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Publications

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Cell Reports

Transcriptional determinants of goal-directed learning and representational drift in the parahippocampal cortex

Jan 09, 2025

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

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Journal of Translational Medicine

CryoSCAPE: Scalable immune profiling using cryopreserved whole blood for multi-omic single cell and functional assays

Jan 03, 2025

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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Nature

Brain-wide cell-type-specific transcriptomic signatures of healthy ageing in mice

Jan 01, 2025

Kelly Jin, Zizhen Yao, Cindy T. J. van Velthoven, Eitan S. Kaplan, Katie Glattfelder, Samuel T. Barlow, Gabriella Boyer, Daniel Carey, Tamara Casper, Anish Bhaswanth Chakka, Rushil Chakrabarty, Michael Clark, Max Departee, Marie Desierto, Amanda Gary, Jessica Gloe, Jeff Goldy, Nathan Guilford, Junitta Guzman, Daniel Hirschstein, Changkyu Lee, Elizabeth Liang, Trangthanh Pham, Melissa Reding, Kara Ronellenfitch, Augustin Ruiz, Josh Sevigny, Nadiya Shapovalova, Lyudmila Shulga, Josef Sulc, Amy Torkelson, Herman Tung, Boaz Levi, Susan M. Sunkin, Nick Dee, Luke Esposito, Kimberly A. Smith, Bosiljka Tasic, Hongkui Zeng

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Nature Neuroscience

The BRAIN initiative: a pioneering program on the precipice

Dec 01, 2024

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

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Nature Neuroscience

Applying single-cell and single-nucleus genomics to studies of cellular heterogeneity and cell fate transitions in the nervous system

Dec 01, 2024

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

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Nature Communications

Neuronal diversity and stereotypy at multiple scales through whole brain morphometry

Nov 26, 2024

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

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Cell Reports

Distinctive physiology of molecularly identified medium spiny neurons in the macaque putamen

Nov 26, 2024

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

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Nature Communications

Developmental mouse brain common coordinate framework

Oct 21, 2024

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

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Nature Neuroscience

Integrated multimodal cell atlas of Alzheimer’s disease

Oct 14, 2024

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

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Nature

Neuronal wiring diagram of an adult brain

Oct 01, 2024

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

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Nature Aging

SEA-AD is a multimodal cellular atlas and resource for Alzheimer’s disease

Oct 01, 2024

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

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Nature Communications

Massive multiplexing of spatially resolved single neuron projections with axonal BARseq

Sep 27, 2024

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

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Cell Reports

Areal specializations in the morpho-electric and transcriptomic properties of primate layer 5 extratelencephalic projection neurons

Sep 24, 2024

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

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Proceedings of the National Academy of Sciences of the United States of America

Unsupervised pattern identification in spatial gene expression atlas reveals mouse brain regions beyond established ontology

Sep 10, 2024

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

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Neuron

SHIELD: Skull-shaped hemispheric implants enabling large-scale electrophysiology datasets in the mouse brain

Sep 04, 2024

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

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Nature Computational Science

Joint inference of discrete cell types and continuous type-specific variability in single-cell datasets with MMIDAS

Sep 01, 2024

Yeganeh Marghi, Rohan Gala, Fahimeh Baftizadeh, Uygar Sümbül

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Science Programs at Allen Institute