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.

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Recent News:
 ​ 

• 06/03/23         Alvin and Carisa graduated from college. Farewell and best wishes!
• 05/17/23         We receive a new R01 from NHGRI in title of "Develop new bioinformatics infrastructures and computational tools for epitranscriptomics data".
• 05/16/23        Dr. Lei Zheng joined the lab as a postdoc, jointly with Dr. Chuan He' lab. Welcome!
• 04/30/23         Yifan's work with Dr. Xin He on factor models has been accepted to Nature Methods. 
• 04/16/23        We received a pilot award from the Diabetes Research and Training Center. 
• 12/08/22         Welcome, Kathryn Li, an undergraduate student,  to join us for research in single cell prediXcan.  
• 10/26/22         Welcome, Yiwei Ding, a graduate student from Chemistry, to join us for a rotation. 
• 10/18/22         Our first HCA paper with Dr. Ernst Lengyel's team has been accepted to Cell Reports. ​
• 10/14/22         Welcome, Alvin Zhang, an undergraduate student in Biology and Statistics, to join us for research in single cell genomics.  
• 09/23/22         Shun Liu's work with Dr. Weixin Tang's Lab on eTAM-seq has been accepted to Nature Biotechnology. ​Nicely done!
• 08/25/22         Welcome, Nick Feng, a master student from Biomedical informatics, to join us as a research assistant. 
• 06/13/22         Welcome, Carisa Zeng, an undergraduate student,  to join us with support from the BSCD Quantitative Biology summer fellowship.  She will work on cell free DNA methylation for her thesis.
• 06/08/22         We received a Breast Cancer SPORE Developmental Research grant to collect more spatial transcriptomics data.   
• 06/01/22         Yifan graduated and moved to GRAIL. Farewell and best wishes!
• 10/28/21         Shun Liu and Yong Peng's work with Lulu on SAC-seq has been accepted to Nature Biotechnology. ​Nice job!​​

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