Senjie Lin

Ph. D. opportunity available to study dinoflagellates using CRISPR/Cas9 and other technologies. Motivated and passionate students with experience in relevant techniques are welcome to apply.

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

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

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 (for full list check

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., …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., 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 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.

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

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.