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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:
 
​   
  • 08/31/20         Welcome, Arpit Panda, a MSTP student, to join us for a rotation. 
  • 08/28/20         Tae moved to Microsoft! Farewell and best wishes! 
  • 07/20/20         Welcome, Allison Rodas, a first-year from the College, to join us for summer research with a Presidents' Scholarship.
  • 07/17/20         Tae successfully defended her PhD thesis! Congratulations! 
  • 07/13/20         Tae's HIPPO paper has been accepted in Genome Biology. Perfectly done!
  • 06/26/20         We received an NSF DMS award to work on statistical methods for intra-tumor heterogeneity studies. 
  • 04/20/20         Welcome, Shuwen Fang, a sophomore from the College, to our lab!​
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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