Gradinaru lab publications in PubMed and bioRxiv.
2023
Removal of a partial genomic duplication restores synaptic transmission and behavior in the MyosinVA mutant mouse Flailer
November 14 2023, BMC Biology
Bustos FJ, Pandian S, Haensgen H, Zhao J-P, Strouf H, Heidenreich M, Swiech L, Deverman BE, Gradinaru V, Zhang F, Constantine-Paton M
Characterization and quantification of adeno-associated virus capsid-loading states by multi-wavelength analytical ultracentrifugation with UltraScan
October 25 2023, Nanomedicine
Henrickson A, Ding X, Seal AG, Qu Z, Tomlinson L, Forsey J, Gradinaru V, Oka K, Demeler B
Immediate responses to ambient light in vivo reveal distinct subpopulations of suprachiasmatic VIP neurons
September 9 2023, iScience
Kahan A, Mahe K, Dutta S, Kassraian P, Wang A, Gradinaru V
Adeno-associated viral vectors for functional intravenous gene transfer throughout the non-human primate brain
July 10 2023, Nature Nanotechnology
Chuapoco MR*, Flytzanis NC*, Goeden N*, Octeau JC, Roxas KM, Chan KY, Scherrer J, Winchester J, Blackburn RJ, Campos LJ, Man KNM, Sun J, Chen X, Lefevre A, Singh VP, Arokiaraj CM, Shay TF, Vendemiatti J, Jang MJ, Mich JK, Bishaw Y, Gore BB, Omstead V, Taskin N, Weed N, Levi BP, Ting JT, Miller CT, Deverman BE, Pickel J, Tian L, Fox AS, Gradinaru V
Functional gene delivery to and across brain vasculature of systemic AAVs with endothelial-specific tropism in rodents and broad tropism in primates
June 8 2023, Nature Communications
Chen X, Wolfe DA, Bindu DS, Zhang M, Taskin N, Goertsen D, Shay TF, Sullivan EE, Huang S-F, Ravindra Kumar S, Arokiaraj CM, Plattner VM, Campos LJ, Mich JK, Monet D, Ngo V, Ding X, Omstead V, Weed N, Bishaw Y, Gore BB, Lein ES, Akrami A, Miller C, Levi BP, Keller A, Ting JT, Fox AS, Eroglu C, Gradinaru V
Primate-conserved carbonic anhydrase IV and murine-restricted LY6C1 enable blood-brain barrier crossing by engineered viral vectors
April 19 2023, Science Advances
Shay TF*+, Sullivan EE*, Ding X*, Chen X, Ravindra Kumar S, Goertsen D, Brown D, Crosby A, Vielmetter J, Borsos M, Wolfe DA, Lam AW, Gradinaru V+
Advances in AAV technology for delivering genetically encoded cargo to the nonhuman primate nervous system
April 12 2023, Current Research in Neurobiology
Campos LJ*, Arokiaraj CM*, Chuapoco MR, Chen X, Goeden N, Gradinaru V+, Fox AS+
CRISPR-clear imaging of melanin-rich B16-derived solid tumors
April 4 2023, Communications Biology
Schubert R, Bae T, Simic B, Smith SN, Park S-H, Nagy-Davidescu G, Gradinaru V, PlĂĽckthun A, Hur JK
Spatial transcriptomics for profiling the tropism of viral vectors in tissues
January 26 2023, Nature Biotechnology
Jang MJ, Coughlin GM, Jackson CR, Chen X, Chuapoco M, Vendemiatti JL, Wang AZ, Gradinaru V
Dysregulated mammalian estrus cycle rescued by timed activation of VIP neurons in the circadian pacemaker and late afternoon light exposure
January 17 2023, bioRxiv
Kahan A, Coughlin GM, Borsos M, Brunton BW, Gradinaru V
Fast, accurate ranking of engineered proteins by receptor binding propensity using structural modeling
January 14 2023, bioRxiv
Ding X, Chen X, Sullivan EE, Shay TF, Gradinaru V
2022
A prebiotic diet modulates microglial states and motor deficits in α-synuclein overexpressing mice
November 8 2022, eLife
Abdel-Haq R, Schlachetzki JCM, Boktor JC, Cantu-Jungles TM, Thron T, Zhang M, Bostick JW, Khazaei T, Chilakala S, Morais LH, Humphrey G, Keshavarzian A, Katz JE, Thomson M, Knight R, Gradinaru V, Hamaker BR, Glass CK, Mazmanian SK
Molecular basis of astrocyte diversity and morphology across the CNS in health and disease
November 4 2022, Science
Endo F, Kasai A, Soto JS, Yu X, Qu Z, Hashimoto H, Gradinaru V, Kawaguchi R, Khakh BS
Targeting the lung epithelium after intravenous delivery by directed evolution of underexplored sites on the AAV capsid
August 9 2022, Molecular Therapy–Methods & Clinical Development
Goertsen D, Goeden N, Flytzanis NC, Gradinaru V
Structural basis of receptor usage by the engineered capsid AAV-PHP.eB
August 9 2022, Molecular Therapy–Methods & Clinical Development
Jang S, Shen HK, Ding X, Miles TF, Gradinaru V
Multimodal imaging of capsid and cargo reveals differential brain targeting and liver detargeting of systemically-administered AAVs
August 6 2022, Biomaterials
Seo JW, Ajenjo J, Wu B, Robinson E, Raie MN, Wang J, Tumbale SK, Buccino P, Anders DA, Shen B, Habte FG, Beinat C, James ML, Reyes ST, Ravindra Kumar S, Miles TF, Lee JT, Gradinaru V, Ferrara KW
Engineered AAVs for non-invasive gene delivery to rodent and non-human primate nervous systems
May 27, 2022, Neuron
Chen X*, Ravindra Kumar S*, Adams CD, Yang D, Wang T, Wolfe DA, Arokiaraj CM, Ngo V, Campos LJ, Griffiths JA, Ichiki T, Mazmanian SK, Osborne PB, Keast JR, Miller CT, Fox AS, Chiu IM, Gradinaru V
Adeno-Associated Virus Toolkit to Target Diverse Brain Cells
Apr 19, 2022, Annu. Rev. Neurosci.
Challis RC, Ravindra Kumar S, Chen X, Goertsen D, Coughlin GM, Hori AM, Chuapoco MR, Otis TS, Miles TF, Gradinaru V
Glutamate in primary afferents is required for itch transmission
Jan 4, 2022, Neuron
Cui L, Guo J, Cranfill SL, Gautam M, Bhattarai J, Olson W, Beattie K, Challis RC, Wu Q, Song X, Raabe T, Gradinaru V, Ma M, Liu Q, Luo W
2021
Multi-Wavelength Analytical Ultracentrifugation of Biopolymer Mixtures and Interactions
Dec 30, 2021, bioRxiv
Henrickson A, Gorbet GE, Savelyev A, Kim M, Schultz SK, Ding X, Hargreaves J, Gradinaru V, Kothe U, Demeler B
AAV capsid variants with brain-wide transgene expression and decreased liver targeting after intravenous delivery in mouse and marmoset
Dec 9, 2021, Nature Neuroscience
Goertsen D, Flytzanis NC, Goeden N, Chuapoco MR, Cummins A, Chen Y, Fan Y, Zhang Q, Sharma J, Duan Y, Wang L, Feng G, Chen Y, Ip NY, Pickel J, Gradinaru V.
Deep Parallel Characterization of AAV Tropism and AAV-Mediated Transcriptional Changes via Single-Cell RNA Sequencing
Oct 12, 2021, Front. Immunol.
Brown D, Altermatt M, Dobreva T, Chen S, Wang A, Thomson M, Gradinaru V.
Light-guided sectioning for precise in situ localization and tissue interface analysis for brain-implanted optical fibers and GRIN lenses
Sep 28, 2021, Cell Rep
Kahan A, Greenbaum A, Jang MJ, Robinson JE, Cho JR, Chen X, Kassraian P, Wagenaar DA, Gradinaru V.
Human embryo polarization requires PLC signaling to mediate trophectoderm specification
Sep 27, 2021, Elife
Zhu M, Shahbazi M, Martin A, Zhang C, Sozen B, Borsos M, Mandelbaum RS, Paulson RJ, Mole MA, Esbert M, Titus S, Scott RT, Campbell A, Fishel S, Gradinaru V, Zhao H, Wu K, Chen Z, Seli E, de Los Santos MJ, Zernicka-Goetz M.
Improved systemic AAV gene therapy with a neurotrophic capsid in Niemann-Pick disease type C1 mice
Aug 18, 2021, Life Sci Alliance
Davidson CD, Gibson AL, Gu T, Baxter LL, Deverman BE, Beadle K, Incao AA, Rodriguez-Gil JL, Fujiwara H, Jiang X, Chandler RJ, Ory DS, Gradinaru V, Venditti CP, Pavan WJ
Brain-wide Cas9-mediated cleavage of a gene causing familial Alzheimer’s disease alleviates amyloid-related pathologies in mice
July 26, 2021, Nat Biomed Eng.
Duan Y, Ye T, Qu Z, Chen Y, Miranda A, Zhou X, Lok KC, Chen Y, Fu AKY, Gradinaru V, Ip NY
Age-dependent alterations in key components of the nigrostriatal dopaminergic system and distinct motor phenotypes
July 09, 2021, Acta Pharmacologica Sinica
Jiang-peng Fan, Hui-zhen Geng, Ya-wei Ji, Tao Jia, Jennifer B. Treweek, An-an Li, Chun-yi Zhou, Viviana Gradinaru & Cheng Xiao
Microbiota regulate social behaviour via stress response neurons in the brain
June 30, 2021, Nature
Wei-Li Wu, Mark D. Adame, Chia-Wei Liou, Jacob T. Barlow, Tzu-Ting Lai, Gil Sharon, Catherine E. Schretter, Brittany D. Needham, Madelyn I. Wang, Weiyi Tang, James Ousey, Yuan-Yuan Lin, Tzu-Hsuan Yao, Reem Abdel-Haq, Keith Beadle, Viviana Gradinaru, Rustem F. Ismagilov & Sarkis K. Mazmanian
Specific and behaviorally consequential astrocyte Gq GPCR signaling attenuation in vivo with iβARK
June 16, 2021, Neuron
Jun Nagai, Arash Bellafard, Zhe Qu, Xinzhu Yu, Matthias Ollivier, Mohitkumar R Gangwani, Blanca Diaz-Castro, Giovanni Coppola, Sarah M Schumacher, Peyman Golshani, Viviana Gradinaru, Baljit S Khakh
The SHREAD gene therapy platform for paracrine delivery improves tumor localization and intratumoral effects of a clinical antibody
May 25, 2021, PNAS
Sheena N. Smith, Rajib Schubert, Branko Simic, Dominik BrĂĽcher, Markus Schmid, Niels Kirk, Patrick C. Freitag, Viviana Gradinaru, and Andreas PlĂĽckthun
Use of high-content imaging to quantify transduction of AAV-PHP viruses in the brain following systemic delivery
May 17, 2021, Brain Communications
Edward J Smith, Pamela P Farshim, Rachel Flomen, Samuel T Jones, Sean J McAteer, Benjamin E Deverman, Viviana Gradinaru, Gillian P Bates
Cholinergic neurons constitutively engage the ISR for dopamine modulation and skill learning in mice
April 23, 2021, Science
Ashley R Helseth, Ricardo Hernandez-Martinez, Victoria L Hall, Matthew L Oliver, Brandon D Turner, Zachary F Caffall, Joseph E Rittiner, Miranda K Shipman, Connor S King, Viviana Gradinaru, Charles Gerfen, Mauro Costa-Mattioli, Nicole Calakos.
Enhancer viruses for combinatorial cell-subclass-specific labeling
March 30, 2021, Neuron
Lucas T. Graybuck, Tanya L. Daigle, Adriana E. Sedeño-Cortés, Miranda Walker, Brian Kalmbach, Garreck H. Lenz, Elyse Morin, Thuc Nghi Nguyen, Emma Garren, Jacqueline L. Bendrick, Tae Kyung Kim, Thomas Zhou, Marty Mortrud, Shenqin Yao, La’ Akea Siverts, Rachael Larsen, Bryan B. Gore, Eric R. Szelenyi, Cameron Trader, Pooja Balaram, Cindy T.J. van Velthoven, Megan Chiang, John K. Mich, Nick Dee, Jeff Goldy, Ali H. Cetin, Kimberly Smith, Sharon W. Way, Luke Esposito, Zizhen Yao, Viviana Gradinaru, Susan M. Sunkin, Ed Lein, Boaz P. Levi, Jonathan T. Ting, Hongkui Zeng, Bosiljka Tasic
Functional enhancer elements drive subclass-selective expression from mouse to primate neocortex
March 30, 2021, Cell Reports
John K Mich, Lucas T Graybuck, Erik E Hess, Joseph T Mahoney, Yoshiko Kojima, Yi Ding, Saroja Somasundaram, Jeremy A Miller, Brian E Kalmbach, Cristina Radaelli, Bryan B Gore, Natalie Weed, Victoria Omstead, Yemeserach Bishaw, Nadiya V Shapovalova, Refugio A Martinez, Olivia Fong, Shenqin Yao, Marty Mortrud, Peter Chong, Luke Loftus, Darren Bertagnolli, Jeff Goldy, Tamara Casper, Nick Dee, Ximena Opitz-Araya, Ali Cetin, Kimberly A Smith, Ryder P Gwinn, Charles Cobbs, Andrew L Ko, Jeffrey G Ojemann, C Dirk Keene, Daniel L Silbergeld, Susan M Sunkin, Viviana Gradinaru, Gregory D Horwitz, Hongkui Zeng, Bosiljka Tasic, Ed S Lein, Jonathan T Ting, Boaz P Levi
Dorsal raphe dopamine neurons signal motivational salience dependent on internal state, expectation, and behavioral context
February 9, 2021, Journal of Neuroscience
Jounhong Ryan Cho, Xinhong Chen, Anat Kahan, J. Elliott Robinson, Daniel A. Wagenaar and Viviana Gradinaru.
2020
Directed Evolution of a Selective and Sensitive Serotonin Sensor via Machine Learning
December 16, 2020, Cell
Elizabeth K. Unger, Jacob P. Keller, Michael Altermatt, Ruqiang Liang, Aya Matsui, Chunyang Dong, Olivia J. Hon, Zi Yao, Junqing Sun, Samba Banala, Meghan E. Flanigan, David A. Jaffe, Samantha Hartanto, Jane Carlen, Grace O. Mizuno, Phillip M. Borden, Amol V. Shivange, Lindsay P. Cameron, Steffen Sinning, Suzanne M. Underhill, David E. Olson, Susan G. Amara, Duncan Temple Lang, Gary Rudnick, Jonathan S. Marvin, Luke D. Lavis, Henry A. Lester, Veronica A. Alvarez, Andrew J. Fisher, Jennifer A. Prescher, Thomas L. Kash, Vladimir Yarov-Yarovoy, Viviana Gradinaru, Loren L. Looger, and Lin Tian.
Negative feedback control of neuronal activity by microglia
September 30, 2020, Nature
Ana Badimon, Hayley J Strasburger, Pinar Ayata, Xinhong Chen, Aditya Nair, Ako Ikegami, Philip Hwang, Andrew T Chan, Steven M Graves, Joseph O Uweru, Carola Ledderose, Munir Gunes Kutlu, Michael A Wheeler, Anat Kahan, Masago Ishikawa, Ying-Chih Wang, Yong-Hwee E Loh, Jean X Jiang, D James Surmeier, Simon C Robson, Wolfgang G Junger, Robert Sebra, Erin S Calipari, Paul J Kenny, Ukpong B Eyo, Marco Colonna, Francisco J Quintana, Hiroaki Wake, Viviana Gradinaru, Anne Schaefer
Dorsal raphe dopamine neurons signal motivational salience dependent on internal and external states
July 27, 2020, BioRxiv
Jounhong Ryan Cho, Xinhong Chen, Anat Kahan, J. Elliott Robinson, Daniel A. Wagenaar, Viviana Gradinaru
Broad gene expression throughout the mouse and marmoset brain after intravenous delivery of engineered AAV capsids
June 17, 2020, BioRxiv
Nicholas C. Flytzanis, Nick Goeden, David Goertsen, Alexander Cummins, James Pickel, Viviana Gradinaru
Positron emission tomography imaging of novel AAV capsids maps rapid brain accumulation
April 30, 2020, Nature Communications
Jai Woong Seo, Elizabeth S. Ingham, Lisa Mahakian, Spencer Tumbale, Bo Wu, Sadaf Aghevlian, Shahin Shams, Mo Baikoghli, Poorva Jain, Xiaozhe Ding, Nick Goeden, Tatyana Dobreva, Nicholas C. Flytzanis, Michael Chavez, Kratika Singhal, Ryan Leib, Michelle L. James, David J. Segal, R. Holland Cheng, Eduardo A. Silva, Viviana Gradinaru, Katherine W. Ferrara
Multiplexed Cre-dependent selection yields systemic AAVs for targeting distinct brain cell types
April 20, 2020, Nature Methods
Sripriya Ravindra Kumar, Timothy F. Miles, Xinhong Chen, David Brown, Tatyana Dobreva, Qin Huang, Xiaozhe Ding, Yicheng Luo, PĂ©tur H. Einarsson, Alon Greenbaum, Min J. Jang, Benjamin E. Deverman, Viviana Gradinaru
LRP1 is a master regulator of tau uptake and spread
April 1, 2020, Nature
Jennifer N. Rauch, Gabriel Luna, Elmer Guzman, Morgane Audouard, Collin Challis, Youssef E. Sibih, Carolina Leshuk, Israel Hernandez, Susanne Wegmann, Bradley T. Hyman, Viviana Gradinaru, Martin Kampmann, Kenneth S. Kosik.
RecV recombinase system for in vivo targeted optogenomic modifications of single cells or cell populations
March 23, 2020, Nature Methods
Shenqin Yao, Peng Yuan, Ben Ouellette, Thomas Zhou, Marty Mortrud, Pooja Balaram, Soumya Chatterjee, Yun Wang, Tanya L. Daigle, Bosiljka Tasic, Xiuli Kuang, Hui Gong, Qingming Luo, Shaoqun Zeng, Andrew Curtright, Ajay Dhaka, Anat Kahan, Viviana Gradinaru, Radosław Chrapkiewicz, Mark Schnitzer, Hongkui Zeng, Ali Cetin
Gut-seeded α-synuclein fibrils promote gut dysfunction and brain pathology specifically in aged mice
February 17, 2020, Nature Neuroscience
Collin Challis, Acacia Hori, Timothy R. Sampson, Bryan B. Yoo, Rosemary C. Challis, Adam M. Hamilton, Sarkis K. Mazmanian, Laura A. Volpicelli-Daley, Viviana Gradinaru
A gut bacterial amyloid promotes α-synuclein aggregation and motor impairment in mice
February 10, 2020, eLife
Timothy R Sampson, Collin Challis, Neha Jain, Anastasiya Moiseyenko, Mark S Ladinsky, Gauri G Shastri, Taren Thron, Brittany D Needham, Istvan Horvath, Justine W Debelius, Stefan Janssen, Rob Knight, Pernilla Wittung-Stafshede, Viviana Gradinaru, Matthew Chapman, Sarkis K Mazmanian
Tissue clearing and its applications in neuroscience
January 2, 2020, Nature Reviews Neuroscience
Hiroki R. Ueda, Ali Ertürk, Kwanghun Chung, Viviana Gradinaru, Alain Chédotal, Pavel Tomancak, Philipp J. Keller
2019
Imaging neuromodulators with high spatiotemporal resolution using genetically encoded indicators
November 15, 2019, Nature Protocols
Tommaso Patriarchi, Jounhong Ryan Cho, Katharina Merten, Aaron Marley, Gerard Joey Broussard, Ruqiang Liang, John Williams, Axel Nimmerjahn, Mark von Zastrow, Viviana Gradinaru, Lin Tian
Machine learning-guided channelrhodopsin engineering enables minimally invasive optogenetics
October 14, 2019, Nature Methods
Claire N. Bedbrook, Kevin K. Yang, J. Elliott Robinson, Elisha D. Mackey, Viviana Gradinaru, Frances H. Arnold
Optical dopamine monitoring with dLight1 reveals mesolimbic phenotypes in a mouse model of neurofibromatosis type 1
September 23, 2019, eLife
J Elliott Robinson, Gerard M Coughlin, Acacia M Hori, Jounhong Ryan Cho, Elisha D Mackey, Zeynep Turan, Tommaso Patriarchi, Lin Tian, Viviana Gradinaru
The Serotonergic Raphe Promote Sleep in Zebrafish and Mice
June 24, 2019, Neuron
Grigorios Oikonomou, Michael Altermatt, Rong-wei Zhang, Gerard M. Coughlin, Christin Montz, Viviana Gradinaru, David A. Prober
Identification of peripheral neural circuits that regulate heart rate using optogenetic and viral vector strategies
April 26, 2019, Nature Communications
Pradeep S. Rajendran, Rosemary C. Challis, Charless C. Fowlkes, Peter Hanna, John D. Tompkins, Maria C. Jordan, Sarah Hiyari, Beth A. Gabris-Weber, Alon Greenbaum, Ken Y. Chan, Benjamin E. Deverman, Heike MĂĽnzberg, Jeffrey L. Ardell, Guy Salama, Viviana Gradinaru, Kalyanam Shivkumar
TRIM9-Mediated Resolution of Neuroinflammation Confers Neuroprotection upon Ischemic Stroke in Mice
April 9, 2019, Cell Reports
Jianxiong Zeng, Yaoming Wang, Zhifei Luo, Lin-Chun Chang, Ji Seung Yoo, Huan Yan, Younho Choi, Xiaochun Xie, Benjamin E. Deverman, Viviana Gradinaru, Stephanie L. Gupton, Berislav V. Zlokovic, Zhen Zhao, Jae U. Jung
Driving the Next Steps with Technology
February 21, 2019, Neuron
Functional enhancer elements drive subclass-selective expression from mouse to primate neocortex
February 19, 2019, BioRxiv
John K. Mich, Lucas T. Graybuck, Erik E. Hess, Joseph T. Mahoney, Yoshiko Kojima, Yi Ding, Saroja Somasundaram, Jeremy A. Miller, Natalie Weed, Victoria Omstead, Yemeserach Bishaw, Nadiya V. Shapovalova, Refugio A. Martinez, Olivia Fong, Shenqin Yao, Marty Mortrud, Peter Chong, Luke Loftus, Darren Bertagnolli, Jeff Goldy, Tamara Casper, Nick Dee, Ximena Opitz-Araya, Ali Cetin, Kimberly A. Smith, Ryder P. Gwinn, Charles Cobbs, Andrew. L. Ko, Jeffrey G. Ojemann, C. Dirk Keene, Daniel. L. Silbergeld, Susan M. Sunkin, Viviana Gradinaru, Gregory D. Horwitz, Hongkui Zeng, Bosiljka Tasic, Ed S. Lein, Jonathan T. Ting, Boaz P. Levi
Systemic AAV vectors for widespread and targeted gene delivery in rodents
January 8, 2019, Nature Protocols
Rosemary C. Challis, Sripriya Ravindra Kumar, Ken Y. Chan, Collin Challis, Keith Beadle, Min J. Jang, Hyun Min Kim, Pradeep S. Rajendran, John D. Tompkins, Kalyanam Shivkumar, Benjamin E. Deverman, Viviana Gradinaru
2018
Whole-Brain Analysis of Cells and Circuits by Tissue Clearing and Light-Sheet Microscopy
October 31, 2018, The Journal of Neuroscience
Tomoyuki Mano, Alexandre Albanese, Hans-Ulrich Dodt, Ali Erturk, Viviana Gradinaru, Jennifer B. Treweek, Atsushi Miyawaki, Kwanghun Chung, Hiroki R. Ueda
Ultrafast neuronal imaging of dopamine dynamics with designed genetically encoded sensors
May 31, 2018, Science
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
Hydrogel-Tissue Chemistry: Principles and Applications
May 24, 2018, Annual Review of Biophysics
Viviana Gradinaru, Jennifer Treweek, Kristin Overton, Karl Deisseroth
The Neuropeptide Tac2 Controls a Distributed Brain State Induced by Chronic Social Isolation Stress
May 17, 2018, Cell
Moriel Zelikowsky, May Hui, Tomomi Karigo, Andrea Choe, Bin Yang, Mario R. Blanco, Keith Beadle, Viviana Gradinaru, Benjamin E. Deverman, David J. Anderson
Viral Strategies for Targeting the Central and Peripheral Nervous Systems
April 30, 2018, Annual Review of Neuroscience
Claire N. Bedbrook, Benjamin E. Deverman, Viviana Gradinaru
2017
Deep tissue optical focusing and optogenetic modulation with time-reversed ultrasonically encoded light
December 8, 2017, Science Advances
Haowen Ruan, Joshua Brake, J. Elliott Robinson, Yan Liu, Mooseok Jang, Cheng Xiao, Chunyi Zhou, Viviana Gradinaru, Changhuei Yang
Overriding sleep
October 26, 2017, Science
Viviana Gradinaru
Machine learning to design integral membrane channelrhodopsins for efficient eukaryotic expression and plasma membrane localization
October 23, 2017, PLOS Computational Biology
Claire N. Bedbrook, Kevin K. Yang, Austin J. Rice, Viviana Gradinaru, Frances H. Arnold
Q&A: How can advances in tissue clearing and optogenetics contribute to our understanding of normal and diseased biology?
September 25, 2017, BMC Biology
Alon Greenbaum, Min J. Jang, Collin Challis, Viviana Gradinaru
The Jellyfish Cassiopea Exhibits a Sleep-like State
September 21, 2017, Current Biology
Ravi D. Nath, Claire N. Bedbrook, Michael J. Abrams, Ty Basinger, Justin S. Bois, David A. Prober, Paul W. Sternberg, Viviana Gradinaru, Lea Goentoro
Dopaminergic dysfunction in neurodevelopmental disorders: recent advances and synergistic technologies to aid basic research
August 30, 2017, Current Opinion in Neurobiology
J Elliott Robinson, Viviana Gradinaru
Engineered AAVs for efficient noninvasive gene delivery to the central and peripheral nervous systems
June 26, 2017, Nature Neuroscience
Ken Y Chan, Min J Jang, Bryan B Yoo, Alon Greenbaum, Namita Ravi, Wei-Li Wu, Luis Sánchez-Guardado, Carlos Lois, Sarkis K Mazmanian, Benjamin E Deverman, Viviana Gradinaru
Dorsal Raphe Dopamine Neurons Modulate Arousal and Promote Wakefulness by Salient Stimuli
June 8, 2017, Neuron
Jounhong Ryan Cho, Jennifer B. Treweek, J. Elliott Robinson, Cheng Xiao, Lindsay R. Bremner, Alon Greenbaum, Viviana Gradinaru
Global Representations of Goal-Directed Behavior in Distinct Cell Types of Mouse Neocortex
May 17, 2017, Neuron
William E. Allen, Isaac V. Kauvar, Michael Z. Chen, Ethan B. Richman, Samuel J. Yang, Ken Chan, Viviana Gradinaru, Benjamin E. Deverman, Liqun Luo, Karl Deisseroth
Bone CLARITY: Clearing, imaging, and computational analysis of osteoprogenitors within intact bone marrow
April 26, 2017, Science Translational Medicine
Alon Greenbaum, Ken Y. Chan, Tatyana Dobreva, David Brown, Deepak H. Balani, Rogely Boyce, Henry M. Kronenberg, Helen J. McBride, Viviana Gradinaru
Structure-guided SCHEMA recombination generates diverse chimeric channelrhodopsins
March 10, 2017, Proceedings of the National Academy of Sciences
Claire N. Bedbrook, Austin J. Rice, Kevin K. Yang, Xiaozhe Ding, Siyuan Chen, Emily M. LeProust, Viviana Gradinaru, Frances H. Arnold
Directed Evolution of a Bright Near-Infrared Fluorescent Rhodopsin Using a Synthetic Chromophore
March 2, 2017, Cell Chemical Biology
Lukas Herwig, Austin J. Rice, Claire N. Bedbrook, Ruijie K. Zhang, Antti Lignell, Jackson K.B. Cahn, Hans Renata, Sheel C. Dodani, Inha Cho, Long Cai, Viviana Gradinaru, Frances H. Arnold
2016
Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson’s Disease
December 1, 2016, Cell
Timothy R. Sampson, Justine W. Debelius, Taren Thron, Stefan Janssen, Gauri G. Shastri, Zehra Esra Ilhan, Collin Challis, Catherine E. Schretter, Sandra Rocha, Viviana Gradinaru, Marie-Francoise Chesselet, Ali Keshavarzian, Kathleen M. Shannon, Rosa Krajmalnik-Brown, Pernilla Wittung-Stafshede, Rob Knight, Sarkis K. Mazmanian
Global Collaboration, Learning from Other Fields
November 2, 2016, Neuron
Exposing the Three-Dimensional Biogeography and Metabolic States of Pathogens in Cystic Fibrosis Sputum via Hydrogel Embedding, Clearing, and rRNA Labeling
September 27, 2016, mBio
William H. DePas, Ruth Starwalt-Lee, Lindsey Van Sambeek, Sripriya Ravindra Kumar, Viviana Gradinaru, Dianne K. Newman
Regional glutamine deficiency in tumours promotes dedifferentiation through inhibition of histone demethylation
September 12, 2016, Nature Cell Biology
Min Pan, Michael A. Reid, Xazmin H. Lowman, Rajan P. Kulkarni, Thai Q. Tran, Xiaojing Liu, Ying Yang, Jenny E. Hernandez-Davies, Kimberly K. Rosales, Haiqing Li, Willy Hugo, Chunying Song, Xiangdong Xu, Dustin E. Schones, David K. Ann, Viviana Gradinaru, Roger S. Lo, Jason W. Locasale, Mei Kong
Extracting structural and functional features of widely distributed biological circuits with single cell resolution via tissue clearing and delivery vectors
July 6, 2016, Current Opinion in Biotechnology
Jennifer Brooke Treweek, Viviana Gradinaru
Single-molecule RNA detection at depth by hybridization chain reaction and tissue hydrogel embedding and clearing
June 24, 2016, Development
Sheel Shah, Eric Lubeck, Maayan Schwarzkopf, Ting-Fang He, Alon Greenbaum, Chang Ho Sohn, Antti Lignell, Harry M. T. Choi, Viviana Gradinaru, Niles A. Pierce, Long Cai
Cholinergic Mesopontine Signals Govern Locomotion and Reward through Dissociable Midbrain Pathways
April 29, 2016, Neuron
Cheng Xiao, Jounhong Ryan Cho, Chunyi Zhou, Jennifer B. Treweek, Ken Chan, Sheri L. McKinney, Bin Yang, Viviana Gradinaru
Cre-dependent selection yields AAV variants for widespread gene transfer to the adult brain
February 1, 2016, Nature Biotechnology
Benjamin E Deverman, Piers L Pravdo, Bryan P Simpson, Sripriya Ravindra Kumar, Ken Y Chan, Abhik Banerjee, Wei-Li Wu, Bin Yang, Nina Huber, Sergiu P Pasca, Viviana Gradinaru
2015
Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping
October 19, 2015, Nature Protocols
Jennifer B Treweek, Ken Y Chan, Nicholas C Flytzanis, Bin Yang, Benjamin E Deverman, Alon Greenbaum, Antti Lignell, Cheng Xiao, Long Cai, Mark S Ladinsky, Pamela J Bjorkman, Charless C Fowlkes, Viviana Gradinaru
2014
Archaerhodopsin variants with enhanced voltage-sensitive fluorescence in mammalian and Caenorhabditis elegans neurons
September 15, 2014, Nature Communications
Nicholas C. Flytzanis, Claire N. Bedbrook, Hui Chiu, Martin K. M. Engqvist, Cheng Xiao, Ken Y. Chan, Paul W. Sternberg, Frances H. Arnold, Viviana Gradinaru
Directed evolution of a far-red fluorescent rhodopsin
August 25, 2014, Proceedings of the National Academy of Sciences
R. S. McIsaac, M. K. M. Engqvist, T. Wannier, A. Z. Rosenthal, L. Herwig, N. C. Flytzanis, E. S. Imasheva, J. K. Lanyi, S. P. Balashov, V. Gradinaru, F. H. Arnold
Single-Cell Phenotyping within Transparent Intact Tissue through Whole-Body Clearing
July 31, 2014, Cell
Bin Yang, Jennifer B. Treweek, Rajan P. Kulkarni, Benjamin E. Deverman, Chun-Kan Chen, Eric Lubeck, Sheel Shah, Long Cai, Viviana Gradinaru
Bioelectronic medicines: a research roadmap
May 30, 2014, Nature Reviews Drug Discovery
Karen Birmingham, Viviana Gradinaru, Polina Anikeeva, Warren M. Grill, Victor Pikov, Bryan McLaughlin, Pankaj Pasricha, Douglas Weber, Kip Ludwig, Kristoffer Famm
2013
Optogenetic Delay of Status Epilepticus Onset in an In Vivo Rodent Epilepsy Model
April 24, 2013, PLoS ONE
Inna Sukhotinsky, Alexander M. Chan, Omar J. Ahmed, Vikram R. Rao, Viviana Gradinaru, Charu Ramakrishnan, Karl Deisseroth, Ania K. Majewska, Sydney S. Cash
Structural and molecular interrogation of intact biological systems
April 9, 2013, Nature
Kwanghun Chung, Jenelle Wallace, Sung-Yon Kim, Sandhiya Kalyanasundaram, Aaron S. Andalman, Thomas J. Davidson, Julie J. Mirzabekov, Kelly A. Zalocusky, Joanna Mattis, Aleksandra K. Denisin, Sally Pak, Hannah Bernstein, Charu Ramakrishnan, Logan Grosenick, Viviana Gradinaru, Karl Deisseroth
2011
Principles for applying optogenetic tools derived from direct comparative analysis of microbial opsins
December 18, 2011, Nature Methods
Joanna Mattis, Kay M Tye, Emily A Ferenczi, Charu Ramakrishnan, Daniel J O’Shea, Rohit Prakash, Lisa A Gunaydin, Minsuk Hyun, Lief E Fenno, Viviana Gradinaru, Ofer Yizhar, Karl Deisseroth
Leptin regulates the reward value of nutrient
November 13, 2011, Nature Neuroscience
Ana I Domingos, Jake Vaynshteyn, Henning U Voss, Xueying Ren, Viviana Gradinaru, Feng Zang, Karl Deisseroth, Ivan E de Araujo, Jeffrey Friedman
Dynamics of Retrieval Strategies for Remote Memories
October 24, 2011, Cell
Inbal Goshen, Matthew Brodsky, Rohit Prakash, Jenelle Wallace, Viviana Gradinaru, Charu Ramakrishnan, Karl Deisseroth
Amygdala circuitry mediating reversible and bidirectional control of anxiety
March 8, 2011, Nature
Kay M. Tye, Rohit Prakash, Sung-Yon Kim, Lief E. Fenno, Logan Grosenick, Hosniya Zarabi, Kimberly R. Thompson, Viviana Gradinaru, Charu Ramakrishnan, Karl Deisseroth
2010
Cholinergic Interneurons Control Local Circuit Activity and Cocaine Conditioning
December 16, 2010, Science
I. B. Witten, S.-C. Lin, M. Brodsky, R. Prakash, I. Diester, P. Anikeeva, V. Gradinaru, C. Ramakrishnan, K. Deisseroth
Global and local fMRI signals driven by neurons defined optogenetically by type and wiring
May 16, 2010, Nature
Jin Hyung Lee, Remy Durand, Viviana Gradinaru, Feng Zhang, Inbal Goshen, Dae-Shik Kim, Lief E. Fenno, Charu Ramakrishnan, Karl Deisseroth
Molecular and Cellular Approaches for Diversifying and Extending Optogenetics
March 22, 2010, Cell
Viviana Gradinaru, Feng Zhang, Charu Ramakrishnan, Joanna Mattis, Rohit Prakash, Ilka Diester, Inbal Goshen, Kimberly R. Thompson, Karl Deisseroth
Optogenetic interrogation of neural circuits: technology for probing mammalian brain structures
February 18, 2010, Nature Protocols
Feng Zhang, Viviana Gradinaru, Antoine R Adamantidis, Remy Durand, Raag D Airan, Luis de Lecea, Karl Deisseroth
2009
Optical Deconstruction of Parkinsonian Neural Circuitry
March 19, 2009, Science
V. Gradinaru, M. Mogri, K. R. Thompson, J. M. Henderson, K. Deisseroth
2008
eNpHR: a Natronomonas halorhodopsin enhanced for optogenetic applications
August 1, 2008, Brain Cell Biology
Viviana Gradinaru, Kimberly R. Thompson, Karl Deisseroth
Controlling Neuronal Activity
May 1, 2008, American Journal of Psychiatry
M. Bret Schneider, Viviana Gradinaru, Feng Zhang, Karl Deisseroth
2007
Targeting and Readout Strategies for Fast Optical Neural Control In Vitro and In Vivo
December 26, 2007, Journal of Neuroscience
V. Gradinaru, K. R. Thompson, F. Zhang, M. Mogri, K. Kay, M. B. Schneider, K. Deisseroth