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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

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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

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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

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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:
 
​ 
  • 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 Li'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!
  • 01/03/22         Welcome, Saideep Gona, a GGSB student, to join us for a rotation. 
  • 10/28/21         Shun Li and Yong Peng's work with Lulu on SAC-seq has been accepted to Nature Biotechnology. ​Nice job!
  • 09/16/21         We received an NHGRI R01 award to work on statistical methods for spatial transcriptomics data. ​
Previous News

Location

Chen Group

Section of Genetic Medicine
​University of Chicago​
5841 S. Maryland Ave N417A
Chicago, IL 60637 USA
Tel: 773-834-3175 
Email: mengjiechen@uchicago.edu

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