Search Search

Publications

2017

  • 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 ]

2016

  • 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 ]

2015

  • 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 ]

2014

  • 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 ]