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publication / 2025
Unexpected Events Trigger Task-Independent Signaling in VIP and Excitatory Neurons of Mouse Visual Cortex
iScience
Neural Dynamics

Farzaneh Najafi, Simone Russo, Jérôme Lecoq

publication / 2024
Applying single-cell and single-nucleus genomics to studies of cellular heterogeneity and cell fate transitions in the nervous system
Nature Neuroscience
Brain Science
MindScope

Igor Adameyko, Trygve Bakken, Aparna Bhaduri, Chintan Chhatbar, Mariella G. Filbin, David Gate, Hannah Hochgerner, Chang Nam Kim, Jordan Krull, Gioele La Manno, Qingyun Li, Sten Linnarsson, Qin Ma, Christian Mayer, Vilas Menon, Patricia Nano, Marco Prinz, Steve Quake, Christopher A. Walsh, Jin Yang, Omer Ali Bayraktar, Ozgun Gokce, Naomi Habib, Genevieve Konopka, Shane A. Liddelow, Tomasz J. Nowakowski

10.1038/s41593-024-01827-9
Brain Science
publication / 2024
The BRAIN initiative: a pioneering program on the precipice
Nature Neuroscience
Brain Science
MindScope

Cory T. Miller, Xiaoke Chen, Zoe R. Donaldson, Bianca Jones Marlin, Doris Y. Tsao, Ziv M. Williams, Moriel Zelikowsky, Hongkui Zeng, Weizhe Hong

10.1038/s41593-024-01811-3
Brain Science
publication / 2024
Distinctive physiology of molecularly identified medium spiny neurons in the macaque putamen
Cell Reports
Brain Science
MindScope

Jonathan T. Ting, Nelson J. Johansen, Brian E. Kalmbach, Naz Taskin, Brian Lee, Jason K. Clark, Rennie Kendrick, Lindsay Ng, Cristina Radaelli, Natalie Weed, Rachel Enstrom, Shea Ransford, Ingrid Redford, Sarah Walling-Bell, Rachel Dalley, Michael Tieu, Jeff Goldy, Nik Jorstad, Kimberly Smith, Trygve Bakken, Ed S. Lein, Scott F. Owen

10.1016/j.celrep.2024.114963
Brain Science
publication / 2024
Neuronal diversity and stereotypy at multiple scales through whole brain morphometry
Nature Communications
Brain Science
MindScope

Yufeng Liu, Shengdian Jiang, Yingxin Li, Sujun Zhao, Zhixi Yun, Zuo-Han Zhao, Lingli Zhang, Gaoyu Wang, Xin Chen, Linus Manubens-Gil, Yuning Hang, Qiaobo Gong, Yuanyuan Li, Penghao Qian, Lei Qu, Marta Garcia-Forn, Wei Wang, Silvia De Rubeis, Zhuhao Wu, Pavel Osten, Hui Gong, Michael Hawrylycz, Partha Mitra, Hongwei Dong, Qingming Luo, Giorgio A. Ascoli, Hongkui Zeng, Lijuan Liu, Hanchuan Peng

10.1038/s41467-024-54745-6
Brain Science
publication / 2024
Developmental mouse brain common coordinate framework
Nature Communications
Brain Science
MindScope

Fae N. Kronman, Josephine K. Liwang, Rebecca Betty, Daniel J. Vanselow, Yuan-Ting Wu, Nicholas J. Tustison, Ashwin Bhandiwad, Steffy B. Manjila, Jennifer A. Minteer, Donghui Shin, Choong Heon Lee, Rohan Patil, Jeffrey T. Duda, Jian Xue, Yingxi Lin, Keith C. Cheng, Luis Puelles, James C. Gee, Jiangyang Zhang, Lydia Ng, Yongsoo Kim

10.1038/s41467-024-53254-w
Brain Science
publication / 2024
Integrated multimodal cell atlas of Alzheimer's disease
Nature Neuroscience
Brain and Consciousness
Brain Science
MindScope
Shanahan
Shanahan Fellowship

Mariano I. Gabitto, Kyle J. Travaglini, Victoria M. Rachleff, Eitan S. Kaplan, Brian Long, Jeanelle Ariza, Yi Ding, Joseph T. Mahoney, Nick Dee, Jeff Goldy, Erica J. Melief, Anamika Agrawal, Omar Kana, Xingjian Zhen, Samuel T. Barlow, Krissy Brouner, Jazmin Campos, John Campos, Ambrose J. Carr, Tamara Casper, Rushil Chakrabarty, Michael Clark, Jonah Cool, Rachel Dalley, Martin Darvas, Song-Lin Ding, Tim Dolbeare, Tom Egdorf, Luke Esposito, Rebecca Ferrer, Lynn E. Fleckenstein, Rohan Gala, Amanda Gary, Emily Gelfand, Jessica Gloe, Nathan Guilford, Junitta Guzman, Daniel Hirschstein, Windy Ho, Madison Hupp, Tim Jarsky, Nelson Johansen, Brian E. Kalmbach, Lisa M. Keene, Sarah Khawand, Mitchell D. Kilgore, Amanda Kirkland, Michael Kunst, Brian R. Lee, Mckaila Leytze, Christine L. Mac Donald, Jocelin Malone, Zoe Maltzer, Naomi Martin, Rachel McCue, Delissa McMillen, Gonzalo Mena, Emma Meyerdierks, Kelly P. Meyers, Tyler Mollenkopf, Mark Montine, Amber L. Nolan, Julie K. Nyhus, Paul A. Olsen, Maiya Pacleb, Chelsea M. Pagan, Nicholas Peña, Trangthanh Pham, Christina Alice Pom, Nadia Postupna, Christine Rimorin, Augustin Ruiz, Giuseppe A. Saldi, Aimee M. Schantz, Nadiya V. Shapovalova, Staci A. Sorensen, Brian Staats, Matt Sullivan, Susan M. Sunkin, Carol Thompson, Michael Tieu, Jonathan T. Ting, Amy Torkelson, Tracy Tran, Nasmil J. Valera Cuevas, Sarah Walling-Bell, Ming-Qiang Wang, Jack Waters, Angela M. Wilson, Ming Xiao, David Haynor, Nicole M. Gatto, Suman Jayadev, Shoaib Mufti, Lydia Ng, Shubhabrata Mukherjee, Paul K. Crane, Caitlin S. Latimer, Boaz P. Levi, Kimberly A. Smith, Jennie L. Close, Jeremy A. Miller, Rebecca D. Hodge, Eric B. Larson, Thomas J. Grabowski, Michael Hawrylycz, C. Dirk Keene, Ed S. Lein

10.1038/s41593-024-01774-5
Shanahan, AIBS First Author, AIBS Last Author, Brain Science
publication / 2024
Network statistics of the whole-brain connectome of Drosophila
Nature
Shanahan

Albert Lin, Runzhe Yang, Sven Dorkenwald, Arie Matsliah, Amy R. Sterling, Philipp Schlegel, Szi-chieh Yu, Claire E. McKellar, Marta Costa, Katharina Eichler, Alexander Shakeel Bates, Nils Eckstein, Jan Funke, Gregory S. X. E. Jefferis, Mala Murthy

publication / 2024
Neuronal wiring diagram of an adult brain
Nature
Brain Science
MindScope
Shanahan
Shanahan Fellowship

Sven Dorkenwald, Arie Matsliah, Amy R. Sterling, Philipp Schlegel, Szi-chieh Yu, Claire E. McKellar, Albert Lin, Marta Costa, Katharina Eichler, Yijie Yin, Will Silversmith, Casey Schneider-Mizell, Chris S. Jordan, Derrick Brittain, Akhilesh Halageri, Kai Kuehner, Oluwaseun Ogedengbe, Ryan Morey, Jay Gager, Krzysztof Kruk, Eric Perlman, Runzhe Yang, David Deutsch, Doug Bland, Marissa Sorek, Ran Lu, Thomas Macrina, Kisuk Lee, J. Alexander Bae, Shang Mu, Barak Nehoran, Eric Mitchell, Sergiy Popovych, Jingpeng Wu, Zhen Jia, Manuel A. Castro, Nico Kemnitz, Dodam Ih, Alexander Shakeel Bates, Nils Eckstein, Jan Funke, Forrest Collman, Davi D. Bock, Gregory S. X. E. Jefferis, H. Sebastian Seung, Mala Murthy, FlyWire Consortium

10.1038/s41586-024-07558-y
Data publication and archiving, Electron microscopy, Image processing, Neural circuits, Shanahan, Brain Science
publication / 2024
SEA-AD is a multimodal cellular atlas and resource for Alzheimer's disease
Nature Aging
Brain Science
MindScope
Brain Health

Michael Hawrylycz, Eitan S. Kaplan, Kyle J. Travaglini, Mariano I. Gabitto, Jeremy A. Miller, Lydia Ng, Jennie L. Close, Rebecca D. Hodge, Brian Long, Tyler Mollenkopf, Shoaib Mufti, Nicole M. Gatto, Eric B. Larson, Paul K. Crane, Thomas J. Grabowski, C. Dirk Keene, Ed S. Lein

10.1038/s43587-024-00719-8
AIBS First Author, AIBS Last Author, Brain Science
publication / 2024
The fly connectome reveals a path to the effectome
Nature
Shanahan

Dean A. Pospisil, Max J. Aragon, Sven Dorkenwald, Arie Matsliah, Amy R. Sterling, Philipp Schlegel, Szi-chieh Yu, Claire E. McKellar, Marta Costa, Katharina Eichler, Gregory S. X. E. Jefferis, Mala Murthy, Jonathan W. Pillow

publication / 2024
Whole-brain annotation and multi-connectome cell typing of Drosophila
Nature
Shanahan

Philipp Schlegel, Yijie Yin, Alexander S. Bates, Sven Dorkenwald, Katharina Eichler, Paul Brooks, Daniel S. Han, Marina Gkantia, Marcia dos Santos, Eva J. Munnelly, Griffin Badalamente, Laia Serratosa Capdevila, Varun A. Sane, Alexandra M. C. Fragniere, Ladann Kiassat, Markus W. Pleijzier, Tomke Stürner, Imaan F. M. Tamimi, Christopher R. Dunne, Irene Salgarella, Alexandre Javier, Siqi Fang, Eric Perlman, Tom Kazimiers, Sridhar R. Jagannathan, Arie Matsliah, Amy R. Sterling, Szi-chieh Yu, Claire E. McKellar, Marta Costa, H. Sebastian Seung, Mala Murthy, Volker Hartenstein, Davi D. Bock, Gregory S. X. E. Jefferis

publication / 2024
Massive multiplexing of spatially resolved single neuron projections with axonal BARseq
Nature Communications
Brain Science
MindScope

Li Yuan, Xiaoyin Chen, Huiqing Zhan, Gilbert L. Henry, Anthony M. Zador

10.1038/s41467-024-52756-x
Brain Science
publication / 2024
Areal specializations in the morpho-electric and transcriptomic properties of primate layer 5 extratelencephalic projection neurons
Cell Reports
Brain Science
MindScope

Nikolai C. Dembrow, Scott Sawchuk, Rachel Dalley, Ximena Opitz-Araya, Mark Hudson, Cristina Radaelli, Lauren Alfiler, Sarah Walling-Bell, Darren Bertagnolli, Jeff Goldy, Nelson Johansen, Jeremy A. Miller, Kamiliam Nasirova, Scott F. Owen, Alejandro Parga-Becerra, Naz Taskin, Michael Tieu, David Vumbaco, Natalie Weed, Julia Wilson, Brian R. Lee, Kimberly A. Smith, Staci A. Sorensen, William J. Spain, Ed S. Lein, Steve I. Perlmutter, Jonathan T. Ting, Brian E. Kalmbach

10.1016/j.celrep.2024.114718
AIBS Last Author, Brian Science
publication / 2024
Unsupervised pattern identification in spatial gene expression atlas reveals mouse brain regions beyond established ontology
Proceedings of the National Academy of Sciences of the United States of America
Brain Science
MindScope

Robert Cahill, Yu Wang, R. Patrick Xian, Alex J. Lee, Hongkui Zeng, Bin Yu, Bosiljka Tasic, Reza Abbasi-Asl

10.1073/pnas.2319804121
Brain Science
publication / 2024
SHIELD: Skull-shaped hemispheric implants enabling large-scale electrophysiology datasets in the mouse brain
Neuron
Neural Dynamics

Corbett Bennett, Ben Ouellette, Tamina K. Ramirez, Alex Cahoon, Hannah Cabasco, Yoni Browning, Anna Lakunina, Galen F. Lynch, Ethan G. McBride, Hannah Belski, Ryan Gillis, Conor Grasso, Robert Howard, Tye Johnson, Henry Loeffler, Heston Smith, David Sullivan, Allison Williford, Shiella Caldejon, Severine Durand, Samuel Gale, Alan Guthrie, Vivian Ha, Warren Han, Ben Hardcastle, Chris Mochizuki, Arjun Sridhar, Lucas Suarez, Jackie Swapp, Joshua Wilkes, Joshua H. Siegle, Colin Farrell, Peter A. Groblewski, Shawn R. Olsen

10.1016/j.neuron.2024.06.015
Neural Dynamics
publication / 2024
Joint inference of discrete cell types and continuous type-specific variability in single-cell datasets with MMIDAS
Nature Computational Science
Brain Science
MindScope

Yeganeh Marghi, Rohan Gala, Fahimeh Baftizadeh, Uygar Sümbül

10.1038/s43588-024-00683-8
AIBS First Author, AIBS Last Author, Brain Science
publication / 2024
Revealing gene function with statistical inference at single-cell resolution
Nature Reviews. Genetics
Synthetic Biology

Cole Trapnell

10.1038/s41576-024-00750-w
Allen Institute, Chan Zuckerberg Inititative, University of Washington
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