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publication / 2025
Enhancer AAV toolbox for accessing and perturbing striatal cell types and circuits
Neuron
Brain Science

Avery C. Hunker, Morgan E. Wirthlin, Gursajan Gill, Nelson J. Johansen, Marcus Hooper, Victoria Omstead, Sara Vargas, M. Nathaly Lerma, Naz Taskin, Natalie Weed, William D. Laird, Yemeserach M. Bishaw, Jacqueline L. Bendrick, Bryan B. Gore, Yoav Ben-Simon, Ximena Opitz-Araya, Refugio A. Martinez, Sharon W. Way, Bargavi Thyagarajan, Sven Otto, Raymond E. A. Sanchez, Jason R. Alexander, Avalon Amaya, Adam Amster, Joel Arbuckle, Angela Ayala, Pam M. Baker, Tyler Barcelli, Stuard Barta, Darren Bertagnolli, Cameron Bielstein, Prajal Bishwakarma, Jessica Bowlus, Gabriella Boyer, Krissy Brouner, Brittny Casian, Tamara Casper, Anish Bhaswanth Chakka, Rushil Chakrabarty, Peter Chong, Michael Clark, Kaity Colbert, Scott Daniel, Tim Dawe, Maxwell Departee, Peter DiValentin, Nicholas P. Donadio, Nadezhda I. Dotson, Deepanjali Dwivedi, Tom Egdorf, Tim Fliss, Amanda Gary, Jeff Goldy, Conor Grasso, Erin L. Groce, Kathryn Gudsnuk, Warren Han, Zeb Haradon, Sam Hastings, Olivia Helback, Windy V. Ho, Cindy Huang, Tye Johnson, Danielle L. Jones, Zoe Juneau, Jaimie Kenney, Madison Leibly, Su Li, Elizabeth Liang, Henry Loeffler, Nicholas A. Lusk, Zachary Madigan, Jessica Malloy, Jocelin Malone, Rachel McCue, Jose Melchor, John K. Mich, Skyler Moosman, Elyse Morin, Robyn Naidoo, Dakota Newman, Kiet Ngo, Katrina Nguyen, Aaron L. Oster, Ben Ouellette, Alana A. Oyama, Nick Pena, Trangthanh Pham, Elliot Phillips, Christina Pom, Lydia Potekhina, Shea Ransford, Patrick L. Ray, Melissa Reding, Dean F. Rette, Cade Reynoldson, Christine Rimorin, Ana Rios Sigler, Dana B. Rocha, Kara Ronellenfitch, Augustin Ruiz, Lane Sawyer, Josh P. Sevigny, Nadiya V. Shapovalova, Noah Shepard, Lyudmila Shulga, Sherif Soliman, Brian Staats, Michael J. Taormina, Michael Tieu, Yimin Wang, Josh Wilkes, Toren Wood, Thomas Zhou, Ali Williford, Nick Dee, Tyler Mollenkopf, Lydia Ng, Luke Esposito, Brian E. Kalmbach, Shenqin Yao, Jeanelle Ariza, Forrest Collman, Shoaib Mufti, Kimberly Smith, Jack Waters, Ina Ersing, Marcella Patrick, Hongkui Zeng, Ed S. Lein, Yoshiko Kojima, Greg Horwitz, Scott F. Owen, Boaz P. Levi, Tanya L. Daigle, Bosiljka Tasic, Trygve E. Bakken, Jonathan T. Ting

publication / 2025
Exploring brain circuits, one cell type-or more- at a time
Neuron
Brain Science

Bosiljka Tasic, Gord Fishell

publication / 2025
Specific targeting of brain endothelial cells using enhancer AAV vectors
Neuron
Brain Science

Eric Velazquez-Rivera, Oyshi Dey, Nayoon S. Kim, Wenhao Cao, Qiao Ye, Pan Gao, Andy Thai, Jason K. Nguyen, Hai Zhang, Jonathan T. Ting, M. Gopi, Bing Ren, Todd C. Holmes, Xiangmin Xu

publication / 2025
An unsupervised map of excitatory neuron dendritic morphology in the mouse visual cortex
Nature Communications
Brain Science

Marissa A. Weis, Stelios Papadopoulos, Laura Hansel, Timo Lüddecke, Brendan Celii, Paul G. Fahey, Eric Y. Wang, J. Alexander Bae, Agnes L. Bodor, Derrick Brittain, JoAnn Buchanan, Daniel J. Bumbarger, Manuel A. Castro, Forrest Collman, Nuno Maçarico da Costa, Sven Dorkenwald, Leila Elabbady, Akhilesh Halageri, Zhen Jia, Chris Jordan, Dan Kapner, Nico Kemnitz, Sam Kinn, Kisuk Lee, Kai Li, Ran Lu, Thomas Macrina, Gayathri Mahalingam, Eric Mitchell, Shanka Subhra Mondal, Shang Mu, Barak Nehoran, Sergiy Popovych, R. Clay Reid, Casey M. Schneider-Mizell, H. Sebastian Seung, William Silversmith, Marc Takeno, Russel Torres, Nicholas L. Turner, William Wong, Jingpeng Wu, Wenjing Yin, Szi-Chieh Yu, Jacob Reimer, Philipp Berens, Andreas S. Tolias, Alexander S. Ecker

publication / 2025
CAVE: Connectome Annotation Versioning Engine
Nature Methods
Brain Science
Shanahan

Sven Dorkenwald, Casey M. Schneider-Mizell, Derrick Brittain, Akhilesh Halageri, Chris Jordan, Nico Kemnitz, Manual A. Castro, William Silversmith, Jeremy Maitin-Shephard, Jakob Troidl, Hanspeter Pfister, Valentin Gillet, Daniel Xenes, J. Alexander Bae, Agnes L. Bodor, JoAnn Buchanan, Daniel J. Bumbarger, Leila Elabbady, Zhen Jia, Daniel Kapner, Sam Kinn, Kisuk Lee, Kai Li, Ran Lu, Thomas Macrina, Gayathri Mahalingam, Eric Mitchell, Shanka Subhra Mondal, Shang Mu, Barak Nehoran, Sergiy Popovych, Marc Takeno, Russel Torres, Nicholas L. Turner, William Wong, Jingpeng Wu, Wenjing Yin, Szi-Chieh Yu, R. Clay Reid, Nuno Maçarico da Costa, H. Sebastian Seung, Forrest Collman

publication / 2025
Layer-specific input to medial prefrontal cortex is linked to stress susceptibility
Translational Psychiatry
Brain Science

Sabahaddin Taha Solakoğlu, Şefik Evren Erdener, Olga Gliko, Alp Can, Uygar Sümbül, Emine Eren-Koçak

publication / 2025
Connectivity of single neurons classifies cell subtypes in mouse brains
Nature Methods
Brain Science

Lijuan Liu, Zhixi Yun, Linus Manubens-Gil, Hanbo Chen, Feng Xiong, Hongwei Dong, Hongkui Zeng, Michael Hawrylycz, Giorgio A. Ascoli, Hanchuan Peng

publication / 2025
Foundation model of neural activity predicts response to new stimulus types
Nature
Brain Science

Eric Y. Wang, Paul G. Fahey, Zhuokun Ding, Stelios Papadopoulos, Kayla Ponder, Marissa A. Weis, Andersen Chang, Taliah Muhammad, Saumil Patel, Zhiwei Ding, Dat Tran, Jiakun Fu, Casey M. Schneider-Mizell, MICrONS Consortium, R. Clay Reid, Forrest Collman, Nuno Maçarico da Costa, Katrin Franke, Alexander S. Ecker, Jacob Reimer, Xaq Pitkow, Fabian H. Sinz, Andreas S. Tolias

publication / 2025
Functional connectomics reveals general wiring rule in mouse visual cortex
Nature
Brain Science
connectomics

Zhuokun Ding, Paul G. Fahey, Stelios Papadopoulos, Eric Y. Wang, Brendan Celii, Christos Papadopoulos, Andersen Chang, Alexander B. Kunin, Dat Tran, Jiakun Fu, Zhiwei Ding, Saumil Patel, Lydia Ntanavara, Rachel Froebe, Kayla Ponder, Taliah Muhammad, J. Alexander Bae, Agnes L. Bodor, Derrick Brittain, JoAnn Buchanan, Daniel J. Bumbarger, Manuel A. Castro, Erick Cobos, Sven Dorkenwald, Leila Elabbady, Akhilesh Halageri, Zhen Jia, Chris Jordan, Dan Kapner, Nico Kemnitz, Sam Kinn, Kisuk Lee, Kai Li, Ran Lu, Thomas Macrina, Gayathri Mahalingam, Eric Mitchell, Shanka Subhra Mondal, Shang Mu, Barak Nehoran, Sergiy Popovych, Casey M. Schneider-Mizell, William Silversmith, Marc Takeno, Russel Torres, Nicholas L. Turner, William Wong, Jingpeng Wu, Wenjing Yin, Szi-Chieh Yu, Dimitri Yatsenko, Emmanouil Froudarakis, Fabian Sinz, Krešimir Josić, Robert Rosenbaum, H. Sebastian Seung, Forrest Collman, Nuno Maçarico da Costa, R. Clay Reid, Edgar Y. Walker, Xaq Pitkow, Jacob Reimer, Andreas S. Tolias

publication / 2025
Inhibitory specificity from a connectomic census of mouse visual cortex
Nature
Brain Science
connectomics

Casey M. Schneider-Mizell, Agnes L. Bodor, Derrick Brittain, JoAnn Buchanan, Daniel J. Bumbarger, Leila Elabbady, Clare Gamlin, Daniel Kapner, Sam Kinn, Gayathri Mahalingam, Sharmishtaa Seshamani, Shelby Suckow, Marc Takeno, Russel Torres, Wenjing Yin, Sven Dorkenwald, J. Alexander Bae, Manuel A. Castro, Akhilesh Halageri, Zhen Jia, Chris Jordan, Nico Kemnitz, Kisuk Lee, Kai Li, Ran Lu, Thomas Macrina, Eric Mitchell, Shanka Subhra Mondal, Shang Mu, Barak Nehoran, Sergiy Popovych, William Silversmith, Nicholas L. Turner, William Wong, Jingpeng Wu, Jacob Reimer, Andreas S. Tolias, H. Sebastian Seung, R. Clay Reid, Forrest Collman, Nuno Maçarico da Costa

publication / 2025
Integrating multimodal data to understand cortical circuit architecture and function
Nature Neuroscience
Brain Science

Anton Arkhipov, Nuno da Costa, Saskia de Vries, Trygve Bakken, Corbett Bennett, Amy Bernard, Jim Berg, Michael Buice, Forrest Collman, Tanya Daigle, Marina Garrett, Nathan Gouwens, Peter A. Groblewski, Julie Harris, Michael Hawrylycz, Rebecca Hodge, Tim Jarsky, Brian Kalmbach, Jerome Lecoq, Brian Lee, Ed Lein, Boaz Levi, Stefan Mihalas, Lydia Ng, Shawn Olsen, Clay Reid, Joshua H. Siegle, Staci Sorensen, Bosiljka Tasic, Carol Thompson, Jonathan T. Ting, Cindy van Velthoven, Shenqin Yao, Zizhen Yao, Christof Koch, Hongkui Zeng

publication / 2025
NEURD offers automated proofreading and feature extraction for connectomics
Nature
Brain Science

Brendan Celii, Stelios Papadopoulos, Zhuokun Ding, Paul G. Fahey, Eric Wang, Christos Papadopoulos, Alexander B. Kunin, Saumil Patel, J. Alexander Bae, Agnes L. Bodor, Derrick Brittain, JoAnn Buchanan, Daniel J. Bumbarger, Manuel A. Castro, Erick Cobos, Sven Dorkenwald, Leila Elabbady, Akhilesh Halageri, Zhen Jia, Chris Jordan, Dan Kapner, Nico Kemnitz, Sam Kinn, Kisuk Lee, Kai Li, Ran Lu, Thomas Macrina, Gayathri Mahalingam, Eric Mitchell, Shanka Subhra Mondal, Shang Mu, Barak Nehoran, Sergiy Popovych, Casey M. Schneider-Mizell, William Silversmith, Marc Takeno, Russel Torres, Nicholas L. Turner, William Wong, Jingpeng Wu, Szi-Chieh Yu, Wenjing Yin, Daniel Xenes, Lindsey M. Kitchell, Patricia K. Rivlin, Victoria A. Rose, Caitlyn A. Bishop, Brock Wester, Emmanouil Froudarakis, Edgar Y. Walker, Fabian Sinz, H. Sebastian Seung, Forrest Collman, Nuno Maçarico da Costa, R. Clay Reid, Xaq Pitkow, Andreas S. Tolias, Jacob Reimer

publication / 2025
Perisomatic ultrastructure efficiently classifies cells in mouse cortex
Nature
Brain Science

Leila Elabbady, Sharmishtaa Seshamani, Shang Mu, Gayathri Mahalingam, Casey M. Schneider-Mizell, Agnes L. Bodor, J. Alexander Bae, Derrick Brittain, JoAnn Buchanan, Daniel J. Bumbarger, Manuel A. Castro, Sven Dorkenwald, Akhilesh Halageri, Zhen Jia, Chris Jordan, Dan Kapner, Nico Kemnitz, Sam Kinn, Kisuk Lee, Kai Li, Ran Lu, Thomas Macrina, Eric Mitchell, Shanka Subhra Mondal, Barak Nehoran, Sergiy Popovych, William Silversmith, Marc Takeno, Russel Torres, Nicholas L. Turner, William Wong, Jingpeng Wu, Wenjing Yin, Szi-Chieh Yu, H. Sebastian Seung, R. Clay Reid, Nuno Maçarico da Costa, Forrest Collman

publication / 2025
Enabling global image data sharing in the life sciences
Nature Methods
Cell Science

Peter Bajcsy, Sreenivas Bhattiprolu, Katy Börner, Beth A. Cimini, Lucy Collinson, Jan Ellenberg, Reto Fiolka, Maryellen Giger, Wojtek Goscinski, Matthew Hartley, Nathan Hotaling, Rick Horwitz, Florian Jug, Isabel Kemmer, Anna Kreshuk, Emma Lundberg, Aastha Mathur, Kedar Narayan, Shuichi Onami, Anne L. Plant, Fred Prior, Jason R. Swedlow, Adam Taylor, Antje Keppler

publication / 2025
VIP-to-SST Cell Circuit Motif Shows Differential Short-Term Plasticity across Sensory Areas of Mouse Cortex
The Journal of Neuroscience: The Official Journal of the Society for Neuroscience
Brain Science

Jenifer Rachel, Martin Möck, Tanya L. Daigle, Bosiljka Tasic, Mirko Witte, Jochen F. Staiger

preprint / 2025
Glutamate indicators with increased sensitivity and tailored deactivation rates
Neural Dynamics

Abhi Aggarwal, Adrian Negrean, Yang Chen, Rishyashring Iyer, Daniel Reep, Anyi Liu, Anirudh Palutla, Michael E. Xie, Bryan J. MacLennan, Kenta M. Hagihara, Lucas W. Kinsey, Julianna L. Sun, Pantong Yao, Jihong Zheng, Arthur Tsang, Getahun Tsegaye, Yonghai Zhang, Ronak H. Patel, Benjamin J. Arthur, Julien Hiblot, Philipp Leippe, Miroslaw Tarnawski, Jonathan S. Marvin, Jason D. Vevea, Srinivas C. Turaga, Alison G. Tebo, Matteo Carandini, L. F. Rossi, David Kleinfeld, Arthur Konnerth, Karel Svoboda, Glenn C. Turner, Jeremy Hasseman, Kaspar Podgorski

publication / 2025
Interneuron-specific dual-AAV SCN1A gene replacement corrects epileptic phenotypes in mouse models of Dravet syndrome
Science Translational Medicine
Brain Science
Brain Health

John K. Mich, Jiyun Ryu, Aguan D. Wei, Bryan B. Gore, Rong Guo, Angela M. Bard, Refugio A. Martinez, Emily M. Luber, Jiatai Liu, Yemeserach M. Bishaw, Robert J. Christian, Luiz M. Oliveira, Nicole Miranda, Jan-Marino Ramirez, Jonathan T. Ting, Ed S. Lein, Boaz P. Levi, Franck K. Kalume

publication / 2025
A versatile cell line for establishing potency of cell type-specific AAV transgenes
Molecular Therapy. Methods & Clinical Development
Brain Science

Refugio A. Martinez, Yemeserach M. Bishaw, Meagan A. Quinlan, Erin L. Groce, Bryan B. Gore, Ed S. Lein, John K. Mich, Boaz P. Levi

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