Gradinaru lab publications in PubMed and bioRxiv.


Fast, accurate ranking of engineered proteins by target binding propensity using structure modeling

April 6 2024, Molecular Therapy

Ding X+, Chen X, Sullivan EE, Shay TF, Gradinaru V+

Peripheral neuronal activation shapes the microbiome and alters gut physiology

March 21 2024, Cell Reports

Griffiths JA*, Yoo BB*, Thuy-Boun P, Cantu VJ, Weldon KC, Challis C, Sweredoski MJ, Chan KY, Thron TM, Sharon G, Moradian A, Humphrey G, Zhu Q, Shaffer JP, Wolan DW, Dorrestein PC, Knight R, Gradinaru V, Mazmanian SK

Synthetic dosage-compensating miRNA circuits allow precision gene therapy for Rett syndrome

March 14 2024, bioRxiv

Flynn MJ*, Mayfield AMH*, Du R, Gradinaru V+, Elowitz MB+

Human cell surface-AAV interactomes identify LRP6 as blood-brain-barrier transcytosis receptor and immune cytokine IL3 as AAV9 binder

January 5 2024, bioRxiv

Shay TF*+, Jang S*, Chen X*, Walker B, Tebbutt C, Wolfe DA, Brittain TJ, Arokiaraj CM, Sullivan EE, Ding X, Wang T-Y, Lei Y, Chuapoco MR, Chou T-F, Gradinaru V+


Spatial genomics of AAVs reveals mechanism of transcriptional crosstalk that enables targeted delivery of large genetic cargo

December 14 2023, bioRxiv

Coughlin GM*, Borsos M*, Appling N†, Barcelona BH†, Mayfield AMH, Mackey ED, Eser RA, Chen X, Ravindra Kumar S, Gradinaru V

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, Plückthun 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


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


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 Brücher, Markus Schmid, Niels Kirk, Patrick C. Freitag, Viviana Gradinaru, and Andreas Plückthun

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.


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, Pétur 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


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 Münzberg, 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


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


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


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


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


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


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


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


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


Optical Deconstruction of Parkinsonian Neural Circuitry

March 19, 2009, Science

V. Gradinaru, M. Mogri, K. R. Thompson, J. M. Henderson, K. Deisseroth


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


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