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Publications

Explore publications from the Allen Institute.

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Cognition

When rules are over-ruled: Virtual bargaining as a contractualist method of moral judgment

Jun 21, 2024

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

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Neuron

Cell-class-specific electric field entrainment of neural activity

May 28, 2024

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

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Entropy (Basel, Switzerland)

Testing the Conjecture That Quantum Processes Create Conscious Experience

May 28, 2024

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

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Nature

Whole-cortex in situ sequencing reveals input-dependent area identity

Apr 24, 2024

Xiaoyin Chen, Stephan Fischer, Mara C. P. Rue, Aixin Zhang, Didhiti Mukherjee, Patrick O. Kanold, Jesse Gillis, Anthony M. Zador

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Cold Spring Harbor Perspectives in Biology

Reimagining Cortical Connectivity by Deconstructing Its Molecular Logic into Building Blocks

Apr 15, 2024

Xiaoyin Chen

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bioRxiv

Thalamic feedback shapes brain responses evoked by cortical stimulation in mice and humans

Apr 12, 2024

Simone Russo, Leslie Claar, Lydia Marks, Giri Krishnan, Giulia Furregoni, Flavia Maria Zauli, Gabriel Hassan, Michela Solbiati, Piergiorgio d’Orio, Ezequiel Mikulan, Simone Sarasso, Mario Rosanova, Ivana Sartori, Maxim Bazhenov, Andrea Pigorini, Marcello Massimini, Christof Koch, Irene Rembado

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Cell Reports

Morpho-electric diversity of human hippocampal CA1 pyramidal neurons

Apr 11, 2024

Eline J. Mertens, Yoni Leibner, Jean Pie, Anna A. Galakhova, Femke Waleboer, Julia Meijer, Tim S. Heistek, René Wilbers, Djai Heyer, Natalia A. Goriounova, Sander Idema, Matthijs B. Verhoog, Brian E. Kalmbach, Brian R. Lee, Ryder P. Gwinn, Ed S. Lein, Eleonora Aronica, Jonathan Ting, Huibert D. Mansvelder, Idan Segev, Christiaan P. J. de Kock

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Cell Reports

Distributed X chromosome inactivation in brain circuitry is associated with X-linked disease penetrance of behavior

Apr 10, 2024

Eric R. Szelenyi, Danielle Fisenne, Joseph E. Knox, Julie A. Harris, James A. Gornet, Ramesh Palaniswamy, Yongsoo Kim, Kannan Umadevi Venkataraju, Pavel Osten

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Cell Reports

Topographical and cell type-specific connectivity of rostral and caudal forelimb corticospinal neuron populations

Mar 27, 2024

Lina Marcela Carmona, Eric D. Thomas, Kimberly Smith, Bosiljka Tasic, Rui M. Costa, Anders Nelson

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Nature Communications

Mapping human tissues with highly multiplexed RNA in situ hybridization

Mar 20, 2024

Kian Kalhor, Chien-Ju Chen, Ho Suk Lee, Matthew Cai, Mahsa Nafisi, Richard Que, Carter R. Palmer, Yixu Yuan, Yida Zhang, Xuwen Li, Jinghui Song, Amanda Knoten, Blue B. Lake, Joseph P. Gaut, C. Dirk Keene, Ed Lein, Peter V. Kharchenko, Jerold Chun, Sanjay Jain, Jian-Bing Fan, Kun Zhang

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Cell

Structurally divergent and recurrently mutated regions of primate genomes

Mar 14, 2024

Yafei Mao, William T. Harvey, David Porubsky, Katherine M. Munson, Kendra Hoekzema, Alexandra P. Lewis, Peter A. Audano, Allison Rozanski, Xiangyu Yang, Shilong Zhang, DongAhn Yoo, David S. Gordon, Tyler Fair, Xiaoxi Wei, Glennis A. Logsdon, Marina Haukness, Philip C. Dishuck, Hyeonsoo Jeong, Ricardo Del Rosario, Vanessa L. Bauer, Will T. Fattor, Gregory K. Wilkerson, Yuxiang Mao, Yongyong Shi, Qiang Sun, Qing Lu, Benedict Paten, Trygve E. Bakken, Alex A. Pollen, Guoping Feng, Sara L. Sawyer, Wesley C. Warren, Lucia Carbone, Evan E. Eichler

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PLoS computational biology

Modeling circuit mechanisms of opposing cortical responses to visual flow perturbations

Mar 01, 2024

J. Galván Fraile, Franz Scherr, José J. Ramasco, Anton Arkhipov, Wolfgang Maass, Claudio R. Mirasso

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Neuron

Behavioral strategy shapes activation of the Vip-Sst disinhibitory circuit in visual cortex

Feb 29, 2024

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

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Hippocampus

Comparison of histological delineations of medial temporal lobe cortices by four independent neuroanatomy laboratories

Feb 28, 2024

Anika Wuestefeld, Hannah Baumeister, Jenna N. Adams, Robin de Flores, Carl J. Hodgetts, Negar Mazloum-Farzaghi, Rosanna K. Olsen, Vyash Puliyadi, Tammy T. Tran, Arnold Bakker, Kelsey L. Canada, Marshall A. Dalton, Ana M. Daugherty, Renaud La Joie, Lei Wang, Madigan L. Bedard, Esther Buendia, Eunice Chung, Amanda Denning, María Del Mar Arroyo-Jiménez, Emilio Artacho-Pérula, David J. Irwin, Ranjit Ittyerah, Edward B. Lee, Sydney Lim, María Del Pilar Marcos-Rabal, Maria Mercedes Iñiguez de Onzoño Martin, Monica Munoz Lopez, Carlos de la Rosa Prieto, Theresa Schuck, Winifred Trotman, Alicia Vela, Paul Yushkevich, Katrin Amunts, Jean C. Augustinack, Song-Lin Ding, Ricardo Insausti, Olga Kedo, David Berron, Laura E. M. Wisse

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Current biology: CB

Dopamine neuron activity encodes the length of upcoming contralateral movement sequences

Feb 12, 2024

Marcelo D. Mendonça, Joaquim Alves da Silva, Ledia F. Hernandez, Ivan Castela, José Obeso, Rui M. Costa

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eLife

Rabies virus-based barcoded neuroanatomy resolved by single-cell RNA and in situ sequencing

Feb 06, 2024

Aixin Zhang, Lei Jin, Shenqin Yao, Makoto Matsuyama, Cindy T. J. van Velthoven, Heather Anne Sullivan, Na Sun, Manolis Kellis, Bosiljka Tasic, Ian Wickersham, Xiaoyin Chen

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Nature Methods

Community-developed checklists for publishing images and image analyses

Feb 01, 2024

Christopher Schmied, Michael S. Nelson, Sergiy Avilov, Gert-Jan Bakker, Cristina Bertocchi, Johanna Bischof, Ulrike Boehm, Jan Brocher, Mariana T. Carvalho, Catalin Chiritescu, Jana Christopher, Beth A. Cimini, Eduardo Conde-Sousa, Michael Ebner, Rupert Ecker, Kevin Eliceiri, Julia Fernandez-Rodriguez, Nathalie Gaudreault, Laurent Gelman, David Grunwald, Tingting Gu, Nadia Halidi, Mathias Hammer, Matthew Hartley, Marie Held, Florian Jug, Varun Kapoor, Ayse Aslihan Koksoy, Judith Lacoste, Sylvia Le Dévédec, Sylvie Le Guyader, Penghuan Liu, Gabriel G. Martins, Aastha Mathur, Kota Miura, Paula Montero Llopis, Roland Nitschke, Alison North, Adam C. Parslow, Alex Payne-Dwyer, Laure Plantard, Rizwan Ali, Britta Schroth-Diez, Lucas Schütz, Ryan T. Scott, Arne Seitz, Olaf Selchow, Ved P. Sharma, Martin Spitaler, Sathya Srinivasan, Caterina Strambio-De-Castillia, Douglas Taatjes, Christian Tischer, Helena Klara Jambor

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Nature Neuroscience

Publisher Correction: Long-term labeling and imaging of synaptically connected neuronal networks in vivo using double-deletion-mutant rabies viruses

Feb 01, 2024

Lei Jin, Heather A. Sullivan, Mulangma Zhu, Thomas K. Lavin, Makoto Matsuyama, Xin Fu, Nicholas E. Lea, Ran Xu, YuanYuan Hou, Luca Rutigliani, Maxwell Pruner, Kelsey R. Babcock, Jacque Pak Kan Ip, Ming Hu, Tanya L. Daigle, Hongkui Zeng, Mriganka Sur, Guoping Feng, Ian R. Wickersham

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Science Programs at Allen Institute