Publications

Gradinaru Lab Publications in PubMed.

 
  • 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., Gut microbiota regulate motor deficits and neuroinflammation in a model of Parkinson's desease. Cell, 2016; 167, 1469-1480.
  • [ Article | Caltech News Release]

  • DePas, W.H., Starwart-Lee, R., Van Sambeek, L., Kumar, S.R., Gradinaru, V.*, Newman, D.K.*, Exposing the three-dimensional biogeography and metabolic states of pathogens in cystic fibrosis sputum via hydrogel embedding, clearing, and rRNA labeling. mBio, 2016; doi:10.1128/mBio.00796-16.
  • [ Article | Caltech News Release | MiPACT Video]


  • 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., Regional glutamine deficiency in tumours promotes dedifferentiation through inhibition of histone demethylation. Nat Cell Biol, 2016; doi:10.1038/ncb3410.
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  • Treweek, J.B., Gradinaru, V., Extracting structural and functional features of widely distributed biological circuits with single cell resolution via tissue clearing and delivery vectors. Curr Opin Biotechnol, 2016; 40, 193-207.
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  • 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.@, Single-molecule RNA detection at depth via hybridization chain reaction and tissue hydrogel embedding and clearing. Development, 2016; 90, doi:10.1242/dev.138560.
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  • Xiao, C.; Cho, J.R.; Zhou, C.; Treweek, J.B.; Chan, K.; McKinney, S.L; Yang, B; Gradinaru, V., Cholinergic mesopontine signals govern locomotion and reward through dissociable midbrain pathways. Neuron, 2016; 90, 333-347.
  • [ Article | Caltech News Release]


  • 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., Cre-dependent selection yields AAV variants for widespread gene transfer to the adult brain. Nat Biotech, 2016; doi:10.1038/nbt.3440.
  • [ Article | Caltech News Release | Video | CIRM Blog | F1000 Exceptional]


  • Gradinaru, V.; Flytzanis, N.C., Neuroscience: Fluorescent boost for voltage sensors. Nature, 2016; 529, 469-470.
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  • Skennerton, C.T.; Ward, L.M.; Michel, A.; Metcalfe, K.; Valiente, C.; Mullin, S.; Chan, K.Y.; Gradinaru, V.; Orphan, V.J., Genomic reconstruction of an uncultured hydrothermal vent gammaproteobacterial methanotroph (family Methylothermaceae) indicates multiple adaptations to oxygen limitation. Front. Microbiol., 2015; doi: 10.3389/fmicb.2015.01425.
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  • 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., Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping. Nat Prot, 2015; doi:10.1038/nprot.2015.122.
  • [ Article | Troubleshooting ]


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


  • 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., Archaerhodopsin variants with enhanced voltage-sensitive fluorescence in mammalian and Caenorhabditis elegans neurons. Nat Commu, 2014; 5: 4894; doi:10.1038/ncomms5894.
  • [ Article | Caltech News Release | Nature Methods Research Highlights | SPIE Newsroom | Archer 1 Plasmid on Addgene ]


  • 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., Directed evolution of a far-red fluorescent rhodopsin. PNAS, 2014; doi: 10.1073/pnas.1413987111.
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  • Yang, B.; Treweek, J.B.; Kulkarni, R.J.; Deverman, B.E.; Chen, C.; Lubeck, E.; Shah, S.; Cai, L.; Gradinaru, V., Single-cell phenotyping within transparent intact tissue through whole-body clearing. 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 ]

  • Birmingham, K.; Gradinaru, V.; Anikeeva, P.; Grill, W.M.; Pikov, V.; McLaughlin, B.; Pasricha, P.; Weber, D.; Ludwig, K.; Famm, K., Bioelectronic Medicines: a research roadmap. Nat Rev Drug Discov., 2014; doi: 10.1038/nrd4351.
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  • 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., Structural and molecular interrogation of intact biological systems. Nature, 2013; doi:10.1038/nature12107.
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  • Sukhotinsky I; Chan AM; Ahmed OJ; Rao VR; Gradinaru, V.; Ramakrishnan C; Deisseroth K; Majewska AK; Cash SS. Optogenetic delay of status epilepticus onset in an in vivo rodent epilepsy model. PLoS One, 2013; Apr 24;8(4):e62013.
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  • 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., Principles for applying optogenetic tools derived from direct comparative analysis of microbial opsins. Nat Methods, 2011; Vol. 9, pp 159-72.
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  • Tye, K. M.; Prakash, R.; Kim, S. Y.; Fenno, L. E.; Grosenick, L.; Zarabi, H.; Thompson, K. R.; Gradinaru, V.; Ramakrishnan, C.; Deisseroth, K., Amygdala circuitry mediating reversible and bidirectional control of anxiety. Nature, 2011; Vol. 471, pp 358-62.
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  • Goshen, I.; Brodsky, M.; Prakash, R.; Wallace, J.; Gradinaru, V.; Ramakrishnan, C.; Deisseroth, K., Dynamics of retrieval strategies for remote memories. Cell, 2011; Vol. 147, pp 678-89.
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  • Domingos, A. I.; Vaynshteyn, J.; Voss, H. U.; Ren, X.; Gradinaru, V.; Zang, F.; Deisseroth, K.; de Araujo, I. E.; Friedman, J., Leptin regulates the reward value of nutrient. Nat Neurosci, 2011; Vol. 14, pp 1562-8.
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  • Zhang, F.*; Gradinaru, V.*; Adamantidis, A. R.*; Durand, R.; Airan, R. D.; de Lecea, L.; Deisseroth, K., Optogenetic interrogation of neural circuits: technology for probing mammalian brain structures. Nat Protoc, 2010; Vol. 5, pp 439-56.
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  • Witten, I. B.; Lin, S. C.; Brodsky, M.; Prakash, R.; Diester, I.; Anikeeva, P.; Gradinaru, V.; Ramakrishnan, C.; Deisseroth, K., Cholinergic interneurons control local circuit activity and cocaine conditioning. Science, 2010; Vol. 330, pp 1677-81.
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  • Lee, J. H.; Durand, R.; Gradinaru, V.; Zhang, F.; Goshen, I.; Kim, D. S.; Fenno, L. E.; Ramakrishnan, C.; Deisseroth, K., Global and local fMRI signals driven by neurons defined optogenetically by type and wiring. Nature, 2010; Vol. 465, pp 788-92.
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  • Gradinaru, V.*; Zhang, F*.; Ramakrishnan, C.; Mattis, J.; Prakash, R.; Diester, I.; Goshen, I.; Thompson, K. R.; Deisseroth, K., Molecular and cellular approaches for diversifying and extending optogenetics. Cell, 2010; Vol. 141, pp 154-65. Commentary by Susumu Tonegawa. F1000 must read.
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  • Gradinaru, V.*; Mogri, M.*; Thompson, K. R.; Henderson, J. M.; Deisseroth, K., Optical deconstruction of parkinsonian neural circuitry. Science, 2009; Vol. 324, pp 354-9. Science News Focus. F1000 medicine exceptional.
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  • Schneider, M. B.; Gradinaru, V.; Zhang, F.; Deisseroth, K., Controlling neuronal activity. Am J Psychiatry, 2008; Vol. 165, p 562.
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  • Gradinaru, V.; Thompson, K. R.; Deisseroth, K., eNpHR: a Natronomonas halorhodopsin enhanced for optogenetic applications. Brain Cell Biol, 2008;36 (1-4), 129-39.
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  • Gradinaru, V.; Thompson, K. R.; Zhang, F.; Mogri, M.; Kay, K.; Schneider, M. B.; Deisseroth, K., Targeting and readout strategies for fast optical neural control in vitro and in vivo. Cover Article.┬áJ Neurosci, 2007; Vol. 27, pp 14231-8.