Gradinaru Lab Publications

Publications

Gradinaru Lab Publications in PubMed.

"Broad gene expression throughout the mouse and marmoset brain after intravenous delivery of engineered AAV capsids" Flytzanis, N. C., Goeden, N., Goertsen, D., Cummins, A., Pickel, J., Gradinaru, V. BioRxiv, 2020; 10.1101/2020.06.16.152975
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"Positron emission tomography imaging of novel AAV capsids maps rapid brain accumulation" Seo, J. W., Ingham, E. S., Mahakian, L., Tumbale, S., Wu, B., Aghevlian, S., Shams, S., Baikoghli, M., Jain, P., Ding, X., Goeden, N., Dobreva, T., Flytzanis, N. C., Chavez, M., Singhal, K., Leib, R., James, M. L., Segal, D. J., Cheng, R. H., Silva, E. A, Gradinaru, V., Ferrara, K. W. Nature Communications, 2020; 10.1038/s41467-020-15818-4
[ Article | Free Access Link ]
"Multiplexed Cre-dependent selection yields systemic AAVs for targeting distinct brain cell types" Kumar, S. R., Miles, T. F., Chen, X., Brown, D., Dobreva, T., Huang, Q., Ding, X., Luo, Y., Einarsson, P., Greenbaum, A., Jang, M. J., Deverman, B. E., Gradinaru, V. Nature Methods, 2020; 10.1038/s41592-020-0799-7
[ Article | Free Access Link | News Article]
"LRP1 is a master regulator of tau uptake and spread" Rauch, J. N., Luna, G., Guzman, E., Audouard, M., Challis, C., Sibih, Y., Leshuk, C., Hernandez, I., Wegmann, S., Hyman, B. T., Gradinaru, V., Kampmann, M., Kosik, K. S. Nature, 2020; 10.1038/s41586-020-2156-5
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"RecV recombinase system for in vivo targeted optogenomic modifications of single cells or cell populations" You, S., Yuan, P., Ouellette, B., Zhou, T., Mortrud, M., Balaram, P., Chatterjee, S., Wang, Y., Daigle, T. L., Bosiljka, T., Kuang, X., Gong, H., Luo, Q., Zeng, S., Curtright, A., Dhaka, A., Kahan, A., Gradinaru, V., Chrapkiewicz, R., Schnitzer, M., Zeng, H., Cetin, A. Nature Methods, 2020; 10.1038/s41592-020-0774-3
[ Article | Free Access Link]
"Gut-seeded α-Synuclein fibrils promote gut dysfunction and brain pathology specifically in aged mice" Challis, C., Hori, A., Sampson, T. R., Yoo, B. B., Challis, R. C., Hamilton, A. M., Mazmanian, S. K., Volpicelli-Daley, L. A., Gradinaru, V. Nature Neuroscience, 2020; 10.1038/s41593-020-0589-7
[ Article | Free Access Link | News Article]
"A Gut Bacterial Amyloid Promotes α-Synuclein Aggregation and Motor Impairment in Mice" Sampson, T. R., Challis, C., Neha, J., Moiseyenko, A., Ladinsky, M. S., Shastri, G. G., Thron, T., Needham, B. D., Horvath, I., Debelius, J., Janssen, S., Knight, R., Wittung-Stafshede, P., Gradinaru, V., Chapman, M., Mazmanian, S. K. eLife, 2020; 10.7554/eLife.53111
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"Tissue Clearing and Its Applications in Neuroscience" Ueda, H. R., Ertürk, A., Chung, K., Gradinaru, V., Chédotal, A., Tomancak, P., Keller, P. J., Nature Reviews Neuroscience, 2020; 10.1038/s41583-019-0250-1
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"Imaging neuromodulators with high spatiotemporal resolution using genetically encoded indicators." Patriarchi, T., Cho, J. R., Merten, K., Marley, A., Broussard, G. J., Liang, R., Williams, J., Nimmerjahn, A., von Zastrow, M., Gradinaru, V., Tian, L. Nature Protocols, 2019; 10.1038/s41596-019-0239-2
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"Machine learning-guided channelrhodopsin engineering enables minimally invasive optogenetics." Bedbrook, C. N., Yang, K. K., Robinson, J. E., Mackey, E. D., Gradinaru, V., & Arnold, F. H. Nature Methods, 2019; 10.1038/s41592-019-0583-8
[ Article | Free Access Link | News Article]
"Optical dopamine monitoring with dLight1 reveals mesolimbic phenotypes in a mouse model of neurofibromatosis type 1." Robinson, J. E., Coughlin, G. M., Hori, A. M., Cho, J. R., Mackey, E. D., Turan, Z., Patriarchi, T., Tian, L., Gradinaru, V. eLife, 2019; 10.7554/eLife.48983
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"The Serotonergic Raphe Promote Sleep in Zebrafish and Mice." Oikonomou, G., Altermatt, M., Zhang, R., Coughlin, G. M., Montz, C., Gradinaru, V., & Prober, D. A. Neuron, 2019; 10.1016/j.neuron.2019.05.038
[ Article | Video Abstract]
"Identification of peripheral neural circuits that regulate heart rate using optogenetic and viral vector strategies." Rajendran, P. S., Challis, R. C., Fowlkes, C. C., Hanna, P., Tompkins, J. D., Jordan, M. C., Hiyari, S., Gabris-Weber, B. A., Greenbaum, A., Chan, K. Y., Deverman, B. E., Münzberg, H., Ardell, J. L., Salama, G., Gradinaru, V., Shivkumar, K. Nature Communications, 2019; 10.1038/s41467-019-09770-1
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"TRIM9-Mediated Resolution of Neuroinflammation Confers Neuroprotection upon Ischemic Stroke in Mice." Zeng, J., Wang, Y., Luo, Z., Chang, L.-C., Yoo, J. S., Yan, H., Choi, Y., Xie, X., Deverman, B. E., Gradinaru, V., Gupton, S. L., Zlokovic, B. V., Zhao, Z., Jung, J. U. Cell Reports, 2019; 10.1016/j.celrep.2018.12.055
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"Driving the Next Steps with Technology." (2019). Neuron, 101(4), 556. 10.1016/j.neuron.2019.02.003
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"Epigenetic landscape and AAV targeting of human neocortical cell classes." Mich, J., Hess, E., Graybuck, L., Somasundaram, S., Miller, J., Ding, Y., Shapovalova, N., Fong, O., Yao, S., Mortrud, M., Chong, P., Bertagnolli, D., Goldy, J., Casper, T., Kroll, M., Hodge, R., Bakken, T., Yao, Z., Dee, N., Cetin, A., Smith, K., Gwinn, R., Cobbs, C., Ko, A., Ojemann, J., Keene, C., Silbergeld, D., Gradinaru, V., Sunkin, S., Zeng, H., Lein, E., Tasic, B., Ting, J. and Levi, B. bioRxiv, 2019; 10.1101/555318
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"RecV recombinase system for spatiotemporally controlled light-inducible genomic modifications." Cetin, A., Yao, S., Ouellette, B., Balaram, P., Zhou, T., Mortrud, M., Chatterjee, S., Wang, Y., Daigle, T., Tasic, B., Kuang, X., Gong, H., Luo, Q., Zeng, S., Kahan, A., Gradinaru, V. and Zeng, H. bioRxiv, 2019; 10.1101/553271
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"Systemic AAV vectors for widespread and targeted gene delivery in rodents." Challis, R. C., Kumar, S. R., Chan, K. Y., Challis, C., Beadle, K., Jang, M. J., Kim, H. M., Rajendran, P. S., Tompkins, J. D., Shivkumar, K., Deverman, B. E., Gradinaru, V. Nature Protocols, 2019; 10.1038/s41596-018-0097-3
[ Article | PDF | High resolution fluorescent images]
"Whole-Brain Analysis of Cells and Circuits by Tissue Clearing and Light-Sheet Microscopy." Mano, T., Albanese, A., Dodt, H.-U., Erturk, A., Gradinaru, V., Treweek, J. B., Miyawaki, A., Chung, K., Ueda, H. R. The Journal of Neuroscience, 2018, 38(44), 9330–9337; 10.1523/jneurosci.1677-18.2018
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"Identification of peripheral neural circuits that regulate heart rate using optogenetic and viral vector strategies." Rajendran, P., Challis, R., Fowlkes, C., Hanna, P., Tompkins, J., Jordan, M., Hiyari, S., Gabris-Weber, B., Greenbaum, A., Chan, K., Deverman, B., Munzberg, H., Ardell, J., Salama, G., Gradinaru, V. and Shivkumar, K. bioRxiv, 2018; 10.1101/456483
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"Ultrafast neuronal imaging of dopamine dynamics with designed genetically encoded sensors." Patriarchi, T.*, Cho, J.R.*, Merten, K., Howe, M.W., Marley, A., Xiong, W.H., Folk, R.W., Broussard, G.J., Liang, R., Jang, M.J., Zhong, H., Dombeck, D., von Zastrow, M., Nimmerjahn, A., Gradinaru, V., Williams, J.T., Tian, L. Science, 2018; 10.1126/science.aat4422
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"Hydrogel-tissue chemistry: principles and applications." Gradinaru, V., Treweek, J.B., Overton, K., Deisseroth, K. Annu Rev Biophys, 2018, 20;47:355-376.

"The neuropeptide Tac2 controls a distributed brain state induced by chronic social isolation stress." Zelikowsky, M., Hui, M., Karigo, T., Choe, A., Yang, B., Blanco, M.R., Beadle, K., Gradinaru, V., Deverman, B.E., Anderson, D.J. Cell ,2018; 173(5), 1256-1279
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"Viral Strategies for Targeting the Central and Peripheral Nervous Systems." Bedbrook, C.N., Deverman, B.E., Gradinaru, V. Annu Rev Neurosci 2018, doi: 10.1146/annurev-neuro-080317-062048

"Widespread and targeted gene expression by systemic AAV vectors: Production, purification, and administration." Challis, R.C., Kumar, S.R., Chan, K.Y., Challis, C., Jang, M.J., Rajendran, P.S., Tompkins, J.D., Shivkumar, K., Deverman, B.E., Gradinaru, V. bioRxiv,2018 doi: https://doi.org/10.1101/246405

"Deep tissue optical focusing and optogenetic modulation with time-reversed ultrasonically encoded light." Ruan, H., Brake, J., Robinson, J.E., Liu, Y., Jang, M., Xiao, C., Zhou, C., Gradinaru, V., Yang, C. Science Advances, 2017; 3(12), eaao5520

"Overriding sleep." Gradinaru, V. Science, 2017; 358(6362):457

"Machine learning to design integral membrane channelrhodopsins for efficient eukaryotic expression and plasma membrane localization." Bedbrook, C.N., Yang, K.K., Rice, A.J., Gradinaru, V., Arnold, F.H. PLoS Comput Biol, 2017; 13(10):e1005786

"Q&A: How can advances in tissue clearing and optogenetics contribute to our understanding of normal and diseased biology?" Greenbaum, A., Jang, M.J., Challis, C., Gradinaru, V. BMC Biol, 2017; 15:87

"The jellyfish Cassiopea exhibits a sleep-like state" Nath, R.D.*, Bedbrook, C.N.*, Abrams, M.J.*, Basinger, T., Bois, J.S., Prober, D.A., Sternberg, P.W., Gradinaru, V., Goentoro, L. Curr Biol, 2017; doi:10.1016/j.cub.2017.08.014

Caltech News Release

Washington Post

"Dopaminergic dysfunction in neurodevelopmental disorders: recent advances and synergistic technologies to aid basic research" Robinson, J.E., Gradinaru, V. Curr Opin Neurobio, 2018; 48, 17-29

"Engineered AAVs for efficient noninvasive gene delivery to the central and peripheral nervous systems" Chan, K.Y., Jang, M.J., Yoo, B.B., Greenbaum, A., Ravi, N., Wu, W.L., Sanchez-Guardado, L., Lois, C., Mazmanian, S.K., Devermen, B.E., Gradinaru, V. Nat Neurosci, 2017; doi:10.1038/nn.4593

Caltech News Release

High-Res Images with Captions

"Dorsal raphe dopamine neurons modulate arousal and promote wakefulness by salient stimuli" Cho, J.R., Treweek, J.B., Robinson, J.E., Xiao, C., Bremner, L.R., Greenbaum, A., Gradinaru, V. Neuron, 2017; 94, 1205-1219.

Caltech News Release

"Global representations of goal-directed behavior in distinct cell types of mouse neocortex" Allen, W.E., Kauvar, I.V., Chen, M.Z., Richman, E.B., Yang, S.J., Chan, K., Gradinaru, V., Deverman, B.E., Luo, L., Deisseroth, K. Neuron, 2017;94, 891-907.

DARPA Highlight

"Bone CLARITY: Clearing, imaging, and computational analysis of osteoprogenitors within intact bone marrow" Greenbaum, A.*, Chan, K.Y.*, Dobreva, T., Brown, D., Balani, D.H., Boyce, R., Kronenberg, H.M., McBride, H.J., Gradinaru, V. Sci Transl Med, 2017; 9, eaah6518.

Caltech News Release

Nature Research Highlights

Popular Science

"Structure-guided SCHEMA recombination generates diverse chimeric channelrhodopsins" Bedbrook, C.N., Rice, A.J., Yang, K.K., Ding, X., Chen, E., LeProust, E.M., Gradinaru, V., Arnold, F.H. Proc Natl Acad Sci, 2017; doi:10.1073/pnas.1700269114.

"Directed evolution of a bright near-infrared fluorescent rhodopsin using a synthetic chromophore" Herwig, L., Rice, A.J., Bedbrook, C.N., Zhang, R.K., Lignell, A., Cahn, J.K.B., Renata, H., Dodani, S.C., Cho, I., Cai, L., Gradinaru, V., Arnold, F.H. Cell Chem Biol, 2017; doi:10.1016/j.chembiol.2017.02.008.

Nature Methods Research Highlights

"Gut microbiota regulate motor deficits and neuroinflammation in a model of Parkinson's desease" Sampson, T.R., Debelius, J.W., Thron, T., Janssen, S., Shastri, G.G., Ilhan, Z.E., Challis, C., Schretter, C.E., Rocha, S., Gradinaru, V., Chesselet, M., Keshavarzian, A., Shannon, K.M., Krajmalnik-Brown, R., Wittung-Stafshede, P., Knight, R., Mazmanian, S.K. Cell, 2016; 167, 1469-1480.

Caltech News Release

Global Collaboration, Learning from Other Fields. (2016). Neuron, 92(3), 561–563. 10.1016/j.neuron.2016.10.040
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"Exposing the three-dimensional biogeography and metabolic states of pathogens in cystic fibrosis sputum via hydrogel embedding, clearing, and rRNA labeling" DePas, W.H., Starwart-Lee, R., Van Sambeek, L., Kumar, S.R., Gradinaru, V.*, Newman, D.K.* mBio, 2016; doi:10.1128/mBio.00796-16.

Caltech News Release

"Regional glutamine deficiency in tumours promotes dedifferentiation through inhibition of histone demethylation" Pan, M., Reid, M.A., Lowman, X.H., Kulkarni, R.P., Tran, T.Q., Liu, X., Yang, Y., Hernandez-Davies, J.E., Rosales, K.K., Li, H., Hugo, W., Song, C., Xu, X., Schones, D.E., Ann, D.K., Gradinaru, V., Lo, R.S., Locasale, J.W., Kong, M. Nat Cell Biol, 2016; doi:10.1038/ncb3410.

"Extracting structural and functional features of widely distributed biological circuits with single cell resolution via tissue clearing and delivery vectors" Treweek, J.B., Gradinaru, V. Curr Opin Biotechnol, 2016; 40, 193-207.

"Single-molecule RNA detection at depth via hybridization chain reaction and tissue hydrogel embedding and clearing" Shah, S.*, Lubeck, E.*, Schwarzkopf, M.*, He, T.*, Greenbaum, A.*, Sohn, C.H., Lignell, A., Choi, H.M.T., Gradinaru, V.@, Pierce, N.A.@, Cai, L.@ Development, 2016; 90, doi:10.1242/dev.138560.

"Cholinergic mesopontine signals govern locomotion and reward through dissociable midbrain pathways" Xiao, C.; Cho, J.R.; Zhou, C.; Treweek, J.B.; Chan, K.; McKinney, S.L; Yang, B; Gradinaru, V. Neuron, 2016; 90, 333-347.

Caltech News Release

"Cre-dependent selection yields AAV variants for widespread gene transfer to the adult brain" Deverman, B.E.; Pravdo, P.L.; Simpson, B.P.; Kumar, S.R.; Chan, K.Y.; Banerjee, A.; Wu, W.L.; Yang, B.; Huber, N.; Pasca, S.P.; Gradinaru, V., Nat Biotech, 2016; doi:10.1038/nbt.3440.

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F1000 Exceptional

"Neuroscience: Fluorescent boost for voltage sensors" Gradinaru, V.; Flytzanis, N.C. Nature, 2016; 529, 469-470.

"Genomic reconstruction of an uncultured hydrothermal vent gammaproteobacterial methanotroph (family Methylothermaceae) indicates multiple adaptations to oxygen limitation" Skennerton, C.T.; Ward, L.M.; Michel, A.; Metcalfe, K.; Valiente, C.; Mullin, S.; Chan, K.Y.; Gradinaru, V.; Orphan, V.J. Front Microbiol, 2015; doi: 10.3389/fmicb.2015.01425.

"Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping" Treweek, J.B.; Chan, K.Y.; Flytzanis, N.C.; Yang, B.; Deverman, B.E.; Greenbaum, A.; Lignell, A.; Xiao, C.; Cai, L.; Ladinsky, M.S.; Bjorkman, P.J.; Fowlkes, C.C.; Gradinaru, V. Nat Prot, 2015; doi:10.1038/nprot.2015.122.

Troubleshooting

"Genetically encoded spy peptide fusion system to detect plasma membrane-localized proteins in vivo" Bedbrook, C.N.; Kato, M.; Kumar, S.R.; Lakshmanan, A.; Nath, R.D.; Sun, F.; Sternberg, P.W.; Arnold, F.H.; Gradinaru, V. Chem Biol, 2015; doi:10.1016/j.chembiol.2015.06.020.

"Archaerhodopsin variants with enhanced voltage-sensitive fluorescence in mammalian and Caenorhabditis elegans neurons" Flytzanis*, N.C.; Bedbrook*, C.N.; Chiu, H.; Engqvist, M.K.M.; Xiao, C.; Chan, K.Y.; Sternberg, P.W.; Arnold, F.H.; Gradinaru, V. Nat Commu, 2014; 5: 4894; doi:10.1038/ncomms5894.

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Nature Methods Research Highlights

Archer 1 Plasmid on Addgene

"Directed evolution of a far-red fluorescent rhodopsin" McIsaac, R.S.; Engqvist, M.K.M.; Wannier, T.; Rosenthal, A.Z.; Herwig, L.; Flytzanis, N.C.; Imasheva, E.S.; Lanyi, J.K.; Balashov, S.P.; Gradinaru, V.; Arnold, F.H. Proc Natl Acad Sci USA 2014; doi: 10.1073/pnas.1413987111.
"Single-cell phenotyping within transparent intact tissue through whole-body clearing." Yang, B.; Treweek, J.B.; Kulkarni, R.J.; Deverman, B.E.; Chen, C.; Lubeck, E.; Shah, S.; Cai, L.; Gradinaru, V. Cell, 2014; doi: 10.1016/j.cell.2014.07.017.
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"Bioelectronic Medicines: a research roadmap" Birmingham, K.; Gradinaru, V.; Anikeeva, P.; Grill, W.M.; Pikov, V.; McLaughlin, B.; Pasricha, P.; Weber, D.; Ludwig, K.; Famm, K. Nat Rev Drug Discov, 2014; doi: 10.1038/nrd4351.
"Structural and molecular interrogation of intact biological systems" Chung, K.; Wallace, J; Kim, S.; Kalyanasundaram, S.; Andalman, A.S.; Davidson, T.J.; Mirzabekov, J.J.; Zalocusky, K.A.; Mattis, J; Denisin, A.K.; Pak, S.; Bernstein, H; Ramakrishnan, C.; Grosenick, L.; Gradinaru, V.; Deisseroth, K. Nature, 2013; doi:10.1038/nature12107.
"Optogenetic delay of status epilepticus onset in an in vivo rodent epilepsy model" Sukhotinsky I; Chan, A.M.; Ahmed, O.J.; Rao, V.R.; Gradinaru, V.; Ramakrishnan, C.; Deisseroth, K.; Majewska, A.K.; Cash, S.S. PLoS One, 2013; Apr 24;8(4):e62013.
"Principles for applying optogenetic tools derived from direct comparative analysis of microbial opsins" Mattis, J.; Tye, K. M.; Ferenczi, E. A.; Ramakrishnan, C.; O'Shea, D. J.; Prakash, R.; Gunaydin, L. A.; Hyun, M.; Fenno, L. E.; Gradinaru, V.; Yizhar, O.; Deisseroth, K. Nat Methods, 2011; Vol. 9, pp 159-72.
"Amygdala circuitry mediating reversible and bidirectional control of anxiety" Tye, K. M.; Prakash, R.; Kim, S. Y.; Fenno, L. E.; Grosenick, L.; Zarabi, H.; Thompson, K. R.; Gradinaru, V.; Ramakrishnan, C.; Deisseroth, K. Nature, 2011; Vol. 471, pp 358-62.
"Dynamics of retrieval strategies for remote memories" Goshen, I.; Brodsky, M.; Prakash, R.; Wallace, J.; Gradinaru, V.; Ramakrishnan, C.; Deisseroth, K. Cell, 2011; Vol. 147, pp 678-89.
"Leptin regulates the reward value of nutrient" Domingos, A. I.; Vaynshteyn, J.; Voss, H. U.; Ren, X.; Gradinaru, V.; Zang, F.; Deisseroth, K.; de Araujo, I. E.; Friedman, J. Nat Neurosci, 2011; Vol. 14, pp 1562-8.
"Optogenetic interrogation of neural circuits: technology for probing mammalian brain structures" Zhang, F.*; Gradinaru, V.*; Adamantidis, A. R.*; Durand, R.; Airan, R. D.; de Lecea, L.; Deisseroth, K. Nat Protoc, 2010; Vol. 5, pp 439-56.
"Cholinergic interneurons control local circuit activity and cocaine conditioning" Witten, I. B.; Lin, S. C.; Brodsky, M.; Prakash, R.; Diester, I.; Anikeeva, P.; Gradinaru, V.; Ramakrishnan, C.; Deisseroth, K. Science, 2010; Vol. 330, pp 1677-81.
"Global and local fMRI signals driven by neurons defined optogenetically by type and wiring" Lee, J. H.; Durand, R.; Gradinaru, V.; Zhang, F.; Goshen, I.; Kim, D. S.; Fenno, L. E.; Ramakrishnan, C.; Deisseroth, K. Nature, 2010; Vol. 465, pp 788-92.
"Molecular and cellular approaches for diversifying and extending optogenetics" Gradinaru, V.*; Zhang, F*.; Ramakrishnan, C.; Mattis, J.; Prakash, R.; Diester, I.; Goshen, I.; Thompson, K. R.; Deisseroth, K. Cell, 2010; Vol. 141, pp 154-65. Commentary by Susumu Tonegawa. F1000 must read.
"Optical deconstruction of parkinsonian neural circuitry" Gradinaru, V.*; Mogri, M.*; Thompson, K. R.; Henderson, J. M.; Deisseroth, K. Science, 2009; Vol. 324, pp 354-9. Science News Focus. F1000 medicine exceptional.
"Controlling neuronal activity" Schneider, M. B.; Gradinaru, V.; Zhang, F.; Deisseroth, K. Am J Psychiatry, 2008; Vol. 165, p 562.
"eNpHR: a Natronomonas halorhodopsin enhanced for optogenetic applications" Gradinaru, V.; Thompson, K. R.; Deisseroth, K. Brain Cell Biol, 2008;36 (1-4), 129-39.
"Targeting and readout strategies for fast optical neural control in vitro and in vivo" Gradinaru, V.; Thompson, K. R.; Zhang, F.; Mogri, M.; Kay, K.; Schneider, M. B.; Deisseroth, K., J Neurosci, 2007; Vol. 27, pp 14231-8.