Xingqi Chen, PhD

Assistant professor, Group leader

Department of Immunology, Genetics and Pathology,

Uppsala University, Sweden

Hi, this is Xingqi Chen

I was trained as a chromatin biologist in both of my PhD (Karolinska Institutet) and postdoc (Stanford University). I am fascinated why cells in our body contain the exact same DNA sequence but turn into different fates,  e.g, some cells in the human bodies become cancer not the others; stem cells could differentiate into totally different cell types.


The recent advance in single-cell technologies ( e.g, single-cell ATAC-seq and single-cell RNA-seq)made it possible to understand the cell heterogeneity by characterizing the epigenetics, transcription or protein expression in the single cell, but the sampling of just one molecular type from individual cells provides incomplete picture since a cell’s state is determined by the complex interplay of molecules within its genome, epigenetics, transcriptome and proteome. At the same time, increasing evidence has shown the spatial information of DNA sequences in the nucleus, and a complex interplay of the genome with specific features of the nuclear architecture are tightly linked to gene expression, replication and DNA repair. To completely understand the cell heterogeneity, we need to characterize multi-layers information, including nucleus architecture, epigenetics, transcriptome and protein expression, as a circuitry loop from the exact same cell.

During my postdoc training at Stanford, I had focused on single-cell technology development, had invented Assay of  Transposase  Accessible  Chromatin-with visualization (ATAC-see, Nature Methods, 2016,  PMID:27749837) and co-invented protein index single-cell ATAC-seq (pi-ATAC, Nature Communications, PMID: 30389926, 2018). Both technologies are single-cell technologies and could be used to understand the chromatin structure at the single-cell level. 

I moved from Stanford university to Sweden at the end of 2018 and was awarded assistant professor position with tenure track from Uppsala University. In my own group, I would like to understand the cell fate decision during the development and human disease, where we are developing state-of-art single-cell technologies to characterize the cell heterogeneity in a systematic manner and identify the key players of controlling the specific cell fates during development and human disease.