ReviewNature neuroscience2024
Applying single-cell and single-nucleus genomics to studies of cellular heterogeneity and cell fate transitions in the nervous system.
Abstract readReview
In one paragraph
Review in Nature neuroscience, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
0numbers the graph read from it
0cells of the map it votes in
15citing papers in PubMed
–field-weighted citation impact
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
15 citing papers in PubMed.
- Article
- A Hierarchical Multimodal Knowledge Graph for Neural Cell-Type-Specific Regulation Integrating Single-Cell Transcriptomics and Literature Evidence.International journal of molecular sciences · 2026Article
- Cellular loci for cagrilintide action identified.Nature metabolism · 2026Article
- Expanding canonical cortical cell type markers in the era of single-cell transcriptomics.Scientific reports · 2026Article
- JUND-driven stress-responsive astrocytes promote neuronal apoptosis via enhanced gap junction signaling in autism spectrum disorder.Molecular autism · 2026Article
- Modern Mining: The Role of Single-cell RNA Sequencing in Advancing Neuroscience Research.BioEssays : news and reviews in molecular, cellular and developmental biology · 2026Review
- A transcriptomic microglia taxonomy across mouse and human pathologies.Nature immunology · 2026Article
- Networked Pathological Mechanisms of Central Sympathetic Nervous System Regulation in Heart Failure and Novel Paradigms for Targeted Intervention.International journal of molecular sciences · 2026Review
- Deep visual proteomics uncovers nociceptor diversity and pain targets.Nature communications · 2026Article
- Review
- Review
- Research progress of single cell RNA sequencing in nervous system.Molecular biology reports · 2025Review
- Single-cell transcriptome of retinal myeloid cells in response to transplantation of human neurons reveals reversibility of microglial activation.bioRxiv : the preprint server for biology · 2025Article
- Targeting TYK2 to target tau.Nature reviews. Neuroscience · 2025Article
- Focus on single-cell genomics.Nature neuroscience · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
26 authors.
Igor AdameykoDepartment of Neuroimmunology, Center for Brain Research, Medical University of Vienna, Vienna, Austria.ORCID http://orcid.org/0000-0001-5471-0356
Trygve BakkenAllen Institute for Brain Science, Seattle, WA, USA.ORCID http://orcid.org/0000-0003-3373-7386
Aparna BhaduriDepartment of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.ORCID http://orcid.org/0000-0003-4625-6899
Chintan ChhatbarInstitute of Neuropathology, Medical Faculty, University of Freiburg, Freiburg, Germany.ORCID http://orcid.org/0000-0002-5824-5209
Mariella G FilbinDepartment of Pediatric Oncology, Dana-Farber Cancer Institute, Boston Children's Hospital, Boston, MA, USA.
David GateThe Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.ORCID http://orcid.org/0000-0003-0481-9657
Hannah HochgernerFaculty of Biotechnology and Food Engineering, Technion Israel Institute of Technology, Haifa, Israel.ORCID http://orcid.org/0000-0002-7739-666X
Chang Nam KimDepartment of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA.ORCID http://orcid.org/0000-0001-7921-4447
Jordan KrullDepartment of Biomedical Informatics, College of Medicine, the Ohio State University, Columbus, OH, USA.ORCID http://orcid.org/0000-0001-6507-8085
Gioele La MannoLaboratory of Neurodevelopmental Systems Biology, Brain Mind Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.ORCID http://orcid.org/0000-0003-1428-8757
Qingyun LiDepartment of Neuroscience, Washington University in St. Louis School of Medicine, St. Louis, MO, USA.ORCID http://orcid.org/0000-0002-3457-5967
Sten LinnarssonDivision of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.ORCID http://orcid.org/0000-0002-3491-3444
Qin MaDepartment of Biomedical Informatics, College of Medicine, the Ohio State University, Columbus, OH, USA.ORCID http://orcid.org/0000-0002-3264-8392
Christian MayerMax Planck Institute for Biological Intelligence, Martinsried, Germany.ORCID http://orcid.org/0000-0003-3152-5574
Vilas MenonDepartment of Neurology, Center for Translational and Computational Neuroimmunology, Columbia University, New York, NY, USA.ORCID http://orcid.org/0000-0002-4096-8601
Patricia NanoDepartment of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.ORCID http://orcid.org/0000-0002-5507-2656
Marco PrinzInstitute of Neuropathology, Medical Faculty, University of Freiburg, Freiburg, Germany.ORCID http://orcid.org/0000-0002-0349-1955
Steve QuakeDepartment of Bioengineering, Stanford University, Stanford, CA, USA.
Christopher A WalshDivision of Genetics and Genomics, Manton Center for Orphan Disease, Boston Children's Hospital, Boston, MA, USA.ORCID http://orcid.org/0000-0002-0156-2238
Jin YangDepartment of Neuroscience, Washington University in St. Louis School of Medicine, St. Louis, MO, USA.
Omer Ali BayraktarWellcome Sanger Institute, Hinxton, UK. ob5@sanger.ac.uk.ORCID http://orcid.org/0000-0001-6055-277X
Ozgun GokceDepartment of Old Age Psychiatry and Cognitive Disorders, University Hospital Bonn, Bonn, Germany. ozgun.goekce@ukbonn.de.ORCID http://orcid.org/0000-0001-6319-404X
Naomi HabibThe Edmond and Lily Safra Center for Brain Sciences, the Hebrew University of Jerusalem, Jerusalem, Israel. naomi.habib@mail.huji.ac.il.ORCID http://orcid.org/0000-0002-6049-2487
Genevieve KonopkaDepartment of Neuroscience, UT Southwestern Medical Center, Dallas, TX, USA. genevieve.konopka@utsouthwestern.edu.ORCID http://orcid.org/0000-0002-3363-7302
Shane A LiddelowNeuroscience Institute, NYU Grossman School of Medicine, New York, NY, USA. shane.liddelow@nyulangone.org.ORCID http://orcid.org/0000-0002-0840-1437
Tomasz J NowakowskiDepartment of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA. tomasz.nowakowski@ucsf.edu.ORCID http://orcid.org/0000-0003-2345-4964
Funding
UCLA SPORE in Brain CancerP50CA211015 · NCI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Yvonne Yu-Hsuan Chen · 2017 to 2026
$25.2MTriState SenNET (Lung and Heart) Tissue Map and Atlas consortiumU54AG075931 · NIA · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI TOREN FINKEL, Melanie Koenigshoff · 2021 to 2026
$14.0MCell Identity Determination In Human Brain: Somatic Mutation and Cell LineageR01NS032457 · NINDS · BOSTON CHILDREN'S HOSPITAL · PI Alice Eunjung Lee, Christopher A. Walsh · 1995 to 2026
$12.7MGenetic Analysis and Manipulation Core (GAEC)P50HD105351 · NICHD · BOSTON CHILDREN'S HOSPITAL · PI Hisashi Umemori · 2021 to 2026
$9.4MUCLA Medical Genetics Training ProgramT32GM008243 · NIGMS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Julian Martinez-Agosto, STANLEY F. NELSON · 1987 to 2026
$6.8MDeciphering the genomic mechanisms underlying the physiology of human brain stimulationRF1NS126143 · NINDS · UT SOUTHWESTERN MEDICAL CENTER · PI KONOPKA, GENEVIEVE, LEGA, BRADLEY C · 2022 to 2024
$4.0MFrom ion channels to graph theory in sensorimotor learningUF1NS115821 · NINDS · UNIVERSITY OF CHICAGO · PI KONOPKA, GENEVIEVE, MACLEAN, JASON NEIL · 2020 to 2020
$3.9MFoxp-regulated signaling pathways in brain development - DiversityR01MH126481 · NIMH · UT SOUTHWESTERN MEDICAL CENTER · PI KONOPKA, GENEVIEVE · 2021 to 2025
$3.4MThe role of apolipoprotein E in Alzheimer's adaptive immunityR01AG078713 · NIA · NORTHWESTERN UNIVERSITY AT CHICAGO · PI David Gate · 2022 to 2026
$3.0MNeurotoxicity of Reactive Astrocyte-secreted Lipids in Neurodegenerative DiseaseR01EY033353 · NEI · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI Shane Liddelow · 2022 to 2026
$2.5MComparative Epigenomics of Primate BrainsR01HG011641 · NHGRI · UNIVERSITY OF CALIFORNIA SANTA BARBARA · PI KONOPKA, GENEVIEVE, SHERWOOD, CHESTER · 2021 to 2024
$2.4MDeciphering the genomic mechanisms underlying the physiology of human brain stimulationR01NS126143 · NINDS · UT SOUTHWESTERN MEDICAL CENTER · PI Genevieve Konopka, Bradley C Lega · 2025 to 2026
$2.2MNCI NIH HHS P50 CA211015NEI NIH HHS R01 EY033353NHGRI NIH HHS R01 HG011641NHGRI NIH HHS R21 HG012482NIA NIH HHS R01 AG078512NIA NIH HHS R01 AG078713NIA NIH HHS U54 AG075931NICHD NIH HHS P50 HD105351NIGMS NIH HHS R01 GM131399NIGMS NIH HHS T32 GM008243NIMH NIH HHS R01 MH126481NINDS NIH HHS R00 NS111731NINDS NIH HHS R00 NS112458NINDS NIH HHS R01 NS032457NINDS NIH HHS R01 NS123263NINDS NIH HHS R01 NS126143NINDS NIH HHS RF1 NS126143NINDS NIH HHS UF1 NS115821
Abstract
Single-cell and single-nucleus genomic approaches can provide unbiased and multimodal insights. Here, we discuss what constitutes a molecular cell atlas and how to leverage single-cell omics data to generate hypotheses and gain insights into cell transitions in development and disease of the nervous system. We share points of reflection on what to consider during study design and implementation as well as limitations and pitfalls.
Indexed as
GenomicsSingle-Cell AnalysisAnimalsCell DifferentiationCell NucleusHumansNervous System
Identifiers
What OpenQuestion holds
Textmetadata
LicenceTDM
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.