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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; link to article
  • 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; link to articlefree access linknews 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; link to rticle
  • 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; link to article; free access link; 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; link to article

  • 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; link to article

  • Machine learning-guided channelrhodopsin engineering enables minimally-invasive optogenetics. Bedbrook, C. N., Yang, K. K., Robinson, J. E., Gradinaru, V., & Arnold, F. H. bioRxiv, 2019; 10.1101/565606; link to article
  • 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; link to article

  • 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; link to article

  • 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; to 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; to pdf

  • 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; link to article
  • Ultrafast neuronal imaging of dopamine dynamics with designed genetically encoded sensors Tommaso Patriarchi, Jounhong Ryan Cho, Katharina Merten, Mark W. Howe, Aaron Marley, Wei-Hong Xiong, Robert W. Folk, Gerard Joey Broussard, Ruqiang Liang, Min Jee Jang, Haining Zhong, Daniel Dombeck, Mark von Zastrow, Axel Nimmerjahn, Viviana Gradinaru, John T. Williams, Lin Tian Science 31 May 2018:eaat4422
    DOI: 10.1126/science.aat4422 link to pdf

  • Hydrogel-Tissue Chemistry: Principles and Applications. Gradinaru V, Treweek J, Overton K, Deisseroth K. Annu Rev Biophys. 2018 May 20;47:355-376. doi: 10.1146/annurev-biophys-070317-032905. PubMed PMID: 29792820; link to pdf

  • The Neuropeptide Tac2 Controls a Distributed Brain State Induced by Chronic Social Isolation Stress Moriel Zelikowsky, May Hui, Tomomi Karigo, Andrea Choe, Bin Yang, Mario R. Blanco, Keith Beadle, Viviana Gradinaru, Benjamin E. Deverman and David J. Anderson. Cell 2018 May 17;  link to pdf
  • Viral Strategies for Targeting the Central and Peripheral Nervous Systems Bedbrook CN, Deverman BE, Gradinaru V. . Annu Rev Neurosci. 2018 Apr 25. doi: 10.1146/annurev-neuro-080317-062048. [Epub ahead of print] PubMed PMID: 29709207.


  • Machine learning to design integral membrane channelrhodopsins for efficient eukaryotic expression and plasma membrane localization. Bedbrook CN, Yang KK, Rice AJ, Gradinaru V, Arnold FH. PLoS Comput Biol. 2017 Oct 23;13(10):e1005786. doi: 10.1371/journal.pcbi.1005786. [Epub ahead of print] PMID:29059183

  • 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; doi: 10.1186/s12915-017-0421-3 [Article
  • 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., Deverman, B.E., Gradinaru, V. Nature Neuroscience, 2017; doi:10.1038/nn.4593. [ Article | Caltech News Release | News and Views | Cover open access link ]
  • 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. [ Article ]
  • 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 ]


  • 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. [ Article ]
  • 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. [ Article ]
  • 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. [ Article ]
  • 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. [ Article ]


  • 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. [ Article ] 
  • 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 ]


  • 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. [ Article ]