A guide to choosing fluorescent proteins

Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein

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p62/SQSTM1 Binds Directly to Atg8/LC3 to Facilitate Degradation of Ubiquitinated Protein Aggregates by Autophagy

Pankiv, S., Clausen, T. H., Lamark, T., Brech, A., Bruun, J.-A., Outzen, H., Øvervatn, A., Bjørkøy, G., & Johansen, T. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.m702824200 · Cited by 4,578

A global double-fluorescent Cre reporter mouse

Muzumdar, M. D., Tasic, B., Miyamichi, K., Li, L., & Luo, L. (2007) · genesis · doi:10.1002/dvg.20335 · Cited by 3,491

Bioorthogonal Chemistry: Fishing for Selectivity in a Sea of Functionality

Sletten, E. M., & Bertozzi, C. R. (2009) · Angewandte Chemie International Edition · doi:10.1002/anie.200900942 · Cited by 3,165

The Fluorescent Toolbox for Assessing Protein Location and Function

Giepmans, B. N. G., Adams, S. R., Ellisman, M. H., & Tsien, R. Y. (2006) · Science · doi:10.1126/science.1124618 · Cited by 2,770

Structural and molecular interrogation of intact biological systems

Chung, K., Wallace, J., Kim, S.-Y., Kalyanasundaram, S., Andalman, A. S., Davidson, T. J., Mirzabekov, J. J., Zalocusky, K. A., Mattis, J., Denisin, A. K., et al. (2013) · Nature · doi:10.1038/nature12107 · Cited by 2,008

Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system

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Biosensors and their applications – A review

Mehrotra, P. (2016) · Journal of Oral Biology and Craniofacial Research · doi:10.1016/j.jobcr.2015.12.002 · Cited by 1,526

Applying systems-level spectral imaging and analysis to reveal the organelle interactome

Valm, A. M., Cohen, S., Legant, W. R., Melunis, J., Hershberg, U., Wait, E., Cohen, A. R., Davidson, M. W., Betzig, E., & Lippincott-Schwartz, J. (2017) · Nature · doi:10.1038/nature22369 · Cited by 1,113

Objective comparison of particle tracking methods

Chenouard, N., Smal, I., de Chaumont, F., Maška, M., Sbalzarini, I. F., Gong, Y., Cardinale, J., Carthel, C., Coraluppi, S., Winter, M., et al. (2014) · Nature Methods · doi:10.1038/nmeth.2808 · Cited by 894

Activity-driven local ATP synthesis is required for synaptic function

Rangaraju, V., Calloway, N., & Ryan, T. A. (2014) · Cell · doi:10.1016/j.cell.2013.12.042 · Cited by 836

A novel sensor to map auxin response and distribution at high spatio-temporal resolution

Brunoud, G., Wells, D. M., Oliva, M., Larrieu, A., Mirabet, V., Burrow, A. H., Beeckman, T., Kepinski, S., Traas, J., Bennett, M. J., et al. (2012) · Nature · doi:10.1038/nature10791 · Cited by 741

Accuracy and precision in quantitative fluorescence microscopy

Waters, J. C. (2009) · Journal of Cell Biology · doi:10.1083/jcb.200903097 · Cited by 613

Immunolabeling artifacts and the need for live-cell imaging

Schnell, U., Dijk, F., Sjollema, K. A., & Giepmans, B. N. G. (2012) · Nature Methods · doi:10.1038/nmeth.1855 · Cited by 506

Fluorescent fusion protein knockout mediated by anti-GFP nanobody

Caussinus, E., Kanca, O., & Affolter, M. (2012) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2180 · Cited by 510

Intravital imaging

Pittet, M. J., & Weissleder, R. (2011) · Cell · doi:10.1016/j.cell.2011.11.004 · Cited by 466

Rapid Synaptic Scaling Induced by Changes in Postsynaptic Firing

Ibata, K., Sun, Q., & Turrigiano, G. G. (2008) · Neuron · doi:10.1016/j.neuron.2008.02.031 · Cited by 446

A platform for brain-wide imaging and reconstruction of individual neurons

Economo, M. N., Clack, N. G., Lavis, L. D., Gerfen, C. R., Svoboda, K., Myers, E. W., & Chandrashekar, J. (2016) · eLife · doi:10.7554/elife.10566 · Cited by 409

De novo design of a fluorescence-activating β-barrel

Dou, J., Vorobieva, A. A., Sheffler, W., Doyle, L. A., Park, H., Bick, M. J., Mao, B., Foight, G. W., Lee, M. Y., Gagnon, L. A., et al. (2018) · Nature · doi:10.1038/s41586-018-0509-0 · Cited by 351

Improving brightness and photostability of green and red fluorescent proteins for live cell imaging and FRET reporting

Bajar, B. T., Wang, E. S., Lam, A. J., Kim, B. B., Jacobs, C. L., Howe, E. S., Davidson, M. W., Lin, M. Z., & Chu, J. (2016) · Scientific Reports · doi:10.1038/srep20889 · Cited by 389

Cell-specific deletion of C1qa identifies microglia as the dominant source of C1q in mouse brain

Fonseca, M. I., Chu, S.-H., Hernandez, M. X., Fang, M. J., Modarresi, L., Selvan, P., MacGregor, G. R., & Tenner, A. J. (2017) · Journal of Neuroinflammation · doi:10.1186/s12974-017-0814-9 · Cited by 337

Imaging molecular interactions in living cells by FRET microscopy

Jares-Erijman, E. A., & Jovin, T. M. (2006) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2006.08.021 · Cited by 313

Bright monomeric near-infrared fluorescent proteins as tags and biosensors for multiscale imaging

Shcherbakova, D. M., Baloban, M., Emelyanov, A. V., Brenowitz, M., Guo, P., & Verkhusha, V. V. (2016) · Nature Communications · doi:10.1038/ncomms12405 · Cited by 312

Local palmitoylation cycles define activity-regulated postsynaptic subdomains

Fukata, Y., Dimitrov, A., Boncompain, G., Vielemeyer, O., Perez, F., & Fukata, M. (2013) · Journal of Cell Biology · doi:10.1083/jcb.201302071 · Cited by 262

New Concepts in Synaptic Biology Derived from Single-Molecule Imaging

Triller, A., & Choquet, D. (2008) · Neuron · doi:10.1016/j.neuron.2008.06.022 · Cited by 262

Living Cells as Test Tubes

Xie, X. S., Yu, J., & Yang, W. Y. (2006) · Science · doi:10.1126/science.1127566 · Cited by 257

Fluorescence lifetime imaging microscopy in life sciences

Borst, J. W., & Visser, A. J. W. G. (2010) · Measurement Science and Technology · doi:10.1088/0957-0233/21/10/102002 · Cited by 168

Accumulation of tau induced in neurites by microglial proinflammatory mediators

Gorlovoy, P., Larionov, S., Pham, T. T. H., & Neumann, H. (2009) · The FASEB Journal · doi:10.1096/fj.08-123877 · Cited by 156

Brainbow: New Resources and Emerging Biological Applications for Multicolor Genetic Labeling and Analysis

Weissman, T. A., & Pan, Y. A. (2015) · Genetics · doi:10.1534/genetics.114.172510 · Cited by 153

Non‐Invasive in vivo Imaging in Small Animal Research

Koo, V., Hamilton, P. W., & Williamson, K. (2006) · Analytical Cellular Pathology · doi:10.1155/2006/245619 · Cited by 145

Fluorescence Spectroscopy and Chemometric Modeling for Bioprocess Monitoring

Faassen, S., & Hitzmann, B. (2015) · Sensors · doi:10.3390/s150510271 · Cited by 120

Labeling and Single-Molecule Methods To Monitor G Protein-Coupled Receptor Dynamics

Tian, H., Fürstenberg, A., & Huber, T. (2017) · Chemical Reviews · doi:10.1021/acs.chemrev.6b00084 · Cited by 114

Genetic dissection of GABAergic neural circuits in mouse neocortex

Taniguchi, H. (2014) · Frontiers in Cellular Neuroscience · doi:10.3389/fncel.2014.00008 · Cited by 106

In vivo dynamics of innate immune sentinels in the CNS

Nayak, D., Zinselmeyer, B. H., Corps, K. N., & McGavern, D. B. (2012) · IntraVital · doi:10.4161/intv.22823 · Cited by 109

Transmembrane/cytoplasmic, rather than catalytic, domains of Mmp14 signal to MAPK activation and mammary branching morphogenesis via binding to integrin β1

Mori, H., Lo, A. T., Inman, J. L., Alcaraz, J., Ghajar, C. M., Mott, J. D., Nelson, C. M., Chen, C. S., Zhang, H., Bascom, J. L., et al. (2013) · Development · doi:10.1242/dev.084236 · Cited by 104

Molecular mechanism of hippocampal long-term potentiation – Towards multiscale understanding of learning and memory

Hayashi, Y. (2022) · Neuroscience Research · doi:10.1016/j.neures.2021.08.001 · Cited by 102

Clearing Up the Signal: Spectral Imaging and Linear Unmixing in Fluorescence Microscopy

Zimmermann, T., Marrison, J., Hogg, K., & O’Toole, P. (2014) · Methods in Molecular Biology · doi:10.1007/978-1-60761-847-8_5 · Cited by 102

A Cell/Cilia Cycle Biosensor for Single-Cell Kinetics Reveals Persistence of Cilia after G1/S Transition Is a General Property in Cells and Mice

Ford, M. J., Yeyati, P. L., Mali, G. R., Keighren, M. A., Waddell, S. H., Mjoseng, H. K., Douglas, A. T., Hall, E. A., Sakaue-Sawano, A., Miyawaki, A., et al. (2018) · Developmental Cell · doi:10.1016/j.devcel.2018.10.027 · Cited by 89

Lighting Up Live-Cell and In Vivo Central Carbon Metabolism with Genetically Encoded Fluorescent Sensors

Zhang, Z., Cheng, X., Zhao, Y., & Yang, Y. (2020) · Annual Review of Analytical Chemistry · doi:10.1146/annurev-anchem-091619-091306 · Cited by 81

Akt regulation of glycolysis mediates bioenergetic stability in epithelial cells

Hung, Y. P., Teragawa, C., Kosaisawe, N., Gillies, T. E., Pargett, M., Minguet, M., Distor, K., Rocha-Gregg, B. L., Coloff, J. L., Keibler, M. A., et al. (2017) · eLife · doi:10.7554/elife.27293 · Cited by 74

A detailed three-step protocol for live imaging of intracellular traffic in polarized primary porcine RPE monolayers

Toops, K. A., Tan, L. X., & Lakkaraju, A. (2014) · Experimental Eye Research · doi:10.1016/j.exer.2014.05.003 · Cited by 73

Two-Photon Microscopy: Shedding Light on the Chemistry of Vision

Imanishi, Y., Lodowski, K. H., & Koutalos, Y. (2007) · Biochemistry · doi:10.1021/bi701055g · Cited by 58

Use of mCherryOpt Fluorescent Protein in Clostridium difficile

Ransom, E. M., Weiss, D. S., & Ellermeier, C. D. (2016) · Methods in Molecular Biology · doi:10.1007/978-1-4939-6361-4_5 · Cited by 28

Identification and In Vivo Characterization of NvFP-7R, a Developmentally Regulated Red Fluorescent Protein of Nematostella vectensis

Ikmi, A., & Gibson, M. C. (2010) · PLoS ONE · doi:10.1371/journal.pone.0011807 · Cited by 26

Fluorescent Protein Applications in Microscopy

Straight, A. F. (2007) · Methods in Cell Biology · doi:10.1016/s0091-679x(06)81006-x · Cited by 24

Unveiling Molecular Events in the Brain by Noninvasive Imaging

Klohs, J., & Rudin, M. (2011) · The Neuroscientist · doi:10.1177/1073858410383433 · Cited by 22

Imaging Approaches for the Study of Metabolism in Real Time Using Genetically Encoded Reporters

Chandris, P., Giannouli, C. C., & Panayotou, G. (2022) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2021.725114 · Cited by 19

Noncytotoxic DsRed Derivatives for Whole-Cell Labeling

Strack, R. L., Keenan, R. J., & Glick, B. S. (2011) · Methods in Molecular Biology · doi:10.1007/978-1-61737-950-5_17 · Cited by 16

Time-lapse imaging of dendritic spines in vitro

Verkuyl, J. M., & Matus, A. (2006) · Nature Protocols · doi:10.1038/nprot.2006.357 · Cited by 13

New Technologies for Studying Biofilms

Franklin, M. J., Chang, C., Akiyama, T., & Bothner, B. (2015) · Microbial Biofilms · doi:10.1128/9781555817466.ch1 · Cited by 11

First-principles simulation of photoreactions in biological systems

Rossle, S. (2009) · Frontiers in Bioscience · doi:10.2741/3574 · Cited by 9

Conformational Dynamics of mCherry Variants: A Link between Side-Chain Motions and Fluorescence Brightness

Mukherjee, S., Manna, P., Douglas, N., Chapagain, P. P., & Jimenez, R. (2023) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.2c05584 · Cited by 8

Visualization of Retroviral Gag-Genomic RNA Cellular Interactions Leading to Genome Encapsidation and Viral Assembly: An Overview

Bernacchi, S. (2022) · Viruses · doi:10.3390/v14020324 · Cited by 8

Influence of Fluorescence Lifetime Selections and Conformational Flexibility on Brightness of FusionRed Variants

Mukherjee, S., Douglas, N., & Jimenez, R. (2024) · The Journal of Physical Chemistry Letters · doi:10.1021/acs.jpclett.3c02765 · Cited by 6

Tracking and measuring local protein synthesis in vivo

Kays, I., & Chen, B. E. (2024) · Development · doi:10.1242/dev.202908 · Cited by 4

Barrel Shape and Chromophore Rigidity Predict Fluorescent-Protein Photophysics

Begg, L. P., Mason, M. L., & Zimmer, M. (2026) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.6c01606 · Cited by 1

Untitled work

(2017) · PubMed