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people

Zizhen Yao

Assistant Investigator

teams /
Allenite

Zizhen Yao joined the Allen Institute for Brain Science in 2014 as part of a large interdisciplinary effort to categorize the diversity of neural cell types and the molecular mechanisms leading to cell type specificity. Prior to joining the Allen Institute for Brain Science, she worked at Fred Hutchinson Cancer Research Center developing computational techniques for analyzing high throughput epigenetic and transcriptomic data to study myogenesis and neurogenesis during normal development and in disease.

Zizhen Yao received a Ph.D. in computer science from University of Washington in Seattle, where she studied in silico genome screening of functional noncoding RNAs.

research focus

I am interested in genetic and epigenetic regulation of transcription factors for cell fate determination during brain development in comparison to development in other systems to understand general principles of cell differentiation.

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news
Scientists complete first drafts of developing mammalian brain cell atlases
New research reveals how early brains form and the critical periods that could help diagnose and treat brain disease.

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featured publications

publication / 2025
Enhancer AAVs for targeting spinal motor neurons and descending motor pathways in rodents and macaque
Cell Reports
publication / 2025
A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types
Cell
publication / 2025
Integrating multimodal data to understand cortical circuit architecture and function
Nature Neuroscience
publication / 2025
Transcriptional determinants of goal-directed learning and representational drift in the parahippocampal cortex
Cell Reports
publication / 2025
Brain-wide cell-type-specific transcriptomic signatures of healthy ageing in mice
Nature
publication / 2023
Brain-wide correspondence of neuronal epigenomics and distant projections
Nature
publication / 2023
A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain
Nature
publication / 2023
Single-cell analysis of chromatin accessibility in the adult mouse brain
Nature
publication / 2023
A transcriptomic taxonomy of mouse brain-wide spinal projecting neurons
Nature
publication / 2023
Single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain
Nature
publication / 2023
Molecularly defined and spatially resolved cell atlas of the whole mouse brain
Nature
publication / 2023
Morphoelectric and transcriptomic divergence of the layer 1 interneuron repertoire in human versus mouse neocortex
Science (New York, N.Y.)
publication / 2023
Robust enhancer-gene regulation identified by single-cell transcriptomes and epigenomes
Cell Genomics
publication / 2023
A guide to the BRAIN Initiative Cell Census Network data ecosystem
PLoS biology
publication / 2022
Single-neuron models linking electrophysiology, morphology, and transcriptomics across cortical cell types
Cell Reports
publication / 2022
Dense functional and molecular readout of a circuit hub in sensory cortex
Science (New York, N.Y.)
publication / 2021
A multimodal cell census and atlas of the mammalian primary motor cortex
Nature
publication / 2021
Human neocortical expansion involves glutamatergic neuron diversification
Nature
publication / 2021
Morphological diversity of single neurons in molecularly defined cell types
Nature
publication / 2021
Isoform cell-type specificity in the mouse primary motor cortex
Nature
publication / 2021
Spatially resolved cell atlas of the mouse primary motor cortex by MERFISH
Nature
publication / 2021
Comparative cellular analysis of motor cortex in human, marmoset and mouse
Nature
publication / 2021
A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex
Nature
publication / 2021
Phenotypic variation of transcriptomic cell types in mouse motor cortex
Nature
publication / 2021
Single-cell and single-nucleus RNA-seq uncovers shared and distinct axes of variation in dorsal LGN neurons in mice, non-human primates, and humans
eLife
publication / 2021
A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation
Cell
publication / 2021
Control of impulsivity by Gi-protein signalling in layer-5 pyramidal neurons of the anterior cingulate cortex
Communications Biology
publication / 2021
Enhancer viruses for combinatorial cell-subclass-specific labeling
Neuron
publication / 2021
Alternating sources of perisomatic inhibition during behavior
Neuron
publication / 2020
Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells
Cell
publication / 2020
Distinct Transcriptomic Cell Types and Neural Circuits of the Subiculum and Prosubiculum along the Dorsal-Ventral Axis
Cell Reports
publication / 2019
Single-cell transcriptomic evidence for dense intracortical neuropeptide networks
eLife
publication / 2019
Multimodal Analysis of Cell Types in a Hypothalamic Node Controlling Social Behavior
Cell
publication / 2019
Conserved cell types with divergent features in human versus mouse cortex
Nature
publication / 2018
Distinct descending motor cortex pathways and their roles in movement
Nature
publication / 2018
Shared and distinct transcriptomic cell types across neocortical areas
Nature
publication / 2018
A Suite of Transgenic Driver and Reporter Mouse Lines with Enhanced Brain-Cell-Type Targeting and Functionality
Cell
publication / 2018
Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding
Science (New York, N.Y.)
publication / 2018
Single-nucleus and single-cell transcriptomes compared in matched cortical cell types
PloS One
publication / 2017
The identification and functional annotation of RNA structures conserved in vertebrates
Genome Research
publication / 2017
Single-Cell Profiling of an In Vitro Model of Human Interneuron Development Reveals Temporal Dynamics of Cell Type Production and Maturation
Neuron
publication / 2017
Layer-specific chromatin accessibility landscapes reveal regulatory networks in adult mouse visual cortex
eLife
publication / 2017
A Single-Cell Roadmap of Lineage Bifurcation in Human ESC Models of Embryonic Brain Development
Cell Stem Cell
publication / 2016
Adult mouse cortical cell taxonomy revealed by single cell transcriptomics
Nature Neuroscience
publication / 2016
Fixed single-cell transcriptomic characterization of human radial glial diversity
Nature Methods
publication / 2015
Canonical genetic signatures of the adult human brain
Nature Neuroscience
publication / 2015
Genome engineering of isogenic human ES cells to model autism disorders
Nucleic Acids Research
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