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Publications

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Nature Neuroscience

Long-term labeling and imaging of synaptically connected neuronal networks in vivo using double-deletion-mutant rabies viruses

Jan 11, 2024

Lei Jin, Heather A. Sullivan, Mulangma Zhu, Thomas K. Lavin, Makoto Matsuyama, Xin Fu, Nicholas E. Lea, Ran Xu, YuanYuan Hou, Luca Rutigliani, Maxwell Pruner, Kelsey R. Babcock, Jacque Pak Kan Ip, Ming Hu, Tanya L. Daigle, Hongkui Zeng, Mriganka Sur, Guoping Feng, Ian R. Wickersham

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Nature

Author Correction: Conserved and divergent gene regulatory programs of the mammalian neocortex

Jan 10, 2024

Nathan R. Zemke, Ethan J. Armand, Wenliang Wang, Seoyeon Lee, Jingtian Zhou, Yang Eric Li, Hanqing Liu, Wei Tian, Joseph R. Nery, Rosa G. Castanon, Anna Bartlett, Julia K. Osteen, Daofeng Li, Xiaoyu Zhuo, Vincent Xu, Lei Chang, Keyi Dong, Hannah S. Indralingam, Jonathan A. Rink, Yang Xie, Michael Miller, Fenna M. Krienen, Qiangge Zhang, Naz Taskin, Jonathan Ting, Guoping Feng, Steven A. McCarroll, Edward M. Callaway, Ting Wang, Ed S. Lein, M. Margarita Behrens, Joseph R. Ecker, Bing Ren

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Nature Neuroscience

Backward masking in mice requires visual cortex

Jan 01, 2024

Samuel D. Gale, Chelsea Strawder, Corbett Bennett, Stefan Mihalas, Christof Koch, Shawn R. Olsen

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eLife

Myomatrix arrays for high-definition muscle recording

Dec 19, 2023

Bryce Chung, Muneeb Zia, Kyle A. Thomas, Jonathan A. Michaels, Amanda Jacob, Andrea Pack, Matthew J. Williams, Kailash Nagapudi, Lay Heng Teng, Eduardo Arrambide, Logan Ouellette, Nicole Oey, Rhuna Gibbs, Philip Anschutz, Jiaao Lu, Yu Wu, Mehrdad Kashefi, Tomomichi Oya, Rhonda Kersten, Alice C. Mosberger, Sean O'Connell, Runming Wang, Hugo Marques, Ana Rita Mendes, Constanze Lenschow, Gayathri Kondakath, Jeong Jun Kim, William Olson, Kiara N. Quinn, Pierce Perkins, Graziana Gatto, Ayesha Thanawalla, Susan Coltman, Taegyo Kim, Trevor Smith, Ben Binder-Markey, Martin Zaback, Christopher K. Thompson, Simon Giszter, Abigail Person, Martyn Goulding, Eiman Azim, Nitish Thakor, Daniel O'Connor, Barry Trimmer, Susana Q. Lima, Megan R. Carey, Chethan Pandarinath, Rui M. Costa, J. Andrew Pruszynski, Muhannad Bakir, Samuel J. Sober

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eLife

Postsynaptic cell type and synaptic distance do not determine efficiency of monosynaptic rabies virus spread measured at synaptic resolution

Dec 14, 2023

Maribel Patiño, Willian N. Lagos, Neelakshi S. Patne, Paula A. Miyazaki, Sai Krishna Bhamidipati, Forrest Collman, Edward M. Callaway

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Nature

Dynamic behaviour restructuring mediates dopamine-dependent credit assignment

Dec 13, 2023

Jonathan C. Y. Tang, Vitor Paixao, Filipe Carvalho, Artur Silva, Andreas Klaus, Joaquim Alves da Silva, Rui M. Costa

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eNeuro

Developing a Toolbox of Antibodies Validated for Array Tomography-Based Imaging of Brain Synapses

Dec 01, 2023

Kristina D. Micheva, Belvin Gong, Forrest Collman, Richard J. Weinberg, Stephen J. Smith, James S. Trimmer, Karl D. Murray

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Nature Methods

Multi-layered maps of neuropil with segmentation-guided contrastive learning

Dec 01, 2023

Sven Dorkenwald, Peter H. Li, Michał Januszewski, Daniel R. Berger, Jeremy Maitin-Shepard, Agnes L. Bodor, Forrest Collman, Casey M. Schneider-Mizell, Nuno Maçarico da Costa, Jeff W. Lichtman, Viren Jain

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Nature

Molecularly defined and spatially resolved cell atlas of the whole mouse brain

Dec 01, 2023

Meng Zhang, Xingjie Pan, Won Jung, Aaron R. Halpern, Stephen W. Eichhorn, Zhiyun Lei, Limor Cohen, Kimberly A. Smith, Bosiljka Tasic, Zizhen Yao, Hongkui Zeng, Xiaowei Zhuang

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Nature

Single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain

Dec 01, 2023

Hanqing Liu, Qiurui Zeng, Jingtian Zhou, Anna Bartlett, Bang-An Wang, Peter Berube, Wei Tian, Mia Kenworthy, Jordan Altshul, Joseph R. Nery, Huaming Chen, Rosa G. Castanon, Songpeng Zu, Yang Eric Li, Jacinta Lucero, Julia K. Osteen, Antonio Pinto-Duarte, Jasper Lee, Jon Rink, Silvia Cho, Nora Emerson, Michael Nunn, Carolyn O'Connor, Zhanghao Wu, Ion Stoica, Zizhen Yao, Kimberly A. Smith, Bosiljka Tasic, Chongyuan Luo, Jesse R. Dixon, Hongkui Zeng, Bing Ren, M. Margarita Behrens, Joseph R. Ecker

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Nature

Single-cell analysis of chromatin accessibility in the adult mouse brain

Dec 01, 2023

Songpeng Zu, Yang Eric Li, Kangli Wang, Ethan J. Armand, Sainath Mamde, Maria Luisa Amaral, Yuelai Wang, Andre Chu, Yang Xie, Michael Miller, Jie Xu, Zhaoning Wang, Kai Zhang, Bojing Jia, Xiaomeng Hou, Lin Lin, Qian Yang, Seoyeon Lee, Bin Li, Samantha Kuan, Hanqing Liu, Jingtian Zhou, Antonio Pinto-Duarte, Jacinta Lucero, Julia Osteen, Michael Nunn, Kimberly A. Smith, Bosiljka Tasic, Zizhen Yao, Hongkui Zeng, Zihan Wang, Jingbo Shang, M. Margarita Behrens, Joseph R. Ecker, Allen Wang, Sebastian Preissl, Bing Ren

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Nature

Conserved and divergent gene regulatory programs of the mammalian neocortex

Dec 01, 2023

Nathan R. Zemke, Ethan J. Armand, Wenliang Wang, Seoyeon Lee, Jingtian Zhou, Yang Eric Li, Hanqing Liu, Wei Tian, Joseph R. Nery, Rosa G. Castanon, Anna Bartlett, Julia K. Osteen, Daofeng Li, Xiaoyu Zhuo, Vincent Xu, Lei Chang, Keyi Dong, Hannah S. Indralingam, Jonathan A. Rink, Yang Xie, Michael Miller, Fenna M. Krienen, Qiangge Zhang, Naz Taskin, Jonathan Ting, Guoping Feng, Steven A. McCarroll, Edward M. Callaway, Ting Wang, Ed S. Lein, M. Margarita Behrens, Joseph R. Ecker, Bing Ren

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Nature

A transcriptomic taxonomy of mouse brain-wide spinal projecting neurons

Dec 01, 2023

Carla C. Winter, Anne Jacobi, Junfeng Su, Leeyup Chung, Cindy T. J. van Velthoven, Zizhen Yao, Changkyu Lee, Zicong Zhang, Shuguang Yu, Kun Gao, Geraldine Duque Salazar, Evgenii Kegeles, Yu Zhang, Makenzie C. Tomihiro, Yiming Zhang, Zhiyun Yang, Junjie Zhu, Jing Tang, Xuan Song, Ryan J. Donahue, Qing Wang, Delissa McMillen, Michael Kunst, Ning Wang, Kimberly A. Smith, Gabriel E. Romero, Michelle M. Frank, Alexandra Krol, Riki Kawaguchi, Daniel H. Geschwind, Guoping Feng, Lisa V. Goodrich, Yuanyuan Liu, Bosiljka Tasic, Hongkui Zeng, Zhigang He

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The Journal of Neuroscience: The Official Journal of the Society for Neuroscience

Responses to pattern-violating visual stimuli evolve differently over days in somata and distal apical dendrites

Nov 21, 2023

Colleen J. Gillon, Jason E. Pina, Jérôme Lecoq, Ruweida Ahmed, Yazan N. Billeh, Shiella Caldejon, Peter A. Groblewski, Timothy M. Henley, India Kato, Eric Lee, Jennifer Luviano, Kyla Mace, Chelsea Nayan, Thuyanh V. Nguyen, Kat North, Jed Perkins, Sam Seid, Matthew T. Valley, Ali Williford, Yoshua Bengio, Timothy P. Lillicrap, Blake A. Richards, Joel Zylberberg

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Nature Communications

Online conversion of reconstructed neural morphologies into standardized SWC format

Nov 16, 2023

Ketan Mehta, Bengt Ljungquist, James Ogden, Sumit Nanda, Ruben G. Ascoli, Lydia Ng, Giorgio A. Ascoli

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Biological Psychiatry

Linking Neurogenetics and Functional Connectivity in Autism

Nov 15, 2023

Michael Hawrylycz, Thomas Nickl-Jockschat

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Science Advances

Single-cell genomics reveals region-specific developmental trajectories underlying neuronal diversity in the human hypothalamus

Nov 10, 2023

Brian R. Herb, Hannah J. Glover, Aparna Bhaduri, Carlo Colantuoni, Tracy L. Bale, Kimberly Siletti, Rebecca Hodge, Ed Lein, Arnold R. Kriegstein, Claudia A. Doege, Seth A. Ament

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Science Programs at Allen Institute