) in incubation-free fashion (in situ). For instance, we have developed PCR-based techniques for analyses of diets of wild-caught copepods, which have revealed surprising diet compositions.

Research Projects

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

Analysis of Phytoplankton in Long Island Sound – CT DEEP

Dinoflagellate bloom mechanism by genomic approach

Oceanography Student

Brittany Sprecher – Ph.D. Student

Lingjie Zhou – Ph.D. Student

Oceanography Alumni

Paola Batta Lona – M.Sc. 2005

Timothy Feinstein – M.Sc. 2007

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

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)

MARN1002 Introduction to Oceanography (Spring)

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

Qiu, D., Lin, L. and Lin, S. 2017. Reply to Johnson et al.: Functionally active cryptophyte cell membrane and cytoplasm indicate intact symbionts within Mesodinium Proc. Natl. Acad. Sci. USA Doi: 10.1073/pnas.1620409114.

Qiu, D., Huang, L. and Lin, S. 2016. Crytophyte farming by symbiotic ciliate host detected in situ. Proc. Natl. Acad. Sci. USA 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.

Lin, X., Shi, X., Wang, L. and Lin, S. 2015. Rapidly diverging evolution of an atypical alkaline phosphatase (PhoAaty) in marine phytoplankton: insights from dinoflagellate alkaline phosphatases. Front. Microbiol. 6: article 868. doi: 10.3389/fmicb.2015.00868

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

Hu, S., Guo, Z., Li, T., Xu, C, Huang, H., Liu, S. and Lin, S. 2015. Molecular analysis of in situ diets of coral reef copepods: evidence of terrestrial plant detritus as food source in Sanya Bay, China. J. Plankton Res. 37(2): 1-9.

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, 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.

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., 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.