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Scientific Publications of the Basal Ganglia Cell Atlas

28 scientific manuscripts across 6 Cell Press Journals.
Published November 12, 2026.

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flagship overview

Towards an Integrated Framework for a Human and Mammalian Brain Cell Atlas

BICAN; Ecker, Hawrylycz, Lein, Ren, Thompson, Zeng, White, Zhang · Cell

https://doi.org/10.1016/j.cell.2026.10.031
perspective

From the human genome to the human brain cell atlas

Hawrylycz · Cell

https://doi.org/10.1016/j.cell.2026.10.034

🧬 Consensus taxonomy and cross-species atlas

Cell type classification, alignment, population variation.

Johansen et al. — Cross-species multiomic atlas of the primate basal gangliaIchihara et al. — Common variation of cell abundances and gene expression in the human striatumFu et al. — Circuit-aligned specialization of human basal ganglia astrocytes

🗺️ Spatial organization

Gradients, striosome–matrix, zonation, cellular communities.

Hewitt et al. — Spatial transcriptomics reveals molecular organization of human and non-human primate basal gangliaKraft et al. — Mesoscale molecular architecture of the striatum across cell types and adult agingBerackey, Xu et al. — Multiscale spatial atlas of human basal ganglia cell types and communitiesDan et al. — Spatial and regulatory organization of cell identity across the primate subcortex

🧩 Epigenomic regulation

Chromatin accessibility, methylation, histone mods, 3D genome.

Ding et al. — Multimodal Single-Cell Epigenomic and 3D Genome Atlas of the Human Basal GangliaChang et al. — Single-cell analysis of chromatin state and transcriptome in the human basal gangliaXie et al. — Single-Cell Multimodal Atlas Reveals Regulatory Programs in the Human BrainLi, Wang — An Integrated Single-Cell and Epigenomic Resource for Comparative Analysis of the Basal Ganglia from BICAN

⚡ Morphology and electrophysiology

Patch-seq linking transcriptomic identity to morphoelectric properties.

Liu et al. — Morphoelectric Diversity and Specialization of Primate Striatal Neuron Types

🧬 Genetic tools

Enhancer-AAV vectors for cell-type-specific targeting.

Chowdhury et al. — Enhancer-based AAV approach for selective AADC delivery reduces motor symptoms and dyskinesia in Parkinson’s mouse models

🩺 Disease relevance

Atlas applied to Alzheimer’s and autism.

Kana et al. — Amyloid and tau display distinct patterns across Alzheimer’s in anterior caudateYuan et al. — Disruption of Cell-Type-Specific Molecular Programs of Striatal Spiny Projection Neurons in Autism

🧫 Development

Progenitor diversity, developmental trajectories.

Heffel et al. — A Single-Cell and Spatial 3D Multi-omic Atlas of the Developing Human Basal Ganglia

⚙️ Infrastructure, standards, and methods

Brain ontology, specimen procurement, data management, mapping tools, and computational methods.

Ding, Lein — Harmonized brain ontology and 3D atlases for human, macaque, and marmoset basal gangliaTao et al. — Tissue-to-bytes: A digital twin for single-cell omics data integration across BICANDaniel et al. — MapMyCells: High-performance mapping of unlabeled cell-by-gene data to reference brain taxonomiesBerry, Xu — UC Irvine’s BICAN Brain Procurement Program for the Center for Multiomic Human Brain Cell Atlas ProjectWang, Krienen — PIANO enables generative modeling of gene expression and scales multi-omics integration to 100 million cellsXu, Babadi, Huo — multiVIB: A unified probabilistic contrastive learning framework for atlas-scale integration of single-cell multi-omics data

🌐 Related cell atlas studies

Analyses in other brain regions and species using the same methods and standards.

Johansen, Schmitz et al. — A consensus spinal cord cell type atlas across mouse, macaque, and humanDalley, Lee — Human Neocortical Glutamatergic Neurons Revealed Through Multimodal ProfilingYang et al. — Single-cell, multi-region profiling of the macaque brain across the lifespanRen — An Integrative Single-Cell Epigenomic Atlas Annotates the Regulatory Genome of the Adult Mouse Brain