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publication / 2023
AI to the rescue of voltage imaging
Cell Reports Methods
Brain Science
MindScope

Jérôme A. Lecoq, Kaspar Podgorski, Benjamin F. Grewe

publication / 2023
Cortico-thalamo-cortical interactions modulate electrically evoked EEG responses in mice
eLife
Brain Science
MindScope
Brain and Consciousness

Leslie D. Claar, Irene Rembado, Jacqulyn R. Kuyat, Simone Russo, Lydia C. Marks, Shawn R. Olsen, Christof Koch

publication / 2023
Reference-based cell type matching of in situ image-based spatial transcriptomics data on primary visual cortex of mouse brain
Scientific Reports
Brain Science
MindScope

Yun Zhang, Jeremy A. Miller, Jeongbin Park, Boudewijn P. Lelieveldt, Brian Long, Tamim Abdelaal, Brian D. Aevermann, Tommaso Biancalani, Charles Comiter, Oleh Dzyubachyk, Jeroen Eggermont, Christoffer Mattsson Langseth, Viktor Petukhov, Gabriele Scalia, Eeshit Dhaval Vaishnav, Yilin Zhao, Ed S. Lein, Richard H. Scheuermann

publication / 2023
Persistent serum protein signatures define an inflammatory subcategory of long COVID
Nature Communications
Immunology

Aarthi Talla, Suhas V. Vasaikar, Gregory Lee Szeto, Maria P. Lemos, Julie L. Czartoski, Hugh MacMillan, Zoe Moodie, Kristen W. Cohen, Lamar B. Fleming, Zachary Thomson, Lauren Okada, Lynne A. Becker, Ernest M. Coffey, Stephen C. De Rosa, Evan W. Newell, Peter J. Skene, Xiaojun Li, Thomas F. Bumol, M. Juliana McElrath, Troy R. Torgerson

publication / 2023
Functional gene delivery to and across brain vasculature of systemic AAVs with endothelial-specific tropism in rodents and broad tropism in primates
Nature Communications
Brain Science
MindScope

Xinhong Chen, Damien A. Wolfe, Dhanesh Sivadasan Bindu, Mengying Zhang, Naz Taskin, David Goertsen, Timothy F. Shay, Erin E. Sullivan, Sheng-Fu Huang, Sripriya Ravindra Kumar, Cynthia M. Arokiaraj, Viktor M. Plattner, Lillian J. Campos, John K. Mich, Deja Monet, Victoria Ngo, Xiaozhe Ding, Victoria Omstead, Natalie Weed, Yeme Bishaw, Bryan B. Gore, Ed S. Lein, Athena Akrami, Cory Miller, Boaz P. Levi, Annika Keller, Jonathan T. Ting, Andrew S. Fox, Cagla Eroglu, Viviana Gradinaru

preprint / 2023
Recurrent pattern completion drives the neocortical representation of sensory inference
Neural Dynamics

Hyeyoung Shin, Mora B. Ogando, Lamiae Abdeladim, Severine Durand, Hannah Belski, Hannah Cabasco, Henry Loefler, Ahad Bawany, Ben Hardcastle, Josh Wilkes, Katrina Nguyen, Lucas Suarez, Tye Johnson, Warren Han, Ben Ouellette, Conor Grasso, Jackie Swapp, Vivian Ha, Ahrial Young, Shiella Caldejon, Ali Williford, Peter Groblewski, Shawn Olsen, Carly Kiselycznyk, Jerome Lecoq, Hillel Adesnik

publication / 2023
A guide to the BRAIN Initiative Cell Census Network data ecosystem
PLoS biology
Brain Science
MindScope

Michael Hawrylycz, Maryann E. Martone, Giorgio A. Ascoli, Jan G. Bjaalie, Hong-Wei Dong, Satrajit S. Ghosh, Jesse Gillis, Ronna Hertzano, David R. Haynor, Patrick R. Hof, Yongsoo Kim, Ed Lein, Yufeng Liu, Jeremy A. Miller, Partha P. Mitra, Eran Mukamel, Lydia Ng, David Osumi-Sutherland, Hanchuan Peng, Patrick L. Ray, Raymond Sanchez, Aviv Regev, Alex Ropelewski, Richard H. Scheuermann, Shawn Zheng Kai Tan, Carol L. Thompson, Timothy Tickle, Hagen Tilgner, Merina Varghese, Brock Wester, Owen White, Hongkui Zeng, Brian Aevermann, David Allemang, Seth Ament, Thomas L. Athey, Cody Baker, Katherine S. Baker, Pamela M. Baker, Anita Bandrowski, Samik Banerjee, Prajal Bishwakarma, Ambrose Carr, Min Chen, Roni Choudhury, Jonah Cool, Heather Creasy, Florence D'Orazi, Kylee Degatano, Benjamin Dichter, Song-Lin Ding, Tim Dolbeare, Joseph R. Ecker, Rongxin Fang, Jean-Christophe Fillion-Robin, Timothy P. Fliss, James Gee, Tom Gillespie, Nathan Gouwens, Guo-Qiang Zhang, Yaroslav O. Halchenko, Nomi L. Harris, Brian R. Herb, Houri Hintiryan, Gregory Hood, Sam Horvath, Bingxing Huo, Dorota Jarecka, Shengdian Jiang, Farzaneh Khajouei, Elizabeth A. Kiernan, Huseyin Kir, Lauren Kruse, Changkyu Lee, Boudewijn Lelieveldt, Yang Li, Hanqing Liu, Lijuan Liu, Anup Markuhar, James Mathews, Kaylee L. Mathews, Chris Mezias, Michael I. Miller, Tyler Mollenkopf, Shoaib Mufti, Christopher J. Mungall, Joshua Orvis, Maja A. Puchades, Lei Qu, Joseph P. Receveur, Bing Ren, Nathan Sjoquist, Brian Staats, Daniel Tward, Cindy T. J. van Velthoven, Quanxin Wang, Fangming Xie, Hua Xu, Zizhen Yao, Zhixi Yun, Yun Renee Zhang, W. Jim Zheng, Brian Zingg

publication / 2023
An integrated cell atlas of the lung in health and disease
Nature Medicine
Brain Science
MindScope

Lisa Sikkema, Ciro Ramírez-Suástegui, Daniel C. Strobl, Tessa E. Gillett, Luke Zappia, Elo Madissoon, Nikolay S. Markov, Laure-Emmanuelle Zaragosi, Yuge Ji, Meshal Ansari, Marie-Jeanne Arguel, Leonie Apperloo, Martin Banchero, Christophe Bécavin, Marijn Berg, Evgeny Chichelnitskiy, Mei-I. Chung, Antoine Collin, Aurore C. A. Gay, Janine Gote-Schniering, Baharak Hooshiar Kashani, Kemal Inecik, Manu Jain, Theodore S. Kapellos, Tessa M. Kole, Sylvie Leroy, Christoph H. Mayr, Amanda J. Oliver, Michael von Papen, Lance Peter, Chase J. Taylor, Thomas Walzthoeni, Chuan Xu, Linh T. Bui, Carlo De Donno, Leander Dony, Alen Faiz, Minzhe Guo, Austin J. Gutierrez, Lukas Heumos, Ni Huang, Ignacio L. Ibarra, Nathan D. Jackson, Preetish Kadur Lakshminarasimha Murthy, Mohammad Lotfollahi, Tracy Tabib, Carlos Talavera-López, Kyle J. Travaglini, Anna Wilbrey-Clark, Kaylee B. Worlock, Masahiro Yoshida, Lung Biological Network Consortium, Maarten van den Berge, Yohan Bossé, Tushar J. Desai, Oliver Eickelberg, Naftali Kaminski, Mark A. Krasnow, Robert Lafyatis, Marko Z. Nikolic, Joseph E. Powell, Jayaraj Rajagopal, Mauricio Rojas, Orit Rozenblatt-Rosen, Max A. Seibold, Dean Sheppard, Douglas P. Shepherd, Don D. Sin, Wim Timens, Alexander M. Tsankov, Jeffrey Whitsett, Yan Xu, Nicholas E. Banovich, Pascal Barbry, Thu Elizabeth Duong, Christine S. Falk, Kerstin B. Meyer, Jonathan A. Kropski, Dana Pe'er, Herbert B. Schiller, Purushothama Rao Tata, Joachim L. Schultze, Sara A. Teichmann, Alexander V. Misharin, Martijn C. Nawijn, Malte D. Luecken, Fabian J. Theis

publication / 2023
BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets
Nature Methods
Brain Science
MindScope

Linus Manubens-Gil, Zhi Zhou, Hanbo Chen, Arvind Ramanathan, Xiaoxiao Liu, Yufeng Liu, Alessandro Bria, Todd Gillette, Zongcai Ruan, Jian Yang, Miroslav Radojević, Ting Zhao, Li Cheng, Lei Qu, Siqi Liu, Kristofer E. Bouchard, Lin Gu, Weidong Cai, Shuiwang Ji, Badrinath Roysam, Ching-Wei Wang, Hongchuan Yu, Amos Sironi, Daniel Maxim Iascone, Jie Zhou, Erhan Bas, Eduardo Conde-Sousa, Paulo Aguiar, Xiang Li, Yujie Li, Sumit Nanda, Yuan Wang, Leila Muresan, Pascal Fua, Bing Ye, Hai-Yan He, Jochen F. Staiger, Manuel Peter, Daniel N. Cox, Michel Simonneau, Marcel Oberlaender, Gregory Jefferis, Kei Ito, Paloma Gonzalez-Bellido, Jinhyun Kim, Edwin Rubel, Hollis T. Cline, Hongkui Zeng, Aljoscha Nern, Ann-Shyn Chiang, Jianhua Yao, Jane Roskams, Rick Livesey, Janine Stevens, Tianming Liu, Chinh Dang, Yike Guo, Ning Zhong, Georgia Tourassi, Sean Hill, Michael Hawrylycz, Christof Koch, Erik Meijering, Giorgio A. Ascoli, Hanchuan Peng

publication / 2023
Cross‐platform immunophenotyping of human peripheral blood mononuclear cells with four high‐dimensional flow cytometry panels
Cytometry Part A
Immunology

Alexander Heubeck, Adam Savage, Katherine Henderson, Charles Roll, Veronica Hernandez, Troy Torgerson, Thomas Bumol, Julian Reading

publication / 2023
Measuring Consciousness in the Intensive Care Unit
Neurocritical Care
Brain Science
MindScope
Brain and Consciousness

Brian L. Edlow, Matteo Fecchio, Yelena G. Bodien, Angela Comanducci, Mario Rosanova, Silvia Casarotto, Michael J. Young, Jian Li, Darin D. Dougherty, Christof Koch, Giulio Tononi, Marcello Massimini, Melanie Boly

publication / 2023
Do not go gently into that good night: The dying brain and its paradoxically heightened electrical activity
Proceedings of the National Academy of Sciences of the United States of America
Brain Science
MindScope
Brain and Consciousness

Christof Koch

publication / 2023
Target cell-specific synaptic dynamics of excitatory to inhibitory neuron connections in supragranular layers of human neocortex
eLife
Brain Science
MindScope

Mean-Hwan Kim, Cristina Radaelli, Elliot R. Thomsen, Deja Monet, Thomas Chartrand, Nikolas L. Jorstad, Joseph T. Mahoney, Michael J. Taormina, Brian Long, Katherine Baker, Trygve E. Bakken, Luke Campagnola, Tamara Casper, Michael Clark, Nick Dee, Florence D'Orazi, Clare Gamlin, Brian E. Kalmbach, Sara Kebede, Brian R. Lee, Lindsay Ng, Jessica Trinh, Charles Cobbs, Ryder P. Gwinn, C. Dirk Keene, Andrew L. Ko, Jeffrey G. Ojemann, Daniel L. Silbergeld, Staci A. Sorensen, Jim Berg, Kimberly A. Smith, Philip R. Nicovich, Tim Jarsky, Hongkui Zeng, Jonathan T. Ting, Boaz P. Levi, Ed Lein

publication / 2023
Responses of pyramidal cell somata and apical dendrites in mouse visual cortex over multiple days
Scientific Data
Brain Science
MindScope

Colleen J. Gillon, Jérôme A. Lecoq, Jason E. Pina, Ruweida Ahmed, Yazan N. Billeh, Shiella Caldejon, Peter 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, Joel Zylberberg, Blake A. Richards

publication / 2023
Deep Imaging to Dissect Microvascular Contributions to White Matter Degeneration in Rodent Models of Dementia
Stroke
Brain Science
MindScope

Stefan Stamenkovic, Yuandong Li, Jack Waters, Andy Shih

publication / 2023
Author Correction: Brain Data Standards - A method for building data-driven cell-type ontologies
Scientific Data
Brain Science
MindScope

Shawn Zheng Kai Tan, Huseyin Kir, Brian D. Aevermann, Tom Gillespie, Nomi Harris, Michael J. Hawrylycz, Nikolas L. Jorstad, Ed S. Lein, Nicolas Matentzoglu, Jeremy A. Miller, Tyler S. Mollenkopf, Christopher J. Mungall, Patrick L. Ray, Raymond E. A. Sanchez, Brian Staats, Jim Vermillion, Ambika Yadav, Yun Zhang, Richard H. Scheuermann, David Osumi-Sutherland

publication / 2023
Evolutionary constraint and innovation across hundreds of placental mammals
Science (New York, N.Y.)
Brain Science
MindScope

Matthew J. Christmas, Irene M. Kaplow, Diane P. Genereux, Michael X. Dong, Graham M. Hughes, Xue Li, Patrick F. Sullivan, Allyson G. Hindle, Gregory Andrews, Joel C. Armstrong, Matteo Bianchi, Ana M. Breit, Mark Diekhans, Cornelia Fanter, Nicole M. Foley, Daniel B. Goodman, Linda Goodman, Kathleen C. Keough, Bogdan Kirilenko, Amanda Kowalczyk, Colleen Lawless, Abigail L. Lind, Jennifer R. S. Meadows, Lucas R. Moreira, Ruby W. Redlich, Louise Ryan, Ross Swofford, Alejandro Valenzuela, Franziska Wagner, Ola Wallerman, Ashley R. Brown, Joana Damas, Kaili Fan, John Gatesy, Jenna Grimshaw, Jeremy Johnson, Sergey V. Kozyrev, Alyssa J. Lawler, Voichita D. Marinescu, Kathleen M. Morrill, Austin Osmanski, Nicole S. Paulat, BaDoi N. Phan, Steven K. Reilly, Daniel E. Schäffer, Cynthia Steiner, Megan A. Supple, Aryn P. Wilder, Morgan E. Wirthlin, James R. Xue, Zoonomia Consortium§, Bruce W. Birren, Steven Gazal, Robert M. Hubley, Klaus-Peter Koepfli, Tomas Marques-Bonet, Wynn K. Meyer, Martin Nweeia, Pardis C. Sabeti, Beth Shapiro, Arian F. A. Smit, Mark S. Springer, Emma C. Teeling, Zhiping Weng, Michael Hiller, Danielle L. Levesque, Harris A. Lewin, William J. Murphy, Arcadi Navarro, Benedict Paten, Katherine S. Pollard, David A. Ray, Irina Ruf, Oliver A. Ryder, Andreas R. Pfenning, Kerstin Lindblad-Toh, Elinor K. Karlsson

publication / 2023
Temporal dynamics of triphasic waves and generalized periodic discharges (P10-1.012)
Neurology
Shanahan

George Plummer, Ryan Raut, Bingni Brunton, Shahin Hakimian

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