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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

preprint / 2024
A human induced pluripotent stem (hiPS) cell model for the holistic study of epithelial to mesenchymal transitions (EMTs)
bioRxiv
Cell Science

Caroline Hookway, Antoine Borensztejn, Leigh K. Harris, Sara Carlson, Gokhan Dalgin, Suraj Mishra, Nivedita Nivedita, Ellen M. Adams, Tiffany Barszczewski, Julie C. Dixon, Jacqueline H. Edmonds, Erik A. Ehlers, Alexandra J. Ferrante, Margaret A. Fuqua, Philip Garrison, Janani Gopalan, Benjamin W. Gregor, Maxwell J. Hedayati, Kyle N. Klein, Chantelle L. Leveille, Sean L. Meharry, Haley S. Morris, Gouthamrajan Nadarajan, Sandra A. Oluoch, Serge E. Parent, Amber Phan, Brock Roberts, Emmanuel E. Sanchez, M. Filip Sluzewski, Lev S. Snyder, Derek J. Thirstrup, John Paul Thottam, Julia R. Torvi, Gaea Turman, Matheus P. Viana, Lyndsay Wilhelm, Chamari S. Wijesooriya, Jie Yao, Julie A. Theriot, Susanne M. Rafelski, Ruwanthi N. Gunawardane

10.1101/2024.08.16.608353
Cell Science, Scientific, Technical Discovery
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

preprint / 2024
4D hybrid model interrogates agent-level rules and parameters driving hiPS cell colony dynamics
bioRxiv
Cell Science

Jessica S. Yu, Blair Lyons, Susanne Rafelski, Julie A. Theriot, Neda Bagheri, Graham T. Johnson

10.1101/2024.08.12.607546
Cell Science, Scientific, Technical Discovery
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

10.1038/s41467-024-50612-6
AIFI, Allen Institute for Immunology, Imran McGrath, Julian Reading, Julie L Czartoski, Lauren Okada, M. Juliana McElrath, MOCHA, MOCHA’s advanced statistical modeling of scATAC-seq data enables functional genomic inference in large human cohorts, Mark-Phillip Pebworth, Morgan Weiss, Peter J Skene, Samir Rachid Zaim, Thomas F Bumol, Troy R Torgerson, Xiao-Jun Li, statistical modeling of scATAC-seq
publication / 2024
Cell-class-specific electric field entrainment of neural activity
Neuron
Brain and Consciousness
Brain Science
MindScope

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

10.1016/j.neuron.2024.05.009
Brain Science, #consciousness
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

10.1038/s41586-024-07706-4
Allen Institute, Chan Zuckerberg Inititative, Seattle Hub for Synthetic Biology, University of Washington
publication / 2024
High-throughput analysis of dendrite and axonal arbors reveals transcriptomic correlates of neuroanatomy
Nature Communications
Brain Science
MindScope

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

10.1038/s41467-024-50728-9
AIBS First Author, AIBS Last Author, Brain Science
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
MindScope

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

10.1038/s41380-024-02620-7
AIBS Last Author, Brain Science
publication / 2024
Behavioral strategy shapes activation of the Vip-Sst disinhibitory circuit in visual cortex
Neuron
Brain and Consciousness
Brain Science
MindScope
Neural Dynamics

Alex Piet, Nick Ponvert, Douglas Ollerenshaw, Marina Garrett, Peter A. Groblewski, Shawn Olsen, Christof Koch, Anton Arkhipov

10.1016/j.neuron.2024.02.008
#consciousness, Neural Dynamics, MindScope Program
publication / 2024
Ultrastructural differences impact cilia shape and external exposure across cell classes in the visual cortex
Current biology: CB
Brain Science
MindScope

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

10.1016/j.cub.2024.04.043
Brain Science
publication / 2024
Simple synaptic modulations implement diverse novelty computations
Cell Reports
Brain Science
MindScope

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

10.1016/j.celrep.2024.114188
Brain Science
publication / 2024
Testing the Conjecture That Quantum Processes Create Conscious Experience
Entropy (Basel, Switzerland)
Brain and Consciousness

Hartmut Neven, Adam Zalcman, Peter Read, Kenneth S. Kosik, Tjitse van der Molen, Dirk Bouwmeester, Eve Bodnia, Luca Turin, Christof Koch

10.3390/e26060460
#consciousness
preprint / 2024
Enhanced endogenous gene tagging in human induced pluripotent stem cells via AAV6-mediated donor delivery
bioRxiv
Cell Science

Erik A. Ehlers, Kyle N. Klein, Margaret A. Fuqua, Julia R. Torvi, Javier Chávez, Lauren M. Kuo, Jacob McCarley, Jacqueline E. Smith, Gaea Turman, Danielle Yi, Ruwanthi N. Gunawardane, Brock Roberts

10.1101/2024.05.24.595765
Cell Science, Scientific, Technical
publication / 2024
Establishing a conceptual framework for holistic cell states and state transitions
Cell
Cell Science

Susanne M. Rafelski, Julie A. Theriot

10.1016/j.cell.2024.04.035
Cell Science, Newsletter, Opinion, Perspective
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