ReviewNature neuroscience2020
A community-based transcriptomics classification and nomenclature of neocortical cell types.
Erratum issuedOpen access · hybridAbstract readReview
In one paragraph
Review in Nature neuroscience, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 149 papers.
0numbers the graph read from it
0cells of the map it votes in
149citing papers in PubMed
1.4field-weighted citation impact, top 19% of its field
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
149 citing papers in PubMed, 25 citations in OpenAlex.
- The misplaced mouse Pax6 interneuron subclass: A cross-species transcriptomic reassignment.iScience · 2026Article
- Neocortical pyramidal cells with axon-carrying basal dendrites: a prominent feature regulated by activity.Brain structure & function · 2026Article
- A massively parallel CRISPR-based screening platform for modifiers of neuronal depolarization.Nature communications · 2026Article
- Interspecific diversity in the neuronal composition of the mammalian cortex arises from heterochrony in neurogenesis.The EMBO journal · 2026Article
- Intrinsic neuronal diversity as a substrate for cortical area specialization in primate vision.Nature communications · 2026Article
- Cortical PV and VIP interneurons similarly influence SST neuron output despite distinct unitary properties.Communications biology · 2026Article
- A Community Standard Multispecies Cell Atlas of the Basal Ganglia.bioRxiv : the preprint server for biology · 2026Article
- Multimodal characterization of transcriptionally defined ventral tegmental area dopamine neurons.bioRxiv : the preprint server for biology · 2026Article
- Article
- Prefrontal cortex interneurons and their contributions to attention, working memory, and adaptive behavior.Progress in neurobiology · 2026Review
- Transport-related effects on intrinsic and synaptic properties of human cortical neurons: A comparative study.The Journal of physiology · 2026Article
- Decoding Alzheimer's Disease One Cell Class at a Time.Cellular and molecular neurobiology · 2026Review
- From the brain cell atlas to precision neurology: a review of the application of AI-driven multi-omics in brain science.GigaScience · 2026Review
- Identity crisis: exploring the boundaries of cell type identification in the age of single-cell transcriptomics.Frontiers in cellular neuroscience · 2026Article
- Single-dose psilocybin promotes cell-type-specific changes of neurons in the orbitofrontal cortex.Neurotherapeutics : the journal of the American Society for Experimental NeuroTherapeutics · 2026Article
- Synthetic Data Generation for Classifying Electrophysiological and Morpho-Electrophysiological Neurons from Mouse Visual Cortex.Neuroinformatics · 2025Article
- Neuron-specific homologous coding genes and non-coding regulatory regions are the most conserved amongst amniotes despite neuron-specific cell size diversity.Scientific reports · 2025Article
- Article
- A consensus definition for deep layer 6 excitatory neurons in mouse somatosensory, visual, and motor cortex.Cell reports · 2025Article
- Functional thalamocortical innervation of VIP- and SST-expressing GABAergic interneurons in mouse barrel cortex.iScience · 2025Article
89 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
- Erratum issued
Authors and funding
73 authors at 20 institutions in 15 countries.
Rafael YusteColumbia University, New York City, NY, USA. rmy5@columbia.edu.ORCID http://orcid.org/0000-0003-4206-497X
Michael HawrylyczAllen Institute for Brain Science, Seattle, WA, USA. MikeH@alleninstitute.org.ORCID http://orcid.org/0000-0002-5741-8024
Nadia AallingUniversity of Copenhagen, Copenhagen, Denmark.ORCID http://orcid.org/0000-0001-6995-1590
Argel Aguilar-VallesDepartment of Neuroscience, Carleton University, Ottawa, Ontario, Canada.
Detlev ArendtEuropean Molecular Biology Laboratory, Heidelberg, Germany.
Ruben ArmañanzasGeorge Mason University, Fairfax, VA, USA.ORCID http://orcid.org/0000-0003-4049-0000
Giorgio A AscoliGeorge Mason University, Fairfax, VA, USA.
Concha BielzaUniversidad Politécnica de Madrid, Madrid, Spain.
Vahid BokharaieMax Planck Institute for Biological Cybernetics, Tübingen, Germany.
Tobias Borgtoft BergmannUniversity of Copenhagen, Copenhagen, Denmark.ORCID http://orcid.org/0000-0002-4610-2585
Irina BystronUniversity of Oxford, Oxford, UK.
Marco CapognaDepartment of Biomedicine, Aarhus University, Aarhus, Denmark.ORCID http://orcid.org/0000-0002-2742-5485
YoonJeung ChangDepartment of Genetics, Harvard Medical School, Boston, MA, USA.
Ann ClemensThe University of Edinburgh, Edinburgh, UK.ORCID http://orcid.org/0000-0001-5488-0902
Christiaan P J de KockVrije Universiteit Amsterdam, Amsterdam, Netherlands.
Javier DeFelipeCajal Institute, Madrid, Spain.
Sandra Esmeralda Dos SantosVanderbilt University, Nashville, TN, USA.
Keagan DunvilleScuola Normale Superior, Pisa, Italy.
Dirk FeldmeyerResearch Centre Jülich, Jülich, Germany.
Richárd FiáthResearch Centre for Natural Sciences, Budapest, Hungary.
Gordon James FishellHarvard Medical School, Cambridge, MA, USA.
Angelica FoggettiChristian-Albrechts-University Kiel, Kiel, Germany.
Xuefan GaoEuropean Molecular Biology Laboratory, Hamburg, Germany.
Parviz GhaderiÉcole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.ORCID http://orcid.org/0000-0001-5405-8951
Natalia A GoriounovaVrije Universiteit Amsterdam, Amsterdam, Netherlands.ORCID http://orcid.org/0000-0002-5917-983X
Onur GüntürkünRuhr University Bochum, Bochum, Germany.
Kenta HagiharaFriedrich Miescher Institute for Biological Research, Basel, Switzerland.
Vanessa Jane HallUniversity of Copenhagen, Copenhagen, Denmark.ORCID http://orcid.org/0000-0002-3598-2214
Moritz HelmstaedterMax Planck Institute for Brain Research, Frankfurt, Germany.ORCID http://orcid.org/0000-0001-7973-0767
Suzana Herculano-HouzelVanderbilt University, Nashville, TN, USA.
Markus M HilscherKarolinska Institutet, Stockholm, Sweden.ORCID http://orcid.org/0000-0001-7782-0830
Hajime HiraseUniversity of Copenhagen, Copenhagen, Denmark.
Jens Hjerling-LefflerKarolinska Institutet, Stockholm, Sweden.ORCID http://orcid.org/0000-0002-4539-1776
Rebecca HodgeAllen Institute for Brain Science, Seattle, WA, USA.ORCID http://orcid.org/0000-0002-5784-9668
Josh HuangCold Spring Harbor Laboratory, Laurel Hollow, NY, USA.ORCID http://orcid.org/0000-0003-0592-028X
Rafiq HudaWM Keck Center for Collaborative Neuroscience, Department of Cell Biology and Neuroscience, Rutgers University - New Brunswick, Piscataway, NJ, USA.ORCID http://orcid.org/0000-0002-6814-9966
Konstantin KhodosevichUniversity of Copenhagen, Copenhagen, Denmark.
Ole KiehnDepartment of Neuroscience, University of Copenhagen, Copenhagen, Denmark.ORCID http://orcid.org/0000-0002-5954-469X
Henner KochRWTH Aachen University, Aachen, Germany.
Eric S KueblerRobarts Research Institute, Western University, London, Ontario, Canada.ORCID http://orcid.org/0000-0002-6816-156X
Malte KühnemundCARTANA, Stockholm, Sweden.
Pedro LarrañagaUniversidad Politécnica de Madrid, Madrid, Spain.
Boudewijn LelieveldtLeiden University Medical Center, Leiden, the Netherlands.
Emma Louise LouthDepartment of Biomedicine, Aarhus University, Aarhus, Denmark.
Jan H LuiStanford University, Stanford, CA, USA.
Huibert D MansvelderVrije Universiteit Amsterdam, Amsterdam, Netherlands.ORCID http://orcid.org/0000-0003-1365-5340
Oscar MarinKing's College London, London, UK.ORCID http://orcid.org/0000-0001-6264-7027
Julio Martinez-TrujilloSchulich School of Medicine and Dentistry, Departments of Physiology, Pharmacology and Psychiatry, University of Western Ontario, London, Ontario, Canada.ORCID http://orcid.org/0000-0003-3338-578X
Homeira Moradi ChamehKrembil Research Institute, Toronto, Ontario, Canada.
Alok Nath MohapatraUniversity of Haifa, Haifa, Israel.ORCID http://orcid.org/0000-0002-9994-6407
Hermany MungubaKarolinska Institutet, Stockholm, Sweden.
Maiken NedergaardUniveristy of Rochester, Rochester, NY, USA.ORCID http://orcid.org/0000-0001-6502-6031
Pavel NěmecCharles University, Prague, Czech Republic.
Netanel OferBar Ilan University, Ramat Gan, Israel.ORCID http://orcid.org/0000-0002-7244-2348
Ulrich Gottfried PfistererUniversity of Copenhagen, Copenhagen, Denmark.
Samuel PontesColumbia University, New York City, NY, USA.ORCID http://orcid.org/0000-0002-4061-2365
William RedmondMacquarie University, Sydney, New South Wales, Australia.ORCID http://orcid.org/0000-0002-6250-1594
Jean RossierSorbonne University, Paris, France.
Joshua R SanesHarvard University, Cambridge, MA, USA.ORCID http://orcid.org/0000-0001-8926-8836
Richard H ScheuermannJ. Craig Venter Institute, La Jolla, CA, USA.ORCID http://orcid.org/0000-0003-1355-892X
Esther Serrano-SaizCentro de Biologia Molecular Severo Ochoa (CSIC), Madrid, Spain.
Jochen F StaigerInstitute for Neuroanatomy, University of Göttingen, Göttingen, Germany.
Peter SomogyiUniversity of Oxford, Oxford, UK.
Gábor TamásUniversity of Szeged, Szeged, Hungary.ORCID http://orcid.org/0000-0002-7905-6001
Andreas Savas ToliasBaylor College of Medicine, Houston, TX, USA.ORCID http://orcid.org/0000-0002-4305-6376
Maria Antonietta ToschesColumbia University, New York City, NY, USA.ORCID http://orcid.org/0000-0001-6338-9357
Miguel Turrero GarcíaDepartment of Neurobiology, Harvard Medical School, Boston, MA, USA.
Christian WoznyUniversity of Strathclyde, Glasgow, UK.ORCID http://orcid.org/0000-0003-4220-2033
Thomas V WuttkeDepartments of Neurosurgery and of Neurology and Epileptology, Hertie-Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.ORCID http://orcid.org/0000-0001-5655-8490
Yong LiuUniversity of Copenhagen, Copenhagen, Denmark.ORCID http://orcid.org/0000-0002-0574-2877
Juan YuanKarolinska Institutet, Stockholm, Sweden.
Hongkui ZengAllen Institute for Brain Science, Seattle, WA, USA. HongkuiZ@alleninstitute.org.ORCID http://orcid.org/0000-0002-0326-5878
Ed LeinAllen Institute for Brain Science, Seattle, WA, USA. EdL@alleninstitute.org.ORCID http://orcid.org/0000-0001-9012-6552
University of Copenhagen · DKAllen Institute · USColumbia University · USHarvard University · USKarolinska Institutet · SEVrije Universiteit Amsterdam · NLAarhus University · DKEuropean Molecular Biology Laboratory · DEGeorge Mason University · USUniversidad Politécnica de Madrid · ESUniversity of Oxford · GBVanderbilt University · USWestern University · CAAllen Institute for Brain Science · USBar-Ilan University · ILBaylor College of Medicine · USCarleton University · CACentro de Biología Molecular Severo Ochoa · ESCharles University · CZChristian-Albrechts-Universität zu Kiel · DE
Funding
Generation of novel cell type specific mouse genetic toolsU19MH114830 · NIMH · ALLEN INSTITUTE · PI ZENG, HONGKUI · 2017 to 2021
$64.7MIMAGING FUNCTIONAL CONNECTIVITY IN VISUAL CORTEXR01EY011787 · NEI · COLUMBIA UNIV NEW YORK MORNINGSIDE · PI YUSTE, RAFAEL · 1998 to 2021
$6.4MPara-Vascular Basis of Small Vessel DiseaseR01NS100366 · NINDS · UNIVERSITY OF ROCHESTER · PI NEDERGAARD, MAIKEN · 2016 to 2020
$3.8MAge and AD related bottlenecks in glymphatic-lymphatic waste transportRF1AG057575 · NIA · UNIVERSITY OF ROCHESTER · PI NEDERGAARD, MAIKEN · 2017 to 2017
$3.2MEffect of GABAergic inhibition of dendritic spines on synaptic pruning in the medial prefrontal cortex during adolescenceR01MH115900 · NIMH · SUNY DOWNSTATE MEDICAL CENTER · PI SMITH, SHERYL S · 2019 to 2023
$3.2MCapillary hyperemia in white matter: Novel mechanistic insight and effect of hypertension and agingRF1NS110049 · NINDS · UNIVERSITY OF ROCHESTER · PI NEDERGAARD, MAIKEN, WAN, JIANDI · 2018 to 2018
$2.9MProbabilistic coding in cortical populationsR01EY026927 · NEI · BAYLOR COLLEGE OF MEDICINE · PI MA, WEI JI, TOLIAS, ANDREAS · 2017 to 2021
$1.9MPrefrontal circuits for attention and motor planningR00MH112855 · NIMH · RUTGERS, THE STATE UNIV OF N.J. · PI HUDA, RAFIQ · 2020 to 2022
$742kMolecular dissection of prefrontal cortex circuit architectureK01MH114022 · NIMH · STANFORD UNIVERSITY · PI LUI, JAN H · 2017 to 2020
$650kNEI NIH HHS R01 EY011787NEI NIH HHS R01 EY026927NIA NIH HHS RF1 AG057575NIMH NIH HHS K01 MH114022NIMH NIH HHS R00 MH112855NIMH NIH HHS R01 MH115900NIMH NIH HHS U19 MH114830NINDS NIH HHS R01 NS100366NINDS NIH HHS RF1 NS110049
Abstract
To understand the function of cortical circuits, it is necessary to catalog their cellular diversity. Past attempts to do so using anatomical, physiological or molecular features of cortical cells have not resulted in a unified taxonomy of neuronal or glial cell types, partly due to limited data. Single-cell transcriptomics is enabling, for the first time, systematic high-throughput measurements of cortical cells and generation of datasets that hold the promise of being complete, accurate and permanent. Statistical analyses of these data reveal clusters that often correspond to cell types previously defined by morphological or physiological criteria and that appear conserved across cortical areas and species. To capitalize on these new methods, we propose the adoption of a transcriptome-based taxonomy of cell types for mammalian neocortex. This classification should be hierarchical and use a standardized nomenclature. It should be based on a probabilistic definition of a cell type and incorporate data from different approaches, developmental stages and species. A community-based classification and data aggregation model, such as a knowledge graph, could provide a common foundation for the study of cortical circuits. This community-based classification, nomenclature and data aggregation could serve as an example for cell type atlases in other parts of the body.
Indexed as
TranscriptomeAnimalsCellsComputational BiologyHumansNeocortexNeurogliaNeuronsSingle-Cell AnalysisTerminology as Topic
Identifiers
What OpenQuestion holds
Textmetadata
LicenceCC BY
Read underepoch 390
Registered trials
None linked
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.