Welcome to Chen Group at U Chicago!

Computational and statistical genomics

Our research group develop computational and statistical tools to address the challenges high-throughput genomics technologies have posed for data analysis and interpretation, particularly for data emerging from biomedical studies.

Single cell genomics

Most of our work focuses on accounting for unwanted variation due to technical artifacts from single cell experiments. Completed and ongoing projects include developing methods to:  

• control for confounding effects for accurate downstream analysis
• preserve gene expression variability across cells after accounting for drop-out and imputing
• align single-cell RNA-seq samples across experiments enabling integrative and comparative analyses. 

Epitranscriptomics

The paradigm-shifting discoveries in RNA modifications have added RNA to the picture of dynamic regulation of gene expression through reversible chemical modifications. Successful transcriptome wide profiling of RNA modifications can significantly advance the frontier of epitranscriptomics research and associate epitranscriptomic variations with human health and diseases. We are developing methods for the following topics:

• Differential methylation analysis
• Integrative analysis of m6A modifications with ENCODE/Roadmap data.​

Cancer genomics

The cancer genome is characterized by genetic heterogeneity that is seen across tumor types, among samples of a particular type (inter-tumor heterogeneity) and within an individual tumor (intratumor heterogeneity). Understanding tumor heterogeneity is a prerequisite for personalized tumor diagnosis and treatment. We are developing methods for integrative tumor heterogeneity analysis using both single cell RNA sequencing and bulk tissue DNA sequencing data.

         Sounds interesting?

We welcome U Chicago students ​from the following programs (but not limited to): Human Genetics, GGSB, Statistics, Data Science and Biophysics. Postdoc positions are also available.

Apply Now

Recent News:
 ​ 

• ​03/28/25        Haoye Yang from Human Genetics started his rotation in the lab. Welcome!
• 03/28/25        Jiannan Rui will join Biostatistics as a PhD student. Congratulations!

• ​11/04/24        Linzhe Teng, a master student from Statistics, joined the lab. Welcome!
• 11/04/24        Chih-Hsuan graduated and joined St Jude children's research hospital as a biostatistician. Farewell and best wishes!
• 09/19/24        Peihong Zhang joined the lab as a joint postdoc with Dr. Chuan He. Welcome!
• 09/09/24        Gu Wang, a master student from NUS, started his visiting quarter at U Chicago.  Welcome!
• 08/12/24        Shun will start his own lab at Sun Yet-Sen Memorial Hospital! Farewell and best wishes!
• 07/31/24        Ken Chen joined the lab as a joint postdoc with Dr. Chuan He.  Welcome!
• 06/15/24         Xiaoyang will start her own lab at Chinese Academy of Science Center for Excellence in Molecular Cell Science! Best wishes!
• 06/05/24        Jianan Rui, a master student from Statistics, joined the lab. Welcome!
• 01/24/24         Yang Li  from PME formally joined the lab. Welcome!
• 09/22/23         Yang Li from PME joined the lab as a rotation student . Welcome!
• 07/11/23         Zhiwei Jiang joined the lab from Chemistry. Welcome!
• 06/07/23         Xiaoyang's paper on RBFOX2 has been accepted to Nature Cell Biology. ​Good job!​​​​​

Previous News