Staff Profiles

Hongkui Zeng, Ph.D.

Executive Director, Structured Science

Hongkui Zeng joined the Allen Institute for Brain Science in 2006. She currently leads the Structured Science Division to develop and operate high-throughput pipelines to generate large-scale, public datasets and tools to fuel neuroscience discovery. Since joining the Allen Institute, she has also 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 and Connectivity program. She has broad scientific experience and a keen interest in using a combined molecular, anatomical 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.


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. My team at the Allen Institute for Brain Science has been working on developing transgenic mouse technologies that enable the identification, labeling, monitoring and manipulation of different neuronal cell types. 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 connectivity, we wish to gain a comprehensive and detailed understanding of how different types of neurons are connected to each other in the brain-wide network. The Mouse Brain Connectivity Atlas project represents the first of such systematic efforts, in which axonal projections from different regions and different cell types within these regions are systematically mapped throughout the brain to generate a 3D 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 neuronal types, and correlate these properties with circuit functions, with the goal of deriving a taxonomy of cell types for this circuit. Through this work, we would like to address some of the most basic questions in neuroscience: What defines a neuronal cell type? How many cell types are there in a specific cortical region, and how similar are they between mouse and human? How are the cells belonging to these types connected to one another to form the circuit? How do these cells work together to process and transform information?


  • Molecular neuroscience
  • Genetics
  • Neuroanatomy
  • Behavior

Research Programs

  • Cell Types
  • Neural Coding
  • Connectivity
  • Atlasing

Selected Publications View on PUBMED

Organization of the connections between claustrum and cortex in the mouse

Journal of Comparative Neurology
May 25, 2016

Wang Q, Ng L, Harris JA, Feng D, Li Y, Royall JJ, Oh SW, Bernard A, Sunkin SM, Koch C, Zeng H

Adult mouse cortical cell taxonomy revealed by single cell transcriptomics

Nature Neuroscience
January 4, 2016

Tasic B, Menon V, Nguyen TN, Kim TK, Jarsky T, Yao Z, Levi B1, Gray LT, Sorensen SA, Dolbeare T, Bertagnolli D, Goldy J, Shapovalova N, Parry S, Lee C, Smith K, Bernard A, Madisen L, Sunkin SM, Hawrylycz M, Koch C, Zeng H

Transgenic mice for intersectional targeting of neural sensors and effectors with high specificity and performance

March 4, 2015

Madisen L, Garner AR, Shimaoka D, Chuong AS, Klapoetke NC, Li L, van der Bourg A, Niino Y, Egolf L, Monetti C, Gu H, Mills M, Cheng A, Tasic B, Nguyen TN, Sunkin SM, Benucci A, Nagy A, Miyawaki A, Helmchen F, Empson RM, Knöpfel T, Boyden ES, Reid RC, Carandini M, Zeng H

A mesoscale connectome of the mouse brain

April 2, 2014

Oh SW, Harris JA, Ng L, Winslow B, Cain N, Mihalas S, Wang Q, Lau C, Kuan L, Henry AM, Mortrud MT, Ouellette B, Nguyen TN, Sorensen SA, Slaughterbeck CR, Wakeman W, Li Y, Feng D, Ho A, Nicholas E, Hirokawa KE, Bohn P, Joines KM, Peng H, Hawrylycz MJ, Phillips JW, Hohmann JG, Wohnoutka P, Gerfen CR, Koch C, Bernard A, Dang C, Jones AR, Zeng H

Genetic approaches to neural circuits in the mouse

Annual Review of Neuroscience
May 17, 2013

Huang JZ & Zeng H

Large-scale cellular-resolution gene profiling in human neocortex reveals species-specific molecular signatures

April 13, 2012

Zeng H, Shen EH, Hohmann JG, Oh SW, Bernard A, Royall JJ, Glattfelder KJ, Sunkin SM, Morris JA, Guillozet-Bongaarts AL, Smith KA, Ebbert AJ, Swanson B, Kuan L, Page DT, Overly CC, Lein ES, Hawrylycz MJ, Hof PR, Hyde TM, Kleinman JE, Jones AR

A toolbox of Cre-dependent optogenetic transgenic mice for light-induced activation and silencing

Nature Neuroscience
March 25, 2012

Madisen L, Mao T, Koch H, Zhuo J, Berenyi A, Fujisawa S, Hsu YW, Garcia AJ, Gu X, Zanella S, Kidney J, Gu H, Mao Y, Hooks BM, Boyden ES, Buzsáki G, Ramirez JM, Jones AR, Svoboda K, Han X, Turner EE, Zeng H

A robust and high-throughput Cre reporting and characterization system for the whole mouse brain

Nature Neuroscience
December 20, 2010

Madisen L, Zwingman TA, Sunkin SM, Oh SW, Zariwala HA, Gu H, Ng LL, Palmiter RD, Hawrylycz MJ, Jones AR, Lein ES, Zeng H

Forebrain-specific calcineurin knockout selectively impairs bidirectional synaptic plasticity and working/episodic-like memory

November 30, 2001

Zeng H, Chattarji S, Barbarosie M, Rondi-Reig L, Philpot BD, Miyakawa T, Bear MF, Tonegawa S

A light-entrainment mechanism for the Drosophila circadian clock

March 14, 1996

Zeng H, Qian Z, Myers MP, Rosbash M