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Cambridge Stem Cell Institute


Dr Joo-Hyeon Lee

Stem cells and niches


Laboratory: Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre

Departmental Affiliation: Physiology, Development and Neuroscience



Joo-Hyeon Lee is an Associate Professor in Stem Cell Medicine, a Wellcome Senior Research Fellow at the Wellcome – MRC Cambridge Stem Cell Institute, and an affiliated faculty member at the Department of Physiology, Development, and Neuroscience (PDN), University of Cambridge. Her research interests focus on understanding the mechanisms of stem cell fate regulation. Her lab particularly studies how stem cells sense environmental changes and determine their cell fate, and how niches develop and remodel the local environment during lung homeostasis, regeneration and the early stages of disease progression. Her group develops the state-of-the art technologies, including in vitro 3D human lung organoids and in vivo genetic labelling models, and employs computational analyses of single cell multi-omics and clonal biophysical modelling to map lineage hierarchy and stem-niche interactions at the single cell level.

Joo-Hyeon received a Wellcome Trust Sir Henry Dale Fellowship, an ERC starting grant, a Suh Kyoungbae Foundation Young Investigator award, and a Wellcome Senior Research Fellowship.



Wellcome Trust, Suh Kyungbae Foundation, BBSRC, AstraZeneca


Lee research

 Clonal expansion of lineage labelled progenitor cells in mouse lungs (Image credit: Catherine Dabrowska)  



What are the regulatory mechanisms that control homeostatic turnover, and how do their perturbation contribute to disease progression? The lung is a very slow cycling organ that is composed of diverse epithelial and stromal cell types, but has capacity to rapidly regenerate new cells after injury. Lee group is trying to understand how stem cells respond to different signals from their local environment and orchestrate the changes in chromatin, transcription, translation, and cellular dynamics in homeostasis and injury repair. We investigate the regulatory networks that need to be turned on and off at the right time and place for stem cells to become activated and generate specialised cell types during regeneration. We are also interested in defining cellular heterogeneity and plasticity during this process. Elucidating the normal process of lung dynamics will provide us a foundation to understand lung diseases and cancer. We couple ex vivo 3D organoid cultures of human and mouse lungs with genetic tools, in vivo transgenic mouse models with lineage tracing techniques, quantitative mathematic modelling of clonal dynamics, and bioinformatics at the single cell level.




Group Members

Frances England, JaeHak Bang, Erik Cardoso, Jakub Chundziak, Christopher Lambert, Minn-E Ng, Bumsoo Kim, Keat Ying Chan



If you are interested in working with us, please contact us at


Plain English

Our interest is focused on understanding how the diverse epithelial and stromal cells are maintained for a lifetime and regenerated following injury in the lungs. We study the regulatory mechanisms that balance stem cell maintenance and differentiation, and how their perturbation contribute to disease progression.


Key Publications


The Lee Group

Lee Group members: 

JaeHak Bang
Erik Cardoso
Keat Ying Chan 
Jakub Chudziak
Bumsoo Kim
Christopher Lambert
Minn-E Ng

If you are interested in working with the Lee Group, please contact