Hongkui Zeng

This study identifies Sst-Chodl inhibitory neurons that promote cortical synchrony and sleep by exerting long-range inhibition during low-arousal states.

This study identifies conserved and clade-specific hypothalamic cell types across vertebrates using single-cell transcriptomics, revealing conserved transcription factors and rewired regulatory linkages.

The paper describes the iterative creation of harmonized ontologies and 3D frameworks for the basal ganglia across human and non-human primates to enable cross-species comparisons of cellular and molecular data.

This paper introduces a new system for activating and recording thousands of neurons over a large field-of-view with pixel-level precision.

This study uses multimodal Patch-seq data to show that gene expression gradients in mouse basal ganglia neurons correlate with spatial location, physiology, and morphology.

The paper maps conserved cell type signatures in the adult mouse brainstem and spinal cord using multi-omics data, revealing shared and region-specific features.

The paper presents a cross-species, multimodal atlas of the basal ganglia using single-cell transcriptomics and integrates epigenomic and spatial genomic data to enable cross-species comparisons.

The paper reveals the external globus pallidus (GPe) as a basal ganglia output hub with distinct subpopulations that mediate specific behaviors through projection-specific circuits.

The paper maps gene expression responses to loss of 1,947 disease-associated genes across the mouse brain using Perturb-seq, revealing cell-type-specific essentiality and transcriptional programs.

MapMyCells maps unlabeled single-cell datasets to reference brain taxonomies, enabling cross-study integration and reproducible cell-type annotation.

The paper develops a cross-species enhancer-AAV toolkit for targeting specific cell types in the basal ganglia across species, validated in mouse and macaque.

The paper analyzes multi-modal Patch-seq data from macaque striatum to reveal morphoelectric diversity and functional specialization of neuronal cell types, highlighting primate-specific features and differences from rodents.

SCALPEL processes large-scale spatial transcriptomics data with improved 3D segmentation, doublet detection, and spatial alignment, showing better performance than previous methods.

The paper creates a cross-species spinal cord cell type atlas integrating data from mouse, macaque, and human, identifying conserved and species-specific features.

The paper creates a cross-species consensus atlas of primate basal ganglia cell types using multiomic data from human, macaque, and marmoset, identifying 61 conserved cell types and a novel hybrid medium spiny neuron type.

This study shows psilocybin alters large-scale cortical network connectivity in mice by strengthening inputs from perceptual and medial regions and weakening cortico-cortical loops, dependent on drug-evoked spiking activity.

This paper creates a cross-species spatial transcriptomic atlas of the basal ganglia in human, rhesus macaque, and common marmoset, revealing conserved molecular organization and cell type-specific compartments.

The paper presents a spatially resolved transcriptomic and gene regulatory atlas of primate subcortical regions, revealing spatially tuned transcriptional and regulatory programs across cell types.

The paper analyzes the transcriptomic and spatial organization of GABAergic neurons in the mouse telencephalon, revealing complex developmental and spatial relationships across multiple brain regions.

The paper investigates how environmental novelty affects cortical plasticity during navigation using optogenetic stimulation and calcium imaging in mice.

The paper introduces a method to monitor and control neural activity at cellular resolution in mice, discovering new cell types with unique functional properties.

This paper introduces CellTransformer, a self-supervised framework for detecting fine-grained spatial domains in mouse brain spatial transcriptomics data, achieving high consistency across large datasets.

The paper introduces xIV-LDDMM, a toolkit for cross-scale and cross-modality mapping of 3D imaging and spatial-omics data using image-varifold measures.

The paper introduces THALMANAC, a resource for analyzing single-cell transcriptomic data of the thalamus, revealing gene expression patterns that support and refine thalamic nucleus parcellation.

This paper introduces two TEMPO voltage-sensing technologies to image high-frequency neural oscillations in behaving mammals, revealing new insights into excitatory-inhibitory dynamics and wave propagation.

This study shows that cholinergic neuron activity promotes both healthy OPC and DMG proliferation through muscarinic receptors, with specific nuclei driving growth in different brain regions.

The paper identifies enhancers for spinal motor neurons and develops AAV vectors to target these cells in rodents and macaques, enabling functional studies and potential therapeutic applications.

This study integrates molecular and morphological data to classify cortical neurons and map their connectomes, revealing organizational principles of brain-wide networks at the single-cell level.

The paper introduces MerQuaCo, an open-source tool to automatically detect and quantify imperfections in spatial transcriptomics data, improving quality assessment.

The paper constructs a high-resolution transcriptomic and epigenomic atlas of the developing mouse visual cortex, revealing continuous cell type diversification across embryonic and postnatal stages.