Skip to main content
impact
about
our story
explore our impact
careers and opportunities
join us
open science
sharing science to speed discovery
open science week
celebrating open science
team science
people & teams
discovery is a team effort
advisors
their input shapes our science
board of directors
they help us fulfill our mission
shanahan foundation fellowship
at the interface of data and neuroscience
studio d3 fellowship
contribute bold ideas to redefine discovery
next generation leaders
fostering emerging leaders in bioscience
research
overview
our approach
science at the scale of greatest impact
additional programs
studio d3
data driven discovery
neurobiology of action
revealing the mechanisms behind movement and learning
science accelerators
brain science
building a blueprint of the brain
cell science
understanding how cells become organs
neural dynamics
revealing the brain’s hidden algorithms
immunology
mapping the immune system
synthetic biology
designing biology to advance health
brain health
accelerating human brain research
ai biodesign
unlocking new frontiers of bioscience
education
overview
science education
science is for everyone
open science
sharing science speeds discovery
engagement
education resources
real science. real skills.
field trips
experience science where it happens
educator development
empowering educators
news
overview
all news
explore the latest news
podcast
the human stories behind discovery
sign up for our newsletter
stay connected to our science
events
overview
all events
public engagement, workshops, seminars and more
conferences
connect with us
science resources
explore
publications
explore our publications
open science
sharing science to speed discovery
science resources
allencell.org
allenimmunology.org
allenneuraldynamics.org
brain-bican.org
brain-map.org
microns-explorer.org
impact
back to menu
overview
our story
explore our impact
careers and opportunities
join us
open science
sharing science to speed discovery
open science week
celebrating open science
team science
people & teams
discovery is a team effort
advisors
their input shapes our science
board of directors
they help us fulfill our mission
shanahan foundation fellowship
at the interface of data and neuroscience
studio d3 fellowship
contributing bold ideas to redefine discovery
next generation leaders
fostering emerging leaders in bioscience
research
back to menu
overview
our approach
science at the scale of greatest impact
publications
explore our publications
open science
sharing science to speed discovery
science accelerators
brain science
building a blueprint of the brain
cell science
understanding how cells become organs
neural dynamics
revealing the brain’s hidden algorithms
immunology
creating the ultimate immune system reference
synthetic biology
seattle hub for synthetic biology
brain health
accelerating human brain research and disease therapeutics
ai biodesign
unlocking new frontiers of bioscience
additional programs
studio d3
data driven discovery
neurobiology of action
revealing the mechanisms behind movement and learning
education
back to menu
overview
science education
science is for everyone
open science
sharing science speeds discovery
engagement
education resources
real science. real skills.
field trips
experience science where it happens
educator development
empowering educators
news
back to menu
overview
all news
explore the latest news
podcast
the human stories behind discovery
newsletter
stay connected to our science
events
back to menu
overview
all events
public engagement, workshops, seminars and more
conferences
connect with us
science resources
back to menu
science resources
allencell.org
allenimmunology.org
allenneuraldynamics.org
brain-bican.org
brain-map.org
microns-explorer.org
explore
publications
explore our publications
open science
sharing science to speed discovery
search

publications

explore publications from the allen institute

latest publications

2026
2025
2024
2023
2022
2021
2020
2019
2018
2017
2016
2015
2014
2013
2012
2011
2010
2009
2008
2007
2006
2005
2004
Brain and Consciousness
Brain Science
Cell Science
Education
Immunology
Neural Dynamics
Seattle Hub Team
Shanahan Fellowship
Thank you! Your submission has been received!
Oops! Something went wrong while submitting the form.
publication / 2021
Perceptual awareness negativity: a physiological correlate of sensory consciousness
Trends in Cognitive Sciences
Brain Science
MindScope

Cole Dembski, Christof Koch, Michael Pitts

publication / 2021
Recent ultra-rare inherited variants implicate new autism candidate risk genes
Nature Genetics
Brain Science
MindScope

Amy B. Wilfert, Tychele N. Turner, Shwetha C. Murali, PingHsun Hsieh, Arvis Sulovari, Tianyun Wang, Bradley P. Coe, Hui Guo, Kendra Hoekzema, Trygve E. Bakken, Lara H. Winterkorn, Uday S. Evani, Marta Byrska-Bishop, Rachel K. Earl, Raphael A. Bernier, SPARK Consortium, Michael C. Zody, Evan E. Eichler

publication / 2021
Interrogating theoretical models of neural computation with emergent property inference
eLife
Brain Science
MindScope

Sean R. Bittner, Agostina Palmigiano, Alex T. Piet, Chunyu A. Duan, Carlos D. Brody, Kenneth D. Miller, John Cunningham

publication / 2021
Remote control of neural function by X-ray-induced scintillation
Nature Communications
Neural Dynamics

Takanori Matsubara, Takayuki Yanagida, Noriaki Kawaguchi, Takashi Nakano, Junichiro Yoshimoto, Maiko Sezaki, Hitoshi Takizawa, Satoshi P. Tsunoda, Shin-ichiro Horigane, Shuhei Ueda, Sayaka Takemoto-Kimura, Hideki Kandori, Akihiro Yamanaka, Takayuki Yamashita

publication / 2021
FR-Match: robust matching of cell type clusters from single cell RNA sequencing data using the Friedman-Rafsky non-parametric test
Briefings in Bioinformatics
Brain Science
MindScope

Yun Zhang, Brian D. Aevermann, Trygve E. Bakken, Jeremy A. Miller, Rebecca D. Hodge, Ed S. Lein, Richard H. Scheuermann

publication / 2021
Reconciling functional differences in populations of neurons recorded with two-photon imaging and electrophysiology
eLife
Brain Science
MindScope

Joshua H. Siegle, Peter Ledochowitsch, Xiaoxuan Jia, Daniel J. Millman, Gabriel K. Ocker, Shiella Caldejon, Linzy Casal, Andy Cho, Daniel J. Denman, Séverine Durand, Peter A. Groblewski, Gregg Heller, India Kato, Sara Kivikas, Jérôme Lecoq, Chelsea Nayan, Kiet Ngo, Philip R. Nicovich, Kat North, Tamina K. Ramirez, Jackie Swapp, Xana Waughman, Ali Williford, Shawn R. Olsen, Christof Koch, Michael A. Buice, Saskia Ej de Vries

publication / 2021
Cell states beyond transcriptomics: Integrating structural organization and gene expression in hiPSC-derived cardiomyocytes
Cell Systems
Cell Science

Kaytlyn A. Gerbin, Tanya Grancharova, Rory M. Donovan-Maiye, Melissa C. Hendershott, Helen G. Anderson, Jackson M. Brown, Jianxu Chen, Stephanie Q. Dinh, Jamie L. Gehring, Gregory R. Johnson, HyeonWoo Lee, Aditya Nath, Angelique M. Nelson, M. Filip Sluzewski, Matheus P. Viana, Calysta Yan, Rebecca J. Zaunbrecher, Kimberly R. Cordes Metzler, Nathalie Gaudreault, Theo A. Knijnenburg, Susanne M. Rafelski, Julie A. Theriot, Ruwanthi N. Gunawardane

publication / 2021
A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation
Cell
Brain Science
MindScope

Zizhen Yao, Cindy T. J. van Velthoven, Thuc Nghi Nguyen, Jeff Goldy, Adriana E. Sedeno-Cortes, Fahimeh Baftizadeh, Darren Bertagnolli, Tamara Casper, Megan Chiang, Kirsten Crichton, Song-Lin Ding, Olivia Fong, Emma Garren, Alexandra Glandon, Nathan W. Gouwens, James Gray, Lucas T. Graybuck, Michael J. Hawrylycz, Daniel Hirschstein, Matthew Kroll, Kanan Lathia, Changkyu Lee, Boaz Levi, Delissa McMillen, Stephanie Mok, Thanh Pham, Qingzhong Ren, Christine Rimorin, Nadiya Shapovalova, Josef Sulc, Susan M. Sunkin, Michael Tieu, Amy Torkelson, Herman Tung, Katelyn Ward, Nick Dee, Kimberly A. Smith, Bosiljka Tasic, Hongkui Zeng

publication / 2021
Cell segmentation-free inference of cell types from in situ transcriptomics data
Nature Communications
Brain Science
MindScope

Jeongbin Park, Wonyl Choi, Sebastian Tiesmeyer, Brian Long, Lars E. Borm, Emma Garren, Thuc Nghi Nguyen, Bosiljka Tasic, Simone Codeluppi, Tobias Graf, Matthias Schlesner, Oliver Stegle, Roland Eils, Naveed Ishaque

publication / 2021
Control of impulsivity by Gi-protein signalling in layer-5 pyramidal neurons of the anterior cingulate cortex
Communications Biology
Brain Science
MindScope

Bastiaan van der Veen, Sampath K. T. Kapanaiah, Kasyoka Kilonzo, Peter Steele-Perkins, Martin M. Jendryka, Stefanie Schulz, Bosiljka Tasic, Zizhen Yao, Hongkui Zeng, Thomas Akam, Janet R. Nicholson, Birgit Liss, Wiebke Nissen, Anton Pekcec, Dennis Kätzel

publication / 2021
Enhancer viruses for combinatorial cell-subclass-specific labeling
Neuron
Brain Science
MindScope

Lucas T. Graybuck, Tanya L. Daigle, Adriana E. Sedeño-Cortés, Miranda Walker, Brian Kalmbach, Garreck H. Lenz, Elyse Morin, Thuc Nghi Nguyen, Emma Garren, Jacqueline L. Bendrick, Tae Kyung Kim, Thomas Zhou, Marty Mortrud, Shenqin Yao, La' Akea Siverts, Rachael Larsen, Bryan B. Gore, Eric R. Szelenyi, Cameron Trader, Pooja Balaram, Cindy T. J. van Velthoven, Megan Chiang, John K. Mich, Nick Dee, Jeff Goldy, Ali H. Cetin, Kimberly Smith, Sharon W. Way, Luke Esposito, Zizhen Yao, Viviana Gradinaru, Susan M. Sunkin, Ed Lein, Boaz P. Levi, Jonathan T. Ting, Hongkui Zeng, Bosiljka Tasic

publication / 2021
Integration of evidence across human and model organism studies: A meeting report
Genes, Brain, and Behavior
Brain Science
MindScope

Rohan H. C. Palmer, Emma C. Johnson, Hyejung Won, Renato Polimanti, Manav Kapoor, Apurva Chitre, Molly A. Bogue, Chelsie E. Benca-Bachman, Clarissa C. Parker, Anurag Verma, Timothy Reynolds, Jason Ernst, Michael Bray, Soo Bin Kwon, Dongbing Lai, Bryan C. Quach, Nathan C. Gaddis, Laura Saba, Hao Chen, Michael Hawrylycz, Shan Zhang, Yuan Zhou, Spencer Mahaffey, Christian Fischer, Sandra Sanchez-Roige, Anita Bandrowski, Qing Lu, Li Shen, Vivek Philip, Joel Gelernter, Laura J. Bierut, Dana B. Hancock, Howard J. Edenberg, Eric O. Johnson, Eric J. Nestler, Peter B. Barr, Pjotr Prins, Desmond J. Smith, Schahram Akbarian, Thorgeir Thorgeirsson, Dave Walton, Erich Baker, Daniel Jacobson, Abraham A. Palmer, Michael Miles, Elissa J. Chesler, Jake Emerson, Arpana Agrawal, Maryann Martone, Robert W. Williams

publication / 2021
Chromatic micromaps in primary visual cortex
Nature Communications
Brain Science
MindScope

Soumya Chatterjee, Kenichi Ohki, R. Clay Reid

publication / 2021
Quantitative visualization of endocytic trafficking through photoactivation of fluorescent proteins
Molecular Biology of the Cell
Brain Science
MindScope

Manuela Ecker, Gregory M. I. Redpath, Philip R. Nicovich, Jérémie Rossy

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

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

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

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

Previous
load more publications

No results found, try reducing your search parameters.

we acceleratedevelopcatalyzeimpact

science done differently. shared openly.

explore our accelerators

brain science

Mapping every cell, connection, and circuit in the brain—openly shared with the world.

cell science

Decoding how cells become tissues, then programming that knowledge into powerful new research tools.

neural dynamics

Revealing the brain's hidden algorithms that transform neural activity into real-world behavior.

immunology

Creating the deepest open reference for the healthy human immune system ever built.

synthetic biology

Engineering cells to record their own histories, transforming how we understand disease over time.

ai biodesign

Advancing evolution to explore biology’s full design space and advance human health

Brain Health

Accelerating human brain research and new therapeutic strategies for neurological conditions

research

Big questions, open answers, and science built to be shared.

education

Inspiring the next generation of scientists through open science resources.

impact

Our science is empowering researchers and advancing health worldwide.
advancing science through open, collaborative research
Get the allen institute newsletter
Stay informed on the latest breakthroughs in neuroscience, bioscience, and AI-driven research.
allen institute
impactpeople & teamscareers & opportunitiesalumnihistory & founder
science resources
allencell.orgallenimmunology.orgallenneuraldynamics.orgbrain-bican.orgbrain-map.orgmicrons-explorer.org
research
brain sciencecell scienceneural dynamicsimmunologysynthetic biologyai biodesignbrain healthpublicationsscience resources
quick links
newseventsopen sciencepodcasthuman brain donationvisit uscontact
education
science educationfield tripsprofessional developmenteducation resources
follow us/

allen institute, 615 Westlake Ave North, Seattle, WA 98109 +12065487055

© 0000 allen institute. all rights reserved.
privacy policyterms of usecitation policyemployee portalpolicy & compliancecookie settings