Peng He

Peng He is an Assistant Professor in the Department of Pathology at the University of California, San Francisco (UCSF) School of Medicine. His research focuses on gene regulatory networks in human tissues, leveraging single-cell and spatial assays combined with innovative computational methods. He has made significant contributions to the Encyclopedia of DNA Elements (ENCODE) project through RNA-centric approaches and to the Human Cell Atlas (HCA) with a focus on developing limbs and lungs.

Dr. He received his BSc in Statistics, Biochemistry and Computer Science from The University of Hong Kong in 2012, followed by a PhD in Functional Genomics and Computational Biology from Caltech in 2019. He completed his postdoctoral training in Single-cell, Spatial and Computational Genomics at the Sanger Institute and EMBL-EBI.

His interdisciplinary research group develops computational methods and profiles transcriptomic and chromatin changes to construct ultra-high resolution cell atlases of healthy and altered tissues and organoids. Their work spans computational biology, single-cell genomics, spatial transcriptomics, and developmental biology, with specific expertise in lung and limb development. The lab follows three main research directions: constructing cell atlases, developing computational workflows, and dissecting gene regulatory networks via organoid perturbations.

Dr. He's publication record shows consistent high-impact output through 2025, with major contributions to understanding human developmental biology. His recent work includes comprehensive single-cell and spatial atlases of human fetal lung, embryonic limb, and prenatal skin, revealing novel insights into cellular differentiation, immune regulation, and tissue morphogenesis. His methodological contributions include computational pipelines for integrated single-cell and spatial data analysis that have become essential tools in the field.

• ISSCR 2022 Abstract Merit Award
• ISSCR 2022 Travel Award
• University of Cambridge 2019-2024 Junior Research Fellowship and MA degree
• University of Hong Kong 2011 Overseas Research Fellowship
• University of Hong Kong & UCLA 2010-2011 Worldwide Exchange Scholarship
• University of Hong Kong 2010 Summer Research Fellowship
• University of Hong Kong 2009-2012 Rosita King Ho Scholarship (Full scholarship)

Dr. He actively mentors UCSF students, residents, fellows, and staff on research projects. His lab offers five main types of projects: genetic perturbation of organoid models, single-cell and spatial profiling, RNA capture optimization, high-resolution omics data analysis, and algorithm development. The He Lab at UCSF includes postdoctoral researchers, PhD students, and technical staff working collaboratively on computational and experimental approaches to understand tissue development and disease.