Hongkui Zeng, Ph.D.

Investigator, Cell and Circuit Genetics

Hongkui Zeng joined the Allen Institute in 2006. She leads the Research and Development program to explore novel technologies and develop high-throughput paradigms for generating large-scale, public datasets and tools to fuel neuroscience discovery. Since joining the Allen Institute, she has led several research programs or projects, including the Transgenic Technology program, the Human Cortex Gene Survey project, the Allen Mouse Brain Connectivity Atlas project, and the Mouse Cell Types program. She has broad scientific experience and a keen interest in using a combined molecular, genetic and physiological approach to unravel mechanisms of brain circuitry and potential approaches for treating brain diseases. Prior to joining the Allen Institute, Zeng worked at a biotechnology start-up where she studied the genomic repertoire of the G-protein coupled receptor (GPCR) gene family, and the function of many GPCR genes in behavioral models of CNS diseases. Zeng received her Ph.D. in molecular and cell biology from Brandeis University, where she studied the molecular mechanisms of the circadian clock in fruit flies. Then as a postdoctoral fellow at Massachusetts Institute of Technology, she used conditional mouse genetic techniques to study the molecular and synaptic mechanisms underlying hippocampus-dependent plasticity and learning.



  • Molecular neuroscience
  • Genetics
  • Neuroanatomy
  • Behavior

Research Programs

  • Cell types
  • Atlasing

Contact Information

  • Email: hongkuiz@alleninstitute.org 

Research Interests

The brain circuit is an intricately interconnected network of a vast number of neurons with diverse molecular, anatomical and physiological properties. To understand the principles of information processing in the brain circuit, it is essential to have a systematic understanding of the common and unique properties for each of its components – the individual and populations of neurons, to monitor their activities while the brain is processing information, and to have the ability to manipulate these neurons to investigate their functions in the brain circuit.

I am leading the Research and Development team at the Allen Institute for Brain Science. My team works on developing technologies that will enable the identification, labeling, monitoring and manipulation of different neuronal cell types, and on using a combined molecular, genetic and physiological approach to unravel the diversity and connectivity of the neuronal cell types that compose of neural circuits. Currently we are focusing on three main research areas – transgenic technology, cell types, and the Allen Mouse Brain Connectivity Atlas.

Modern neuroscience is powered by technology innovations in microscopy and imaging, molecular genetic engineering, genomics and computer science. Genetic tools (such as transgenic mice and recombinant viral vectors) can integrate these different approaches at the level of specific circuit components for precisely targeted investigation. In our transgenic technology efforts, we build transgenic mouse lines that target sensors and effectors to specific types of neurons. In connectivity, we wish to gain a comprehensive and detailed understanding of how different types of neurons are connected to each other. The Allen Mouse Brain Connectivity Atlas represents the first of such large-scale efforts, in which axonal projections from different regions and different cell types within these regions are systematically mapped throughout the brain to generate a 3-D whole-brain projectome. Finally, in the mouse cell types program, we use the mouse visual system as a model to systematically characterize the transcriptomic, morphological, connectional and electrophysiological properties of different kinds of neurons, and correlate these properties with circuit functions, in the hope of deriving a taxonomy of cell types for this circuit.