Shaner Lab


Our lab is focused on biological tool-building. Many of the most useful tools in modern biomedical research are derived from naturally evolved systems. Among the most well known biological tools are the fluorescent proteins, derived from a variety of marine invertebrates such as jellyfish and corals. We are continuing to engineer improved fluorescent protein variants optimized for use in specific imaging techniques, such as the newly minted field of superresolution imaging, which uses fluorescent labels to allow reconstruction of optical images far beyond the traditional diffraction limit.

We are also interested in bioluminescence, the process by which biological organisms produce light. Every known bioluminescence reaction involves an enzyme (a luciferase or a photoprotein) and a small molecule substrate (a luciferin). While a great many luciferases and photoproteins have been cloned, very little is understood about the biosynthesis of eukaryotic luciferins. We are using massively parallel RNA-Seq and biochemical approaches to delineate the biosynthetic pathways for a number of important eukaryotic luciferins, including firefly luciferin ("d-luciferin"), dinoflagellate luciferin, and coelenterazine (in collaboration wi Dr. Steven Haddock at MBARI). Eventually, we hope to use these pathways to generate the next generation of optogenetic tools for biomedical research.

Apart from optical tools, we are also exploring ways to improve induced pluripotent stem cell (iPSC) reprogramming and directed differentiation.


Dr. Nathan C. Shaner - Principal Investigator

  • B.A. in Physics, Oberlin College, 1999
  • Ph.D. in Biomedical Sciences, University of California, San Diego, 2006

Gerard Lambert - Lab Manager/Research Technician


  • Shaner, N.C., Campbell, R.E., Steinbach, P.A., Giepmans, B.N., Palmer, A.E. & Tsien R.Y. (2004). "Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein." Nature Biotechnology, 22(12), 1567-72. (Download PDF)

  • Shaner, N.C., Steinbach, P.A. & Tsien, R.Y. (2005). "A guide to choosing fluorescent proteins." Nature Methods, 2(12), 905-9. (Download PDF)

  • Shu, X., Shaner, N.C., Yarbrough, C.A., Tsien, R.Y. & Remington, S.J. (2006). "Novel chromophores and buried charges control color in mFruits." Biochemistry, 45(32), 9639-47. (Download PDF)

  • Ai, H.W., Shaner, N.C., Cheng, Z., Tsien, R.Y. & Campbell, R.E. (2007). "Exploration of new chromophore structures leads to the identification of improved blue fluorescent proteins." Biochemistry, 46(20), 5904-10. (Download PDF)

  • Shaner, N.C., Patterson, G.H. & Davidson, M.W. (2007). "Advances in fluorescent protein technology." Journal of Cell Science, 120(Pt 24) 4247-60. (Download PDF)

  • Shaner, N.C., Lin, M.Z., McKeown, M.R., Steinbach, P.A., Hazelwood, K.L., Davidson, M.W. & Tsien, R.Y. (2008). "Improving the photostability of bright monomeric orange and red fluorescent proteins." Nature Methods, 5(6), 545-51. PMC2853173 (Download PDF)

  • Lin, M.Z., McKeown, M.R., Ng, H.L., Aguilera, T.A., Shaner, N.C., Campbell, R.E., Adams, S.R., Gross, L.A., Ma, W., Alber, T. & Tsien, R.Y. (2009). "Autofluoresent proteins with excitation in the optical window for intravital imaging in mammals." Chemistry & Biology, 16(11), 1169-79. PMC2814181 (Download PDF)

  • Ouyang, M., Huang, H., Shaner, N.C., Remacle, A.G., Shiryaev, S.A., Strongin, A.Y., Tsien, R.Y. & Wang, Y. (2010). "Simultaneous visualization of pro-tumorigenic Src and MT1-MMP activities with fluorescence resonance energy transfer." Cancer Research, 70(6): 2204-12. PMC2840183 (Download PDF)

  • Hoi, H., Shaner, N.C., Davidson, M.W., Cairo, C.W., Wang, J. & Campbell, R.E. (2010). "A monomeric photoconvertible fluorescent protein for imaging of dynamic protein localization." Journal of Molecular Biology, 401(5), 776-91. (Download PDF)

  • Ewen-Campen, B., Shaner, N.C., Panfilio, K.A., Suzuki, Y., Roth, S. & Extavour, C.G. (2011). "The maternal and early embryonic transcriptome of the milkweed bug Oncopeltus fasciatus." BMC Genomics, 12:61. PMC3040728 (Download PDF)

  • Siebert, S., Robinson, M.D., Tintori, S.C., Goetz, F., Helm, R.R., Smith, S.A., Shaner, N.C., Haddock, S.H., & Dunn, C.W. (2011). "Differential gene expression in the siphonophore Nanomia bijuga (Cnidaria) assessed with multiple next-generation sequencing workflows." PloS One, 6(7):e22953. PMC3146525 (Download PDF)

  • Li, H., Foss, S.M., Dobryy, Y.L., Park, C.K., Hires, S.A., Shaner, N.C., Tsien, R.Y., Osborne, L.C. & Voglmaier, S.M. (2011). "Concurrent imaging of synaptic vesicle recycling and calcium dynamics." Frontiers in Molecular Neuroscience, 4:34. PMC3206542 (Download PDF)

  • Powers, M.L., McDermott, A.G., Shaner, N.C., & Haddock, S.H. (2012). "Expression and characterization of the calcium-activated photoprotein from the ctenophore Bathocyroe fosteri: Insights into light-sensitive photoproteins." Biochemical and Biophysical Research Communications, Feb 8;431(2):360-6. PMC3570696 (Download PDF)

  • Francis, W.R., Christianson, L.M., Kiko, R., Powers, M.L., Shaner, N.C., & Haddock, S.H. (2013). "A comparison across non-model animals suggests an optimal sequencing depth for de novo transcriptome assembly." BMC Genomics, Mar 12;14(1):167. (Download PDF)

  • Shaner, N.C. (2013). "The mFruit collection of monomeric fluorescent proteins." Clin Chem 59(2):440-441. (commentary) (Download PDF)

  • Shaner, N.C., Lambert, G.G., Chammas, A., Ni, Y., Cranfill, P.J., Baird, M.A., Sell, B.R., Allen, J.R., Day, R.N., Israelsson, M., Davidson, M.W., & Wang, J. (2013) "A bright monomeric green fluorescent protein derived from Branchiostoma lanceolatum." Nature Methods (Epub March 24). (Download PDF)

  • Shaner, N.C. (2014) "Fluorescent proteins for quantitative microscopy: Important properties and practical evaluation." Methods in Cell Biology, 123:95-111. doi: 10.1016/B978-0-12-420138-5.00006-9.

Data and Sample Requests

Due to the very high volume of sample requests coming into my lab, Allele Biotechnology is handling all distribution of the mNeonGreen plasmids, including all of the published fusion constructs, through a low-cost academic licensing model intended to facilitate collaborations between end users of this fluorescent protein. Keep in mind that certain fusion constructs, including those to mTurquoise, will require additional MTAs from other institutions.

Raw data for mNeonGreen absorbance, excitation, and emission spectra can be downloaded here:


Ctenophore image photographed by Dr. Nathan Shaner