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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

publication / 2025
Provide proactive reproducible analysis transparency with every publication
Royal Society Open Science
Immunology

Paul Meijer, Nicole Howard, Jessica Liang, Autumn Kelsey, Sathya Subramanian, Ed Johnson, Paul Mariz, James Harvey, Madeline Ambrose, Vitalii Tereshchenko, Aldan Beaubien, Neelima Inala, Yousef Aggoune, Stark Pister, Anne Vetto, Melissa Kinsey, Tom Bumol, Ananda Goldrath, Xiaojun Li, Troy Torgerson, Peter Skene, Lauren Okada, Christian La France, Zach Thomson, Lucas Graybuck

publication / 2025
A large field of view 2- and 3-photon microscope
Light, Science & Applications
Brain Science

Jack Waters

publication / 2025
Multiplex generation and single-cell analysis of structural variants in mammalian genomes
Science
Synthetic Biology

Sudarshan Pinglay, Jean-Benoît Lalanne, Riza M. Daza, Sanjay Kottapalli, Faaiz Quaisar, Jonas Koeppel, Riddhiman K. Garge, Xiaoyi Li, David S. Lee, Jay Shendure

publication / 2025
Tissue-resident memory CD8 T cell diversity is spatiotemporally imprinted
Nature
Immunology
Tissue Immunity

Miguel Reina-Campos, Alexander Monell, Amir Ferry, Vida Luna, Kitty P. Cheung, Giovanni Galletti, Nicole E. Scharping, Kennidy K. Takehara, Sara Quon, Peter P. Challita, Brigid Boland, Yun Hsuan Lin, William H. Wong, Cynthia S. Indralingam, Hayley Neadeau, Suzie Alarcón, Gene W. Yeo, John T. Chang, Maximilian Heeg, Ananda W. Goldrath

preprint / 2025
Adaptation, not prediction, drives neuronal spiking responses in mammalian sensory cortex
Neural Dynamics

Jacob A. Westerberg, Yihan S. Xiong, Hamed Nejat, Eli Sennesh, Séverine Durand, Ben Hardcastle, Hannah Cabasco, Hannah Belski, Ahad Bawany, Ryan Gillis, Henry Loeffler, Carter R. Peene, Warren Han, Katrina Nguyen, Vivian Ha, Tye Johnson, Conor Grasso, Ahrial Young, Jackie Swapp, Ben Ouellette, Shiella Caldejon, Ali Williford, Peter A. Groblewski, Shawn R. Olsen, Carly Kiselycznyk, Jerome A. Lecoq, Alexander Maier, André M. Bastos

publication / 2025
Transcriptional determinants of goal-directed learning and representational drift in the parahippocampal cortex
Cell Reports
Brain Science

Caroline A. McLachlan, David G. Lee, Osung Kwon, Kevin M. Delgado, Nikita Manjrekar, Zizhen Yao, Hongkui Zeng, Bosiljka Tasic, Jerry L. Chen

publication / 2025
CryoSCAPE: Scalable immune profiling using cryopreserved whole blood for multi-omic single cell and functional assays
Journal of Translational Medicine
Immunology

Alexander T. Heubeck, Cole Phalen, Neel Kaul, Peter J. Wittig, Jessica Garber, Morgan Weiss, Palak C. Genge, Zachary Thomson, Claire Gustafson, Julian Reading, Peter J. Skene

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