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preprint / 2023
Attention for Causal Relationship Discovery from Biological Neural Dynamics
Shanahan

Ziyu Lu, Anika Tabassum, Shruti Kulkarni, Lu Mi, J. Nathan Kutz, Eric Shea-Brown, Seung-Hwan Lim

publication / 2023
Responses to pattern-violating visual stimuli evolve differently over days in somata and distal apical dendrites
The Journal of Neuroscience: The Official Journal of the Society for Neuroscience
Brain Science

Colleen J. Gillon, Jason E. Pina, Jérôme Lecoq, Ruweida Ahmed, Yazan N. Billeh, Shiella Caldejon, Peter A. Groblewski, Timothy M. Henley, India Kato, Eric Lee, Jennifer Luviano, Kyla Mace, Chelsea Nayan, Thuyanh V. Nguyen, Kat North, Jed Perkins, Sam Seid, Matthew T. Valley, Ali Williford, Yoshua Bengio, Timothy P. Lillicrap, Blake A. Richards, Joel Zylberberg

publication / 2023
Online conversion of reconstructed neural morphologies into standardized SWC format
Nature Communications
Brain Science

Ketan Mehta, Bengt Ljungquist, James Ogden, Sumit Nanda, Ruben G. Ascoli, Lydia Ng, Giorgio A. Ascoli

publication / 2023
Linking Neurogenetics and Functional Connectivity in Autism
Biological Psychiatry
Brain Science

Michael Hawrylycz, Thomas Nickl-Jockschat

publication / 2023
Single-cell genomics reveals region-specific developmental trajectories underlying neuronal diversity in the human hypothalamus
Science Advances
Brain Science

Brian R. Herb, Hannah J. Glover, Aparna Bhaduri, Carlo Colantuoni, Tracy L. Bale, Kimberly Siletti, Rebecca Hodge, Ed Lein, Arnold R. Kriegstein, Claudia A. Doege, Seth A. Ament

publication / 2023
Trimodal single-cell profiling reveals a novel pediatric CD8αα+ T cell subset and broad age-related molecular reprogramming across the T cell compartment
Nature Immunology
Immunology

Zachary Thomson, Ziyuan He, Elliott Swanson, Katherine Henderson, Cole Phalen, Samir Rachid Zaim, Mark-Phillip Pebworth, Lauren Y. Okada, Alexander T. Heubeck, Charles R. Roll, Veronica Hernandez, Morgan Weiss, Palak C. Genge, Julian Reading, Josephine R. Giles, Sasikanth Manne, Jeanette Dougherty, C. J. Jasen, Allison R. Greenplate, Lynne A. Becker, Lucas T. Graybuck, Suhas V. Vasaikar, Gregory L. Szeto, Adam K. Savage, Cate Speake, Jane H. Buckner, Xiao-Jun Li, Thomas F. Bumol, E. John Wherry, Troy R. Torgerson, Laura A. Vella, Sarah E. Henrickson, Peter J. Skene, Claire E. Gustafson

preprint / 2023
Coordinated changes in a cortical circuit sculpt effects of novelty on neural dynamics
Neural Dynamics

Shinya Ito, Alex Piet, Corbett Bennett, Séverine Durand, Hannah Belski, Marina Garrett, Shawn R. Olsen, Anton Arkhipov

publication / 2023
A comparative atlas of single-cell chromatin accessibility in the human brain
Science (New York, N.Y.)
Brain Science
MindScope

Yang Eric Li, Sebastian Preissl, Michael Miller, Nicholas D. Johnson, Zihan Wang, Henry Jiao, Chenxu Zhu, Zhaoning Wang, Yang Xie, Olivier Poirion, Colin Kern, Antonio Pinto-Duarte, Wei Tian, Kimberly Siletti, Nora Emerson, Julia Osteen, Jacinta Lucero, Lin Lin, Qian Yang, Quan Zhu, Nathan Zemke, Sarah Espinoza, Anna Marie Yanny, Julie Nyhus, Nick Dee, Tamara Casper, Nadiya Shapovalova, Daniel Hirschstein, Rebecca D. Hodge, Sten Linnarsson, Trygve Bakken, Boaz Levi, C. Dirk Keene, Jingbo Shang, Ed Lein, Allen Wang, M. Margarita Behrens, Joseph R. Ecker, Bing Ren

publication / 2023
Comparative transcriptomics reveals human-specific cortical features
Science (New York, N.Y.)
Brain Science
MindScope

Nikolas L. Jorstad, Janet H. T. Song, David Exposito-Alonso, Hamsini Suresh, Nathan Castro-Pacheco, Fenna M. Krienen, Anna Marie Yanny, Jennie Close, Emily Gelfand, Brian Long, Stephanie C. Seeman, Kyle J. Travaglini, Soumyadeep Basu, Marc Beaudin, Darren Bertagnolli, Megan Crow, Song-Lin Ding, Jeroen Eggermont, Alexandra Glandon, Jeff Goldy, Katelyn Kiick, Thomas Kroes, Delissa McMillen, Trangthanh Pham, Christine Rimorin, Kimberly Siletti, Saroja Somasundaram, Michael Tieu, Amy Torkelson, Guoping Feng, William D. Hopkins, Thomas Höllt, C. Dirk Keene, Sten Linnarsson, Steven A. McCarroll, Boudewijn P. Lelieveldt, Chet C. Sherwood, Kimberly Smith, Christopher A. Walsh, Alexander Dobin, Jesse Gillis, Ed S. Lein, Rebecca D. Hodge, Trygve E. Bakken

publication / 2023
Interindividual variation in human cortical cell type abundance and expression
Science (New York, N.Y.)
Brain Science
MindScope

Nelson Johansen, Saroja Somasundaram, Kyle J. Travaglini, Anna Marie Yanny, Maya Shumyatcher, Tamara Casper, Charles Cobbs, Nick Dee, Richard Ellenbogen, Manuel Ferreira, Jeff Goldy, Junitta Guzman, Ryder Gwinn, Daniel Hirschstein, Nikolas L. Jorstad, C. Dirk Keene, Andrew Ko, Boaz P. Levi, Jeffrey G. Ojemann, Thanh Pham, Nadiya Shapovalova, Daniel Silbergeld, Josef Sulc, Amy Torkelson, Herman Tung, Kimberly Smith, Ed S. Lein, Trygve E. Bakken, Rebecca D. Hodge, Jeremy A. Miller

publication / 2023
Morphoelectric and transcriptomic divergence of the layer 1 interneuron repertoire in human versus mouse neocortex
Science (New York, N.Y.)
Brain Science
MindScope
Brain and Consciousness

Thomas Chartrand, Rachel Dalley, Jennie Close, Natalia A. Goriounova, Brian R. Lee, Rusty Mann, Jeremy A. Miller, Gabor Molnar, Alice Mukora, Lauren Alfiler, Katherine Baker, Trygve E. Bakken, Jim Berg, Darren Bertagnolli, Thomas Braun, Krissy Brouner, Tamara Casper, Eva Adrienn Csajbok, Nick Dee, Tom Egdorf, Rachel Enstrom, Anna A. Galakhova, Amanda Gary, Emily Gelfand, Jeff Goldy, Kristen Hadley, Tim S. Heistek, DiJon Hill, Nik Jorstad, Lisa Kim, Agnes Katalin Kocsis, Lauren Kruse, Michael Kunst, Gabriela Leon, Brian Long, Matthew Mallory, Medea McGraw, Delissa McMillen, Erica J. Melief, Norbert Mihut, Lindsay Ng, Julie Nyhus, Gáspár Oláh, Attila Ozsvár, Victoria Omstead, Zoltan Peterfi, Alice Pom, Lydia Potekhina, Ramkumar Rajanbabu, Marton Rozsa, Augustin Ruiz, Joanna Sandle, Susan M. Sunkin, Ildiko Szots, Michael Tieu, Martin Toth, Jessica Trinh, Sara Vargas, David Vumbaco, Grace Williams, Julia Wilson, Zizhen Yao, Pal Barzo, Charles Cobbs, Richard G. Ellenbogen, Luke Esposito, Manuel Ferreira, Nathan W. Gouwens, Benjamin Grannan, Ryder P. Gwinn, Jason S. Hauptman, Tim Jarsky, C. Dirk Keene, Andrew L. Ko, Christof Koch, Jeffrey G. Ojemann, Anoop Patel, Jacob Ruzevick, Daniel L. Silbergeld, Kimberly Smith, Staci A. Sorensen, Bosiljka Tasic, Jonathan T. Ting, Jack Waters, Christiaan P. J. de Kock, Huib D. Mansvelder, Gabor Tamas, Hongkui Zeng, Brian Kalmbach, Ed S. Lein

publication / 2023
Signature morphoelectric properties of diverse GABAergic interneurons in the human neocortex
Science (New York, N.Y.)
Brain Science
MindScope

Brian R. Lee, Rachel Dalley, Jeremy A. Miller, Thomas Chartrand, Jennie Close, Rusty Mann, Alice Mukora, Lindsay Ng, Lauren Alfiler, Katherine Baker, Darren Bertagnolli, Krissy Brouner, Tamara Casper, Eva Csajbok, Nicholas Donadio, Stan L. W. Driessens, Tom Egdorf, Rachel Enstrom, Anna A. Galakhova, Amanda Gary, Emily Gelfand, Jeff Goldy, Kristen Hadley, Tim S. Heistek, Dijon Hill, Wen-Hsien Hou, Nelson Johansen, Nik Jorstad, Lisa Kim, Agnes Katalin Kocsis, Lauren Kruse, Michael Kunst, Gabriela León, Brian Long, Matthew Mallory, Michelle Maxwell, Medea McGraw, Delissa McMillen, Erica J. Melief, Gabor Molnar, Marty T. Mortrud, Dakota Newman, Julie Nyhus, Ximena Opitz-Araya, Attila Ozsvár, Trangthanh Pham, Alice Pom, Lydia Potekhina, Ram Rajanbabu, Augustin Ruiz, Susan M. Sunkin, Ildikó Szöts, Naz Taskin, Bargavi Thyagarajan, Michael Tieu, Jessica Trinh, Sara Vargas, David Vumbaco, Femke Waleboer, Sarah Walling-Bell, Natalie Weed, Grace Williams, Julia Wilson, Shenqin Yao, Thomas Zhou, Pál Barzó, Trygve Bakken, Charles Cobbs, Nick Dee, Richard G. Ellenbogen, Luke Esposito, Manuel Ferreira, Nathan W. Gouwens, Benjamin Grannan, Ryder P. Gwinn, Jason S. Hauptman, Rebecca Hodge, Tim Jarsky, C. Dirk Keene, Andrew L. Ko, Anders Rosendal Korshoej, Boaz P. Levi, Kaare Meier, Jeffrey G. Ojemann, Anoop Patel, Jacob Ruzevick, Daniel L. Silbergeld, Kimberly Smith, Jens Christian Sørensen, Jack Waters, Hongkui Zeng, Jim Berg, Marco Capogna, Natalia A. Goriounova, Brian Kalmbach, Christiaan P. J. de Kock, Huib D. Mansvelder, Staci A. Sorensen, Gabor Tamas, Ed S. Lein, Jonathan T. Ting

publication / 2023
Single-cell DNA methylation and 3D genome architecture in the human brain
Science (New York, N.Y.)
Brain Science
MindScope

Wei Tian, Jingtian Zhou, Anna Bartlett, Qiurui Zeng, Hanqing Liu, Rosa G. Castanon, Mia Kenworthy, Jordan Altshul, Cynthia Valadon, Andrew Aldridge, Joseph R. Nery, Huaming Chen, Jiaying Xu, Nicholas D. Johnson, Jacinta Lucero, Julia K. Osteen, Nora Emerson, Jon Rink, Jasper Lee, Yang E. Li, Kimberly Siletti, Michelle Liem, Naomi Claffey, Carolyn O'Connor, Anna Marie Yanny, Julie Nyhus, Nick Dee, Tamara Casper, Nadiya Shapovalova, Daniel Hirschstein, Song-Lin Ding, Rebecca Hodge, Boaz P. Levi, C. Dirk Keene, Sten Linnarsson, Ed Lein, Bing Ren, M. Margarita Behrens, Joseph R. Ecker

publication / 2023
Transcriptomic cytoarchitecture reveals principles of human neocortex organization
Science (New York, N.Y.)
Brain Science
MindScope

Nikolas L. Jorstad, Jennie Close, Nelson Johansen, Anna Marie Yanny, Eliza R. Barkan, Kyle J. Travaglini, Darren Bertagnolli, Jazmin Campos, Tamara Casper, Kirsten Crichton, Nick Dee, Song-Lin Ding, Emily Gelfand, Jeff Goldy, Daniel Hirschstein, Katelyn Kiick, Matthew Kroll, Michael Kunst, Kanan Lathia, Brian Long, Naomi Martin, Delissa McMillen, Trangthanh Pham, Christine Rimorin, Augustin Ruiz, Nadiya Shapovalova, Soraya Shehata, Kimberly Siletti, Saroja Somasundaram, Josef Sulc, Michael Tieu, Amy Torkelson, Herman Tung, Edward M. Callaway, Patrick R. Hof, C. Dirk Keene, Boaz P. Levi, Sten Linnarsson, Partha P. Mitra, Kimberly Smith, Rebecca D. Hodge, Trygve E. Bakken, Ed S. Lein

publication / 2023
Transcriptomic diversity of cell types across the adult human brain
Science (New York, N.Y.)
Brain Science
MindScope

Kimberly Siletti, Rebecca Hodge, Alejandro Mossi Albiach, Ka Wai Lee, Song-Lin Ding, Lijuan Hu, Peter Lönnerberg, Trygve Bakken, Tamara Casper, Michael Clark, Nick Dee, Jessica Gloe, Daniel Hirschstein, Nadiya V. Shapovalova, C. Dirk Keene, Julie Nyhus, Herman Tung, Anna Marie Yanny, Ernest Arenas, Ed S. Lein, Sten Linnarsson

preprint / 2023
HyperSINDy: Deep Generative Modeling of Nonlinear Stochastic Governing Equations
Shanahan

Mozes Jacobs, Bingni W. Brunton, Steven L. Brunton, J. Nathan Kutz, Ryan V. Raut

publication / 2023
Modeling functional cell types in spike train data
PLoS computational biology
Brain Science
MindScope

Daniel N. Zdeblick, Eric T. Shea-Brown, Daniela M. Witten, Michael A. Buice

publication / 2023
Building the next generation of virtual cells to understand cellular biology
Biophysical Journal
Cell Science

Graham T. Johnson, Eran Agmon, Matthew Akamatsu, Emma Lundberg, Blair Lyons, Wei Ouyang, Omar A. Quintero-Carmona, Megan Riel-Mehan, Susanne Rafelski, Rick Horwitz

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