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publication / 2024
Development of a high-throughput image cytometric screening method as a research tool for immunophenotypic characterization of patient samples from clinical studies
Journal of Immunological Methods
Immunology

Samir Patel, James I. McDonald, Hamza Mohammed, Vaishnavi Parthasarathy, Veronica Hernandez, Tyanna Stuckey, Allen H. Lin, Srinivas Koushik Gundimeda, Bo Lin, Julian Reading, Leo Li-Ying Chan

publication / 2024
Editorial: 15 years of frontiers in neuroanatomy: the circuits behind the visual cortex
Frontiers in Neuroanatomy
Brain Science

Toru Takahata, Song-Lin Ding

publication / 2024
Hierarchical Bayesian inference to model continuous phenotypical progression in Alzheimer's Disease
bioRxiv
Shanahan

Anamika Agrawal, Victoria Mallett Rachleff, Kyle J. Travaglini, Shubhabrata Mukherjee, Paul Crane, Michael Hawrylycz, C. Dirk Keene, Ed Lein, Gonzalo E. Mena, Mariano I. Gabitto

publication / 2024
Information-Theoretic Tools to Understand Distributed Source Coding in Neuroscience
IEEE Journal on Selected Areas in Information Theory
Shanahan

Ariel K. Feldman, Praveen Venkatesh, Douglas J. Weber, Pulkit Grover

publication / 2024
Taste for discovery: a conversation with neuroscientist Serge Charpak
Neurophotonics
Brain Science

Jérôme Lecoq

publication / 2023
Myomatrix arrays for high-definition muscle recording
eLife
Brain Science

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

publication / 2023
Gaussian Partial Information Decomposition: Bias Correction and Application to High-dimensional Data
Advances in Neural Information Processing Systems
Shanahan

Praveen Venkatesh, Corbett Bennett, Sam Gale, Tamina Ramirez, Greggory Heller, Severine Durand, Shawn Olsen, Stefan Mihalas

publication / 2023
Postsynaptic cell type and synaptic distance do not determine efficiency of monosynaptic rabies virus spread measured at synaptic resolution
eLife
Brain Science

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

publication / 2023
Dynamic behaviour restructuring mediates dopamine-dependent credit assignment
Nature
Brain Science

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

publication / 2023
A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain
Nature
Brain Science

Zizhen Yao, Cindy T. J. van Velthoven, Michael Kunst, Meng Zhang, Delissa McMillen, Changkyu Lee, Won Jung, Jeff Goldy, Aliya Abdelhak, Matthew Aitken, Katherine Baker, Pamela Baker, Eliza Barkan, Darren Bertagnolli, Ashwin Bhandiwad, Cameron Bielstein, Prajal Bishwakarma, Jazmin Campos, Daniel Carey, Tamara Casper, Anish Bhaswanth Chakka, Rushil Chakrabarty, Sakshi Chavan, Min Chen, Michael Clark, Jennie Close, Kirsten Crichton, Scott Daniel, Peter DiValentin, Tim Dolbeare, Lauren Ellingwood, Elysha Fiabane, Timothy Fliss, James Gee, James Gerstenberger, Alexandra Glandon, Jessica Gloe, Joshua Gould, James Gray, Nathan Guilford, Junitta Guzman, Daniel Hirschstein, Windy Ho, Marcus Hooper, Mike Huang, Madie Hupp, Kelly Jin, Matthew Kroll, Kanan Lathia, Arielle Leon, Su Li, Brian Long, Zach Madigan, Jessica Malloy, Jocelin Malone, Zoe Maltzer, Naomi Martin, Rachel McCue, Ryan McGinty, Nicholas Mei, Jose Melchor, Emma Meyerdierks, Tyler Mollenkopf, Skyler Moonsman, Thuc Nghi Nguyen, Sven Otto, Trangthanh Pham, Christine Rimorin, Augustin Ruiz, Raymond Sanchez, Lane Sawyer, Nadiya Shapovalova, Noah Shepard, Cliff Slaughterbeck, Josef Sulc, Michael Tieu, Amy Torkelson, Herman Tung, Nasmil Valera Cuevas, Shane Vance, Katherine Wadhwani, Katelyn Ward, Boaz Levi, Colin Farrell, Rob Young, Brian Staats, Ming-Qiang Michael Wang, Carol L. Thompson, Shoaib Mufti, Chelsea M. Pagan, Lauren Kruse, Nick Dee, Susan M. Sunkin, Luke Esposito, Michael J. Hawrylycz, Jack Waters, Lydia Ng, Kimberly Smith, Bosiljka Tasic, Xiaowei Zhuang, Hongkui Zeng

publication / 2023
A transcriptomic taxonomy of mouse brain-wide spinal projecting neurons
Nature
Brain Science

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

publication / 2023
Brain-wide correspondence of neuronal epigenomics and distant projections
Nature
Brain Science

Jingtian Zhou, Zhuzhu Zhang, May Wu, Hanqing Liu, Yan Pang, Anna Bartlett, Zihao Peng, Wubin Ding, Angeline Rivkin, Will N. Lagos, Elora Williams, Cheng-Ta Lee, Paula Assakura Miyazaki, Andrew Aldridge, Qiurui Zeng, J. L. Angelo Salinda, Naomi Claffey, Michelle Liem, Conor Fitzpatrick, Lara Boggeman, Zizhen Yao, Kimberly A. Smith, Bosiljka Tasic, Jordan Altshul, Mia A. Kenworthy, Cynthia Valadon, Joseph R. Nery, Rosa G. Castanon, Neelakshi S. Patne, Minh Vu, Mohammad Rashid, Matthew Jacobs, Tony Ito, Julia Osteen, Nora Emerson, Jasper Lee, Silvia Cho, Jon Rink, Hsiang-Hsuan Huang, António Pinto-Duartec, Bertha Dominguez, Jared B. Smith, Carolyn O'Connor, Hongkui Zeng, Shengbo Chen, Kuo-Fen Lee, Eran A. Mukamel, Xin Jin, M. Margarita Behrens, Joseph R. Ecker, Edward M. Callaway

publication / 2023
Conserved and divergent gene regulatory programs of the mammalian neocortex
Nature
Brain Science

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

publication / 2023
Developing a Toolbox of Antibodies Validated for Array Tomography-Based Imaging of Brain Synapses
eNeuro
Brain Science

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

publication / 2023
Molecularly defined and spatially resolved cell atlas of the whole mouse brain
Nature
Brain Science

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

publication / 2023
Multi-layered maps of neuropil with segmentation-guided contrastive learning
Nature Methods
Brain Science

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

publication / 2023
Single-cell analysis of chromatin accessibility in the adult mouse brain
Nature
Brain Science

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

publication / 2023
Single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain
Nature
Brain Science

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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