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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

publication / 2024
Symbolic recording of signalling and cis-regulatory element activity to DNA
Nature
Synthetic Biology

Wei Chen, Junhong Choi, Xiaoyi Li, Jenny F. Nathans, Beth Martin, Wei Yang, Nobuhiko Hamazaki, Chengxiang Qiu, Jean-Benoît Lalanne, Samuel Regalado, Haedong Kim, Vikram Agarwal, Eva Nichols, Anh Leith, Choli Lee, Jay Shendure

publication / 2024
High-throughput analysis of dendrite and axonal arbors reveals transcriptomic correlates of neuroanatomy
Nature Communications
Brain Science

Olga Gliko, Matt Mallory, Rachel Dalley, Rohan Gala, James Gornet, Hongkui Zeng, Staci A. Sorensen, Uygar Sümbül

publication / 2024
Colony context and size-dependent compensation mechanisms give rise to variations in nuclear growth trajectories
bioRxiv: The Preprint Server for Biology
Cell Science

Julie C. Dixon, Christopher L. Frick, Chantelle L. Leveille, Philip Garrison, Peyton A. Lee, Saurabh S. Mogre, Benjamin Morris, Nivedita Nivedita, Ritvik Vasan, Jianxu Chen, Cameron L. Fraser, Clare R. Gamlin, Leigh K. Harris, Melissa C. Hendershott, Graham T. Johnson, Kyle N. Klein, Sandra A. Oluoch, Derek J. Thirstrup, M. Filip Sluzewski, Lyndsay Wilhelm, Ruian Yang, Daniel M. Toloudis, Matheus P. Viana, Julie A. Theriot, Susanne M. Rafelski

publication / 2024
When rules are over-ruled: Virtual bargaining as a contractualist method of moral judgment
Cognition
Brain Science

Sydney Levine, Max Kleiman-Weiner, Nick Chater, Fiery Cushman, Joshua B. Tenenbaum

publication / 2024
The single-cell opioid responses in the context of HIV (SCORCH) consortium
Molecular Psychiatry
Brain Science

Seth A. Ament, Rianne R. Campbell, Mary Kay Lobo, Joseph P. Receveur, Kriti Agrawal, Alejandra Borjabad, Siddappa N. Byrareddy, Linda Chang, Declan Clarke, Prashant Emani, Dana Gabuzda, Kyle J. Gaulton, Michelle Giglio, Federico M. Giorgi, Busra Gok, Chittibabu Guda, Eran Hadas, Brian R. Herb, Wen Hu, Anita Huttner, Mohammad R. Ishmam, Michelle M. Jacobs, Jennifer Kelschenbach, Dong-Wook Kim, Cheyu Lee, Shuhui Liu, Xiaokun Liu, Bertha K. Madras, Anup A. Mahurkar, Deborah C. Mash, Eran A. Mukamel, Meng Niu, Richard M. O'Connor, Chelsea M. Pagan, Alina P. S. Pang, Piya Pillai, Vez Repunte-Canonigo, W. Brad Ruzicka, Jay Stanley, Timothy Tickle, Shang-Yi A. Tsai, Allen Wang, Lauren Wills, Alyssa M. Wilson, Susan N. Wright, Siwei Xu, Junchen Yang, Maryam Zand, Le Zhang, Jing Zhang, Schahram Akbarian, Shilpa Buch, Christine S. Cheng, Michael J. Corley, Howard S. Fox, Mark Gerstein, Suryaram Gummuluru, Myriam Heiman, Ya-Chi Ho, Manolis Kellis, Paul J. Kenny, Yuval Kluger, Teresa A. Milner, David J. Moore, Susan Morgello, Lishomwa C. Ndhlovu, Tariq M. Rana, Pietro Paolo Sanna, John S. Satterlee, Nenad Sestan, Stephen A. Spector, Serena Spudich, Hagen U. Tilgner, David J. Volsky, Owen R. White, Dionne W. Williams, Hongkui Zeng

publication / 2024
Ultrastructural differences impact cilia shape and external exposure across cell classes in the visual cortex
Current biology: CB
Brain Science

Carolyn M. Ott, Russel Torres, Tung-Sheng Kuan, Aaron Kuan, JoAnn Buchanan, Leila Elabbady, Sharmishtaa Seshamani, Agnes L. Bodor, Forrest Collman, Davi D. Bock, Wei Chung Lee, Nuno Maçarico da Costa, Jennifer Lippincott-Schwartz

publication / 2024
Simple synaptic modulations implement diverse novelty computations
Cell Reports
Brain Science

Kyle Aitken, Luke Campagnola, Marina E. Garrett, Shawn R. Olsen, Stefan Mihalas

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