The focus of our work is to understand cell fate decisions during development and human disease. We are developing state-of-art single-cell technologies to characterize cell heterogeneity in a systematic manner and to identify key players involved in controlling specific cell fates.

In our group, we are fascinated by why cells in our body contain the exact same DNA sequence but turn into different fates. For instance, what is it that makes some cells in human bodies become cancer and not others? And how can stem cells differentiate into totally different cell types?


Our main aim is to understand the role of epigenetics in controlling cell fate in human disease and we have adopted two main approaches to accomplish this:

  1. Deciphering the tumour microenvironment across multiple primary clinical cancer types with single-cell technologies.

  2. Developing start-of-art single-cell technologies.


The insight from our research could give us better knowledge of cancer progression at the single-cell level, and provide a potential clinical diagnosis toolkit. A long-term goal is to reveal a target for cancer therapy.

Characterising multi-layers of information in single cells


The recent advance in single-cell technologies (e.g, single-cell ATAC-seq and single-cell RNA-seq) has made it possible to understand the cell heterogeneity by characterizing epigenetics, transcription or protein expression in the single cell.


However, sampling of just one molecular type from individual cells provides an incomplete picture since a cell’s state is determined by the complex interplay of molecules within its genome, epigenetics, transcriptome and proteome. To completely understand cell heterogeneity, we need to characterize multi-layers of information, including nucleus architecture, epigenetics, transcriptome and protein expression, as a circuitry loop from the exact same cell. 


My previous work has focused on single-cell technology development and I have invented Assay of Transposase Accessible Chromatin-with visualization (ATAC-see) and protein index single-cell ATAC-seq (pi-ATAC). Both technologies are single-cell technologies and can be used to analyse multi-layers of cell features at the same time either in vitro or in situ. These will now be employed in my planned projects.



We aim to build up a multidisciplinary research team and are looking for highly motivated master students, PhD students and postdoc researches with an interest in single-cell biology.

Please contact xingqi.chen@igp.uu.se 

if you are interested.



Xingqi Chen, PhD

Assistant professor, Group leader

email: xingqi.chen@igp.uu.se

Department of Immunology,  Genetics and Pathology, Uppsala University,  Sweden