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
allenites
the people who make our work possible
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
next generation leaders
fostering emerging leaders in bioscience
research
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
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
science resources
allencell.org
allenimmunology.org
allenneuraldynamics.org
brain-bican.org
brain-map.org
microns-explorer.org
impact
back to menu
team science
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
allenites
the people who make our work possible
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
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
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
Heading
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 / 2023
Spatial transcriptomics for profiling the tropism of viral vectors in tissues
Nature Biotechnology
No items found.

Min J. Jang, Gerard M. Coughlin, Cameron R. Jackson, Xinhong Chen, Miguel R. Chuapoco, Julia L. Vendemiatti, Alexander Z. Wang, Viviana Gradinaru

publication / 2023
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
Influence of claustrum on cortex varies by area, layer, and cell type
Neuron
Brain Science
MindScope

Ethan G. McBride, Saurabh R. Gandhi, Jacqulyn R. Kuyat, Douglas R. Ollerenshaw, Anton Arkhipov, Christof Koch, Shawn R. Olsen

publication / 2023
Neural assemblies uncovered by generative modeling explain whole-brain activity statistics and reflect structural connectivity
eLife
Brain Science
MindScope

Thijs L. van der Plas, Jérôme Tubiana, Guillaume Le Goc, Geoffrey Migault, Michael Kunst, Herwig Baier, Volker Bormuth, Bernhard Englitz, Georges Debrégeas

publication / 2023
Magnify is a universal molecular anchoring strategy for expansion microscopy
Nature Biotechnology
No items found.

Aleksandra Klimas, Brendan R. Gallagher, Piyumi Wijesekara, Sinda Fekir, Emma F. DiBernardo, Zhangyu Cheng, Donna B. Stolz, Franca Cambi, Simon C. Watkins, Steven L. Brody, Amjad Horani, Alison L. Barth, Christopher I. Moore, Xi Ren, Yongxin Zhao

publication / 2023
A survey of neurophysiological differentiation across mouse visual brain areas and timescales
Frontiers in Computational Neuroscience
Brain Science
MindScope

Saurabh R. Gandhi, William G. P. Mayner, William Marshall, Yazan N. Billeh, Corbett Bennett, Samuel D. Gale, Chris Mochizuki, Joshua H. Siegle, Shawn Olsen, Giulio Tononi, Christof Koch, Anton Arkhipov

publication / 2023
Endothelial structure contributes to heterogeneity in brain capillary diameter
Vascular Biology (Bristol, England)
Brain Science
MindScope

Sheridan M. Sargent, Stephanie K. Bonney, Yuandong Li, Stefan Stamenkovic, Marc M. Takeno, Vanessa Coelho-Santos, Andy Y. Shih

publication / 2023
Integrated intracellular organization and its variations in human iPS cells
Nature
Cell Science

Matheus P. Viana, Jianxu Chen, Theo A. Knijnenburg, Ritvik Vasan, Calysta Yan, Joy E. Arakaki, Matte Bailey, Ben Berry, Antoine Borensztejn, Eva M. Brown, Sara Carlson, Julie A. Cass, Basudev Chaudhuri, Kimberly R. Cordes Metzler, Mackenzie E. Coston, Zach J. Crabtree, Steve Davidson, Colette M. DeLizo, Shailja Dhaka, Stephanie Q. Dinh, Thao P. Do, Justin Domingus, Rory M. Donovan-Maiye, Alexandra J. Ferrante, Tyler J. Foster, Christopher L. Frick, Griffin Fujioka, Margaret A. Fuqua, Jamie L. Gehring, Kaytlyn A. Gerbin, Tanya Grancharova, Benjamin W. Gregor, Lisa J. Harrylock, Amanda Haupt, Melissa C. Hendershott, Caroline Hookway, Alan R. Horwitz, H. Christopher Hughes, Eric J. Isaac, Gregory R. Johnson, Brian Kim, Andrew N. Leonard, Winnie W. Leung, Jordan J. Lucas, Susan A. Ludmann, Blair M. Lyons, Haseeb Malik, Ryan McGregor, Gabe E. Medrash, Sean L. Meharry, Kevin Mitcham, Irina A. Mueller, Timothy L. Murphy-Stevens, Aditya Nath, Angelique M. Nelson, Sandra A. Oluoch, Luana Paleologu, T. Alexander Popiel, Megan M. Riel-Mehan, Brock Roberts, Lisa M. Schaefbauer, Magdalena Schwarzl, Jamie Sherman, Sylvain Slaton, M. Filip Sluzewski, Jacqueline E. Smith, Youngmee Sul, Madison J. Swain-Bowden, W. Joyce Tang, Derek J. Thirstrup, Daniel M. Toloudis, Andrew P. Tucker, Veronica Valencia, Winfried Wiegraebe, Thushara Wijeratna, Ruian Yang, Rebecca J. Zaunbrecher, Ramon Lorenzo D. Labitigan, Adrian L. Sanborn, Graham T. Johnson, Ruwanthi N. Gunawardane, Nathalie Gaudreault, Julie A. Theriot, Susanne M. Rafelski

publication / 2023
Mapping Human Neuronal Diversity in the Search for New Therapeutics: Using Real Human Neuron Data Sets to Build Student Quantitative Skills
Journal of undergraduate neuroscience education: JUNE: a publication of FUN, Faculty for Undergraduate Neuroscience
Brain Science

Emma C. Milligan, Kaitlyn Casimo, Laurie Buchanan, Bryant Hutson, Sabrina Robertson

publication / 2023
Mapping Human Neuronal Diversity in the Search for New Therapeutics: Using Real Human Neuron Data Sets to Build Student Quantitative Skills
Journal of Undergraduate Neuroscience Education
Education and Engagement

Emma C Milligan, Kaitlyn Casimo, Laurie Buchanan, Bryant Huston, Sabrina Robertson

publication / 2023
Modeling the cell-type-specific mesoscale murine connectome with anterograde tracing experiments
Network Neuroscience (Cambridge, Mass.)
Brain Science
MindScope

Samson Koelle, Dana Mastrovito, Jennifer D. Whitesell, Karla E. Hirokawa, Hongkui Zeng, Marina Meila, Julie A. Harris, Stefan Mihalas

publication / 2023
Possible rodent equivalent of the posterior cingulate cortex (area 23) interconnects with multimodal cortical and subcortical regions
Frontiers in Neuroscience
Brain Science
MindScope

Xiao-Jun Xiang, Sheng-Qiang Chen, Xue-Qin Zhang, Chang-Hui Chen, Shun-Yu Zhang, Hui-Ru Cai, Song-Lin Ding

publication / 2023
Sleep-mediated regulation of reward circuits: implications in substance use disorders
Neuropsychopharmacology: Official Publication of the American College of Neuropsychopharmacology
Brain Science
MindScope

Rong Guo, Dylan Thomas Vaughan, Ana Lourdes Almeida Rojo, Yanhua H. Huang

publication / 2022
A novel subdivision of the bed nucleus of stria terminalis in monkey, rat, and mouse brains
The Journal of Comparative Neurology
Brain Science
MindScope

Song-Lin Ding

publication / 2022
Multi-modal characterization and simulation of human epileptic circuitry
Cell Reports
Brain Science
MindScope

Anatoly Buchin, Rebecca de Frates, Anirban Nandi, Rusty Mann, Peter Chong, Lindsay Ng, Jeremy Miller, Rebecca Hodge, Brian Kalmbach, Soumita Bose, Ueli Rutishauser, Stephen McConoughey, Ed Lein, Jim Berg, Staci Sorensen, Ryder Gwinn, Christof Koch, Jonathan Ting, Costas A. Anastassiou

publication / 2022
Simulations of cortical networks using spatially extended conductance-based neuronal models
The Journal of Physiology
Brain Science
MindScope
Brain and Consciousness

Darrell Haufler, Shinya Ito, Christof Koch, Anton Arkhipov

publication / 2022
Mesolimbic dopamine release conveys causal associations
Science (New York, N.Y.)
Brain Science
MindScope

Huijeong Jeong, Annie Taylor, Joseph R. Floeder, Martin Lohmann, Stefan Mihalas, Brenda Wu, Mingkang Zhou, Dennis A. Burke, Vijay Mohan K. Namboodiri

publication / 2022
Joint coding of visual input and eye/head position in V1 of freely moving mice
Neuron
No items found.

Philip R. L. Parker, Elliott T. T. Abe, Emmalyn S. P. Leonard, Dylan M. Martins, Cristopher M. Niell

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.

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 biologybrain healthpublications
education
science educationfield tripsprofessional developmenteducation resources
quick links
newseventsopen sciencepodcastscience resourceshuman brain donationvisit uscontact
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