Xingqi Chen

Senior Lecturer/Associate Professor at Department of Immunology, Genetics and Pathology; Research programme: Molecular Tools and Functional Genomics; Research group Xingqi Chen

Telephone:
+46 18 471 40 72
E-mail:
xingqi.chen@igp.uu.se
Visiting address:
BMC, Husargatan 3
751 22 Uppsala
Postal address:
IGP / BMC
Box 815
751 08 Uppsala

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Short presentation

  • 2022,Nov-, Associate Professor, Uppsala University
  • 2019-2022, Assistant Professor, Uppsala University
  • 2015-2018, Postdoc, Stanford University
  • 2009-2014 PhD, Karolinska Institute

see more from: https://www.chenlabuppsala.com

Keywords

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

Biography

  • 2022,Nov-, Associate Professor, Uppsala University
  • 2019-2022, Assistant Professor, Uppsala University
  • 2015-2018, Postdoc, Stanford University
  • 2009-2014 PhD, Karolinska Institute

see more from: https://www.chenlabuppsala.com

Research

Research Focus

Research Overview

Recent advances in single-cell technologies—such as single-cell ATAC-seq and single-cell RNA-seq—have made it possible to explore cellular heterogeneity by profiling epigenetic, transcriptional, and protein-level information at single-cell resolution.

However, the analysis of a single molecular layer provides only a partial understanding of cellular identity. A cell’s state is determined by the complex interplay among the genome, epigenome, transcriptome, and proteome. To achieve a comprehensive understanding of cellular heterogeneity, our research aims to integrate multiple layers of molecular information—including nuclear architecture, epigenetics, transcriptomics, and proteomics—from the same individual cell, thereby reconstructing a detailed regulatory circuitry of cell function and fate.

The overarching goal of our research is to elucidate the mechanisms governing cell fate decisions during development and in human disease. We are developing state-of-the-art single-cell technologies to systematically characterize cellular heterogeneity and to identify the key regulatory factors that control specific cell fates.

A central question motivating our work is why cells in the human body, despite sharing an identical DNA sequence, adopt markedly different functional identities. For example, what determines why certain cells undergo malignant transformation while others remain normal? Similarly, what molecular mechanisms enable stem cells to differentiate into distinct cell types?

Our primary objective is to uncover the epigenetic mechanisms that regulate cell fate in the context of human disease. To address this, we pursue two major research directions:

  1. Deciphering the tumour microenvironment across multiple primary human cancer types using advanced single-cell technologies.
  2. Developing novel single-cell platforms to achieve deeper, more accurate, and multi-dimensional cellular analyses.

The insights generated from our research will provide a deeper understanding of cancer progression at the single-cell level and may contribute to the development of novel diagnostic tools and therapeutic strategies. Our long-term goal is to identify actionable molecular targets for precision cancer therapy.

Xingqi Chen

Publications

Selection of publications

Recent publications

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Articles, review/survey

Chapters in book

Manuscripts (preprints)