Publications

Gradinaru Lab Publications in PubMed.

 
  • "Overriding sleep." Gradinaru, V. Science, 2017; 358(6362):457
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  • "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
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  • "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
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  • "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
  • [ Article | Caltech News Release | Science News | Nature News | New York Times | 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
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  • "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
  • [ ReadCube PDF | Article | Caltech News Release | News and Views | 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.
  • [ Article | 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.
  • [ Article | 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.
  • [ Article | 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.
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  • "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.
  • [ Article | 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.
  • [ Article | Caltech News Release]

  • "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.
  • [ Article | Caltech News Release | MiPACT Video]


  • "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.
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  • "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.
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  • "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.
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  • "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.
  • [ Article | 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.
  • [ Article | Caltech News Release | Video | CIRM Blog | F1000 Exceptional]


  • "Neuroscience: Fluorescent boost for voltage sensors" Gradinaru, V.; Flytzanis, N.C. Nature, 2016; 529, 469-470.
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  • "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.
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  • "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.
  • [ Article | 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.
  • [ PDF | Article ]


  • "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.
  • [ Article | Caltech News Release | Nature Methods Research Highlights | SPIE Newsroom | 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.
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  • "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.
    [ PDF | Videos and Images | Caltech News Release | CBS News | BBC News | Nature Research Highlights | Alzforum | NIH Highlights | Faculty of 1000 Exceptional | Nature Biotechnology News and Views ]

  • "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.
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  • "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.
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  • "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.
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  • "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.
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  • "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.
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  • "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.
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  • "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.
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  • "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.
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  • "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.
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  • "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.
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  • "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.
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  • "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.
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  • "Controlling neuronal activity" Schneider, M. B.; Gradinaru, V.; Zhang, F.; Deisseroth, K. Am J Psychiatry, 2008; Vol. 165, p 562.
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  • "eNpHR: a Natronomonas halorhodopsin enhanced for optogenetic applications" Gradinaru, V.; Thompson, K. R.; Deisseroth, K. Brain Cell Biol, 2008;36 (1-4), 129-39.
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  • "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.