ReviewNature neuroscience2024
Opportunities and challenges of single-cell and spatially resolved genomics methods for neuroscience discovery.
Erratum issuedAbstract 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. An erratum has been issued. Cited by 23 papers.
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0cells of the map it votes in
23citing papers in PubMed
–field-weighted citation impact
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
23 citing papers in PubMed.
- A single-nuclei multiomics resource across four brain regions prioritises human neural cell types influencing brain-related traits.bioRxiv : the preprint server for biology · 2026Article
- Type-I IFNs in EAE drive synaptic transcriptional responses in neurons and astrocytes in the brain.bioRxiv : the preprint server for biology · 2026Article
- Real-time, cross-modal genotype mapping of free-movingScience advances · 2026Article
- STcompare: comparative spatial transcriptomics data analysis of structurally matched tissues to characterize differentially spatially patterned genes.Bioinformatics (Oxford, England) · 2026Article
- Single-Cell Annotation and Localization via Integrating Spatial Transcriptomics Maps the Mouse Ocular Atlas and RAO Dynamics.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- A Hierarchical Multimodal Knowledge Graph for Neural Cell-Type-Specific Regulation Integrating Single-Cell Transcriptomics and Literature Evidence.International journal of molecular sciences · 2026Article
- Innate immune signaling and functions in astrocytes.Nature immunology · 2026Review
- A comparative transcriptomic analysis of mouse demyelination models and multiple sclerosis lesions.Nature communications · 2026Article
- Molecular dynamics of Brodmann Area 22 in development and autism.bioRxiv : the preprint server for biology · 2026Article
- The Future of Epigenetics: Emerging Technologies and Clinical Applications.ACS pharmacology & translational science · 2026Review
- High-parameter spatial multi-omics through histology-anchored integration.Nature methods · 2026Article
- Grand challenges for systems neuroscience: perspectives and opportunities.Frontiers in systems neuroscience · 2026Article
- Integrated Single-Cell and Bulk RNA Sequencing Reveals Inflammatory Microenvironment and Glycolysis-Driven Epithelial Proliferation in Benign Prostatic Hyperplasia.Journal of inflammation research · 2026Article
- Spatially Resolved Profiling of Compartmentalized Muscle and Brain Inflammation.European journal of immunology · 2025Review
- Review
- Review
- SpaTM: topic models for inferring spatially informed transcriptional programs.Briefings in bioinformatics · 2025Article
- Research progress of single cell RNA sequencing in nervous system.Molecular biology reports · 2025Review
- GASTON-Mix: a unified model of spatial gradients and domains using spatial mixture-of-experts.Bioinformatics (Oxford, England) · 2025Article
- Single-cell sequencing and transcriptomic data reveal that P65 activation significantly promotes microglia-mediated neuroinflammation after ischemic stroke.Scientific reports · 2025Article
Corrections and comments
- Erratum issued
Authors and funding
31 authors.
Boyan BonevHelmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany.
Gonçalo Castelo-BrancoLaboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.ORCID http://orcid.org/0000-0003-2247-9393
Fei ChenThe Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0003-2308-3649
Simone CodeluppiMoleculent, Stockholm, Sweden.ORCID http://orcid.org/0000-0002-7053-0520
M Ryan CorcesGladstone Institute of Neurological Disease, San Francisco, CA, USA.ORCID http://orcid.org/0000-0001-7465-7652
Jean FanDepartment of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.ORCID http://orcid.org/0000-0002-0212-5451
Myriam HeimanDepartment of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-6365-8673
Kenneth HarrisUCL Queen Square Institute of Neurology, University College London, London, UK.ORCID http://orcid.org/0000-0002-5930-6456
Fumitaka InoueInstitute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.ORCID http://orcid.org/0000-0003-0657-434X
Manolis KellisThe Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0001-7113-9630
Ariel LevineSpinal Circuits and Plasticity Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA.ORCID http://orcid.org/0000-0002-0335-0730
Mo LotfollahiInstitute of Computational Biology, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Germany.ORCID http://orcid.org/0000-0001-6858-7985
Chongyuan LuoDepartment of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA.
Kristen R MaynardLieber Institute for Brain Development, Baltimore, MD, USA.ORCID http://orcid.org/0000-0003-0031-8468
Mor NitzanSchool of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel.ORCID http://orcid.org/0000-0003-0074-9196
Vijay RamaniGladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.
Rahul SatijiaNew York Genome Center, New York, NY, USA.
Lucas SchirmerDepartment of Neurology, Mannheim Center for Translational Neuroscience, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.ORCID http://orcid.org/0000-0001-7142-4116
Yin ShenDepartment of Neurology, University of California, San Francisco, San Francisco, CA, USA.ORCID http://orcid.org/0000-0001-9901-5613
Na SunThe Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Gilad S GreenThe Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
Fabian TheisWellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.ORCID http://orcid.org/0000-0002-2419-1943
Xiao WangThe Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-3090-9894
Joshua D WelchDepartment of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.ORCID http://orcid.org/0000-0002-5869-2391
Ozgun GokceGerman Center for Neurodegenerative Diseases (DZNE), Bonn, Germany. Ozgun.Goekce@ukbonn.de.ORCID http://orcid.org/0000-0001-6319-404X
Genevieve KonopkaDepartment of Neuroscience, UT Southwestern Medical Center, Dallas, TX, USA. genevieve.konopka@utsouthwestern.edu.ORCID http://orcid.org/0000-0002-3363-7302
Shane LiddelowNeuroscience Institute, NYU Grossman School of Medicine, New York, NY, USA. shane.liddelow@nyulangone.org.ORCID http://orcid.org/0000-0002-0840-1437
Evan MacoskoThe Broad Institute of MIT and Harvard, Cambridge, MA, USA. emacosko@broadinstitute.org.ORCID http://orcid.org/0000-0002-2794-5165
Omer Ali BayraktarWellcome Sanger Institute, Hinxton, UK. ob5@sanger.ac.uk.ORCID http://orcid.org/0000-0001-6055-277X
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
Tomasz J NowakowskiWeill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA. tomasz.nowakowski@ucsf.edu.ORCID http://orcid.org/0000-0003-2345-4964
Funding
Comprehensive single-cell atlas of the developing mouse brainU01MH130962 · NIMH · HARVARD UNIVERSITY · PI Paola Arlotta, Tomasz Nowakowski · 2022 to 2026
$33.3MProject 4: Cross-species Dissection of Cellular Response to APOE Genotype and AD Pathology Using Single-cell Multi-omicsP01AG073082 · NIA · J. DAVID GLADSTONE INSTITUTES · PI HUANG, YADONG, MUCKE, LENNART · 2021 to 2025
$23.4MMechanisms of Plasticity in the Spinal CordZIANS003153 · NINDS · NATIONAL INSTITUTE OF NEUROLOGICAL DISORDERS AND STROKE · PI LEVINE, ARIEL · 2016 to 2025
$20.9MSingle-cell Mapping Center for Human Regulatory Elements and Gene ActivityUM1HG012076 · NHGRI · STANFORD UNIVERSITY · PI Michael Ryan Corces, Ansuman Satpathy · 2021 to 2026
$13.8MMulti-omic functional assessment of novel AD variants using high-throughput and single-cell technologiesU01AG072573 · NIA · STANFORD UNIVERSITY · PI KUNDAJE, ANSHUL, MONTGOMERY, STEPHEN · 2021 to 2025
$8.3MElucidate the roles of Alzheimer's disease risk genes and variants in gene expression and AD-related phenotypesRF1AG079557 · NIA · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI GAN, LI, SHEN, YIN · 2022 to 2025
$6.1MStudy of Selective Cell and System Vulnerability in Alzheimer's DiseaseR01AG079291 · NIA · UNIV OF NORTH CAROLINA CHAPEL HILL · PI Li Gan, Yun Li · 2023 to 2026
$5.4MSpatiotemporal epigenomic and chromosomal architectural cell atlas of developing human brainsU01MH130995 · NIMH · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Chongyuan Luo, Mercedes Paredes · 2022 to 2026
$4.4MDeciphering 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
$3.9MAssessing Genomic, Regulatory and Transcriptional Variation at Single Nuclei Resolution in the Brains of Individuals with Autism Spectrum DisorderR01MH125516 · NIMH · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI ARNOLD KRIEGSTEIN, Tomasz Nowakowski · 2021 to 2026
$3.8MSINGLE-CELL MULTI-OMIC APPROACHES TO MECHANISTICALLY CHARACTERIZE PSYCHIATRIC DISORDER RISK LOCI IN THE HUMAN BRAINR01MH125252 · NIMH · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI LUO, CHONGYUAN · 2021 to 2025
$3.7MIntramural NIH HHS ZIA NS003153NEI NIH HHS R01 EY033353NHGRI NIH HHS R01 HG011641NHGRI NIH HHS UM1 HG012076NIA NIH HHS P01 AG073082NIA NIH HHS R01 AG079291NIA NIH HHS RF1 AG079557NIA NIH HHS U01 AG072573NIDA NIH HHS R01 DA055823NIDA NIH HHS U01 DA052713NIGMS NIH HHS R35 GM142889NIMH NIH HHS R01 MH103517NIMH NIH HHS R01 MH125516NIMH NIH HHS R01 MH126481NIMH NIH HHS R01 MH128364NIMH NIH HHS U01 MH130962NINDS NIH HHS R01 NS123263NINDS NIH HHS R01 NS126143NINDS NIH HHS RF1 NS126143NINDS NIH HHS RF1 NS128908NINDS NIH HHS UF1 NS115821U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI) HG011641U.S. Department of Health & Human Services | NIH | National Institute of Mental Health (NIMH) MH103517U.S. Department of Health & Human Services | NIH | National Institute of Mental Health (NIMH) MH126481U.S. Department of Health & Human Services | NIH | National Institute of Mental Health (NIMH) R01MH125516U.S. Department of Health & Human Services | NIH | National Institute of Mental Health (NIMH) R01MH128364U.S. Department of Health & Human Services | NIH | National Institute of Neurological Disorders and Stroke (NINDS) NS115821U.S. Department of Health & Human Services | NIH | National Institute of Neurological Disorders and Stroke (NINDS) NS126143Wellcome Trust
Abstract
Over the past decade, single-cell genomics technologies have allowed scalable profiling of cell-type-specific features, which has substantially increased our ability to study cellular diversity and transcriptional programs in heterogeneous tissues. Yet our understanding of mechanisms of gene regulation or the rules that govern interactions between cell types is still limited. The advent of new computational pipelines and technologies, such as single-cell epigenomics and spatially resolved transcriptomics, has created opportunities to explore two new axes of biological variation: cell-intrinsic regulation of cell states and expression programs and interactions between cells. Here, we summarize the most promising and robust technologies in these areas, discuss their strengths and limitations and discuss key computational approaches for analysis of these complex datasets. We highlight how data sharing and integration, documentation, visualization and benchmarking of results contribute to transparency, reproducibility, collaboration and democratization in neuroscience, and discuss needs and opportunities for future technology development and analysis.
Indexed as
GenomicsNeurosciencesSingle-Cell AnalysisAnimalsEpigenomicsHumans
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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.