Mengjie Chen, Ph.D.

Assistant Professor of Medicine

Office: KCBD 3220A
Telephone number: 773-834-3175

My primary research is driven by the need for powerful statistical methods to address the challenges those technologies have posed for data analysis and interpretation, particularly for data emerging from biological and biomedical studies, such as epigenetic and cancer genomics related research. I have developed novel methodologies for a variety of problems, including change point detection methods for identifying somatic copy number aberration, nonparametric Bayesian methods to integrate the heterogeneity in somatic mutations into gene expression analysis, Gaussian graphical models for eQTL analysis and methods for the analysis of single cell sequencing data. My ultimate goal is to develop methods that can integrate genomic features into the prediction of clinical outcomes, which will potentially shed new lights on personalized disease diagnosis and prognosis.

JOURNAL PUBLICATIONS

 

* Joint 1st author

1. *Silva G, *Siegel MB, Mose LE, Parker JS, Sun W, Perou CM, Chen M: SynthEx: A Synthetic-normal based DNA sequencing tool for copy number alteration detection and tumor heterogeneity proling. Genome Biology (Accepted) 2017

2. *Chang J, *Tan W, *Lin Z, *Xi R, *Shao M, *Chen M, Luo Y, Zhao Y, Liu Y, Huang X, XiaY, Hu J, Parker J, Marron D, Cui Q, Peng L, Chu J, Li H, Du Z, Han Y, Tan W, Liu Z, Zhan Q, Li YL, Mao W, Wu C, Lin D: Comprehensive analysis of esophageal squamous-cell carcinoma identies alcohol drinking-related mutation signature and novel genomic alterations. Nature communications (Accepted) 2017

3. Dinh T, Vitucci EC, Wauthier E, Graham PR, Oikawa T, Chen M, Silva OG, Greene GK, Tor-benson M, Reid LM, Sethupathy P: Comprehensive analysis of The Cancer Genome Atlas reveals a unique, predictive gene and non-coding RNA signature of brolamellar carcinoma. Scientic Report (To appear) 2017

4. Chen M, Gao C, Ren Z: A General Decision Theory for Huber's -Contamination Model. Electronic Journal of Statistics (To appear) 2016

5. Wang T, Chen M, Zhao H, Zhu L: Model-free dimension reduction and variable selection for general regression in high dimensions. Statistics and computing (Accepted) 2016

6. Allott EH, Geradts J, Sun X, Cohen SM, Zirpoli GR, Khoury T, Bshara W, Chen M, Sherman ME, Palmer JR, Ambrosone CB, Olshan AF, Troester MA: Intratumoral heterogeneity as a source of inter-laboratory disagreement in breast cancer biomarker classication. Breast Cancer Research (To appear) 2016

7. Chen M, Lin H, Zhao H: Change point analysis of histone modications reveals epigenetic blocks with distinct regulatory activity and biological functions. Annals of Applied Statistics 2016, 10:506{526}

8. Wang X, Chen M, Yu X, Pornputtapong N, Chen H, Zhang NR, Powers S, Krauthammer M: Global copy number proling of cancer genomes. Bioinformatics 2016, 32(6):926{928}

9. Xu Z, Zhang G, Jin F, Chen M, Furey TS, Sullivan PF, Qin Z, Hu M, Li Y: A hidden Markov random eld based Bayesian method for the detection of long-range chromosomal interactions in Hi-C Data. Bioinformatics 2015

10. Wang T, Chen M, Zhao H: Estimating DNA methylation levels by joint modeling of multiple methylation proles from microarray data. Biometrics 2015 (In print), URL [http://dx.doi.org/10.1111/biom.12422]