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Publications

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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 Communications

MOCHA’s advanced statistical modeling of scATAC-seq data enables functional genomic inference in large human cohorts

Aug 09, 2024

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

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Nature

Symbolic recording of signalling and cis-regulatory element activity to DNA

Aug 01, 2024

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

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Neuron

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

Jun 05, 2024

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

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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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Proceedings of the National Academy of Sciences

Incomplete-penetrant hypertrophic cardiomyopathy MYH7 G256E mutation causes hypercontractility and elevated mitochondrial respiration

May 07, 2024

Soah Lee, Alison S. Vander Roest, Cheavar A. Blair, Kerry Kao, Samantha B. Bremner, Matthew C. Childers, Divya Pathak, Paul Heinrich, Daniel Lee, Orlando Chirikian, Saffie E. Mohran, Brock Roberts, Jacqueline E. Smith, James W. Jahng, David T. Paik, Joseph C. Wu, Ruwanthi N. Gunawardane, Kathleen M. Ruppel, David L. Mack, Beth L. Pruitt, Michael Regnier, Sean M. Wu, James A. Spudich, Daniel Bernstein

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bioRxiv: The Preprint Server for Biology

Multiplex, single-cell CRISPRa screening for cell type specific regulatory elements

Apr 30, 2024

Florence M. Chardon, Troy A. McDiarmid, Nicholas F. Page, Riza M. Daza, Beth Martin, Silvia Domcke, Samuel G. Regalado, Jean-Benoît Lalanne, Diego Calderon, Xiaoyi Li, Lea M. Starita, Stephan J. Sanders, Nadav Ahituv, Jay Shendure

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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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Science Programs at Allen Institute