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What is a cell type and how to define it?

https://doi.org/10.1016/j.cell.2022.06.031

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Outgoing claims: the papers this work cites, builds on, or argues with.

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Spatially resolved single-cell genomics and transcriptomics by imaging

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Single-cell analysis of experience-dependent transcriptomic states in the mouse visual cortex

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Viral manipulation of functionally distinct interneurons in mice, non-human primates and humans

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Circuit and molecular architecture of a ventral hippocampal network

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Revisiting the neurovascular unit

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Single-neuron projectome of mouse prefrontal cortex

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Single-cell genomic profiling of human dopamine neurons identifies a population that selectively degenerates in Parkinson’s disease

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A survey of human brain transcriptome diversity at the single cell level

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The Expanding Cell Diversity of the Brain Vasculature

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Designed optogenetic tool for bridging single-neuronal multimodal information in intact animals

inferred← citeshttps://doi.org/10.1038/s41467-025-63429-8openalex-snapshot

Aging in mice alters regionally enriched striatal astrocytes

inferred← citeshttps://doi.org/10.1038/s41467-025-66613-yopenalex-snapshot

Laminar organization of pyramidal neuron cell types defines distinct CA1 hippocampal subregions

inferred← citeshttps://doi.org/10.1038/s41467-026-71371-6openalex-snapshot

Molecular and functional dissection using CaMPARI-seq reveals the neuronal organization for dissociating optic flow-dependent behaviors

inferred← citeshttps://doi.org/10.1038/s41467-026-75680-8openalex-snapshot

Efficient differential expression analysis of large-scale single-cell transcriptomics data using Dreamlet

inferred← citeshttps://doi.org/10.1038/s41467-026-75681-7openalex-snapshot

Fast, flexible analysis of differences in cellular composition with crumblr

inferred← citeshttps://doi.org/10.1038/s41467-026-76522-3openalex-snapshot

Transcriptomic analysis of spinal V1 interneurons informs their multifunctional role in motor output

inferred← citeshttps://doi.org/10.1038/s41556-023-01316-4openalex-snapshot

Single-cell spatial multi-omics and deep learning dissect enhancer-driven gene regulatory networks in liver zonation

inferred← citeshttps://doi.org/10.1038/s41559-026-03164-5openalex-snapshot

Flexible use of conserved motifs constrains genome access in cell type evolution

inferred← citeshttps://doi.org/10.1038/s41559-026-03186-zopenalex-snapshot

Ancient vocabulary for evolving cells

inferred← citeshttps://doi.org/10.1038/s41576-023-00626-5openalex-snapshot

Genetics of human brain development

inferred← citeshttps://doi.org/10.1038/s41583-024-00856-4openalex-snapshot

Genetically defined neuron types underlying visuomotor transformation in the superior colliculus

inferred← citeshttps://doi.org/10.1038/s41583-025-00941-2openalex-snapshot

Molecular and functional diversity of the autonomic nervous system

inferred← citeshttps://doi.org/10.1038/s41584-023-01031-2openalex-snapshot

A roadmap for delivering a human musculoskeletal cell atlas

inferred← citeshttps://doi.org/10.1038/s41586-023-06638-9openalex-snapshot

Evolution of neuronal cell classes and types in the vertebrate retina

inferred← citeshttps://doi.org/10.1038/s41586-023-06805-yopenalex-snapshot

Single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain

inferred← citeshttps://doi.org/10.1038/s41586-023-06812-zopenalex-snapshot

A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain

inferred← citeshttps://doi.org/10.1038/s41586-023-06817-8openalex-snapshot

A transcriptomic taxonomy of mouse brain-wide spinal projecting neurons

inferred← citeshttps://doi.org/10.1038/s41586-023-06818-7openalex-snapshot

The molecular cytoarchitecture of the adult mouse brain

inferred← citeshttps://doi.org/10.1038/s41586-024-07405-0openalex-snapshot

Large-scale neurophysiology and single-cell profiling in human neuroscience

inferred← citeshttps://doi.org/10.1038/s41586-024-07780-8openalex-snapshot

Inhibitory specificity from a connectomic census of mouse visual cortex

inferred← citeshttps://doi.org/10.1038/s41586-024-07915-xopenalex-snapshot

Causal evidence of a line attractor encoding an affective state

inferred← citeshttps://doi.org/10.1038/s41586-024-08518-2openalex-snapshot

Transcriptomic neuron types vary topographically in function and morphology

inferred← citeshttps://doi.org/10.1038/s41586-025-09037-4openalex-snapshot

Molecular gradients shape synaptic specificity of a visuomotor transformation

inferred← citeshttps://doi.org/10.1038/s41586-025-09312-4openalex-snapshot

The Biodiversity Cell Atlas: mapping the tree of life at cellular resolution

inferred← citeshttps://doi.org/10.1038/s41586-025-09644-1openalex-snapshot

Continuous cell-type diversification in mouse visual cortex development

inferred← citeshttps://doi.org/10.1038/s41586-025-09652-1openalex-snapshot

The new frontier in understanding human and mammalian brain development

inferred← citeshttps://doi.org/10.1038/s41586-026-10269-1openalex-snapshot

A mechanism for adaptive genome regulation in cancer

inferred← citeshttps://doi.org/10.1038/s41586-026-10424-8openalex-snapshot

Connecting single-cell transcriptomes to projectomes in the mouse visual cortex

inferred← citeshttps://doi.org/10.1038/s41588-024-01920-6openalex-snapshot

Defining heritability, plasticity, and transition dynamics of cellular phenotypes in somatic evolution

inferred← citeshttps://doi.org/10.1038/s41588-025-02329-5openalex-snapshot

A multi-tissue single-cell expression atlas in cattle

inferred← citeshttps://doi.org/10.1038/s41592-024-02503-3openalex-snapshot

Mapping the topography of spatial gene expression with interpretable deep learning

inferred← citeshttps://doi.org/10.1038/s41592-025-02622-5openalex-snapshot

Spotiphy enables single-cell spatial whole transcriptomics across an entire section

inferred← citeshttps://doi.org/10.1038/s41592-025-02687-2openalex-snapshot

NeuroXiv: AI-powered open databasing and dynamic mining of brain-wide neuron morphometry

inferred← citeshttps://doi.org/10.1038/s41592-025-02867-0openalex-snapshot

Scalable spatial single-cell transcriptomics and translatomics in 3D thick tissue blocks

inferred← citeshttps://doi.org/10.1038/s41593-022-01222-2openalex-snapshot

Insights into Alzheimer’s disease from single-cell genomic approaches

inferred← citeshttps://doi.org/10.1038/s41593-024-01812-2openalex-snapshot

The cell-type underpinnings of the human functional cortical connectome

inferred← citeshttps://doi.org/10.1038/s41593-024-01814-0openalex-snapshot

Implementation and validation of single-cell genomics experiments in neuroscience

inferred← citeshttps://doi.org/10.1038/s41593-025-01978-3openalex-snapshot

A dynamic and multimodal framework to define microglial states

inferred← citeshttps://doi.org/10.1038/s41593-025-02085-zopenalex-snapshot

Dendritome mapping reveals the spatial organization of striatal neuron morphology

inferred← citeshttps://doi.org/10.1038/s41593-025-02097-9openalex-snapshot

Roadmap for direct and indirect translation of optogenetics into discoveries and therapies for humans

inferred← citeshttps://doi.org/10.1038/s41593-025-02119-6openalex-snapshot

A mouse brain atlas based on dendritic microenvironments

inferred← citeshttps://doi.org/10.1038/s41593-025-02134-7openalex-snapshot

Electrophysiological classification of human layer 2–3 pyramidal neurons reveals subtype-specific synaptic interactions

inferred← citeshttps://doi.org/10.1038/s41597-025-04379-0openalex-snapshot

A Multi-Scale Neuron Morphometry Dataset from Peta-voxel Mouse Whole-Brain Images

inferred← citeshttps://doi.org/10.1038/s41597-025-04528-5openalex-snapshot

Divergence in cellular markers observed in single-cell transcriptomics datasets between cultured primary trabecular meshwork cells and tissues

inferred← citeshttps://doi.org/10.1038/s41598-023-42883-8openalex-snapshot

Defining and identifying cell sub-crosstalk pairs for characterizing cell–cell communication patterns

inferred← citeshttps://doi.org/10.1038/s41598-024-53098-wopenalex-snapshot

Single-cell analysis reveals the spatial-temporal expression of genes associated with esophageal malformations

inferred← citeshttps://doi.org/10.1038/s41598-026-39703-0openalex-snapshot

Attention-guided enhanced deconvolution enables reference-free cell type estimation in spatial transcriptomics

inferred← citeshttps://doi.org/10.1038/s42003-024-06564-0openalex-snapshot

Building a learnable universal coordinate system for single-cell atlas with a joint-VAE model

inferred← citeshttps://doi.org/10.1038/s42003-026-09940-0openalex-snapshot

Dynamic gut responses to sepsis uncovered by multi-omics profiling in a rodent model

inferred← citeshttps://doi.org/10.1038/s42003-026-10803-xopenalex-snapshot

A who’s who of cell types in skeletal muscle

inferred← citeshttps://doi.org/10.1038/s42256-022-00600-6openalex-snapshot

Translating single-cell genomics into cell types

inferred← citeshttps://doi.org/10.1038/s43588-024-00683-8openalex-snapshot

Joint inference of discrete cell types and continuous type-specific variability in single-cell datasets with MMIDAS

inferred← citeshttps://doi.org/10.1038/s43588-024-00689-2openalex-snapshot

Biophysically interpretable inference of cell types from multimodal sequencing data

inferred← citeshttps://doi.org/10.1038/s44277-025-00041-0openalex-snapshot

A practical guide to sequencing in neuropsychiatric research

inferred← citeshttps://doi.org/10.1042/bcj20220572openalex-snapshot

Respiratory epithelial cell types, states and fates in the era of single-cell RNA-sequencing

inferred← citeshttps://doi.org/10.1042/bst20230878openalex-snapshot

Cell-free genomics: transcription factor interactions in reconstituted naïve embryonic chromatin

inferred← citeshttps://doi.org/10.1063/5.0165773openalex-snapshot

Diversity-induced trivialization and resilience of neural dynamics

inferred← citeshttps://doi.org/10.1073/pnas.2218841120openalex-snapshot

Intrinsic neural diversity quenches the dynamic volatility of neural networks

inferred← citeshttps://doi.org/10.1073/pnas.2317083121openalex-snapshot

Hox gene–specific cellular targeting using split intein Trojan exons

inferred← citeshttps://doi.org/10.1073/pnas.2319804121openalex-snapshot

Unsupervised pattern identification in spatial gene expression atlas reveals mouse brain regions beyond established ontology

inferred← citeshttps://doi.org/10.1073/pnas.2416987121openalex-snapshot

Dissecting the cellular architecture and genetic circuitry of the soybean seed

inferred← citeshttps://doi.org/10.1073/pnas.2512872122openalex-snapshot

Geometrical compartmentalization of trigger waves

inferred← citeshttps://doi.org/10.1073/pnas.2516083122openalex-snapshot

High-resolution single-cell analyses reveal evolutionary constraints and evolvability of sexual circuits in Drosophila

inferred← citeshttps://doi.org/10.1080/00029890.2025.2460411openalex-snapshot

Reviews

inferred← citeshttps://doi.org/10.1093/bfgp/elad033openalex-snapshot

Cell type and gene regulatory network approaches in the evolution of spiralian biomineralisation

inferred← citeshttps://doi.org/10.1093/bib/bbaf013openalex-snapshot

BIOTIC: a Bayesian framework to integrate single-cell multi-omics for transcription factor activity inference and improve identity characterization of cells

inferred← citeshttps://doi.org/10.1093/bib/bbaf312openalex-snapshot

A data-intelligence-intensive bioinformatics copilot system for large-scale omics research and scientific insights

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