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publication / 2021
Simultaneous trimodal single-cell measurement of transcripts, epitopes, and chromatin accessibility using TEA-seq
eLife
Immunology

Elliott Swanson, Cara Lord, Julian Reading, Alexander T Heubeck, Palak C Genge, Zachary Thomson, Morgan Da Weiss, Xiao-jun Li, Adam K Savage, Richard R Green, Troy R Torgerson, Thomas F Bumol, Lucas T Graybuck, Peter J Skene

10.7554/elife.63632
AIFI, Adam K Savage, Alexander T Heubeck, Allen Institute for Immunology, Cara Lord, Elliott Swanson, Immunology, Julian Reading, Lucas T Graybuck, Morgan DA Weiss, Palak C Genge, Peter J Skene, Richard R. Green, Simultaneous trimodal single-cell measurement of transcripts epitopes and chromatin accessibility using TEA-seq, Thomas F Bumol, Troy R Torgerson, Xiaojun Li, Zachary Thomson
publication / 2021
Survey of spiking in the mouse visual system reveals functional hierarchy
Nature
Brain Science
MindScope

Joshua H. Siegle, Xiaoxuan Jia, Séverine Durand, Sam Gale, Corbett Bennett, Nile Graddis, Greggory Heller, Tamina K. Ramirez, Hannah Choi, Jennifer A. Luviano, Peter A. Groblewski, Ruweida Ahmed, Anton Arkhipov, Amy Bernard, Yazan N. Billeh, Dillan Brown, Michael A. Buice, Nicolas Cain, Shiella Caldejon, Linzy Casal, Andrew Cho, Maggie Chvilicek, Timothy C. Cox, Kael Dai, Daniel J. Denman, Saskia E. J. de Vries, Roald Dietzman, Luke Esposito, Colin Farrell, David Feng, John Galbraith, Marina Garrett, Emily C. Gelfand, Nicole Hancock, Julie A. Harris, Robert Howard, Brian Hu, Ross Hytnen, Ramakrishnan Iyer, Erika Jessett, Katelyn Johnson, India Kato, Justin Kiggins, Sophie Lambert, Jerome Lecoq, Peter Ledochowitsch, Jung Hoon Lee, Arielle Leon, Yang Li, Elizabeth Liang, Fuhui Long, Kyla Mace, Jose Melchior, Daniel Millman, Tyler Mollenkopf, Chelsea Nayan, Lydia Ng, Kiet Ngo, Thuyahn Nguyen, Philip R. Nicovich, Kat North, Gabriel Koch Ocker, Doug Ollerenshaw, Michael Oliver, Marius Pachitariu, Jed Perkins, Melissa Reding, David Reid, Miranda Robertson, Kara Ronellenfitch, Sam Seid, Cliff Slaughterbeck, Michelle Stoecklin, David Sullivan, Ben Sutton, Jackie Swapp, Carol Thompson, Kristen Turner, Wayne Wakeman, Jennifer D. Whitesell, Derric Williams, Ali Williford, Rob Young, Hongkui Zeng, Sarah Naylor, John W. Phillips, R. Clay Reid, Stefan Mihalas, Shawn R. Olsen, Christof Koch

10.1038/s41586-020-03171-x
Brain Science
publication / 2021
Functional enhancer elements drive subclass-selective expression from mouse to primate neocortex
Cell Reports
Brain Science
MindScope

John K. Mich, Lucas T. Graybuck, Erik E. Hess, Joseph T. Mahoney, Yoshiko Kojima, Yi Ding, Saroja Somasundaram, Jeremy A. Miller, Brian E. Kalmbach, Cristina Radaelli, Bryan B. Gore, Natalie Weed, Victoria Omstead, Yemeserach Bishaw, Nadiya V. Shapovalova, Refugio A. Martinez, Olivia Fong, Shenqin Yao, Marty Mortrud, Peter Chong, Luke Loftus, Darren Bertagnolli, Jeff Goldy, Tamara Casper, Nick Dee, Ximena Opitz-Araya, Ali Cetin, Kimberly A. Smith, Ryder P. Gwinn, Charles Cobbs, Andrew L. Ko, Jeffrey G. Ojemann, C. Dirk Keene, Daniel L. Silbergeld, Susan M. Sunkin, Viviana Gradinaru, Gregory D. Horwitz, Hongkui Zeng, Bosiljka Tasic, Ed S. Lein, Jonathan T. Ting, Boaz P. Levi

10.1016/j.celrep.2021.108754
AIBS First Author, AIBS Last Author, Brain Science
publication / 2021
Dorsal Raphe Dopamine Neurons Signal Motivational Salience Dependent on Internal State, Expectation, and Behavioral Context
The Journal of Neuroscience
Neural Dynamics

Jounhong Ryan Cho, Xinhong Chen, Anat Kahan, J. Elliott Robinson, Daniel A. Wagenaar, Viviana Gradinaru

publication / 2021
Alternating sources of perisomatic inhibition during behavior
Neuron
Brain Science
MindScope

Barna Dudok, Peter M. Klein, Ernie Hwaun, Brian R. Lee, Zizhen Yao, Olivia Fong, John C. Bowler, Satoshi Terada, Fraser T. Sparks, Gergely G. Szabo, Jordan S. Farrell, Jim Berg, Tanya L. Daigle, Bosiljka Tasic, Jordane Dimidschstein, Gord Fishell, Attila Losonczy, Hongkui Zeng, Ivan Soltesz

10.1016/j.neuron.2021.01.003
Brain Science
publication / 2021
Relationship between simultaneously recorded spiking activity and fluorescence signal in GCaMP6 transgenic mice
eLife
Brain Science
MindScope

Lawrence Huang, Peter Ledochowitsch, Ulf Knoblich, Jérôme Lecoq, Gabe J. Murphy, R. Clay Reid, Saskia Ej de Vries, Christof Koch, Hongkui Zeng, Michael A. Buice, Jack Waters, Lu Li

10.7554/elife.51675
AIBS First Author, AIBS Last Author, Brain Science
publication / 2021
Predictive learning as a network mechanism for extracting low-dimensional latent space representations
Nature Communications
Brain Science
MindScope

Stefano Recanatesi, Matthew Farrell, Guillaume Lajoie, Sophie Deneve, Mattia Rigotti, Eric Shea-Brown

publication / 2021
Analysis of spiking synchrony in visual cortex reveals distinct types of top-down modulation signals for spatial and object-based attention
PLoS computational biology
Brain Science
MindScope

Nobuhiko Wagatsuma, Brian Hu, Rüdiger von der Heydt, Ernst Niebur

publication / 2021
Highlights from the Era of Open Source Web-Based Tools
The Journal of Neuroscience: The Official Journal of the Society for Neuroscience
Brain Science
MindScope

Kristin R. Anderson, Julie A. Harris, Lydia Ng, Pjotr Prins, Sara Memar, Bengt Ljungquist, Daniel Fürth, Robert W. Williams, Giorgio A. Ascoli, Dani Dumitriu

10.1523/jneurosci.1657-20.2020
Brain Science
publication / 2021
Patch-seq: Past, Present, and Future
The Journal of Neuroscience: The Official Journal of the Society for Neuroscience
Brain Science
MindScope

Marcela Lipovsek, Cedric Bardy, Cathryn R. Cadwell, Kristen Hadley, Dmitry Kobak, Shreejoy J. Tripathy

publication / 2021
Regional, Layer, and Cell-Type-Specific Connectivity of the Mouse Default Mode Network
Neuron
Brain Science
MindScope

Jennifer D. Whitesell, Adam Liska, Ludovico Coletta, Karla E. Hirokawa, Phillip Bohn, Ali Williford, Peter A. Groblewski, Nile Graddis, Leonard Kuan, Joseph E. Knox, Anh Ho, Wayne Wakeman, Philip R. Nicovich, Thuc Nghi Nguyen, Cindy T. J. van Velthoven, Emma Garren, Olivia Fong, Maitham Naeemi, Alex M. Henry, Nick Dee, Kimberly A. Smith, Boaz Levi, David Feng, Lydia Ng, Bosiljka Tasic, Hongkui Zeng, Stefan Mihalas, Alessandro Gozzi, Julie A. Harris

10.1016/j.neuron.2020.11.011
AIBS First Author, AIBS Last Author, Brain Science
publication / 2021
Consistent cross-modal identification of cortical neurons with coupled autoencoders
Nature Computational Science
Brain Science
MindScope

Rohan Gala, Agata Budzillo, Fahimeh Baftizadeh, Jeremy Miller, Nathan Gouwens, Anton Arkhipov, Gabe Murphy, Bosiljka Tasic, Hongkui Zeng, Michael Hawrylycz, Uygar Sümbül

10.1038/s43588-021-00030-1
AIBS First Author, AIBS Last Author, Brain Science
publication / 2021
The Effect of Inclusion Criteria on the Functional Properties Reported in Mouse Visual Cortex
eNeuro
Brain Science
MindScope

Natalia Mesa, Jack Waters, Saskia E. J. de Vries

10.1523/eneuro.0188-20.2021
Brain Science, MindScope Program
publication / 2021
Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems
Science (New York, N.Y.)
Brain Science
MindScope

Shahar Alon, Daniel R. Goodwin, Anubhav Sinha, Asmamaw T. Wassie, Fei Chen, Evan R. Daugharthy, Yosuke Bando, Atsushi Kajita, Andrew G. Xue, Karl Marrett, Robert Prior, Yi Cui, Andrew C. Payne, Chun-Chen Yao, Ho-Jun Suk, Ru Wang, Chih-Chieh Jay Yu, Paul Tillberg, Paul Reginato, Nikita Pak, Songlei Liu, Sukanya Punthambaker, Eswar P. R. Iyer, Richie E. Kohman, Jeremy A. Miller, Ed S. Lein, Ana Lako, Nicole Cullen, Scott Rodig, Karla Helvie, Daniel L. Abravanel, Nikhil Wagle, Bruce E. Johnson, Johanna Klughammer, Michal Slyper, Julia Waldman, Judit Jané-Valbuena, Orit Rozenblatt-Rosen, Aviv Regev, IMAXT Consortium, George M. Church, Adam H. Marblestone, Edward S. Boyden

publication / 2021
Multiple Alu Exonization in 3'UTR of a Primate-Specific Isoform of CYP20A1 Creates a Potential miRNA Sponge
Genome Biology and Evolution
Brain Science
MindScope

Aniket Bhattacharya, Vineet Jha, Khushboo Singhal, Mahar Fatima, Dayanidhi Singh, Gaura Chaturvedi, Dhwani Dholakia, Rintu Kutum, Rajesh Pandey, Trygve E. Bakken, Pankaj Seth, Beena Pillai, Mitali Mukerji

publication / 2021
A course-based research experience using the Allen Brain Map: from research question to poster session
Journal of Undergraduate Neuroscience Education
Education and Engagement

Jim Ryan, Kaitlyn Casimo

publication / 2021
A Course-Based Research Experience Using the Allen Brain Map: From Research Question to Poster Session
Journal of undergraduate neuroscience education: JUNE: a publication of FUN, Faculty for Undergraduate Neuroscience
Brain Science
MindScope

Jim Ryan, Kaitlyn Casimo

publication / 2021
A Multisubcellular Compartment Model of AMPA Receptor Trafficking for Neuromodulation of Hebbian Synaptic Plasticity
Frontiers in Synaptic Neuroscience
Brain Science
MindScope

Stefan Mihalas, Alvaro Ardiles, Kaiwen He, Adrian Palacios, Alfredo Kirkwood

10.3389/fnsyn.2021.703621
Brain Science
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