ArticleCell2025
A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types.
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Article in Cell, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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50citing papers in PubMed
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Who cites it
50 citing papers in PubMed.
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- Astrocytes viewed through the lens of their proteomes and subproteomes.Nature reviews. Neuroscience · 2026Review
- Learning how to experience the world: From circuits to cell types to genes.Current opinion in neurobiology · 2026Review
- Acute in vivo proximity labeling for membrane targeted proteomics in neuronal circuits.bioRxiv : the preprint server for biology · 2026Article
- TRACR: an anterograde transneuronal tracing system for genetic access across synapses and longitudinal circuit analysis.bioRxiv : the preprint server for biology · 2026Article
- Neural Control of Homeothermy, Torpor, and Hibernation.Annual review of neuroscience · 2026Review
- Search, organize, aggregate and share image data with BioFile Finder (BFF).Nature methods · 2026Article
- Multimodal characterization of variation in neuronal types in the mouse basal ganglia.bioRxiv : the preprint server for biology · 2026Article
- Expression-linked promoter selection (ELiPS) engineers short, strong ubiquitous promoters for gene therapy applications.bioRxiv : the preprint server for biology · 2026Article
- POINTseq: Cell-type-specific barcoding reveals single-cell projection architecture of the mouse dopaminergic system.Neuron · 2026Article
- Synthetic multicolor antigen-stabilizable nanobody platform for intersectional labeling and functional imaging.Nature methods · 2026Article
- Systemic delivery of synapsin-promoted caveolin-1 overexpression ameliorates pathological TDP-43-induced cognitive decline and neurodegenerative changes.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2026Article
- CREsted: modeling genomic and synthetic cell-type-specific enhancers across tissues and species.Nature methods · 2026Article
- Technical and biological sources of noise confound multiplexed enhancer AAV screening.Nature communications · 2026Article
- Transforming healthcare through in-body bioelectronic systems.Nature communications · 2026Review
Corrections and comments
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Authors and funding
149 authors.
Yoav Ben-SimonAllen Institute for Brain Science, Seattle, WA 98109, USA.
Marcus HooperAllen Institute for Brain Science, Seattle, WA 98109, USA.
Sujatha NarayanAllen Institute for Brain Science, Seattle, WA 98109, USA.
Tanya L DaigleAllen Institute for Brain Science, Seattle, WA 98109, USA.
Deepanjali DwivediAllen Institute for Brain Science, Seattle, WA 98109, USA.
Sharon W WayAllen Institute for Brain Science, Seattle, WA 98109, USA.
Aaron OsterAllen Institute for Brain Science, Seattle, WA 98109, USA.
David A StaffordUniversity of California, Berkeley, Berkeley, CA 94720, USA.
John K MichAllen Institute for Brain Science, Seattle, WA 98109, USA.
Michael J TaorminaAllen Institute for Brain Science, Seattle, WA 98109, USA.
Refugio A MartinezAllen Institute for Brain Science, Seattle, WA 98109, USA.
Ximena Opitz-ArayaAllen Institute for Brain Science, Seattle, WA 98109, USA.
Jada R RothAllen Institute for Brain Science, Seattle, WA 98109, USA.
Jason R AlexanderAllen Institute for Brain Science, Seattle, WA 98109, USA.
Shona AllenUniversity of California, Berkeley, Berkeley, CA 94720, USA.
Adam AmsterAllen Institute for Brain Science, Seattle, WA 98109, USA.
Joel ArbuckleAllen Institute for Brain Science, Seattle, WA 98109, USA.
Angela AyalaAllen Institute for Brain Science, Seattle, WA 98109, USA.
Pamela M BakerAllen Institute for Brain Science, Seattle, WA 98109, USA.
Trygve E BakkenAllen Institute for Brain Science, Seattle, WA 98109, USA.
Tyler BarcelliAllen Institute for Brain Science, Seattle, WA 98109, USA.
Stuard BartaAllen Institute for Brain Science, Seattle, WA 98109, USA.
Jacqueline BendrickAllen Institute for Brain Science, Seattle, WA 98109, USA.
Darren BertagnolliAllen Institute for Brain Science, Seattle, WA 98109, USA.
Cameron BielsteinAllen Institute for Brain Science, Seattle, WA 98109, USA.
Prajal BishwakarmaAllen Institute for Brain Science, Seattle, WA 98109, USA.
Jessica BowlusAllen Institute for Brain Science, Seattle, WA 98109, USA.
Gabriella BoyerAllen Institute for Brain Science, Seattle, WA 98109, USA.
Krissy BrounerAllen Institute for Brain Science, Seattle, WA 98109, USA.
Brittny CasianAllen Institute for Brain Science, Seattle, WA 98109, USA.
Tamara CasperAllen Institute for Brain Science, Seattle, WA 98109, USA.
Anish B ChakkaAllen Institute for Brain Science, Seattle, WA 98109, USA.
Rushil ChakrabartyAllen Institute for Brain Science, Seattle, WA 98109, USA.
Rebecca K ChanceUniversity of California, Berkeley, Berkeley, CA 94720, USA.
Sakshi ChavanAllen Institute for Brain Science, Seattle, WA 98109, USA.
Michael ClarkAllen Institute for Brain Science, Seattle, WA 98109, USA.
Kaity ColbertAllen Institute for Brain Science, Seattle, WA 98109, USA.
Forrest CollmanAllen Institute for Brain Science, Seattle, WA 98109, USA.
Scott DanielAllen Institute for Brain Science, Seattle, WA 98109, USA.
Maxwell DeparteeAllen Institute for Brain Science, Seattle, WA 98109, USA.
Peter DiValentinAllen Institute for Brain Science, Seattle, WA 98109, USA.
Nicholas DonadioAllen Institute for Brain Science, Seattle, WA 98109, USA.
Nadezhda DotsonAllen Institute for Brain Science, Seattle, WA 98109, USA.
Tom EgdorfAllen Institute for Brain Science, Seattle, WA 98109, USA.
Tim FlissAllen Institute for Brain Science, Seattle, WA 98109, USA.
Mariano GabittoAllen Institute for Brain Science, Seattle, WA 98109, USA.
Jazmin GarciaAllen Institute for Brain Science, Seattle, WA 98109, USA.
Amanda GaryAllen Institute for Brain Science, Seattle, WA 98109, USA.
Molly GasperiniAllen Institute for Brain Science, Seattle, WA 98109, USA.
Jessica GloeAllen Institute for Brain Science, Seattle, WA 98109, USA.
Jeff GoldyAllen Institute for Brain Science, Seattle, WA 98109, USA.
Bryan B GoreAllen Institute for Brain Science, Seattle, WA 98109, USA.
Lucas GraybuckAllen Institute for Brain Science, Seattle, WA 98109, USA.
Noah GreismanAllen Institute for Brain Science, Seattle, WA 98109, USA.
Francoise HaeseleerAllen Institute for Brain Science, Seattle, WA 98109, USA.
Carliana HaltermanAllen Institute for Brain Science, Seattle, WA 98109, USA.
Zeb HaradonAllen Institute for Brain Science, Seattle, WA 98109, USA.
Samantha D HastingsAllen Institute for Brain Science, Seattle, WA 98109, USA.
Olivia HelbackAllen Institute for Brain Science, Seattle, WA 98109, USA.
Windy HoAllen Institute for Brain Science, Seattle, WA 98109, USA.
Dirk HockemeyerUniversity of California, Berkeley, Berkeley, CA 94720, USA.
Cindy HuangAllen Institute for Brain Science, Seattle, WA 98109, USA.
Sydney HuffAllen Institute for Brain Science, Seattle, WA 98109, USA.
Avery HunkerAllen Institute for Brain Science, Seattle, WA 98109, USA.
Nelson JohansenAllen Institute for Brain Science, Seattle, WA 98109, USA.
Danielle JonesAllen Institute for Brain Science, Seattle, WA 98109, USA.
Zoe JuneauAllen Institute for Brain Science, Seattle, WA 98109, USA.
Brian KalmbachAllen Institute for Brain Science, Seattle, WA 98109, USA.
Madhav KannanAllen Institute for Brain Science, Seattle, WA 98109, USA.
Shannon KhemAllen Institute for Brain Science, Seattle, WA 98109, USA.
Emily KussickAllen Institute for Brain Science, Seattle, WA 98109, USA.
Rana KutsalAllen Institute for Brain Science, Seattle, WA 98109, USA.
Rachael LarsenAllen Institute for Brain Science, Seattle, WA 98109, USA.
Changkyu LeeAllen Institute for Brain Science, Seattle, WA 98109, USA.
Angus Y LeeUniversity of California, Berkeley, Berkeley, CA 94720, USA.
Madison LeiblyAllen Institute for Brain Science, Seattle, WA 98109, USA.
Garreck H LenzAllen Institute for Brain Science, Seattle, WA 98109, USA.
Su LiAllen Institute for Brain Science, Seattle, WA 98109, USA.
Elizabeth LiangAllen Institute for Brain Science, Seattle, WA 98109, USA.
Nicholas LuskAllen Institute for Brain Science, Seattle, WA 98109, USA.
Zachary MadiganAllen Institute for Brain Science, Seattle, WA 98109, USA.
Jessica MalloyAllen Institute for Brain Science, Seattle, WA 98109, USA.
Jocelin MaloneAllen Institute for Brain Science, Seattle, WA 98109, USA.
Rachel McCueAllen Institute for Brain Science, Seattle, WA 98109, USA.
Jose MelchorAllen Institute for Brain Science, Seattle, WA 98109, USA.
Tyler MollenkopfAllen Institute for Brain Science, Seattle, WA 98109, USA.
Skyler MoosmanAllen Institute for Brain Science, Seattle, WA 98109, USA.
Elyse MorinAllen Institute for Brain Science, Seattle, WA 98109, USA.
Dakota NewmanAllen Institute for Brain Science, Seattle, WA 98109, USA.
Lydia NgAllen Institute for Brain Science, Seattle, WA 98109, USA.
Kiet NgoAllen Institute for Brain Science, Seattle, WA 98109, USA.
Victoria OmsteadAllen Institute for Brain Science, Seattle, WA 98109, USA.
Sven OttoAllen Institute for Brain Science, Seattle, WA 98109, USA.
Alana OyamaAllen Institute for Brain Science, Seattle, WA 98109, USA.
Nick PenaAllen Institute for Brain Science, Seattle, WA 98109, USA.
Trangthanh PhamAllen Institute for Brain Science, Seattle, WA 98109, USA.
Elliot PhillipsAllen Institute for Brain Science, Seattle, WA 98109, USA.
Christina A PomAllen Institute for Brain Science, Seattle, WA 98109, USA.
Lydia PotekhinaAllen Institute for Brain Science, Seattle, WA 98109, USA.
Shea RansfordAllen Institute for Brain Science, Seattle, WA 98109, USA.
Patrick L RayAllen Institute for Brain Science, Seattle, WA 98109, USA.
Dean RetteAllen Institute for Brain Science, Seattle, WA 98109, USA.
Cade ReynoldsonAllen Institute for Brain Science, Seattle, WA 98109, USA.
Christine RimorinAllen Institute for Brain Science, Seattle, WA 98109, USA.
Dana RochaAllen Institute for Brain Science, Seattle, WA 98109, USA.
Augustin RuizAllen Institute for Brain Science, Seattle, WA 98109, USA.
Raymond E A SanchezAllen Institute for Brain Science, Seattle, WA 98109, USA.
Lane SawyerAllen Institute for Brain Science, Seattle, WA 98109, USA.
Adriana Sedeno-CortesAllen Institute for Brain Science, Seattle, WA 98109, USA.
Joshua P SevignyAllen Institute for Brain Science, Seattle, WA 98109, USA.
Nadiya ShapovalovaAllen Institute for Brain Science, Seattle, WA 98109, USA.
Noah ShepardAllen Institute for Brain Science, Seattle, WA 98109, USA.
Lyudmila ShulgaAllen Institute for Brain Science, Seattle, WA 98109, USA.
Ana R SiglerAllen Institute for Brain Science, Seattle, WA 98109, USA.
La'Akea SivertsAllen Institute for Brain Science, Seattle, WA 98109, USA.
Sherif SolimanAllen Institute for Brain Science, Seattle, WA 98109, USA.
Saroja SomasundaramAllen Institute for Brain Science, Seattle, WA 98109, USA.
Brian StaatsAllen Institute for Brain Science, Seattle, WA 98109, USA.
Kaiya StewartAllen Institute for Brain Science, Seattle, WA 98109, USA.
Eric SzelenyiAllen Institute for Brain Science, Seattle, WA 98109, USA.
Michael TieuAllen Institute for Brain Science, Seattle, WA 98109, USA.
Cameron TraderAllen Institute for Brain Science, Seattle, WA 98109, USA.
Alex TranAllen Institute for Brain Science, Seattle, WA 98109, USA.
Cindy T J van VelthovenAllen Institute for Brain Science, Seattle, WA 98109, USA.
Miranda WalkerAllen Institute for Brain Science, Seattle, WA 98109, USA.
Yimin WangAllen Institute for Brain Science, Seattle, WA 98109, USA.
Natalie WeedAllen Institute for Brain Science, Seattle, WA 98109, USA.
Morgan WirthlinAllen Institute for Brain Science, Seattle, WA 98109, USA.
Toren WoodAllen Institute for Brain Science, Seattle, WA 98109, USA.
Brooke WynaldaAllen Institute for Brain Science, Seattle, WA 98109, USA.
Zizhen YaoAllen Institute for Brain Science, Seattle, WA 98109, USA.
Thomas ZhouAllen Institute for Brain Science, Seattle, WA 98109, USA.
Jeanelle ArizaAllen Institute for Brain Science, Seattle, WA 98109, USA.
Nick DeeAllen Institute for Brain Science, Seattle, WA 98109, USA.
Melissa RedingAllen Institute for Brain Science, Seattle, WA 98109, USA.
Kara RonellenfitchAllen Institute for Brain Science, Seattle, WA 98109, USA.
Shoaib MuftiAllen Institute for Brain Science, Seattle, WA 98109, USA.
Susan M SunkinAllen Institute for Brain Science, Seattle, WA 98109, USA.
Kimberly A SmithAllen Institute for Brain Science, Seattle, WA 98109, USA.
Luke EspositoAllen Institute for Brain Science, Seattle, WA 98109, USA.
Jack WatersAllen Institute for Brain Science, Seattle, WA 98109, USA.
Bargavi ThyagarajanAllen Institute for Brain Science, Seattle, WA 98109, USA.
Shenqin YaoAllen Institute for Brain Science, Seattle, WA 98109, USA.
Ed S LeinAllen Institute for Brain Science, Seattle, WA 98109, USA.
Hongkui ZengAllen Institute for Brain Science, Seattle, WA 98109, USA.
Boaz P LeviAllen Institute for Brain Science, Seattle, WA 98109, USA.
John NgaiUniversity of California, Berkeley, Berkeley, CA 94720, USA.
Jonathan T TingAllen Institute for Brain Science, Seattle, WA 98109, USA.
Bosiljka TasicAllen Institute for Brain Science, Seattle, WA 98109, USA. Electronic address: bosiljkat@alleninstitute.org.
Funding
Generation of novel cell type specific mouse genetic toolsU19MH114830 · NIMH · ALLEN INSTITUTE · PI NGAI, JOHN J. · 2017 to 2021
$64.7MOpen-Access AAV Toolbox for Basal Ganglia Cell Types and CircuitsUF1MH128339 · NIMH · ALLEN INSTITUTE · PI BAKKEN, TRYGVE, DAIGLE, TANYA LYNN · 2021 to 2021
$7.3MEnhancer AAV toolbox for cell classes and subclasses in the brains of mouse, macaque and marmoset.U01MH139778 · NIMH · ALLEN INSTITUTE · PI JONATHAN T TING, Bosiljka Tasic · 2025 to 2026
$5.7MDevelopment of tools for cell-type specific labeling of human and mouse neocortical neuronsRF1MH114126 · NIMH · ALLEN INSTITUTE · PI LEIN, ED, LEVI, BOAZ PIRIE · 2017 to 2017
$4.5MCell type selective viral tools to interrogate and correct non-human primate and human brain circuitryUG3MH120095 · NIMH · ALLEN INSTITUTE · PI KALUME, FRANCK K, LEIN, ED · 2020 to 2022
$3.8MCell class- or type-specific viruses for brain-wide labeling and neural circuit examinationRF1MH121274 · NIMH · ALLEN INSTITUTE · PI TASIC, BOSILJKA · 2019 to 2019
$2.6MNIMH NIH HHS RF1 MH114126NIMH NIH HHS RF1 MH121274NIMH NIH HHS U01 MH139778NIMH NIH HHS U19 MH114830NIMH NIH HHS UF1 MH128339NIMH NIH HHS UG3 MH120095
Abstract
The mammalian cortex is comprised of cells classified into types according to shared properties. Defining the contribution of each cell type to the processes guided by the cortex is essential for understanding its function in health and disease. We use transcriptomic and epigenomic cortical cell-type taxonomies from mouse and human to define marker genes and putative enhancers and create a large toolkit of transgenic lines and enhancer adeno-associated viruses (AAVs) for selective targeting of cortical cell populations. We report creation and evaluation of fifteen transgenic driver lines, two reporter lines, and >1,000 different enhancer AAV vectors covering most subclasses of cortical cells. The tools reported here have been made publicly available, and along with the scaled process of tool creation, evaluation, and modification, they will enable diverse experimental strategies toward understanding mammalian cortex and brain function.
Indexed as
Cerebral CortexDependovirusEnhancer Elements, GeneticAnimalsGenetic VectorsHumansMiceMice, TransgenicNeuronsTranscriptomeAAVcell typeenhancerepigeneticshumanmouseneocortexrecombinasetranscriptomicstransgenic
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