Optimized ratiometric calcium sensors for functional in vivo imaging of neurons and T lymphocytes

UCSF Chimera—A visualization system for exploratory research and analysis

Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004) · Journal of Computational Chemistry · doi:10.1002/jcc.20084 · Cited by 45,828

The Psychophysics Toolbox

Brainard, D. H. (1997) · Spatial Vision · doi:10.1163/156856897x00357 · Cited by 19,702

NMRPipe: A multidimensional spectral processing system based on UNIX pipes

Delaglio, F., Grzesiek, S., Vuister, G., Zhu, G., Pfeifer, J., & Bax, A. (1995) · Journal of Biomolecular NMR · doi:10.1007/bf00197809 · Cited by 15,965

The VideoToolbox software for visual psychophysics: transforming numbers into movies

Pelli, D. G. (1997) · Spatial Vision · doi:10.1163/156856897x00366 · Cited by 11,098

MOLMOL: A program for display and analysis of macromolecular structures

Koradi, R., Billeter, M., & Wüthrich, K. (1996) · Journal of Molecular Graphics · doi:10.1016/0263-7855(96)00009-4 · Cited by 7,163

AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR

Laskowski, R., Rullmann, J. A., MacArthur, M., Kaptein, R., & Thornton, J. (1996) · Journal of Biomolecular NMR · doi:10.1007/bf00228148 · Cited by 5,502

MolProbity: all-atom contacts and structure validation for proteins and nucleic acids

Davis, I. W., Leaver-Fay, A., Chen, V. B., Block, J. N., Kapral, G. J., Wang, X., Murray, L. W., Arendall, W. B., Snoeyink, J., Richardson, J. S., et al. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm216 · Cited by 3,896

Fluorescent indicators for Ca2+based on green fluorescent proteins and calmodulin

Miyawaki, A., Llopis, J., Heim, R., McCaffery, J. M., Adams, J. A., Ikura, M., & Tsien, R. Y. (1997) · Nature · doi:10.1038/42264 · Cited by 3,248

A variant of yellow fluorescent protein with fast and efficient maturation for cell-biological applications

Nagai, T., Ibata, K., Park, E. S., Kubota, M., Mikoshiba, K., & Miyawaki, A. (2002) · Nature Biotechnology · doi:10.1038/nbt0102-87 · Cited by 2,753

DAMMIF , a program for rapid ab-initio shape determination in small-angle scattering

Franke, D., & Svergun, D. I. (2009) · Journal of Applied Crystallography · doi:10.1107/s0021889809000338 · Cited by 2,021

Imaging neural activity in worms, flies and mice with improved GCaMP calcium indicators

Tian, L., Hires, S. A., Mao, T., Huber, D., Chiappe, M. E., Chalasani, S. H., Petreanu, L., Akerboom, J., McKinney, S. A., Schreiter, E. R., et al. (2009) · Nature Methods · doi:10.1038/nmeth.1398 · Cited by 1,967

Uniqueness of ab initio shape determination in small-angle scattering

Volkov, V. V., & Svergun, D. I. (2003) · Journal of Applied Crystallography · doi:10.1107/s0021889803000268 · Cited by 1,932

New developments in the ATSAS program package for small-angle scattering data analysis

Petoukhov, M. V., Franke, D., Shkumatov, A. V., Tria, G., Kikhney, A. G., Gajda, M., Gorba, C., Mertens, H. D. T., Konarev, P. V., & Svergun, D. I. (2012) · Journal of Applied Crystallography · doi:10.1107/s0021889812007662 · Cited by 1,903

Regulation of Contraction in Striated Muscle

Gordon, A. M., Homsher, E., & Regnier, M. (2000) · Physiological Reviews · doi:10.1152/physrev.2000.80.2.853 · Cited by 1,737

A high signal-to-noise Ca2+ probe composed of a single green fluorescent protein

Nakai, J., Ohkura, M., & Imoto, K. (2001) · Nature Biotechnology · doi:10.1038/84397 · Cited by 1,616

Defective TCR expression in transgenic mice constructed using cDNA‐based α‐ and β‐chain genes under the control of heterologous regulatory elements

Barnden, M. J., Allison, J., Heath, W. R., & Carbone, F. R. (1998) · Immunology & Cell Biology · doi:10.1046/j.1440-1711.1998.00709.x · Cited by 1,489

Determination of Domain Structure of Proteins from X-Ray Solution Scattering

Svergun, D. I., Petoukhov, M. V., & Koch, M. H. J. (2001) · Biophysical Journal · doi:10.1016/s0006-3495(01)76260-1 · Cited by 1,420

In vivo two-photon calcium imaging of neuronal networks

Stosiek, C., Garaschuk, O., Holthoff, K., & Konnerth, A. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1232232100 · Cited by 1,312

An Expanded Palette of Genetically Encoded Ca 2+ Indicators

Zhao, Y., Araki, S., Wu, J., Teramoto, T., Chang, Y.-F., Nakano, M., Abdelfattah, A. S., Fujiwara, M., Ishihara, T., Nagai, T., et al. (2011) · Science · doi:10.1126/science.1208592 · Cited by 1,260

Optimization of a GCaMP Calcium Indicator for Neural Activity Imaging

Akerboom, J., Chen, T.-W., Wardill, T. J., Tian, L., Marvin, J. S., Mutlu, S., Calderón, N. C., Esposti, F., Borghuis, B. G., Sun, X. R., et al. (2012) · The Journal of Neuroscience · doi:10.1523/jneurosci.2601-12.2012 · Cited by 1,223

X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution

Putnam, C. D., Hammel, M., Hura, G. L., & Tainer, J. A. (2007) · Quarterly Reviews of Biophysics · doi:10.1017/s0033583507004635 · Cited by 1,184

Functional imaging with cellular resolution reveals precise micro-architecture in visual cortex

Ohki, K., Chung, S., Ch'ng, Y. H., Kara, P., & Reid, R. C. (2005) · Nature · doi:10.1038/nature03274 · Cited by 1,183

Highly selective receptive fields in mouse visual cortex

Niell, C. M., & Stryker, M. P. (2008) · The Journal of Neuroscience · doi:10.1523/jneurosci.0623-08.2008 · Cited by 1,081

Expanded dynamic range of fluorescent indicators for Ca 2+ by circularly permuted yellow fluorescent proteins

Nagai, T., Yamada, S., Tominaga, T., Ichikawa, M., & Miyawaki, A. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0400417101 · Cited by 1,030

Correlating backbone amide and side chain resonances in larger proteins by multiple relayed triple resonance NMR

Grzesiek, S., & Bax, A. (1992) · Journal of the American Chemical Society · doi:10.1021/ja00042a003 · Cited by 1,022

Quantitative J correlation: a new approach for measuring homonuclear three-bond J(HNH.alpha.) coupling constants in 15N-enriched proteins

Vuister, G. W., & Bax, A. (1993) · Journal of the American Chemical Society · doi:10.1021/ja00070a024 · Cited by 978

Measurement ofJand Dipolar Couplings from Simplified Two-Dimensional NMR Spectra

Ottiger, M., Delaglio, F., & Bax, A. (1998) · Journal of Magnetic Resonance · doi:10.1006/jmre.1998.1361 · Cited by 967

A novel approach for sequential assignment of proton, carbon-13, and nitrogen-15 spectra of larger proteins: heteronuclear triple-resonance three-dimensional NMR spectroscopy. Application to calmodulin

Ikura, M., Kay, L. E., & Bax, A. (1990) · Biochemistry · doi:10.1021/bi00471a022 · Cited by 918

Consistent blind protein structure generation from NMR chemical shift data

Shen, Y., Lange, O., Delaglio, F., Rossi, P., Aramini, J. M., Liu, G., Eletsky, A., Wu, Y., Singarapu, K. K., Lemak, A., et al. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0800256105 · Cited by 855

Genetically encoded calcium indicators for multi-color neural activity imaging and combination with optogenetics

Akerboom, J., Carreras Calderón, N., Tian, L., Wabnig, S., Prigge, M., Tolö, J., Gordus, A., Orger, M. B., Severi, K. E., Macklin, J. J., et al. (2013) · Frontiers in Molecular Neuroscience · doi:10.3389/fnmol.2013.00002 · Cited by 719

Tunable alignment of macromolecules by filamentous phage yields dipolar coupling interactions

Hansen, M. R., Mueller, L., & Pardi, A. (1998) · Nature Structural Biology · doi:10.1038/4176 · Cited by 703

Aβ plaques lead to aberrant regulation of calcium homeostasis in vivo resulting in structural and functional disruption of neuronal networks

Kuchibhotla, K. V., Goldman, S. T., Lattarulo, C. R., Wu, H.-Y., Hyman, B. T., & Bacskai, B. J. (2008) · Neuron · doi:10.1016/j.neuron.2008.06.008 · Cited by 614

Broadly tuned response properties of diverse inhibitory neuron subtypes in mouse visual cortex

Kerlin, A. M., Andermann, M. L., Berezovskii, V. K., & Reid, R. C. (2010) · Neuron · doi:10.1016/j.neuron.2010.08.002 · Cited by 613

ATSAS 2.1, a program package for small-angle scattering data analysis

Konarev, P. V., Petoukhov, M. V., Volkov, V. V., & Svergun, D. I. (2006) · Journal of Applied Crystallography · doi:10.1107/s0021889806004699 · Cited by 609

Ca2+ Indicators Based on Computationally Redesigned Calmodulin-Peptide Pairs

Palmer, A. E., Giacomello, M., Kortemme, T., Hires, S. A., Lev-Ram, V., Baker, D., & Tsien, R. Y. (2006) · Chemistry & Biology · doi:10.1016/j.chembiol.2006.03.007 · Cited by 508

A genetically encoded calcium indicator for chronic in vivo two-photon imaging

Mank, M., Santos, A. F., Direnberger, S., Mrsic-Flogel, T. D., Hofer, S. B., Stein, V., Hendel, T., Reiff, D. F., Levelt, C., Borst, A., et al. (2008) · Nature Methods · doi:10.1038/nmeth.1243 · Cited by 475

[14] Measurement of cytosolic free Ca2+ with quin2

Tsien, R., & Pozzan, T. (1989) · Methods in Enzymology · doi:10.1016/s0076-6879(89)72017-6 · Cited by 469

Ion channels and transporters in lymphocyte function and immunity

Feske, S., Skolnik, E. Y., & Prakriya, M. (2012) · Nature Reviews Immunology · doi:10.1038/nri3233 · Cited by 441

Calmodulin bifurcates the local Ca2+ signal that modulates P/Q-type Ca2+ channels

DeMaria, C. D., Soong, T. W., Alseikhan, B. A., Alvania, R. S., & Yue, D. T. (2001) · Nature · doi:10.1038/35078091 · Cited by 407

An efficient experiment for sequential backbone assignment of medium-sized isotopically enriched proteins

Grzesiek, S., & Bax, A. (1992) · Journal of Magnetic Resonance (1969) · doi:10.1016/0022-2364(92)90169-8 · Cited by 391

Use of Chemical Shifts in Macromolecular Structure Determination

Wishart, D. S., & Case, D. A. (2002) · Methods in Enzymology · doi:10.1016/s0076-6879(02)38214-4 · Cited by 368

A Cre-Dependent GCaMP3 Reporter Mouse for Neuronal Imaging In Vivo

Zariwala, H. A., Borghuis, B. G., Hoogland, T. M., Madisen, L., Tian, L., De Zeeuw, C. I., Zeng, H., Looger, L. L., Svoboda, K., & Chen, T.-W. (2012) · The Journal of Neuroscience · doi:10.1523/jneurosci.4469-11.2012 · Cited by 353

Developmental profile and synaptic origin of early network oscillations in the CA1 region of rat neonatal hippocampus

Garaschuk, O., Hanse, E., & Konnerth, A. (1998) · The Journal of Physiology · doi:10.1111/j.1469-7793.1998.219bu.x · Cited by 348

Spontaneous network activity visualized by ultrasensitive Ca2+ indicators, yellow Cameleon-Nano

Horikawa, K., Yamada, Y., Matsuda, T., Kobayashi, K., Hashimoto, M., Matsu-ura, T., Miyawaki, A., Michikawa, T., Mikoshiba, K., & Nagai, T. (2010) · Nature Methods · doi:10.1038/nmeth.1488 · Cited by 338

In vivo imaging of partially reversible th17 cell-induced neuronal dysfunction in the course of encephalomyelitis

Siffrin, V., Radbruch, H., Glumm, R., Niesner, R., Paterka, M., Herz, J., Leuenberger, T., Lehmann, S. M., Luenstedt, S., Rinnenthal, J. L., et al. (2010) · Immunity · doi:10.1016/j.immuni.2010.08.018 · Cited by 325

A FRET-Based Calcium Biosensor with Fast Signal Kinetics and High Fluorescence Change

Mank, M., Reiff, D. F., Heim, N., Friedrich, M. W., Borst, A., & Griesbeck, O. (2006) · Biophysical Journal · doi:10.1529/biophysj.105.073536 · Cited by 296

Crystal Structures of the GCaMP Calcium Sensor Reveal the Mechanism of Fluorescence Signal Change and Aid Rational Design

Akerboom, J., Rivera, J. D. V., Guilbe, M. M. R., Malavé, E. C. A., Hernandez, H. H., Tian, L., Hires, S. A., Marvin, J. S., Looger, L. L., & Schreiter, E. R. (2009) · Journal of Biological Chemistry · doi:10.1074/jbc.m807657200 · Cited by 285

Genetically Encoded Calcium Indicators

Mank, M., & Griesbeck, O. (2008) · Chemical Reviews · doi:10.1021/cr078213v · Cited by 283

Bright cyan fluorescent protein variants identified by fluorescence lifetime screening

Goedhart, J., van Weeren, L., Hink, M. A., Vischer, N. O. E., Jalink, K., & Gadella, T. W. J. (2010) · Nature Methods · doi:10.1038/nmeth.1415 · Cited by 283

NMR Structure Determination for Larger Proteins Using Backbone-Only Data

Raman, S., Lange, O. F., Rossi, P., Tyka, M., Wang, X., Aramini, J., Liu, G., Ramelot, T. A., Eletsky, A., Szyperski, T., et al. (2010) · Science · doi:10.1126/science.1183649 · Cited by 268

Genetically Encoded Green Fluorescent Ca2+ Indicators with Improved Detectability for Neuronal Ca2+ Signals

Ohkura, M., Sasaki, T., Sadakari, J., Gengyo-Ando, K., Kagawa-Nagamura, Y., Kobayashi, C., Ikegaya, Y., & Nakai, J. (2012) · PLoS ONE · doi:10.1371/journal.pone.0051286 · Cited by 268

An Improved Cerulean Fluorescent Protein with Enhanced Brightness and Reduced Reversible Photoswitching

Markwardt, M. L., Kremers, G.-J., Kraft, C. A., Ray, K., Cranfill, P. J. C., Wilson, K. A., Day, R. N., Wachter, R. M., Davidson, M. W., & Rizzo, M. A. (2011) · PLoS ONE · doi:10.1371/journal.pone.0017896 · Cited by 267

Genetically Encoded Indicators of Cellular Calcium Dynamics Based on Troponin C and Green Fluorescent Protein

Heim, N., & Griesbeck, O. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m312751200 · Cited by 259

Design and application of genetically encoded biosensors

Palmer, A. E., Qin, Y., Park, J. G., & McCombs, J. E. (2011) · Trends in Biotechnology · doi:10.1016/j.tibtech.2010.12.004 · Cited by 238

Monitoring Neural Activity and [Ca2+] with Genetically Encoded Ca2+Indicators

Pologruto, T. A., Yasuda, R., & Svoboda, K. (2004) · The Journal of Neuroscience · doi:10.1523/jneurosci.2854-04.2004 · Cited by 209

Genetically encoded optical indicators for the analysis of neuronal circuits

Knöpfel, T. (2012) · Nature reviews. Neuroscience · doi:10.1038/nrn3293 · Cited by 205

Crystal structure of troponin C in complex with troponin I fragment at 2.3-Å resolution

Vassylyev, D. G., Takeda, S., Wakatsuki, S., Maeda, K., & Maéda, Y. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.9.4847 · Cited by 197

Genetically encoded neural activity indicators

Looger, L. L., & Griesbeck, O. (2012) · Current Opinion in Neurobiology · doi:10.1016/j.conb.2011.10.024 · Cited by 179

Optical recording of neuronal activity with a genetically-encoded calcium indicator in anesthetized and freely moving mice

Lütcke, H. (2010) · Frontiers in Neural Circuits · doi:10.3389/fncir.2010.00009 · Cited by 178

Structural Basis for Calcium Sensing by GCaMP2

Wang, Q., Shui, B., Kotlikoff, M. I., & Sondermann, H. (2008) · Structure · doi:10.1016/j.str.2008.10.008 · Cited by 170

Ensemble Calculations of Unstructured Proteins Constrained by RDC and PRE Data: A Case Study of Urea-Denatured Ubiquitin

Huang, J., & Grzesiek, S. (2009) · Journal of the American Chemical Society · doi:10.1021/ja907974m · Cited by 114

UsingSitusfor the registration of protein structures with low-resolution bead models from X-ray solution scattering

Wriggers, W. R., & Chacón, P. (2001) · Journal of Applied Crystallography · doi:10.1107/s0021889801012869 · Cited by 107

Real-time in vivo analysis of T cell activation in the central nervous system using a genetically encoded calcium indicator

Mues, M., Bartholomäus, I., Thestrup, T., Griesbeck, O., Wekerle, H., Kawakami, N., & Krishnamoorthy, G. (2013) · Nature Medicine · doi:10.1038/nm.3180 · Cited by 100

A Neuron-Based Screening Platform for Optimizing Genetically-Encoded Calcium Indicators

Wardill, T. J., Chen, T., Schreiter, E. R., Hasseman, J. P., Tsegaye, G., Fosque, B. F., Behnam, R., Shields, B. C., Ramirez, M. H., Kimmel, B. E., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0077728 · Cited by 67

Functional immunoimaging: the revolution continues

Bousso, P., & Moreau, H. D. (2012) · Nature reviews. Immunology · doi:10.1038/nri3342 · Cited by 63

Biocompatibility of a genetically encoded calcium indicator in a transgenic mouse model

Direnberger, S., Mues, M., Micale, V., Wotjak, C. T., Dietzel, S., Schubert, K., Scharr, A., Hassan, S., Wahl‐Schott, C., Biel, M., et al. (2012) · Nature Communications · doi:10.1038/ncomms2035 · Cited by 46

Correlating Calcium Binding, Förster Resonance Energy Transfer, and Conformational Change in the Biosensor TN-XXL

Geiger, A., Russo, L., Gensch, T., Thestrup, T., Becker, S., Hopfner, K., Griesinger, C., Witte, G., & Griesbeck, O. (2012) · Biophysical Journal · doi:10.1016/j.bpj.2012.03.065 · Cited by 46

The revolution continues

Linden, H. R. (1995) · The Electricity Journal · doi:10.1016/1040-6190(95)90142-6 · Cited by 31

In vivo functional properties of juxtaglomerular neurons in the mouse olfactory bulb

Homma, R., Kovalchuk, Y., Konnerth, A., Cohen, L. B., & Garaschuk, O. (2013) · Frontiers in Neural Circuits · doi:10.3389/fncir.2013.00023 · Cited by 26

Ratiometric optical nanoprobes enable accurate molecular detection and imaging

Huang, X., Song, J., Yung, B. C., Huang, X., Xiong, Y., & Chen, X. (2018) · Chemical Society Reviews · doi:10.1039/c7cs00612h · Cited by 820

Thy1-GCaMP6 transgenic mice for neuronal population imaging in vivo

Dana, H., Chen, T.-W., Hu, A., Shields, B. C., Guo, C., Looger, L. L., Kim, D. S., & Svoboda, K. (2014) · PLoS ONE · doi:10.1371/journal.pone.0108697 · Cited by 574

Glioblastoma hijacks neuronal mechanisms for brain invasion

Venkataramani, V., Yang, Y., Schubert, M. C., Reyhan, E., Tetzlaff, S. K., Wißmann, N., Botz, M., Soyka, S. J., Beretta, C. A., Pramatarov, R. L., et al. (2022) · Cell · doi:10.1016/j.cell.2022.06.054 · Cited by 632

A Critical and Comparative Review of Fluorescent Tools for Live-Cell Imaging

Specht, E. A., Braselmann, E., & Palmer, A. E. (2017) · Annual Review of Physiology · doi:10.1146/annurev-physiol-022516-034055 · Cited by 444

Transplanted embryonic neurons integrate into adult neocortical circuits

Falkner, S., Grade, S., Dimou, L., Conzelmann, K.-K., Bonhoeffer, T., Götz, M., & Hübener, M. (2016) · Nature · doi:10.1038/nature20113 · Cited by 174