Xingqi Chen

biträdande universitetslektor vid Institutionen för immunologi, genetik och patologi, Molekylära verktyg; Forskargrupp Xingqi Chen

018-471 4072
BMC, Husargatan 3
751 22 Uppsala
Box 815
751 08 Uppsala

Nyckelord: epigenetics gene expression single cell atac-seq chromatin biology atac-seq single cell biology functional genomics

Mina kurser


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Higher education degrees:

  • 2009-2014 PhD degree in medical science, Karolinska Institute, Sweden

Postdoctoral positions:

  • March 2015- Dec 2018, Postdoc researcher in Dr. Howard Chang’s group at Stanford University


more detail see the group link:

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. To completely understand the cell heterogeneity, we need characterize multi-layers information, including nucleus architecture, epigenetics, transcriptome and protein expression, as a circuitry loop from the exactly same cell.

We had focused on single cell technology development in the past, had invented Assay of Transposase Accessible Chromatin-with visualization (ATAC-see, Chen, X et al, Nature Methods, PMID: 27749837, 2016) and protein index single cell ATAC-seq (pi-ATAC, Chen, X et al, Nature Communications, PMID: 30389926, 2018). Both technologies are single cell technologiesand could be used to analyze multi-layers of cell features at the same time either in vitro or in situ.

In our group, we arefascinated why cells in our body contain the exactly 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. We are aiming to understand the role of epigenetic in control the cell fate in human disease by 1)deciphering the tumor microenvironment across multiple primary clinical cancer types with single cell technologies and 2) developing the start-of-art single cell technologies. The insight from our research could give us better knowledge of cancer progression at single cell level, and provide a potential clinical diagnosis toolkit, and reveal a target for cancer therapy in the long term.


We aim to build up multidisciplinary research team and are looking for highly motivated Master students, PhD students and Postdoc researches, who are interested in single cell biology. The Ad-hoc applications are welcome. Please e-mail to Xingqi:


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