ArticleNature2021
A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex.
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In one paragraph
Article in Nature, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 244 papers.
0numbers the graph read from it
0cells of the map it votes in
244citing papers in PubMed
22.8field-weighted citation impact, top 1% of its field
What it found
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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.
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Who cites it
244 citing papers in PubMed, 363 citations in OpenAlex.
- The misplaced mouse Pax6 interneuron subclass: A cross-species transcriptomic reassignment.iScience · 2026Article
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- Transcriptome Analysis of Hippocampus After Weekly Binge Alcohol Exposure and Voluntary Exercise in Rats.Alcohol, clinical & experimental research · 2026Article
- scASprofiler: profiling single-cell RNA splicing with a deep convolutional generative network.Briefings in bioinformatics · 2026Article
- The deficiency of KIF2C leads to abnormal distribution of cortical neurons and behavioral deficits in mice.iScience · 2026Article
- Regional specialization of upper-layer inhibitory interneuron organization in the human prefrontal cortex.Journal of anatomy · 2026Article
- Lhx2 Regulates Distinct Dendritic Architecture of Pyramidal Neurons across Primary Sensory Areas.eNeuro · 2026Article
- Pericyte KNature cardiovascular research · 2026Article
- NodoMap: A single-cell and spatial transcriptomic atlas of the mouse nodose ganglion.Cell press blue · 2026Article
- Brain Spatial Genomics Atlases.Genes · 2026Review
- Compound models and Pearson residuals for single-cell RNA-seq data without UMIs.Genome biology · 2026Article
- Cluster replicability in single-cell and single-nucleus atlases of the mouse brain.Nature communications · 2026Article
- The molecular asynchrony of single cells.bioRxiv : the preprint server for biology · 2026Article
- Tissueformer: extending single-cell foundation models to predict population-level phenotypes.BMC bioinformatics · 2026Article
- Temporal single-cell atlas of full-length Huntington's disease mouse model defines stage-specific signatures of corticostriatal dysfunction.Molecular neurodegeneration · 2026Article
- Tbx1 heterozygosity in the oligodendrocyte lineage shifts myelinated axon composition in the mouse fimbria without behavioral impairments.Molecular brain · 2026Article
- Network clustering algorithms and preprocessing pipelines for robust cell type identification in single-cell RNA sequencing data.Scientific reports · 2026Article
- Robust integration of single-cell datasets with imbalanced modality composition.Nature communications · 2026Article
- A layered standards framework for integrating single-cell and spatial omics data into brain cell atlases.bioRxiv : the preprint server for biology · 2026Article
184 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
83 authors at 17 institutions in 3 countries.
Zizhen Yao *Allen Institute for Brain Science, Seattle, WA, USA.ORCID http://orcid.org/0000-0002-9361-5607
Hanqing Liu *Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
Fangming Xie *Department of Physics, University of California, San Diego, La Jolla, CA, USA.
Stephan Fischer *Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
Ricky S AdkinsInstitute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.ORCID http://orcid.org/0000-0002-7983-5486
Andrew I AldridgeGenomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.ORCID http://orcid.org/0000-0003-1962-8802
Seth A AmentInstitute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.ORCID http://orcid.org/0000-0001-6443-7509
Anna BartlettGenomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
M Margarita BehrensComputational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-7168-8186
Koen Van den BergeDepartment of Statistics, University of California, Berkeley, Berkeley, CA, USA.
Darren BertagnolliAllen Institute for Brain Science, Seattle, WA, USA.
Hector Roux de BézieuxDivision of Biostatistics, School of Public Health, University of California, Berkeley, Berkeley, CA, USA.ORCID http://orcid.org/0000-0002-1489-8339
Tommaso BiancalaniBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0001-9104-9755
A Sina BooeshaghiCalifornia Institute of Technology, Pasadena, CA, USA.ORCID http://orcid.org/0000-0002-6442-4502
Héctor Corrada BravoCenter for Bioinformatics and Computational Biology, University of Maryland, College Park, College Park, MD, USA.
Tamara CasperAllen Institute for Brain Science, Seattle, WA, USA.
Carlo ColantuoniJohns Hopkins School of Medicine, Department of Neurology, Baltimore, MD, USA.
Jonathan CrabtreeInstitute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.ORCID http://orcid.org/0000-0002-7286-5690
Heather CreasyInstitute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.ORCID http://orcid.org/0000-0002-1369-6882
Kirsten CrichtonAllen Institute for Brain Science, Seattle, WA, USA.
Megan CrowStanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.ORCID http://orcid.org/0000-0002-1172-5897
Nick DeeAllen Institute for Brain Science, Seattle, WA, USA.
Elizabeth L DoughertyBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Wayne I DoyleDepartment of Cognitive Science, University of California, San Diego, La Jolla, CA, USA.
Sandrine DudoitDepartment of Statistics, University of California, Berkeley, Berkeley, CA, USA.ORCID http://orcid.org/0000-0002-6069-8629
Rongxin FangBioinformatics and Systems Biology Graduate Program, University of California, San Diego, San Diego, CA, USA.
Victor FelixInstitute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
Olivia FongAllen Institute for Brain Science, Seattle, WA, USA.
Michelle GiglioInstitute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.ORCID http://orcid.org/0000-0001-7628-5565
Jeff GoldyAllen Institute for Brain Science, Seattle, WA, USA.
Mike HawrylyczAllen Institute for Brain Science, Seattle, WA, USA.ORCID http://orcid.org/0000-0002-5741-8024
Brian R HerbInstitute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
Ronna HertzanoInstitute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
Xiaomeng HouCenter for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA.
Qiwen HuDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
Jayaram KancherlaCenter for Bioinformatics and Computational Biology, University of Maryland, College Park, College Park, MD, USA.
Matthew KrollAllen Institute for Brain Science, Seattle, WA, USA.
Kanan LathiaAllen Institute for Brain Science, Seattle, WA, USA.
Yang Eric LiLudwig Institute for Cancer Research, La Jolla, CA, USA.ORCID http://orcid.org/0000-0001-6997-6018
Jacinta D LuceroComputational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
Chongyuan LuoGenomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
Anup MahurkarInstitute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.ORCID http://orcid.org/0000-0002-4999-2296
Delissa McMillenAllen Institute for Brain Science, Seattle, WA, USA.
Naeem M NadafBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Joseph R NeryGenomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.ORCID http://orcid.org/0000-0003-0153-5659
Thuc Nghi NguyenAllen Institute for Brain Science, Seattle, WA, USA.ORCID http://orcid.org/0000-0002-6466-5883
Sheng-Yong NiuGenomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
Vasilis NtranosUniversity of California, San Francisco, San Francisco, CA, USA.
Joshua OrvisInstitute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
Julia K OsteenComputational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.ORCID http://orcid.org/0000-0001-7058-3297
Thanh PhamAllen Institute for Brain Science, Seattle, WA, USA.ORCID http://orcid.org/0000-0002-4738-5062
Antonio Pinto-DuarteComputational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-2215-7653
Olivier PoirionCenter for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA.
Sebastian PreisslCenter for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA.ORCID http://orcid.org/0000-0001-8971-5616
Elizabeth PurdomDepartment of Statistics, University of California, Berkeley, Berkeley, CA, USA.ORCID http://orcid.org/0000-0001-9455-7990
Christine RimorinAllen Institute for Brain Science, Seattle, WA, USA.
Davide RissoDepartment of Statistical Sciences, University of Padova, Padova, Italy.
Angeline C RivkinHoward Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA, USA.
Kimberly SmithAllen Institute for Brain Science, Seattle, WA, USA.ORCID http://orcid.org/0000-0002-3142-1970
Kelly StreetDepartment of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA.
Josef SulcAllen Institute for Brain Science, Seattle, WA, USA.
Valentine SvenssonCalifornia Institute of Technology, Pasadena, CA, USA.
Michael TieuAllen Institute for Brain Science, Seattle, WA, USA.
Amy TorkelsonAllen Institute for Brain Science, Seattle, WA, USA.
Herman TungAllen Institute for Brain Science, Seattle, WA, USA.ORCID http://orcid.org/0000-0002-0812-3318
Eeshit Dhaval VaishnavBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0003-3720-8051
Charles R VanderburgBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Cindy van VelthovenAllen Institute for Brain Science, Seattle, WA, USA.ORCID http://orcid.org/0000-0001-5120-4546
Xinxin WangCenter for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA.ORCID http://orcid.org/0000-0001-6393-2276
Owen R WhiteInstitute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
Z Josh HuangCold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.ORCID http://orcid.org/0000-0003-0592-028X
Peter V KharchenkoDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0000-0002-6036-5875
Lior PachterCalifornia Institute of Technology, Pasadena, CA, USA.
John NgaiDepartment of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
Aviv RegevBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0003-3293-3158
Bosiljka TasicAllen Institute for Brain Science, Seattle, WA, USA.ORCID http://orcid.org/0000-0002-6861-4506
Joshua D WelchDepartment of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.ORCID http://orcid.org/0000-0002-5869-2391
Jesse GillisStanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
Evan Z MacoskoBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-2794-5165
Bing RenCenter for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-5435-1127
Joseph R EckerGenomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.ORCID http://orcid.org/0000-0001-5799-5895
Hongkui ZengAllen Institute for Brain Science, Seattle, WA, USA. HongkuiZ@alleninstitute.org.ORCID http://orcid.org/0000-0002-0326-5878
Eran A MukamelDepartment of Cognitive Science, University of California, San Diego, La Jolla, CA, USA. emukamel@ucsd.edu.ORCID http://orcid.org/0000-0003-3203-9535
Allen Institute for Brain Science · USSalk Institute for Biological Studies · USUniversity of Maryland, Baltimore · USUniversity of California San Diego · USBroad Institute · USCold Spring Harbor Laboratory · USUniversity of California, Berkeley · USCalifornia Institute of Technology · USHarvard University · USUniversity of Maryland, College Park · USDana-Farber Cancer Institute · USGhent University · BEJames S. McDonnell Foundation · USLudwig Cancer Research · USUniversity of California, San Francisco · USUniversity of Michigan · USUniversity of Padua · IT
Funding
Viral Vector Core (VVC)P30CA014195 · NCI · SALK INSTITUTE FOR BIOLOGICAL STUDIES · PI Reuben Shaw · 1985 to 2026
$82.8MGeneration of novel cell type specific mouse genetic toolsU19MH114830 · NIMH · ALLEN INSTITUTE · PI ANDERSON, DAVID J, PACHTER, LIOR S · 2017 to 2021
$64.7MTool and Technology Development CoreU19MH114821 · NIMH · COLD SPRING HARBOR LABORATORY · PI ARLOTTA, PAOLA, HUANG, Z JOSH · 2017 to 2021
$64.5MA BRAIN Initiative Resource: The Neuroscience Multi-omic Data ArchiveR24MH114788 · NIMH · UNIVERSITY OF MARYLAND BALTIMORE · PI Anup Mahurkar, Owen R White · 2017 to 2026
$17.2MA Community Resource for Single Cell Data in the BrainU24MH114827 · NIMH · ALLEN INSTITUTE · PI HAWRYLYCZ, MICHAEL, MARTONE, MARYANN E · 2017 to 2021
$14.4MEpigenomic cell-type classification and regulatory element identification in the human brainU01MH121282 · NIMH · SALK INSTITUTE FOR BIOLOGICAL STUDIES · PI BEHRENS, M MARGARITA, ECKER, JOSEPH R · 2019 to 2021
$5.4MCell Type Specific Transcriptional Cascades in Inner Ear DevelopmentR01DC013817 · NIDCD · UNIVERSITY OF MARYLAND BALTIMORE · PI HERTZANO, RONNA · 2015 to 2022
$3.6MIlluminating Neurodevelopment through Integrated Analysis and Vizualization of Multi-Omic DataR24MH114815 · NIMH · UNIVERSITY OF MARYLAND BALTIMORE · PI HERTZANO, RONNA, WHITE, OWEN R · 2018 to 2020
$2.3MIntegrative Visual and Computational Exploratory Analysis of Genomics DataR01GM114267 · NIGMS · UNIV OF MARYLAND, COLLEGE PARK · PI CORRADA BRAVO, HECTOR · 2015 to 2018
$1.8MCell Type Specific Transcriptional Cascades in Inner Ear DevelopmentU01DC013817 · NIDCD · UNIVERSITY OF MARYLAND BALTIMORE · PI AHMED, ZUBAIR M. · 2023 to 2025
$1.6MThe gEAR portal - Advancing Data Sharing, Analysis and Discovery for Hearing and Balance ResearchR01DC019370 · NIDCD · UNIVERSITY OF MARYLAND BALTIMORE · PI MAHURKAR, ANUP · 2021 to 2022
$1.5MLinking molecular and anatomical features of brain cell identity through computational data integrationRF1MH123199 · NIMH · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI WELCH, JOSHUA · 2020 to 2020
$1.1MNCI NIH HHS P30 CA014195NIDCD NIH HHS R01 DC013817NIDCD NIH HHS R01 DC019370NIDCD NIH HHS U01 DC013817NIGMS NIH HHS R01 GM114267NIH HHS DC013817NIH HHS GM114267NIMH NIH HHS R24 MH114788NIMH NIH HHS R24 MH114815NIMH NIH HHS RF1 MH123199NIMH NIH HHS U01 MH121282NIMH NIH HHS U19 MH114821NIMH NIH HHS U19 MH114830NIMH NIH HHS U24 MH114827
Abstract
Single-cell transcriptomics can provide quantitative molecular signatures for large, unbiased samples of the diverse cell types in the brain
Indexed as
EpigenomicsGene Expression ProfilingSingle-Cell AnalysisTranscriptomeAnimalsAtlases as TopicDatasets as TopicEpigenesis, GeneticFemaleMaleMiceMotor CortexNeuronsOrgan SpecificityReproducibility of Results
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