Invited Bookchapters

  1. 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.
  2. Lin, S. and Carpenter, E. J. 1999. Molecular ecology of marine Phytoplankton: A practical procedure. In: Xu, H. and Colwell, R. R. (eds.) Proceedings of the International Symposium on Progress and Prospect of Marine Biotechnology (ISPPMB’98). China Ocean Press. 255-268.
  3. Carpenter, E. J., Lin, S. and Chang, J. 1998. Phytoplankton growth studies by cell Cycle analysis. In: K. E. Cooksey [Ed.] Some Molecular Approaches to the Study of the Ocean. Chapman & Hall. p227-245.


Journal articles

  1. 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.
  2. Zhang, X., Lin, S. and Liu, D. 2020. Transcriptomic and physiological responses of Skeletonema costatum to ATP utilization. Environ. Microbiol. https://Doi.10.111/1462-2920.14944
  3. Su, Y., Zhang, K., Zhou, Z., Wang, J., Yang, X., Tang, J., Li, H. and Lin, S. Microplastic exposure represses the growth of endosymbiotic dinoflagellate Cladocopium goreaui in culture through affecting its apoptosis and metabolism. Chemosphere 244: 125485.
  4. Wu, Z., Luo, H., Yu, L., Lee, W. H., Li, L., Mak, Y. L., Lin, S. and Lam, P, K. S. 2020. Characterizing ciguatoxin (CTX)- and non-CTX-producing strains of Gambierdiscus balechii using comparative transcriptomics. Science of Total Environment 717: 137184.
  5. Sprecher, B. N., Zhang, H. and Lin, S. Nuclear gene transformation in a dinoflagellate. Microorganisms 18(1):126. Preprint published in BioRxiv,
  6. Li, T., Yu, L., Song, B., Song, Y., Li, L., Lin, X. Lin, S. Genome improvement and core gene set refinement of Fugacium kawagutii. Microorganisms 8(1): 102.
  7. Ji, N., Huang, J., Zhang, Z., Zhou, L., Shen, X. and Lin, S. Identification and expression analysis of meiosis-related genes in the harmful alga Heterosigma akashiwo (Raphidophyceae). Harmful Algae
  8. Li, T., Lin, X., Yu, L., Lin, S., Rodriguez, I., and Ho, T.-Y. 2020. RNA-seq profiling of Fugacium kawagutii reveals strong responses in metabolic processes and symbiosis potential to deficiencies of iron and other trace metals. Science of the Total Environment 705: 135767. Doi:10.1016/j.scitotenv.2019.135767.
  9. Liu, C., Cheng, B. H. and Lin, S. 2020. Illuminating the dark depths inside coral. Microbiol. 22(1):e13122. doi: 10.1111/cmi.13122. (Cover paper)
  10. Yu, L., Zhang, Y., Li, M., Wang, C., Lin, X., Li, L., Shi, Xi, Guo, C. and Lin, S. Comparative metatranscriptomic profiling and microRNA sequencing to reveal active metabolic pathways associated with a dinoflagellate bloom. Science of the Total Environment 699: 134323.
  11. Pan, Y., Yang, J., McManus, G. B., Lin, S. and Zhang, W. 2019. Insights into protist diversity and biogeography in intertidal sediments sampled across a range of spatial scales. Oceanogr. doi: 10.1002/lno.11375.
  12. Lin, X., Guo, C., Li, L., Li, T. and Lin, S. Non-conventional metal ion cofactor requirement of dinoflagellate alkaline phosphatase and translational regulation by phosphorus limitation. Microorganisms 7: 232. doi:10.3390/microorganisms7080232.
  13. Qiu, D., Huang, L., Liu, X. and Lin, S. Flourishing deep-sea AAP bacteria detected by flow cytometric sorting and molecular analysis. PLoS ONE 14(6): e0218753.
  14. Lin, S., Yu, L. and Zhang, H. 2019. Transcriptomic responses to thermal stress and varied phosphorus conditions in Fugacium kawagutii. Microorganisms 74(4): 96.
  15. Zhou, Z., Zhao, S., Tang, J., Liu, Z., Wu, Y., Wang, Y. and Lin, S. Altered immune landscape and disrupted coral-Symbiodiniaceae symbiosis in the scleractinian coral Pocillopora damicornis by Vibrio coralliilyticus challenge. Front. Physiol. 10: 366. doi: 10.3389/phys2019.00366.
  16. Zhang, Y., Lin, X., Shi, X., Lin, L.-X., Luo, H., Li, L. and Lin, S. Metatranscriptomic signatures associated with regime shift from diatom dominance to a dinoflagellate bloom. Front. Microbiol. 10: 590. doi:10.3389/fmicb.2019.00590
  17. Li, H. and Lin, S. Research progresses of phytoplankton ecology in the South China Sea. Journal of Xiamen University (Natural Science) 58(1): 1-10. doi:10.6043/j.issn.0438-0479.20180503. (In Chinese with English abstract)
  18. Gomez, F., Wang, L. and Lin, S. Molecular phylogeny suggests the affinity of the planktonic diatoms Climacodiumand Bellerochea (Lithodesmidales, Mediophyceae). Diatom Res. 33(3): 349-354.
  19. Zhang, C and Lin, S. Initial evidence of functional siRNA machinery in dinoflagellates. Harmful Algae 81: 53-58.
  20. Pan, Y., Zhang, W. and Lin, S. Transcriptomic and microRNAomic profiling reveals molecular mechanisms to cope with silver nanoparticle exposure in the ciliate Euplotes vannus. Environ. Sci.: Nano. Doi: 10.1039/C8EN00924D
  21. Shi, X., Liu, L., Li, Y., Xiao, Y., Ding, G., Lin, S. and Chen J. 2018. Isolation of an algicidal bacterium and its effects against the harmful-algal-bloom dinoflagellate Prorocentrum donghaiense (Dinophyceae). Harmful Algae 80: 72-79.
  22. Wohlrab, S., Falcke, J., Lin, S., Zhang, H., Elferink, S., Neuhaus, S., Voss, D., Zielinski, O. and John, U. 2018. Metatranscriptome profiling indicates size-dependent differentiation in plastic and conserved community traits and functional diversification in dinoflagellate communities. Mar. Sci. 5: 358. Doi: 10.3389/fmars.2018.00358.
  23. Hou, Y., Ji, N., Zhang, H., Shi, X., Han, H. and Lin, S. Genome size-dependent PCNA gene copy number in dinoflagellates and molecular evidence of retroposition as a major evolutionary mechanism. J. Phycol. 55: 37-46.
  24. Li, T., Guo, C., Zhang, Y., Wang, C., Lin, X. and Lin, S. Identification and expression analysis of an atypical alkaline phosphatase in Emiliania huxleyi. Front. Microbiol. 9: 2156. Doi: 10.3389/fmicb.2018.02156.
  25. Tang, J., Ni, X., Zhou Z., Wang, L. and Lin, S. Acute microplastic exposure raises stress response and suppresses detoxification and immune capabilities in the scleractinian coral Pocillopora damicornis. Environ. Poll. 243: 66-74.
  26. Mo, Y., Zhang, W., Yang, J., Lin, Y., Yu, Z. and Lin, S. Biogeographic patterns of abundant and rare bacterioplankton in three subtropical bays resulting from selective and neutral processes. ISME J. 12: 2198-2210.
  27. Shi, X., Li, L. and Lin, S. Circadian and irradiance effects on expression of antenna protein genes and pigment contents in dinoflagellate Prorocentrum donghaiense (Dinophyceae). Harmful Algae 75: 27-34.
  28. 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 Comm. 9: 1342. Doi: 10.1038/s41467-018-03724-9.
  29. Gomez, F., Wang, L. and Lin, S. Morphology and molecular phylogeny of epizoic araphid diatoms on marine zooplankton, including Pseudofalcula hyalina gen. & comb. nov (Fragilariophyceae, Bacillariophyta). J. Phycol. 54(4): 557-570
  30. Gomez, F., Wang, L. and Lin, S. 2018. Morphology and molecular phylogeny of peritrich ciliate epibionts on pelagic diatoms: Vorticella oceanica and Pseudovorticella coscinodisci nov. (Ciliophora, Peritrichia). Protist 169: 268-279.
  31. Ji, N., Lin, L., Li, L., Yu, L., Zhang, Y., Luo, H., Li, M., Shi, X., Wang, D.-Z. and Lin, S. 2018. Metatranscriptome analysis reveals environmental and diel regulation of a Heterosigma akashiwo (Raphidophyceae) bloom. Microbiol. Doi:10.1111/1462-2920.14045.
  32. Jing, X., Lin, S., Zhang, H., Koerting, C. and Yu, Z. 2017. Utilization of urea and expression profiles of related genes in the dinoflagellte Prorocentrum donghaiense. PLoS ONE 13(1): e0191521.
  33. Wang, C., Lin, X., Li, L., Lin, L. and Lin, S. Glyphosate shapes a dinoflagellate-associated bacteria community while supporting algal growth as sole phosphorus source. Front. Microbiol. 8: 2530. Doi: 10.3389/fmicb.2017.02530.
  34. Augyte, S., Lewis, L., Lin, S., Neefus, C. D. and Yarish, C. 2017. Speciation in the exposed intertidal zone: the case of Saccharina angustisima Nov. & stat. nov. (Laminariales, Phaeophycae). Phycologia 57: 100-112.
  35. Gomez, F., Qiu, D. and Lin, S. The synonymy of the toxic dinoflagellate Prorocentrum mexicanum and P. rhathymum and the description of P. steidingerae sp. nov. (Prorocentrales, Dinophyceae). J. Euk. Microbiol. 64: 668-677.
  36. Zhang, W., Pan, Y., Yang, J., Chen, H., Holohan, B. and Vaudrey, J., Lin, S. and McManus, G. B. 2017. The diversity and biogeography of abundant and rare intertidal marine microeukaryotes explained by environment and dispersal limitation. Microbiol. Doi:10.1111/1462-2920.13916.
  37. Luo, H., Lin, X., Li, L., Lin, L., Zhang, C. and Lin, S. 2017 Transcriptomic and physiological analyses of the dinoflagellate Karenia mikimotoi reveal non-alkaline phosphatase-based molecular machinery of ATP utilization. Microbiol. 19: 4506-4518. Doi: 10.1111/1462-2920.13899.
  38. Song, B., Morse, D., Song, Y., Fu, Y., Lin, X., Wang, W., Cheng, S., Chen, W., Liu, X. and Lin, S. Comparative genomics reveals two major bouts of gene retroposition coinciding with crucial periods of Symbiodinium evolution. Genome Biol. Evol. 9(8): 2037-2047.
  39. Gomez, F., Qiu, D., Lopes, R. M. and Lin, S. Morphological and molecular characterization of the toxic dinoflagellate Ostreopsis cf. ovate (Gonyaulacales: Dinophyceae) from Brazil (South Atlantic Ocean). Rev. Biol. Trop.65: 1022-1032.
  40. 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). Natl. Acad. Sci. USA 114: E6361-6370. doi/10.1073/pnas.1703088114.
  41. Zhang, C., Luo, H., Huang, L. and Lin, S. Molecular mechanism of glucose-6-phosphate utilization in the dinoflagellate Karenia mikimotoi. Harmful Algae 67: 74-84.
  42. Shi, X., Ma, M. and Lin, S. 2017. Cell cycle-dependent expression dynamics of G1/S specific cyclin, cellulose synthase and cellulase in the dinoflagellate Prorocentrum donghaiense. Front. Microbiol. 8: 1118. doi: 10.3389/fmicb.2017.01118
  43. 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
  44. Kraemer, G., Yarish, C., Kim, J., Zhang, H. and Lin, S. 2017. Life history interactions between the red algae Chondrus crispus and Grateloupia tururu in a changing global environment. Phycologia 56: 176-185.
  45. Cui, Y., Zhang, H. and Lin, S. 2017. Enhancement of non-photochemical quenching as an adaptive strategy under phosphorus deprivation in the dinoflagellate Karlodinium veneficum. Front. Microbiol. 8: 404. Doi: 10.3389/fmicb.2017.00404.
  46. Gomez, F., Wang, L., Hernandez-Becerril, D. U., Liunova, Y. O., Lopes, R. M. and Lin, S. 2017. Molecular phylogeny suggests transfer of Hemidiscus into Actinocyclus (Coscinodiscales, Coscinodiscophyceae). Diatom Res. 32: 21-28.
  47. 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.
  48. Ji, N., Li, L., Lin, L. and Lin, S. 2017. Identification and expression analysis of blue light receptor aureochrome in the harmful alga Heterosigma akashiwo (Raphidophyceae). Harmful Algae 61: 71-79.
  49. Johnson, M. D., Beaudoin, D.J., Dyhrman,S., Fensin, E., Laza-Martinez, A., Lin, S., Merculief, A., Nagai, S., Pompeu, M., Setala, O. and Stoecker, D. K. 2016. The genetic diversity of Mesodinum and associated cryptophytes. Front. Microbiol. 7: 2017. Doi: 10.3389/fmicb.2016.02017.
  50. 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.
  51. Gomez, F., Qiu, D., Dodge, J. D., Lopes, R. M. and Lin, S. 2016. Morphological and molecular characterization of Ptychodiscus noctiluca revealed the polyphyletic nature of the order Ptychodiscales (Dinophyceae). J. Phycol. 52: 793-805. Doi: 10.1111/jpy.12438.
  52. Gomez, F., Qiu, D., Otero-Morales, E., Lopes, R. M. and Lin, S. 2016. Circumtropical distribution of the epiphytic dinoflagellate Coolia malayensis (Dinophyceae): Morphology and molecular phylogeny from Puerto Rico and Brazil. Phycol. Res. 64: 194-199.
  53. Li, M., Shi, X., Guo, C. and Lin, S. 2016. Phosphorus deficiency inhibits cell division but not growth in the dinoflagellate Amphidinium carterae. Front. Microbiol. 7: 826. Doi: 10.3389/fmicb.2016.00826.
  54. Wang, C., Lin, X., Li, L. and Lin, S. 2016. Differential growth responses of marine phytoplankton to herbicide glyphosate. PLoSONE 11(3): e0151633. Doi:10.1371/journal.pone.0151633.
  55. Wang, L., Lin, X., Goes, J. I. and Lin, S. 2016. Phylogenetic analyses of three genes of Pedinomonas noctilucae, the green endosymbiont of the marine dinoflagellate Noctiluca scintillans, reveal its affiliation to the order Marsupiomonas(Chlorophyta, Pedinophyceae) under the reinstated name Protoeuglena noctilucae. Protist 167: 205-216.
  56. Rodriguez, I. B., Lin, S. Ho, J. and Ho, T.-Y. 2016. Effects of trace metal concentrations on the growth of the coral endosymbiont Symbiodinium kawagutii. Front. Microbiol. 7: 82. doi: 10.3389/fmicb.2016.00082
  57. Pan, Y., Wang, L., Zhang, W., Liu, G. and Lin, S. 2016. Genetic analysis of Noctiluca scintillans populations indicates low latitudinal differentiation in China but high China-America differences. J. Exp. Mar. Biol. Ecol. 477: 31-39.
  58. Cui, Y., Lin, X., Zhang, H., Lin, L. and Lin, S. 2015. PhnW-PhnX pathway in dinoflagellates not functional to utilize extracellular phosphonates. Front. Mar. Sci. 2: article 120.
  59. Yang, F., Xu, D., Zhuang, Y., Yi, X., Huang, S., Chen, H., Lin, S., Campbell, D., Sturm, N., Liu, G. and Zhang, H. 2015. Spliced leader RNA trans-splicing discovered in copepods. Sci. Rep. 5: 17411. Doi: 10.1038/Srep17411
  60. 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. 112: 14783-14787.
  61. Kuo, R. C., Zhang, H., Stuart, J. D., Provatas, A. A., Hannick, L. and Lin, S. Unique lipid biosynthesis pathways in Eutreptiella sp. revealed by chromatographic and transcriptomic analyses. J. Phycol. (in revision)
  62. Lin, S., Litaker, R. W. and Sunda, W. 2015. Phosphorus physiological ecology and molecular mechanisms in marine phytoplankton. J. Phycol. 52: 10-36. doi: 10.1111/jpy.12365.
  63. Lin, S., Cheng, S., Song, B., Zhong, X., Lin, X., Li, W., Li, L., Zhang, Y., Zhang, H., Ji, Z., Cai, M., Zhuang, Y., Shi, X., Lin, L.-X., Wang, L., Wang, Z., Liu, X., Yu, S., Zeng, P., Hao, H., Zou, Q., Chen, C., Li, Y., Wang, Y., Xu, C., Meng, S., Xu, X., Wang, J., Yang, H., Campbell, D. A., Sturm, N. R., Dagenais-Bellefeuille, S. and Morese, D. 2015. The genome of Symbiodinium kawagutii illuminates dinoflagellate gene expression and coral symbiosis. Science 350: 691-694.
  64. Li, M., Li, L., Shi, X., Lin, L. and Lin, S. 2015. Effects of phosphorus deficiency and adenosine 5’-triphosphate (ATP) on growth and cell cycle of the dinoflagellate Prorocentrum donghaiense. Harmful Algae 47: 35-41.
  65. Ji, N., Li, L., Lin, L. and Lin, S. 2015. Screening for suitable reference genes for quantitative real-time PCR in Heterosigma akashiwo (Raphidophyceae). PLoSONE 10(7): e0132183. Doi:10.1371/journal.pone.0132183.
  66. Yuan, J., Li, M. and Lin, S. 2015. An improved DNA extraction method for efficient and quantitative recovery of phytoplankton diversity in natural assemblages. PLoSONE 10(7): e0133060.
  67. 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
  68. 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
  69. Chen, L., Zhang, H., Finiguerra, M., Bobkov, Y., Bouchard, C., Avery. D. E., Anderson, P. A. V., Lin, S. and Dam, H. G. 2015. A novel mutation from the gene splicing of a voltage-gated sodium channel in a marine copepod and its potential effect on channel function. J. Exp. Mar. Biol. Ecol. 489: 131-142.
  70. Gomez, F., Qiu, D., Lopes, R. M. and Lin, S. 2015. Fukuyoa paulensis gen. et sp. nov, a new genus for the globular species of the dinoflagellate Gambierdiscus (Dinophyceae). PLoSONE 10(4): e0119676.doi:10.1371/journal.pone.0119676.
  71. 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.
  72. Zhuang, Y., Zhang, H., Hannick, L. and Lin, S. 2015. Metatranscriptome profiling reveals versatile N-nutrient utilization, CO2 limitation, oxidative stress, and active toxin production in an Alexandrium fundyense bloom. Harmful Algae 42: 60-70.
  73. Lin, S., Wang, L., Zheng, L., Dong, Y., Liu, S., Ding, S., Ye, N., Cao, W. and Zhuang, Z. 2014. Current status and future prospect of DNA barcoding in marine biology. Acta Oceanologica Sinica 36(12): 1-17 (In Chinese with English abstract).
  74. Guo, Z., Zhang, H. and Lin, S. 2014 Light-promoted rhodopsin expression and starvation survival in the marine dinoflagellate Oxyrrhis marina. PLoSONE 9(12): e114941. doi:10.1371/journal.pone.0114941.
  75. Keeling, P., Burki, F., Wilcox, H. M., Allam, B., Allen, E., Amaral-Zettler, L. A., Armbrust, E. V., Archibald, J. M., Bharti, A. K., Bell, C. J.,….Lin, S….2014. The marine microbial eukaryote transcriptome sequencing project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing. PLoS Biol. 12(6): e1001889. doi:10.1371/journal.pbio.1001889.
  76. Hu, S., Guo, Z., Li, T., Carpenter, E. J., Liu, S. and Lin, S. 2014. Detecting in situ copepod diet diversity using molecular technique: development of a copepod/symbiotic ciliate-excluding eukaryote-inclusive PCR protocol. PLoSONE 9(7): e103528. doi:10.1371/journal.pone.0103528.
  77. Mungpakdee, S., Shinzato, C., Takeuchi, T., Kawashima, T., Koyanagi, R., Kisata, K., Tanaka, M., Goto, H., Fujie, M., Lin, S., Satoh, N. and Shoguchi E. 2014. Massive gene transfer and extensive RNA editing of a symbiotic dinoflagellate plastid genome. Genome Biol. Evol. 6(6): 1408-1422.
  78. Zhang, C., Lin, S., Huang, L., Wang, L. Li, M. and Liu, S. 2014. Suppression subtraction hybridization analysis revealed regulation of some cell cycle and toxin genes in Alexandrium catenella by phosphate limitation. Harmful Algae 39: 26-39.
  79. Huang, Y-S., Xu, D.-H., Chen, H.-J., Zhang, H., Lin, S. and Liu, G.-X. 2014. PCR-based in situ dietary analysis of Calanus sinicus Brodsky in Yellow River Estuary and adjacent waters. Periodical of Ocean Univ. China 44(3): 83-91.
  80. 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.
  81. Guo, Z., Zhang, H., Liu, S. and Lin, S. 2013. Biology of the marine heterotrophic dinoflagellate Oxyrrhis marina: current status and future directions. Microorganisms 1: 33-57. doi: 10.3390/microorganisms 10x00x.
  82. Zhang, H., Campbell, D. A., Sturm, N. R., Rosenblad, M. A., Dungan, C. F. and Lin, S. 2013. Detection of signal recognition particle RNA in Dinoflagellata and Perkinsozoa. Protist 164: 748-761.
  83. Qiu, D., Huang, L., Liu, S., Zhang, H. and Lin, S. 2013. Apical groove and molecular phylogeny suggest reclassification of Cochlodinium geminatum as Polykrikos geminatum. PLoSONE 8(8): e71346. doi:10.1371/journal.pone.0071346.
  84. Shi, X., Zhang, H. and Lin, S. 2013. Tandem repeats, high copy number and remarkable diel rhythm in transcription of form II Rubisco in dinoflagellate Prorocentrum donghaiense. PLoSONE 8(8): e71232. doi:10.1371/journal.pone.0071232.
  85. Castillo-Medina, R. E., Islas-Flores, T., Thome, P. E., Iglesias-Prieto, R., Lin, S., Zhang, H. and Villanueva,, M. A. 2013. Oxygen-evolving enhancer 1 homolog (oee1/psbo/msp) in Symbiodinium kawagutii (Dinophyceae) characterized using biochemical and molecular methods. Photosynthesis Res. 115: 167-178.
  86. Zhang, H., Zhuang, Y., Gill, J. and Lin, S. 2013. Proof that dinoflagellate spliced leader (DinoSL) is a useful hook for fishing dinoflagellate transcripts from mixed microbial samples: Symbiodinium kawagutii as a case study. Protist 164: 510-527.
    1. Zhuang, Y., Zhang, H. and Lin, S. 2013. Polyadenylation of 18S rRNA in algae. Phycol. 49: 570-579. DOI: 10.1111/jpy.12068.
    2. Zhuang, Y., Zhang, H. and Lin, S. 2013. Cyclin B and its cell cycle-dependent differential expression in the toxic dinoflagellate Alexandrium fundyense Atama Group I/Clade I. Harmful Algae 26: 71-79.
    3. Bergman, B., Sandh, G., Lin, S., Larsson, J. and Carpenter, E. J. 2013. Tichodesmium – a widespread marine cyanobacterium with unusual nitrogen fixation properties. FEMS Microbiol. Rev. 37: 286–302. DOI:10.1111/j.1574-6976.2012.00352.x
    4. Kuo, R. C.-Y., Zhang, H., Zhuang, Y. and Lin, S. 2013. Transcriptomic study reveals widespread spliced leader trans-splicing, short 5′-UTRs and potential complex carbon fixation mechanisms in the euglenoid alga Eutreptiella sp. PLoS ONE 8(4): e60826. doi:10.1371/journal.pone.0060826.
    5. Kuo, R. C. and Lin, S. 2012. Ectobiotic and endobiotic bacteria associated with Eutreptiella sp. Isolated from long island sound. Protist 164: 60-74.
    6. Chan, C. X., Blouin, N. A., Zhuang, Y., Zäuner, S., Prochnik, S. E., Lindquist, E., Lin, S., Benning, C., Lohr, M., Yarish, C., Gantt, E., Grossman, A. R., Lu, S., Müller, K., Stiller, J., Brawley, S. H. and Bhattacharya, D. 2012. Porphyra(Bangiophyceae) transcriptomes provide insights into red algal development and metabolism. J. Phycol. 48: 1328–1342.
    7. Zheng, S., Wang, G. and Lin, S. 2012. Heat shock effects and population survival in the polar dinoflagellate Polarella glacialis. J. Exp. Mar. Biol. Ecol. 438: 100-108.
    8. Ndu, U. Mason, R., Zhang, H., Lin, S. and Visscher, P. 2012. The effect of inorganic and organic ligands on the bioavailability of methylmercury as determined by a merlux bioreporter. Appl. Environ. Microbiol. 78: 7276–7282.
    9. Guo, Z., Liu, S., Hu, S., Li, T., Huang, Y., Liu, G., Zhang, H. and Lin, S. 2012. Prevalent ciliate symbiosis on copepods: high genetic diversity and wide distribution detected using small subunit ribosomal RNA gene. PLoS ONE 7(9): e44847. doi:10.1371/ journal.pone.0044847.
    10. 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. Front. Microbiol. 3: article 235. doi: 10.3389/fmicb.2012.00235.
    11. Stiller, J. W., Perry, J., Raymaquis, L. A., Green, P. J., Prochnik, S., Lindquist, E., Chan, C. X., Yarish, C., Lin, S., Zhuang, Y., Blouin, N. A. and Brawley, S. H. 2012. Major developmental regulators and their expression in two closely related species of Porphyra (Rhodophyta). J. Phycol. 48: 883–896.
    12. Stefaniak, L., Zhang, H., Gittenberger, A., Smith, K., Holsinger, K., Lin, S. and Whitlatch, R. B. 2012. Determining the native region of the putatively invasive ascidian Didemnum vexillum Kott, 2002. J. Exp. Mar. Biol. Ecol. 422-423: 64-71.
    13. Lin, X., Zhang, H., Huang, B. and Lin, S. 2012. Alkaline phosphatase gene sequence characteristics and transcriptional regulation by phosphate limitation in Karenia brevis (Dinophyceae).Harmful Algae 17: 14-24.
    14. Chan, C. X., Zauner, S., Wheeler, G. et al. (Lin, S. in 13th position). 2012. Analysis of Porphyra membrane transporters demonstrate gene transfer among photosynthetic eukaryotes and numerous sodium-coupled transport systems. Plant Physiol. Doi:10.1104/pp.112.193896.
    15. Miranda, L. N., Zhang, H., Zhuang, Y. and Lin, S. 2012. Phylogenetic analysis guided by intragenomic SSU rDNA polymorphism refines classification of “Alexandrium tamarense” species complex. Harmful Algae 16: 35-48. doi:10.1016/j.hal.2012.01.002.
    16. Haska, C. L., Yarish, C., Kraemer, G., Blaschik, N., Whitlatch, R., Zhang, H. and Lin, S. 2012. Bait worm packaging as a potential vector of invasive species. Biol. Invasions 14: 481-493. DOI: 10.1007/s10530-011-0091-y.
    17. Qiu, D., Huang, L., Liu, S. and Lin, S. 2011. Nuclear, mitochondrial and plastid gene phylogenies of Dinophysis miles(Dinophyceae): evidence of variable types of chloroplasts. PLoS ONE 6(12): e29398. doi:10.1371/journal.pone.0029398.
    18. Zhang, H., Campbell, D. A, Strum, N. R., Dungan, C. F. and Lin, S. 2011. Spliced leader RNA, mitochondrial gene frameshifts, and multi-protein phylogeny expand support for Perkinsus as a unique alveolate. PLoS ONE 6(5): e19933. Doi:10.1371/ journal.pone.0019933.
    19. Liu, S., Guo, Z., Li, T., Huang, H. and Lin, S. 2011. Photosynthetic efficiency, cell volume, and elemental stoichiometric ratios in Thalassirosira weissflogii under phosphorus limitation. Chin. J. Oceanol. Limnol. 29: 1048-1056.
    20. Wong, G. T. F., Hong, H. S., Lin, S. J., Liu, H. B. and Xue, H. J. 2011. Upwelling ecosystem in the southern Taiwan Strait Preface and Introduction. Cont. Shelf Res. 31: S1-S2.
    21. Li, T., Liu, S., Huang, L., Huang, H., Lian, J., Yan, Y. and Lin, S. 2011. Diatoms to dinoflagellates shift in the summer phytoplankton community in a bay impacted by nuclear power plant thermal effluent. Mar. Ecol. Prog. Ser. 424: 75-85. doi: 10.3354/meps08974.
    22. 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. doi: 10.1111/j.1529-8817.2011.01038.x
    23. Lin, S. 2011. Genomic understanding of dinoflagellates. Res. Microbiol. (invited review). 162: 551-569. doi: 10.1016/j.resmic.2011.04.006.
    24. 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.
    25. Ying, C.-Q., Yin, S.-J., Shen, Y., Lin, S., He, P.-M. 2011. Cloning and analysis of the full-length Rubisco large subunit (rbc L) cDNA from Ulva linza (Chlorophyceae, Chlorophyta). Bot. Mar. 54: 303–312.
    26. Lin, S. and Zhang, H. 2010. Dinoflagellate meta-transcriptomics enabled by spliced leader. In C. K. Ho (ed.) Proceedings of 13th International Conference on Harmful Alge. Pp166-170.
    27. 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.
    28. Gantt, E., Berg, G. M., Bhattacharya, D., Bluoin, N. A., Brodie, J. A., Chan, C. X., Collen, J., Cunningham, F. X., Gross, J., Grossman, A., Karpowicz, S., Kitade, Y., Klein, A. S., Levine, I. A., Lin, S., Lu, S., Lynch, M., Minocha, S. C., Muller, K., Neffus, C. D., Olieira, M. C., Rymarquis, L., Smith, Al, Stiller, J. W., Wu, W.-K., Yarish, C., Zhuang, Y. and Brawley, S. 2010. Porphyra: Complex Life Histories in a Harsh Environment: P. umbilicalis, an Intertidal Red Alga for Genomic Analysis. Red Algae in the Genomic Age: Cellular Origin, Life in Extreme Habitats and Astrobiology, Vol. 13 (Part 3): 129-148. DOI: 10.1007/978-90-481-3795-4_7.
    29. Qiu, D., Huang, L., Huang, H. Yang, J., and Lin, S. 2010. Two functionally distinct ciliates dwelling in Acropora corals in Sanya, South China Sea. Appl. Environ. Microbiol. 76: 5639-5643.
    30. 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. doi:10.1371/journal.pone.0009545.
    31. Qiu, D., Huang, L., Zhang, J. and Lin, S. 2010. Phytoplankton dynamics in and near the highly eutrophic Pearl River Estuary, South China Sea. Cont. Shelf Res. 30: 177-186.
    32. 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.
    33. Zhang, H., Campbell, D. A., Strum, N. R. and Lin, S. 2009. Dinoflagellate spliced leader RNA genes display a variety of sequences and genomic arrangements. Mol. Biol. Evol. 26: 1757-1771.
    34. Lin, S., Sandh, G., Zhang, H., Cheng, J., Perkins, K., Carpenter, E. J. and Bergman, B. 2009. Two flavodoxin genes in Trichodesmium (Oscillatoriales, Cyanophyceae): remarkable sequence divergence and possible functional diversification. J. Exp. Mar. Biol. Ecol. 371: 93-101.
    35. Stefaniak, L., Lambert, G., Gittenberger, A. Zhang, H., Lin, S. and Whitlatch, R. B. 2009. Genetic conspecificity of the worldwide populations of Didemnum vexillum Kott, 2002. Aquat. Invasion. 4: 29-44.
    36. 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.
    37. Zhang, H. and Lin, S. 2009. Retrieval of missing spliced leader in dinoflagellates. PLoS ONE 4(1): e4129. doi:10.1371/journal.pone.0004129.
    38. 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.
    39. Zhang, H., Bhattacharya, D., Maranda, L. and Lin, S. 2008. Mitochondrial cob and cox1 and their mRNA editing in Dinophysis acuminata from Narragansett Bay, with special reference to the phylogenetic position of Dinophysis. Appl. Envion. Microbiol. 74: 1546-1554.
    40. Zhang, H. and Lin, S. 2008. Status of mRNA editing and SL RNA trans-splicing group Oxyrrhis, Noctiluca, Heterocapsa, and Amphidinium as basal lineages of dinoflagellates. J. Phycol. 44: 703-711.
    41. Huang, B., Hou, J., Lin, S., Chen, J. and Hong, H. 2008. Development of a PNA probe for the detection of the toxic dinoflagellate Takayama pulchellum. Harmful Algae 7: 495-503.
    42. Lin, S. 2008. Use of molecular markers for early warning detection of harmful algal blooms. Int. J. Environ. Pollution 33: 381-400.
    43. He, P., Xu, S., Zhang, H., Wen, S., Dai, Y., Lin, S. and Yarish, C. 2008. Bioremediation efficiency in the removal of dissolved inorganic nutrients by the red seaweed, Porphyra yezoensis, cultivated in the open sea. Water Res. 42: 1281 – 1289.
    44. Zhang, H., Bhattacharya, D. and Lin, S. 2007. A three-gene dinoflagellate phylogeny suggests monophyly ofProrocentrales and a basal position for Amphidinium and Heterocapsa  J. Mol. Evol. 65: 463-474.
    45. 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.
    46. Beauchamp, K. and Lin, S. 2006. Stimulation of Pfiesteria piscicida (Dinophyceae) growth by animal sera. J. Xiamen Univ. (Natural Science) 45 (no.z2): 225-232.
    47. Lin, S., Zhang, H., Hou, Y., Miranda, L. and Bhattacharya, D. 2006. Development of a dinoflagellate-oriented PCR primer set leads to the detection of picoplanktonic dinoflagellates from Long Island Sound. Appl. Environ. Microbiol. 72: 5626-5630.
    48. Lin, S., Zhang, H. and Dubois, A. 2006. Low abundance distribution and of Pfiesteria piscicida in Pacific and Western Atlantic as detected by mtDNA-18S rDNA Real-Time PCR. J. Plankton Res. 28: 667-681.
    49. Lin, S., Zhang, H. and Jiao, N. 2006. Potential utility of mitochondrial cytochrome b and its mRNA editing in resolving closely related dinoflagellates: a case study of Prorocentrum (Dinophyceae). J. Phycol. 42: 646-654.
    50. Lin, S. 2006. The Smallest dinoflagellate genome is yet to be found: A comment on LaJeunesse et al. “Symbiodinium(Pyrrhophyta) genome sizes (DNA content) are smallest among dinoflagellates” J. Phycol. 42: 746-748.
    51. Zhang, H., Hou, Y. and Lin, S. 2006. Isolation and characterization of PCNA from the dinoflagellate Pfiesteria piscicida. J. Euk. Microbiol. 53: 142-150.
    52. Zhang, H. and Lin, S. 2005. Development of a cob-18S rDNA Real-Time PCR assay for quantifying Pfiesteria shumwayaein the natural environment. Appl. Environ. Microbiol. 71: 7053-7063.
    53. Lin, S. and Zhang, H. 2005. Isolation of mitochondrial cytochrome b gene and development of a Real-Time quantitative PCR technique for detecting Neoparamoeba aestuarina. J. Shellfish Res. 24: 733-739.
    54. Zhang, H. Bhattacharya, D. and Lin, S. 2005. Phylogeny of dinoflagellates based on mitochondrial cytochrome b and nuclear small subunit rDNA sequence comparisons. J. Phycol. 41: 411-420.
    55. Lin, S., Mulholland, M. R., Zhang, H., Feinstein, T. N., Jochem, F. J., and Carpenter, E. J. 2004. Intense grazing and prey-dependent growth of Pfiesteria piscicida (Dinophyceae). J. Phycol. 40: 1062-1073.
    56. McManus, G., Zhang, H. and Lin, S. 2004. The marine planktonic ciliates that prey on macroalgae and enslave their chloroplasts. Limnol. Oceanogr. 49: 308-313.
    57. Zhang, H. and Lin, S. 2003. Complex gene structure of the form II Rubisco in the dinoflagellate Prorocentrum minimum (dinophyceae). J. Phycol. 39: 1160-1171.
    58. Lin, S., Feinstein, T. N., Zhang, H. and Carpenter, E. J. 2003. Development of an immunofluorescence technique for detecting Pfiesteria piscicida. Harmful Algae 2: 223-231.
    59. Lin, S. and Zhang, H. 2003. Mitogen-activated protein kinase (MAPK) in Pfiesteria piscicida and its growth rate-related expression. Appl. Environ. Microbiol. 69: 343-349.
    60. Feinstein, T. N. Traslavina, R., Sun, M.-Y., Lin, S. 2002.
    61. Lin, S., Zhang, H., Spencer, D., Norman, J. and Gray, M. W. 2002. Widespread and extensive editing of mitochondrial mRNAs in dinoflagellates. J. Mol. Biol. 320:727-739.
    62. Zhang, H. and Lin, S. 2002. Detection and quantification of Pfiesteria piscicida by using the mitochondrial cytochrome bgene. Appl. Environ. Microbiol. 68: 989-994.
    63. Lin, S. and Corstjens, P. L. A. M. 2002. Molecular cloning and expression of the Proliferating Cell Nuclear Antigen gene from the coccolithorid  Pleurochrysis carterae (Haptophyceae). J. Phycol. 38: 164-173.
    64. Lin, S., Gobler, C. and Carpenter, E. J. 2001. Cytological and biochemical responses to iron stress in Dunaliella tertiolecta. Phycologia 40: 403-410.
    65. Lin, S., Magaletti, E., and Carpenter, E. J. 2000. Molecular cloning and antibody development of cyclin box in the brown tide alga Aureococcus anophagefferens. Mar. Biotech. 2: 577-586.
    66. Carpenter, E. J., Lin, S. and Capone, D. 2000. Bacterial activity in South Pole snow. Appl. Environ. Microbiol. 66: 4514-4517.
    67. Lin, S. and Carpenter, E. J. 1999. A PSTTLRE-form of cdc2-like gene in the marine microalga Dunaliella tertiolecta. Gene 239: 39-48.
    68. Lin, S., Henze, S., Lundgren, P., Bergman, B. and Carpenter, E. J. 1998. Whole-cell immunolocalization of nitrogenase in marine diazotrophic cyanobacteria Trichodesmium spp. App. Environ. Microbiol. 64: 3052-3058.
    69. Lin, S. and Carpenter, E. J. 1998. Detection and preliminary characterization of the PCNA gene in marine phytoplankton. Mol. Mar. Biol. Biotech. 7: 62-71.
    70. Lin, S., Chang, J., and Carpenter, E. J. 1997. Can a non-terminal event of the cell cycle be used for estimating species-specific growth rates of phytoplankton?  Mar. Ecol. Prog. Ser. 151:283-290.
    71. Lin, S. and Carpenter, E. J. 1997. Pyrenoid-Rubisco in relation to the cell cycle and growth phase in Dunaliella tertiolecta(Chlorophyceae). Phycologia 36: 24-31.
    72. Lin, S. and Carpenter, E. J. 1997. Rubisco of Dunaliella tertiolecta is redistributed between the pyrenoid and the stroma as a light-shade response. Mar. Biol. 127: 521-529.
    73. Lin, S. and Carpenter, E. J. 1996. An empirical protocol of immunofluorescence for marine phytoplankton. J. Phycol. 32: 1083-1094.
    74. Lin, S., Carpenter, E. J., and Chang, J. 1996. Detection of p34cdc2- and cyclin B-like proteins in Dunaliella tertiolecta. Mar. Biol. 125: 603-610.
    75. Lin, S. and Carpenter, E. J. 1995. Growth characteristics of phytoplankton determined by cell cycle proteins: The cell cycle of Ethmodiscus rex in the southwestern North Atlantic Ocean and Caribbean Sea. J. Phycol.  31: 778-785.
    76. Lin, S. Chang, J., and Carpenter, E. J. 1995. Growth characteristics of phytoplankton determined by cell cycle proteins: PCNA immunostaining of Dunaliella tertiolecta. J. Phycol. 31: 388-395.
    77. Lin, S., Chang, J., and Carpenter, E. J. 1994. Detection of proliferating cell nuclear antigen (PCNA) analog in four species of marine phytoplankton. J. Phycol. 30: 449-456.
    78. Lin, S. and Li, S. 1991. Reproductive rate of a marine planktonic copepod Labidocera euchaeta Giesbrecht in Xiamen Harbor. Chin. J. Oceanol. Limnol. 9(4): 319-328.
    79. Lin, S. and Li, S. 1990. Development rate of Labidocera euchaeta Giesbrecht in Xiamen Harbor. Acta Oceanologica Sinica, 9(3): 439-447.
    80. Lin, S. and Li, S. 1990. Growth rate of a marine planktonic copepod Labidocera euchaeta Giesbrecht. J. Oceanogr. Taiwan Strait 9(1): 48-55.
    81. Lin, S. 1989. Studies on biochemical genetic mechanisms in metabolism, growth, and ecological adaptation of marine planktonic copepods. In: Selected Symp. Nation. Confer. Young Mar. Sci. China. Chinese Society of Oceanography. Ocean Press, Beijing.