Hongkui Zeng

Hongkui Zeng serves as Executive Vice President and Director of the Allen Institute for Brain Science, a position she assumed in 2020 after joining the institute in 2006 and leading its Structured Science Division from 2016-2020. She directs one of the world's leading neuroscience research organizations focused on creating comprehensive brain atlases and accelerating neuroscience discovery through open science principles.

Dr. Zeng earned her Ph.D. in molecular and cell biology from Brandeis University studying circadian clock mechanisms in fruit flies, followed by postdoctoral research at MIT investigating hippocampus-dependent plasticity and learning. Her scientific journey has evolved toward systematic understanding of brain circuitry through large-scale, multidisciplinary approaches.

Her research program centers on understanding neuronal diversity and connectivity in the mouse visual cortical circuit, employing a combined molecular, anatomical, and physiological approach. She has pioneered the development of multiple research platforms including single-cell transcriptomics, electrophysiology, 3D neuronal reconstruction, brain-wide connectivity mapping, and neuronal activity imaging to characterize neuronal cell types and their interconnections.

Analysis of her recent publications (2023-2025) reveals a strong emphasis on creating multi-scale brain atlases that integrate transcriptomic, epigenomic, morphological, and connectivity data. Her work demonstrates increasing sophistication in mapping brain organization from molecular to circuit levels, with significant contributions to understanding healthy aging, cortical architecture, and cell-type-specific brain organization.

• Leading the BRAIN Initiative Cell Census Network
• Developing the Allen Mouse Brain Connectivity Atlas
• Creating comprehensive cell-type taxonomies
• Establishing standardized physiological survey methods

As Director, she oversees major research programs, mentors scientific staff, and guides strategic direction for large-scale neuroscience projects that produce foundational resources for the global neuroscience community. Her leadership has positioned the Allen Institute at the forefront of systematic brain mapping initiatives that are transforming how we understand brain structure and function.