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Shenqin Yao

Assistant Investigator

teams /
Allenite

Shenqin Yao joined the Allen Institute for Brain Science in 2015 as a scientist in the research and development group. Her role will focus on the development and optimization of novel molecular genetic tools, in an effort to understand the neural connectivity of the mouse brain. She received her Ph.D. in Molecular Biology and Genetics with Phillip Beachy at the Johns Hopkins University, where she identified novel signaling molecules that govern embryogenesis and adult tissue homeostasis via genome-wide screening in cultured cells. Prior to joining the Allen Institute, she received postdoctoral training and worked as a staff scientist with Catherine Dulac at Harvard University. There, she studied neural circuits underlying mouse social recognition using advanced molecular, genetic and behavioral approaches.

research focus

My research interest is to understand the molecular basis of neural circuitry that translates sensory inputs into behavioral outputs. At the Allen Institute, I will contribute to the development of viral vector tools that enable us to mark and trace the connectivities from molecularly defined populations of neurons. On the basis of anatomical dissection of circuit connectivity, I will also develop tools that will allow functional perturbation of distinct circuit components by combining genetic engineering with optogenetics and chemogenetics. Development and optimization of the above tools will facilitate the ongoing effort of the Allen Institute in characterizing different cell types in the brain and understanding the nature of the connections between cells of various types.

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technique built off rabies virus lets scientists trace backward flow of neural activity in the mouse brain

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featured publications

publication / 2025
Data-driven fine-grained region discovery in the mouse brain with transformers
Nature Communications
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
Enhancer AAV toolbox for accessing and perturbing striatal cell types and circuits
Neuron
publication / 2025
Integrating multimodal data to understand cortical circuit architecture and function
Nature Neuroscience
publication / 2024
Rabies virus-based barcoded neuroanatomy resolved by single-cell RNA and in situ sequencing
eLife
publication / 2023
Signature morphoelectric properties of diverse GABAergic interneurons in the human neocortex
Science (New York, N.Y.)
publication / 2023
Linking connectome with transcriptome using a self-inactivating rabies virus
Nature Methods
publication / 2023
Regional and cell-type-specific afferent and efferent projections of the mouse claustrum
Cell Reports
publication / 2023
A whole-brain monosynaptic input connectome to neuron classes in mouse visual cortex
Nature Neuroscience
publication / 2022
Cardiovascular baroreflex circuit moonlights in sleep control
Neuron
publication / 2022
Dense functional and molecular readout of a circuit hub in sensory cortex
Science (New York, N.Y.)
publication / 2021
Cellular anatomy of the mouse primary motor cortex
Nature
publication / 2021
Enhancer viruses for combinatorial cell-subclass-specific labeling
Neuron
publication / 2021
Functional enhancer elements drive subclass-selective expression from mouse to primate neocortex
Cell Reports
publication / 2020
RecV recombinase system for in vivo targeted optogenomic modifications of single cells or cell populations
Nature Methods
publication / 2019
Connectional architecture of a mouse hypothalamic circuit node controlling social behavior
Proceedings of the National Academy of Sciences of the United States of America
publication / 2018
Nontoxic, double-deletion-mutant rabies viral vectors for retrograde targeting of projection neurons
Nature Neuroscience
publication / 2017
Identification of preoptic sleep neurons using retrograde labelling and gene profiling
Nature
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