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publication / 2024
Developmental mouse brain common coordinate framework
Nature Communications
Brain Science

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

publication / 2024
Integrated multimodal cell atlas of Alzheimer's disease
Nature Neuroscience
Brain and Consciousness
Brain Science
Shanahan
Brain Health

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

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
Shanahan

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

publication / 2024
SEA-AD is a multimodal cellular atlas and resource for Alzheimer's disease
Nature Aging
Brain Science
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

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

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

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

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

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

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

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

publication / 2024
Joint inference of discrete cell types and continuous type-specific variability in single-cell datasets with MMIDAS
Nature Computational Science
Brain Science

Yeganeh Marghi, Rohan Gala, Fahimeh Baftizadeh, Uygar Sümbül

publication / 2024
Revealing gene function with statistical inference at single-cell resolution
Nature Reviews. Genetics
Synthetic Biology

Cole Trapnell

publication / 2024
Expansion-assisted selective plane illumination microscopy for nanoscale imaging of centimeter-scale tissues
eLife
Neural Dynamics

Adam Glaser, Jayaram Chandrashekar, Sonya Vasquez, Cameron Arshadi, Naveen Ouellette, Xiaoyun Jiang, Judith Baka, Gabor Kovacs, Micah Woodard, Sharmishtaa Seshamani, Kevin Cao, Nathan Clack, Andrew Recknagel, Anna Grim, Pooja Balaram, Emily Turschak, Marcus Hooper, Alan Liddell, John Rohde, Ayana Hellevik, Kevin Takasaki, Lindsey Erion Barner, Molly Logsdon, Chris Chronopoulos, Saskia de Vries, Jonathan Ting, Steve Perlmutter, Brian Kalmbach, Nikolai Dembrow, Bosiljka Tasic, R. Clay Reid, David Feng, Karel Svoboda

publication / 2024
Interpretable representation learning for 3D multi-piece intracellular structures using point clouds
bioRxiv: The Preprint Server for Biology
Cell Science

Ritvik Vasan, Alexandra J. Ferrante, Antoine Borensztejn, Christopher L. Frick, Nathalie Gaudreault, Saurabh S. Mogre, Benjamin Morris, Guilherme G. Pires, Susanne M. Rafelski, Julie A. Theriot, Matheus P. Viana

publication / 2024
MOCHA’s advanced statistical modeling of scATAC-seq data enables functional genomic inference in large human cohorts
Nature Communications
Immunology

Samir Rachid Zaim, Mark-Phillip Pebworth, Imran McGrath, Lauren Okada, Morgan Weiss, Julian Reading, Julie L. Czartoski, Troy R. Torgerson, M. Juliana McElrath, Thomas F. Bumol, Peter J. Skene, Xiao-jun Li

publication / 2024
Cell-class-specific electric field entrainment of neural activity
Neuron
Brain and Consciousness
Brain Science

Soo Yeun Lee, Konstantinos Kozalakis, Fahimeh Baftizadeh, Luke Campagnola, Tim Jarsky, Christof Koch, Costas A. Anastassiou

publication / 2024
A Case for the Use of Open Data as a Tool to Incorporate Socioscientific Topics into Neuroscience Education
Journal of Undergraduate Neuroscience Education
Education and Engagement

Allen Institute, Madison Meuler, Kaitlyn Casimo, Allen Institute

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