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 / 2019
Mouse embryo geometry drives formation of robust signaling gradients through receptor localization
Nature Communications
Brain Science
MindScope

Zhechun Zhang, Steven Zwick, Ethan Loew, Joshua S. Grimley, Sharad Ramanathan

publication / 2019
Aberration-free multi-plane imaging of neural activity from the mammalian brain using a fast-switching liquid crystal spatial light modulator
Biomedical Optics Express
Brain Science
MindScope

Rui Liu, Neil Ball, James Brockill, Leonard Kuan, Daniel Millman, Cassandra White, Arielle Leon, Derric Williams, Shig Nishiwaki, Saskia de Vries, Josh Larkin, David Sullivan, Cliff Slaughterbeck, Colin Farrell, Peter Saggau

publication / 2019
Single-trial neural dynamics are dominated by richly varied movements
Nature Neuroscience
Neural Dynamics

Simon Musall, Matthew T. Kaufman, Ashley L. Juavinett, Steven Gluf, Anne K. Churchland

publication / 2019
Automatic navigation system for the mouse brain
The Journal of Comparative Neurology
Brain Science
MindScope

Susan J. Tappan, Brian S. Eastwood, Nathan O'Connor, Quanxin Wang, Lydia Ng, David Feng, Bryan M. Hooks, Charles R. Gerfen, Patrick R. Hof, Christoph Schmitz, Jack R. Glaser

publication / 2019
Conserved cell types with divergent features in human versus mouse cortex
Nature
Brain Science
MindScope

Rebecca D. Hodge, Trygve E. Bakken, Jeremy A. Miller, Kimberly A. Smith, Eliza R. Barkan, Lucas T. Graybuck, Jennie L. Close, Brian Long, Nelson Johansen, Osnat Penn, Zizhen Yao, Jeroen Eggermont, Thomas Höllt, Boaz P. Levi, Soraya I. Shehata, Brian Aevermann, Allison Beller, Darren Bertagnolli, Krissy Brouner, Tamara Casper, Charles Cobbs, Rachel Dalley, Nick Dee, Song-Lin Ding, Richard G. Ellenbogen, Olivia Fong, Emma Garren, Jeff Goldy, Ryder P. Gwinn, Daniel Hirschstein, C. Dirk Keene, Mohamed Keshk, Andrew L. Ko, Kanan Lathia, Ahmed Mahfouz, Zoe Maltzer, Medea McGraw, Thuc Nghi Nguyen, Julie Nyhus, Jeffrey G. Ojemann, Aaron Oldre, Sheana Parry, Shannon Reynolds, Christine Rimorin, Nadiya V. Shapovalova, Saroja Somasundaram, Aaron Szafer, Elliot R. Thomsen, Michael Tieu, Gerald Quon, Richard H. Scheuermann, Rafael Yuste, Susan M. Sunkin, Boudewijn Lelieveldt, David Feng, Lydia Ng, Amy Bernard, Michael Hawrylycz, John W. Phillips, Bosiljka Tasic, Hongkui Zeng, Allan R. Jones, Christof Koch, Ed S. Lein

publication / 2019
New insights into the development of the human cerebral cortex
Journal of Anatomy
Brain Science
MindScope

Zoltán Molnár, Gavin J. Clowry, Nenad Šestan, Ayman Alzu'bi, Trygve Bakken, Robert F. Hevner, Petra S. Hüppi, Ivica Kostović, Pasko Rakic, E. S. Anton, David Edwards, Patricia Garcez, Anna Hoerder-Suabedissen, Arnold Kriegstein

publication / 2019
Whole brain imaging reveals distinct spatial patterns of amyloid beta deposition in three mouse models of Alzheimer's disease
The Journal of Comparative Neurology
Brain Science
MindScope

Jennifer D. Whitesell, Alex R. Buckley, Joseph E. Knox, Leonard Kuan, Nile Graddis, Andrew Pelos, Alice Mukora, Wayne Wakeman, Phillip Bohn, Anh Ho, Karla E. Hirokawa, Julie A. Harris

publication / 2019
Bright and photostable chemigenetic indicators for extended in vivo voltage imaging
Science (New York, N.Y.)
Brain Science
MindScope

Ahmed S. Abdelfattah, Takashi Kawashima, Amrita Singh, Ondrej Novak, Hui Liu, Yichun Shuai, Yi-Chieh Huang, Luke Campagnola, Stephanie C. Seeman, Jianing Yu, Jihong Zheng, Jonathan B. Grimm, Ronak Patel, Johannes Friedrich, Brett D. Mensh, Liam Paninski, John J. Macklin, Gabe J. Murphy, Kaspar Podgorski, Bei-Jung Lin, Tsai-Wen Chen, Glenn C. Turner, Zhe Liu, Minoru Koyama, Karel Svoboda, Misha B. Ahrens, Luke D. Lavis, Eric R. Schreiter

publication / 2019
Automated segmentation of medial temporal lobe subregions on in vivo T1-weighted MRI in early stages of Alzheimer's disease
Human Brain Mapping
Brain Science
MindScope

Long Xie, Laura E. M. Wisse, John Pluta, Robin de Flores, Virgine Piskin, Jose V. Manjón, Hongzhi Wang, Sandhitsu R. Das, Song-Lin Ding, David A. Wolk, Paul A. Yushkevich, Alzheimer's Disease Neuroimaging Initiative

publication / 2019
TeraVR empowers precise reconstruction of complete 3-D neuronal morphology in the whole brain
Nature Communications
Brain Science
MindScope

Yimin Wang, Qi Li, Lijuan Liu, Zhi Zhou, Zongcai Ruan, Lingsheng Kong, Yaoyao Li, Yun Wang, Ning Zhong, Renjie Chai, Xiangfeng Luo, Yike Guo, Michael Hawrylycz, Qingming Luo, Zhongze Gu, Wei Xie, Hongkui Zeng, Hanchuan Peng

publication / 2019
DynMat, a network that can learn after learning
Neural Networks: The Official Journal of the International Neural Network Society
Brain Science
MindScope

Jung Hoon Lee

publication / 2019
Multi-immersion open-top light-sheet microscope for high-throughput imaging of cleared tissues
Nature Communications
Brain Science
MindScope

Adam K. Glaser, Nicholas P. Reder, Ye Chen, Chengbo Yin, Linpeng Wei, Soyoung Kang, Lindsey A. Barner, Weisi Xie, Erin F. McCarty, Chenyi Mao, Aaron R. Halpern, Caleb R. Stoltzfus, Jonathan S. Daniels, Michael Y. Gerner, Philip R. Nicovich, Joshua C. Vaughan, Lawrence D. True, Jonathan T. C. Liu

publication / 2019
Classification of electrophysiological and morphological neuron types in the mouse visual cortex
Nature Neuroscience
Brain Science
MindScope

Nathan W. Gouwens, Staci A. Sorensen, Jim Berg, Changkyu Lee, Tim Jarsky, Jonathan Ting, Susan M. Sunkin, David Feng, Costas A. Anastassiou, Eliza Barkan, Kris Bickley, Nicole Blesie, Thomas Braun, Krissy Brouner, Agata Budzillo, Shiella Caldejon, Tamara Casper, Dan Castelli, Peter Chong, Kirsten Crichton, Christine Cuhaciyan, Tanya L. Daigle, Rachel Dalley, Nick Dee, Tsega Desta, Song-Lin Ding, Samuel Dingman, Alyse Doperalski, Nadezhda Dotson, Tom Egdorf, Michael Fisher, Rebecca A. de Frates, Emma Garren, Marissa Garwood, Amanda Gary, Nathalie Gaudreault, Keith Godfrey, Melissa Gorham, Hong Gu, Caroline Habel, Kristen Hadley, James Harrington, Julie A. Harris, Alex Henry, DiJon Hill, Sam Josephsen, Sara Kebede, Lisa Kim, Matthew Kroll, Brian Lee, Tracy Lemon, Katherine E. Link, Xiaoxiao Liu, Brian Long, Rusty Mann, Medea McGraw, Stefan Mihalas, Alice Mukora, Gabe J. Murphy, Lindsay Ng, Kiet Ngo, Thuc Nghi Nguyen, Philip R. Nicovich, Aaron Oldre, Daniel Park, Sheana Parry, Jed Perkins, Lydia Potekhina, David Reid, Miranda Robertson, David Sandman, Martin Schroedter, Cliff Slaughterbeck, Gilberto Soler-Llavina, Josef Sulc, Aaron Szafer, Bosiljka Tasic, Naz Taskin, Corinne Teeter, Nivretta Thatra, Herman Tung, Wayne Wakeman, Grace Williams, Rob Young, Zhi Zhou, Colin Farrell, Hanchuan Peng, Michael J. Hawrylycz, Ed Lein, Lydia Ng, Anton Arkhipov, Amy Bernard, John W. Phillips, Hongkui Zeng, Christof Koch

publication / 2019
Dimensionality in recurrent spiking networks: Global trends in activity and local origins in connectivity
PLoS computational biology
Brain Science
MindScope

Stefano Recanatesi, Gabriel Koch Ocker, Michael A. Buice, Eric Shea-Brown

publication / 2019
Single-cell activity tracking reveals that orbitofrontal neurons acquire and maintain a long-term memory to guide behavioral adaptation
Nature Neuroscience
Brain Science
MindScope

Vijay Mohan K. Namboodiri, James M. Otis, Kay van Heeswijk, Elisa S. Voets, Rizk A. Alghorazi, Jose Rodriguez-Romaguera, Stefan Mihalas, Garret D. Stuber

publication / 2019
Neuronal cell-subtype specificity of neural synchronization in mouse primary visual cortex
Nature Communications
Brain Science
MindScope

Ulf Knoblich, Lawrence Huang, Hongkui Zeng, Lu Li

publication / 2019
Autonomous patch-clamp robot for functional characterization of neurons in vivo: development and application to mouse visual cortex
Journal of Neurophysiology
Brain Science
MindScope

Gregory L. Holst, William Stoy, Bo Yang, Ilya Kolb, Suhasa B. Kodandaramaiah, Lu Li, Ulf Knoblich, Hongkui Zeng, Bilal Haider, Edward S. Boyden, Craig R. Forest

publication / 2019
Fluorescent Gene Tagging of Transcriptionally Silent Genes in hiPSCs
Stem Cell Reports
Cell Science

Brock Roberts, Melissa C. Hendershott, Joy Arakaki, Kaytlyn A. Gerbin, Haseeb Malik, Angelique Nelson, Jamie Gehring, Caroline Hookway, Susan A. Ludmann, Ruian Yang, Amanda Haupt, Tanya Grancharova, Veronica Valencia, Margaret A. Fuqua, Andrew Tucker, Susanne M. Rafelski, Ruwanthi N. Gunawardane

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