Nathan Shaner

Title(s)Associate Adjunct Professor, Neurosciences
SchoolVc-health Sciences-schools
Address9500 Gilman Drive #
La Jolla CA 92093
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    Transformative Optical Imaging of Brain & Behavior in Navigating Genetic Species
    NIH R34DA059500Mar 15, 2024 - Feb 28, 2026
    Role: Co-Investigator
    New tools for quantitative non-invasive recording of biochemical signals
    NIH R01CA279813Jan 1, 2024 - Dec 31, 2028
    Role: Principal Investigator
    Engineering photostable fluorescent proteins and biosensors using transcriptomic mining and massive-throughput single-cell screening
    NIH R01EB032854May 1, 2022 - Jan 31, 2026
    Role: Co-Investigator
    Selective Control of Synaptically-Connected Circuit Elements by Interluminescence
    NIH R01NS120832Apr 15, 2021 - Mar 31, 2024
    Role: Co-Investigator
    From seaside to bedside: evolution of bioluminescent genetically encoded Neurotransmitter Indicators and activators for neuromodulation
    NSF 2027113Jun 16, 2020 - Sep 30, 2024
    Role: Co-investigator
    Designing and deploying an expanded color palette of voltage indicators engineered for multiphoton microscopy
    NIH U01NS113294Aug 15, 2019 - Jul 31, 2022
    Role: Co-Investigator
    Highly specific control of neurons with photoswitchable bioluminescent optogenetics.
    NIH R21EY030716Aug 1, 2019 - Jul 31, 2021
    Role: Principal Investigator
    NeuroNex Technology Hub: Bioluminescence for Optimal Brain Control and Imaging
    NSF 1707352Aug 1, 2017 - Jul 31, 2023
    Role: Co-investigator
    Probes for Luminescence-based Superresolution Microscopy
    NIH R01GM121944Feb 16, 2017 - Jan 31, 2021
    Role: Principal Investigator
    BioLuminescent OptoGenetics (BL-OG): A Novel and Versatile Strategy for Neuromodulation
    NIH U01NS099709Sep 30, 2016 - Jun 30, 2020
    Role: Co-Principal Investigator
    Fluorescent proteins for superresolution imaging
    NIH R01GM109984Sep 30, 2014 - Aug 31, 2020
    Role: Principal Investigator
    BRAIN EAGER: Genetically Encoded Light Sources for Non-Invasive Optogenetics
    NSF 1450216Sep 1, 2014 - Feb 28, 2015
    Role: Co-investigator

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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Toward a brighter constellation: multiorgan neuroimaging of neural and vascular dynamics in the spinal cord and brain. Neurophotonics. 2024 Apr; 11(2):024209. Celinskis D, Black CJ, Murphy J, Barrios-Anderson A, Friedman NG, Shaner NC, Saab CY, Gomez-Ramirez M, Borton DA, Moore CI. PMID: 38725801; PMCID: PMC11079446.
      View in: PubMed   Mentions:
    2. Engineering luminopsins with improved coupling efficiencies. Neurophotonics. 2024 Apr; 11(2):024208. Slaviero AN, Gorantla N, Simkins J, Crespo EL, Ikefuama EC, Tree MO, Prakash M, Björefeldt A, Barnett LM, Lambert GG, Lipscombe D, Moore CI, Shaner NC, Hochgeschwender U. PMID: 38559366; PMCID: PMC10980360.
      View in: PubMed   Mentions:
    3. Efficient opto- and chemogenetic control in a single molecule driven by FRET-modified bioluminescence. Neurophotonics. 2024 Apr; 11(2):021005. Björefeldt A, Murphy J, Crespo EL, Lambert GG, Prakash M, Ikefuama EC, Friedman N, Brown TM, Lipscombe D, Moore CI, Hochgeschwender U, Shaner NC. PMID: 38450294; PMCID: PMC10917299.
      View in: PubMed   Mentions:
    4. Towards a Brighter Constellation: Multi-Organ Neuroimaging of Neural and Vascular Dynamics in the Spinal Cord and Brain. bioRxiv. 2023 Dec 27. Celinskis D, Black CJ, Murphy J, Barrios-Anderson A, Friedman N, Shaner NC, Saab C, Gomez-Ramirez M, Lipscombe D, Borton DA, Moore CI. PMID: 38234789; PMCID: PMC10793404.
      View in: PubMed   Mentions:
    5. A New Highly Efficient Molecule for Both Optogenetic and Chemogenetic Control Driven by FRET Amplification of BioLuminescence. bioRxiv. 2023 Dec 04. Bjorefeldt A, Murphy J, Crespo EL, Lambert GG, Prakash M, Ikefuama EC, Friedman N, Brown TM, Lipscombe D, Moore CI, Hochgeschwender U, Shaner NC. PMID: 37425735; PMCID: PMC10327108.
      View in: PubMed   Mentions:
    6. Engineering luminopsins with improved coupling efficiencies. bioRxiv. 2023 Nov 22. Slaviero A, Gorantla N, Simkins J, Crespo EL, Ikefuama EC, Tree MO, Prakash M, Björefeldt A, Barnett LM, Lambert GG, Lipscombe D, Moore CI, Shaner NC, Hochgeschwender U. PMID: 38045286; PMCID: PMC10690276.
      View in: PubMed   Mentions:
    7. A Bioluminescent Activity Dependent (BLADe) Platform for Converting Neuronal Activity to Photoreceptor Activation. bioRxiv. 2023 Oct 18. Crespo EL, Pal A, Prakash M, Silvagnoli AD, Zaidi Z, Gomez-Ramirez M, Tree MO, Shaner NC, Lipscombe D, Moore C, Hochgeschwender U. PMID: 37425742; PMCID: PMC10327117.
      View in: PubMed   Mentions:
    8. CaBLAM! A high-contrast bioluminescent Ca2+ indicator derived from an engineered Oplophorus gracilirostris luciferase. bioRxiv. 2023 Oct 04. Lambert GG, Crespo EL, Murphy J, Boassa D, Luong S, Celinskis D, Venn S, Hu J, Sprecher B, Tree MO, Orcutt R, Heydari D, Bell AB, Torreblanca-Zanca A, Hakimi A, Lipscombe D, Moore CI, Hochgeschwender U, Shaner NC. PMID: 37425712; PMCID: PMC10327125.
      View in: PubMed   Mentions:
    9. Bioluminescent Genetically Encoded Glutamate Indicators for Molecular Imaging of Neuronal Activity. ACS Synth Biol. 2023 08 18; 12(8):2301-2309. Petersen ED, Lapan AP, Castellanos Franco EA, Fillion AJ, Crespo EL, Lambert GG, Grady CJ, Zanca AT, Orcutt R, Hochgeschwender U, Shaner NC, Gilad AA. PMID: 37450884; PMCID: PMC10443529.
      View in: PubMed   Mentions: 7     Fields:    Translation:Humans
    10. Selective control of synaptically-connected circuit elements by all-optical synapses. Commun Biol. 2022 01 11; 5(1):33. Prakash M, Murphy J, St Laurent R, Friedman N, Crespo EL, Bjorefeldt A, Pal A, Bhagat Y, Kauer JA, Shaner NC, Lipscombe D, Moore CI, Hochgeschwender U. PMID: 35017641; PMCID: PMC8752598.
      View in: PubMed   Mentions: 11  Translation:AnimalsCells
    11. Endoplasmic reticulum tubules limit the size of misfolded protein condensates. Elife. 2021 09 01; 10. Parashar S, Chidambaram R, Chen S, Liem CR, Griffis E, Lambert GG, Shaner NC, Wortham M, Hay JC, Ferro-Novick S. PMID: 34467852; PMCID: PMC8486381.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansAnimalsCells
    12. Bioluminescent optogenetic (BL-OG) activation of neurons during mouse postnatal brain development. STAR Protoc. 2021 09 17; 2(3):100667. Crespo EL, Prakash M, Bjorefeldt A, Medendorp WE, Shaner NC, Lipscombe D, Moore CI, Hochgeschwender U. PMID: 34286295; PMCID: PMC8273415.
      View in: PubMed   Mentions: 3     Fields:    Translation:AnimalsCells
    13. Local Electric Field Controls Fluorescence Quantum Yield of Red and Far-Red Fluorescent Proteins. Front Mol Biosci. 2021; 8:633217. Drobizhev M, Molina RS, Callis PR, Scott JN, Lambert GG, Salih A, Shaner NC, Hughes TE. PMID: 33763453; PMCID: PMC7983054.
      View in: PubMed   Mentions: 7  
    14. Aequorea's secrets revealed: New fluorescent proteins with unique properties for bioimaging and biosensing. PLoS Biol. 2020 11; 18(11):e3000936. Lambert GG, Depernet H, Gotthard G, Schultz DT, Navizet I, Lambert T, Adams SR, Torreblanca-Zanca A, Chu M, Bindels DS, Levesque V, Nero Moffatt J, Salih A, Royant A, Shaner NC. PMID: 33137097; PMCID: PMC7660908.
      View in: PubMed   Mentions: 19     Fields:    Translation:Animals
    15. Miniaturized Devices for Bioluminescence Imaging in Freely Behaving Animals. Annu Int Conf IEEE Eng Med Biol Soc. 2020 07; 2020:4385-4389. Celinskis D, Friedman N, Koksharov M, Murphy J, Gomez-Ramirez M, Borton D, Shaner N, Hochgeschwender U, Lipscombe D, Moore C. PMID: 33018967.
      View in: PubMed   Mentions: 5     Fields:    Translation:AnimalsCells
    16. Alkynamide phthalazinones as a new class of TbrPDEB1 inhibitors (Part 2). Bioorg Med Chem. 2019 09 15; 27(18):4013-4029. de Heuvel E, Singh AK, Boronat P, Kooistra AJ, van der Meer T, Sadek P, Blaazer AR, Shaner NC, Bindels DS, Caljon G, Maes L, Sterk GJ, Siderius M, Oberholzer M, de Esch IJP, Brown DG, Leurs R. PMID: 31378593.
      View in: PubMed   Mentions: 6     Fields:    Translation:Humans
    17. Assay for Detecting Gαi-Mediated Decreases in cAMP in Living Cells. SLAS Discov. 2018 10; 23(9):898-906. Tewson P, Martinka S, Shaner N, Berlot C, Quinn AM, Hughes T. PMID: 29991302.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansAnimalsCells
    18. Spatiotemporal manipulation of ciliary glutamylation reveals its roles in intraciliary trafficking and Hedgehog signaling. Nat Commun. 2018 04 30; 9(1):1732. Hong SR, Wang CL, Huang YS, Chang YC, Chang YC, Pusapati GV, Lin CY, Hsu N, Cheng HC, Chiang YC, Huang WE, Shaner NC, Rohatgi R, Inoue T, Lin YC. PMID: 29712905; PMCID: PMC5928066.
      View in: PubMed   Mentions: 34     Fields:    Translation:AnimalsCells
    19. Characterization of a spectrally diverse set of fluorescent proteins as FRET acceptors for mTurquoise2. Sci Rep. 2017 09 20; 7(1):11999. Mastop M, Bindels DS, Shaner NC, Postma M, Gadella TWJ, Goedhart J. PMID: 28931898; PMCID: PMC5607329.
      View in: PubMed   Mentions: 39     Fields:    Translation:HumansAnimalsCells
    20. Blue-Shifted Green Fluorescent Protein Homologues Are Brighter than Enhanced Green Fluorescent Protein under Two-Photon Excitation. J Phys Chem Lett. 2017 Jun 15; 8(12):2548-2554. Molina RS, Tran TM, Campbell RE, Lambert GG, Salih A, Shaner NC, Hughes TE, Drobizhev M. PMID: 28530831; PMCID: PMC5474692.
      View in: PubMed   Mentions: 18     Fields:    
    21. Engineering of mCherry variants with long Stokes shift, red-shifted fluorescence, and low cytotoxicity. PLoS One. 2017; 12(2):e0171257. Shen Y, Chen Y, Wu J, Shaner NC, Campbell RE. PMID: 28241009; PMCID: PMC5328254.
      View in: PubMed   Mentions: 36     Fields:    Translation:AnimalsCells
    22. Structural analysis of the bright monomeric yellow-green fluorescent protein mNeonGreen obtained by directed evolution. Acta Crystallogr D Struct Biol. 2016 12 01; 72(Pt 12):1298-1307. Clavel D, Gotthard G, von Stetten D, De Sanctis D, Pasquier H, Lambert GG, Shaner NC, Royant A. PMID: 27917830; PMCID: PMC5137226.
      View in: PubMed   Mentions: 17  Translation:AnimalsCells
    23. New DAG and cAMP Sensors Optimized for Live-Cell Assays in Automated Laboratories. J Biomol Screen. 2016 Mar; 21(3):298-305. Tewson PH, Martinka S, Shaner NC, Hughes TE, Quinn AM. PMID: 26657040; PMCID: PMC4766961.
      View in: PubMed   Mentions: 54     Fields:    Translation:HumansCells
    24. Special Section Guest Editorial: Protein Photonics for Imaging, Sensing, and Manipulation: Honoring Prof. Osamu Shimomura, a Pioneer of Photonics for Biomedical Research. J Biomed Opt. 2015 Oct; 20(10):101201. Fujita K, Nagai T, Shaner N, Egner A. PMID: 26527157.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimals
    25. Occurrence of Isopenicillin-N-Synthase Homologs in Bioluminescent Ctenophores and Implications for Coelenterazine Biosynthesis. PLoS One. 2015; 10(6):e0128742. Francis WR, Shaner NC, Christianson LM, Powers ML, Haddock SH. PMID: 26125183; PMCID: PMC4488382.
      View in: PubMed   Mentions: 13     Fields:    Translation:AnimalsCells
    26. Fluorescent proteins for quantitative microscopy: important properties and practical evaluation. Methods Cell Biol. 2014; 123:95-111. Shaner NC. PMID: 24974024.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansAnimals
    27. A bright monomeric green fluorescent protein derived from Branchiostoma lanceolatum. Nat Methods. 2013 May; 10(5):407-9. Shaner NC, Lambert GG, Chammas A, Ni Y, Cranfill PJ, Baird MA, Sell BR, Allen JR, Day RN, Israelsson M, Davidson MW, Wang J. PMID: 23524392; PMCID: PMC3811051.
      View in: PubMed   Mentions: 607     Fields:    Translation:Animals
    28. A comparison across non-model animals suggests an optimal sequencing depth for de novo transcriptome assembly. BMC Genomics. 2013 Mar 12; 14:167. Francis WR, Christianson LM, Kiko R, Powers ML, Shaner NC, Haddock SH. PMID: 23496952; PMCID: PMC3655071.
      View in: PubMed   Mentions: 48     Fields:    Translation:AnimalsCells
    29. Expression and characterization of the calcium-activated photoprotein from the ctenophore Bathocyroe fosteri: insights into light-sensitive photoproteins. Biochem Biophys Res Commun. 2013 Feb 08; 431(2):360-6. Powers ML, McDermott AG, Shaner NC, Haddock SH. PMID: 23262181; PMCID: PMC3570696.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    30. The mFruit collection of monomeric fluorescent proteins. Clin Chem. 2013 Feb; 59(2):440-1. Shaner NC. PMID: 23213078.
      View in: PubMed   Mentions: 1     Fields:    Translation:Animals
    31. Concurrent imaging of synaptic vesicle recycling and calcium dynamics. Front Mol Neurosci. 2011; 4:34. Li H, Foss SM, Dobryy YL, Park CK, Hires SA, Shaner NC, Tsien RY, Osborne LC, Voglmaier SM. PMID: 22065946; PMCID: PMC3206542.
      View in: PubMed   Mentions: 38  
    32. Differential gene expression in the siphonophore Nanomia bijuga (Cnidaria) assessed with multiple next-generation sequencing workflows. PLoS One. 2011; 6(7):e22953. Siebert S, Robinson MD, Tintori SC, Goetz F, Helm RR, Smith SA, Shaner N, Haddock SH, Dunn CW. PMID: 21829563; PMCID: PMC3146525.
      View in: PubMed   Mentions: 24     Fields:    Translation:Animals
    33. The maternal and early embryonic transcriptome of the milkweed bug Oncopeltus fasciatus. BMC Genomics. 2011 Jan 25; 12:61. Ewen-Campen B, Shaner N, Panfilio KA, Suzuki Y, Roth S, Extavour CG. PMID: 21266083; PMCID: PMC3040728.
      View in: PubMed   Mentions: 75     Fields:    Translation:Animals
    34. A monomeric photoconvertible fluorescent protein for imaging of dynamic protein localization. J Mol Biol. 2010 Sep 03; 401(5):776-91. Hoi H, Shaner NC, Davidson MW, Cairo CW, Wang J, Campbell RE. PMID: 20603133.
      View in: PubMed   Mentions: 28     Fields:    Translation:Cells
    35. Simultaneous visualization of protumorigenic Src and MT1-MMP activities with fluorescence resonance energy transfer. Cancer Res. 2010 Mar 15; 70(6):2204-12. Ouyang M, Huang H, Shaner NC, Remacle AG, Shiryaev SA, Strongin AY, Tsien RY, Wang Y. PMID: 20197470; PMCID: PMC2840183.
      View in: PubMed   Mentions: 69     Fields:    Translation:HumansCells
    36. Autofluorescent proteins with excitation in the optical window for intravital imaging in mammals. Chem Biol. 2009 Nov 25; 16(11):1169-79. Lin MZ, McKeown MR, Ng HL, Aguilera TA, Shaner NC, Campbell RE, Adams SR, Gross LA, Ma W, Alber T, Tsien RY. PMID: 19942140; PMCID: PMC2814181.
      View in: PubMed   Mentions: 120     Fields:    Translation:AnimalsCells
    37. Improving the photostability of bright monomeric orange and red fluorescent proteins. Nat Methods. 2008 Jun; 5(6):545-51. Shaner NC, Lin MZ, McKeown MR, Steinbach PA, Hazelwood KL, Davidson MW, Tsien RY. PMID: 18454154; PMCID: PMC2853173.
      View in: PubMed   Mentions: 481     Fields:    Translation:AnimalsCells
    38. Advances in fluorescent protein technology. J Cell Sci. 2007 Dec 15; 120(Pt 24):4247-60. Shaner NC, Patterson GH, Davidson MW. PMID: 18057027.
      View in: PubMed   Mentions: 265     Fields:    Translation:AnimalsCells
    39. Exploration of new chromophore structures leads to the identification of improved blue fluorescent proteins. Biochemistry. 2007 May 22; 46(20):5904-10. Ai HW, Shaner NC, Cheng Z, Tsien RY, Campbell RE. PMID: 17444659.
      View in: PubMed   Mentions: 118     Fields:    Translation:Animals
    40. Novel chromophores and buried charges control color in mFruits. Biochemistry. 2006 Aug 15; 45(32):9639-47. Shu X, Shaner NC, Yarbrough CA, Tsien RY, Remington SJ. PMID: 16893165.
      View in: PubMed   Mentions: 210     Fields:    Translation:Animals
    41. A guide to choosing fluorescent proteins. Nat Methods. 2005 Dec; 2(12):905-9. Shaner NC, Steinbach PA, Tsien RY. PMID: 16299475.
      View in: PubMed   Mentions: 1105     Fields:    Translation:HumansAnimals
    42. Dynamics of Z-band based proteins in developing skeletal muscle cells. Cell Motil Cytoskeleton. 2005 May; 61(1):34-48. Wang J, Shaner N, Mittal B, Zhou Q, Chen J, Sanger JM, Sanger JW. PMID: 15810059; PMCID: PMC1993831.
      View in: PubMed   Mentions: 72     Fields:    Translation:AnimalsCells
    43. Actin and alpha-actinin dynamics in the adhesion and motility of EPEC and EHEC on host cells. Cell Motil Cytoskeleton. 2005 Feb; 60(2):104-20. Shaner NC, Sanger JW, Sanger JM. PMID: 15627283.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansAnimalsCells
    44. Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein. Nat Biotechnol. 2004 Dec; 22(12):1567-72. Shaner NC, Campbell RE, Steinbach PA, Giepmans BN, Palmer AE, Tsien RY. PMID: 15558047.
      View in: PubMed   Mentions: 2088     Fields:    Translation:AnimalsCells
    45. Myofibrillogenesis in skeletal muscle cells. Clin Orthop Relat Res. 2002 Oct; (403 Suppl):S153-62. Sanger JW, Chowrashi P, Shaner NC, Spalthoff S, Wang J, Freeman NL, Sanger JM. PMID: 12394464.
      View in: PubMed   Mentions: 51     Fields:    Translation:HumansAnimalsCells
    46. Expression of green or red fluorescent protein (GFP or DsRed) linked proteins in nonmuscle and muscle cells. Mol Biotechnol. 2001 Jan; 17(1):65-71. Ayoob JC, Shaner NC, Sanger JW, Sanger JM. PMID: 11280932.
      View in: PubMed   Mentions: 6     Fields:    Translation:AnimalsCells
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