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Hongkui Zeng

Allen Institute for Brain Science · US
🔎 Find collaborators in Cognitive Neuroscience · Molecular Biology →
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Area of research
Cognitive Neuroscience · Molecular Biology
Research interest
Research interests include Neural dynamics and brain function, Single-cell and spatial transcriptomics, Cell Image Analysis Techniques, and Neuroinflammation and Neurodegeneration Mechanisms.
h-index
95
citations
55,455
works
375
NIH funding
primary concept
Biology
email

Recent publications

Three-photon holographic microscopy for deep precise optogenetics
Research Square 2026cited by 0position: middledoi
Brain-wide cell-type-specific transcriptomic signatures of healthy ageing in mice
Nature 2025cited by 102position: lastdoi
Cholinergic neuronal activity promotes diffuse midline glioma growth through muscarinic signaling
Cell 2025cited by 35position: middledoi
Connectomics of predicted Sst transcriptomic types in mouse visual cortex
Nature 2025cited by 19position: middledoi
Enhancer AAVs for targeting spinal motor neurons and descending motor pathways in rodents and macaque
Cell Reports 2025cited by 19position: middledoi
Continuous cell-type diversification in mouse visual cortex development
Nature 2025cited by 15position: lastdoi
Transcriptomic and spatial organization of telencephalic GABAergic neurons
Nature 2025cited by 13position: lastdoi
Imaging high-frequency voltage dynamics in multiple neuron classes of behaving mammals
Cell 2025cited by 10position: middledoi
Connectivity of single neurons classifies cell subtypes in mouse brains
Nature Methods 2025cited by 9position: middledoi
Cross-species consensus atlas of the primate basal ganglia
bioRxiv (Cold Spring Harbor Laboratory) 2025cited by 8position: middledoi
A cross-species spatial transcriptomic atlas of the human and non-human primate basal ganglia
bioRxiv (Cold Spring Harbor Laboratory) 2025cited by 7position: middledoi
The new frontier in understanding human and mammalian brain development
Nature 2025cited by 6position: lastdoi
Transcriptional determinants of goal-directed learning and representational drift in the parahippocampal cortex
Cell Reports 2025cited by 4position: middledoi
epDevAtlas: mapping GABAergic cells and microglia in the early postnatal mouse brain
Nature Communications 2025cited by 4position: middledoi
Roadmap for direct and indirect translation of optogenetics into discoveries and therapies for humans
Nature Neuroscience 2025cited by 4position: middledoi
Data-driven fine-grained region discovery in the mouse brain with transformers
Nature Communications 2025cited by 3position: middledoi
MerQuaCo: a computational tool for quality control in image-based spatial transcriptomics
eLife 2025cited by 1position: middledoi
MerQuaCo: a computational tool for quality control in image-based spatial transcriptomics
eLife 2025cited by 1position: middledoi
Enhancer-AAVs allow genetic access to oligodendrocytes and diverse populations of astrocytes across species
eLife 2025cited by 1position: middledoi
Large-scale cellular-resolution read/write of activity enables discovery of cell types defined by complex circuit properties
bioRxiv (Cold Spring Harbor Laboratory) 2025cited by 1position: middledoi
Integrated Classification of Cortical Cells and Quantitative Projectomic Mapping Unveil Organizational Principles of Brain-Wide Connectomes at Single Cell Level
bioRxiv (Cold Spring Harbor Laboratory) 2025cited by 0position: middledoi
The xIV-LDDMM toolkit of image-varifold based technologies for mapping 3D images and spatial-omics across scales
Communications Biology 2025cited by 0position: middledoi
Exploring the correspondence between gene expression and thalamic nuclei using the THALMANAC resource
bioRxiv (Cold Spring Harbor Laboratory) 2025cited by 0position: middledoi
Enhancer-AAVs allow genetic access to oligodendrocytes and diverse populations of astrocytes across species
eLife 2025cited by 0position: middledoi
MerQuaCo: a computational tool for quality control in image-based spatial transcriptomics
eLife 2025cited by 0position: middledoi
Spatial patterning of transcriptional and regulatory programs in the primate subcortex
bioRxiv (Cold Spring Harbor Laboratory) 2025cited by 0position: middledoi
Neural circuit basis of placebo pain relief
Nature 2024cited by 70position: middledoi
Long-term labeling and imaging of synaptically connected neuronal networks in vivo using double-deletion-mutant rabies viruses
Nature Neuroscience 2024cited by 19position: middledoi
The single-cell opioid responses in the context of HIV (SCORCH) consortium
Molecular Psychiatry 2024cited by 16position: lastdoi
Neuronal diversity and stereotypy at multiple scales through whole brain morphometry
Nature Communications 2024cited by 16position: middledoi

Grants

No grants ingested yet.

Frequent collaborators

Bosiljka Tasic · Allen Institute for Brain Science53 papers (2016–2026)Tanya L. Daigle · Allen Institute for Brain Science37 papers (2017–2025)Michael Hawrylycz · Allen Institute27 papers (2012–2025)Zizhen Yao · Allen Institute for Brain Science23 papers (2016–2025)Linda Madisen · Allen Institute for Brain Science21 papers (2012–2022)Christof Koch · Allen Institute for Brain Science19 papers (2016–2023)Julie A. Harris · Allen Institute for Brain Science17 papers (2012–2023)Ed S. Lein · Allen Institute for Brain Science14 papers (2012–2020)Thuc Nghi Nguyen · Cajal Neuroscience (United States)13 papers (2016–2022)Hong‐Wei Dong · Shandong University of Traditional Chinese Medicine12 papers (2020–2025)Shenqin Yao · Allen Institute for Brain Science12 papers (2017–2025)Karla E. Hirokawa · Allen Institute11 papers (2013–2023)Amy Bernard · Carnegie Mellon University10 papers (2012–2023)Jack Waters · Allen Institute for Brain Science10 papers (2018–2025)Gabe J. Murphy · Allen Institute10 papers (2018–2022)Ali Çetin · Eskişehir Osmangazi University10 papers (2017–2023)Lydia Ng · Allen Institute for Brain Science10 papers (2016–2025)Qingming Luo · Southern Medical University9 papers (2017–2023)Kimberly A. Smith · Allen Institute for Brain Science9 papers (2012–2023)Seung Wook Oh · Marine Biodiversity Institute of Korea9 papers (2012–2020)
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