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Mengjie Chen

TitleAssistant Professor
InstitutionUniversity of Chicago
DepartmentMedicine-Genetic Medicine
AddressChicago IL 60637
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    Collapse Overview 
    Collapse overview
    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.


    Collapse Biography 
    Collapse education and training
    Yale University, New Haven, CT, USAPhD05/2014Computational Biology
    Collapse awards and honors
    2015 Junior Faculty Development Award, University of North Carolina - Chapel Hill
    2014Student Marshal, Yale Graduate School of Arts and Sciences
    2009 - 2012China Scholarship Council-Yale World Scholarship, Yale University
    2007 - 2008National Scholarship, HUST, China

    Collapse ORNG Applications 
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    Collapse Research 
    Collapse research activities and funding
    1R01GM126553-01     (Mengjie Chen)Aug 1, 2017 - May 31, 2022
    NIH/NIGMS
    COLLABORATIVE RESEARCH: ADVANCED STATISTICAL METHODS FOR SINGLE CELL RNA SEQUENCING STUDIES
    Role Description: Single cell RNA sequencing has emerged as a powerful tool in genomics. The technology is essential for understanding the heterogeneity of tissue compositions and the genetic architecture of complex traits and diseases. This project aims to develop new methods to address statistical and computational challenges in scRNAseq data analysis and facilitate the usage of scRNAseq technology.
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
    List All   |   Timeline
    1. Chen M, Zhou X. VIPER: variability-preserving imputation for accurate gene expression recovery in single-cell RNA sequencing studies. Genome Biol. 2018 11 12; 19(1):196. PMID: 30419955.
      View in: PubMed
    2. Chen M, Zhou X. Controlling for Confounding Effects in Single Cell RNA Sequencing Studies Using both Control and Target Genes. Sci Rep. 2017 10 19; 7(1):13587. PMID: 29051597.
      View in: PubMed
    3. Chang J, Tan W, Ling Z, Xi R, Shao M, Chen M, Luo Y, Zhao Y, Liu Y, Huang X, Xia Y, Hu J, Parker JS, Marron D, Cui Q, Peng L, Chu J, Li H, Du Z, Han Y, Tan W, Liu Z, Zhan Q, Li Y, Mao W, Wu C, Lin D. Genomic analysis of oesophageal squamous-cell carcinoma identifies alcohol drinking-related mutation signature and genomic alterations. Nat Commun. 2017 05 26; 8:15290. PMID: 28548104.
      View in: PubMed
    4. Silva GO, 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 profiling. Genome Biol. 2017 04 08; 18(1):66. PMID: 28390427.
      View in: PubMed
    5. Dinh TA, Vitucci EC, Wauthier E, Graham RP, Pitman WA, Oikawa T, Chen M, Silva GO, Greene KG, Torbenson MS, Reid LM, Sethupathy P. Comprehensive analysis of The Cancer Genome Atlas reveals a unique gene and non-coding RNA signature of fibrolamellar carcinoma. Sci Rep. 2017 03 17; 7:44653. PMID: 28304380.
      View in: PubMed
    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 discordance in breast cancer biomarker classification. Breast Cancer Res. 2016 06 28; 18(1):68. PMID: 27349894.
      View in: PubMed
    7. Chen M, Ren Z, Zhao H, Zhou H. Asymptotically Normal and Efficient Estimation of Covariate-Adjusted Gaussian Graphical Model. J Am Stat Assoc. 2016 Mar; 111(513):394-406. PMID: 27499564.
      View in: PubMed
    8. Chen M, Lin H, Zhao H. CHANGE POINT ANALYSIS OF HISTONE MODIFICATIONS REVEALS EPIGENETIC BLOCKS LINKING TO PHYSICAL DOMAINS. Ann Appl Stat. 2016 Mar; 10(1):506-526. PMID: 27231496.
      View in: PubMed
    9. Wang X, Chen M, Yu X, Pornputtapong N, Chen H, Zhang NR, Powers RS, Krauthammer M. Global copy number profiling of cancer genomes. Bioinformatics. 2016 03 15; 32(6):926-8. PMID: 26576652.
      View in: PubMed
    10. Xu Z, Zhang G, Jin F, Chen M, Furey TS, Sullivan PF, Qin Z, Hu M, Li Y. A hidden Markov random field-based Bayesian method for the detection of long-range chromosomal interactions in Hi-C data. Bioinformatics. 2016 03 01; 32(5):650-6. PMID: 26543175.
      View in: PubMed
    11. Wang T, Chen M, Zhao H. Estimating DNA methylation levels by joint modeling of multiple methylation profiles from microarray data. Biometrics. 2016 06; 72(2):354-63. PMID: 26433612.
      View in: PubMed
    12. Chen M, Gao C, Zhao H. Posterior Contraction Rates of the Phylogenetic Indian Buffet Processes. Bayesian Anal. 2016 Jun; 11(2):477-497. PMID: 27087886.
      View in: PubMed
    13. Lin H, Chen M, Kundaje A, Valouev A, Yin H, Liu N, Neuenkirchen N, Zhong M, Snyder M. Reassessment of Piwi binding to the genome and Piwi impact on RNA polymerase II distribution. Dev Cell. 2015 Mar 23; 32(6):772-4. PMID: 25805139.
      View in: PubMed
    14. Huang KC, Sun W, Wu Y, Chen M, Mohlke KL, Lange LA, Li Y. Association studies with imputed variants using expectation-maximization likelihood-ratio tests. PLoS One. 2014; 9(11):e110679. PMID: 25383782.
      View in: PubMed
    15. Chen M, Yang C, Li C, Hou L, Chen X, Zhao H. Admixture mapping analysis in the context of GWAS with GAW18 data. BMC Proc. 2014; 8(Suppl 1):S3. PMID: 25519317.
      View in: PubMed
    16. Li C, Yang C, Chen M, Chen X, Hou L, Zhao H. Adjustment of familial relatedness in association test for rare variants. BMC Proc. 2014; 8(Suppl 1 Genetic Analysis Workshop 18Vanessa Olmo):S39. PMID: 25519384.
      View in: PubMed
    17. Yang C, Li C, Chen M, Chen X, Hou L, Zhao H. A penalized linear mixed model for genomic prediction using pedigree structures. BMC Proc. 2014; 8(Suppl 1 Genetic Analysis Workshop 18Vanessa Olmo):S67. PMID: 25519399.
      View in: PubMed
    18. Zhu Y, Watson J, Chen M, Shen DR, Yarde M, Agler M, Burford N, Alt A, Jayachandra S, Cvijic ME, Zhang L, Dyckman A, Xie J, O'Connell J, Banks M, Weston A. Integrating High-Content Analysis into a Multiplexed Screening Approach to Identify and Characterize GPCR Agonists. J Biomol Screen. 2014 Aug; 19(7):1079-89. PMID: 24789006.
      View in: PubMed
    19. Chen M, Gunel M, Zhao H. SomatiCA: identifying, characterizing and quantifying somatic copy number aberrations from cancer genome sequencing data. PLoS One. 2013; 8(11):e78143. PMID: 24265680.
      View in: PubMed
    20. Saxe JP, Chen M, Zhao H, Lin H. Tdrkh is essential for spermatogenesis and participates in primary piRNA biogenesis in the germline. EMBO J. 2013 Jul 03; 32(13):1869-85. PMID: 23714778.
      View in: PubMed
    21. Chen M, Svicher V, Artese A, Costa G, Alteri C, Ortuso F, Parrotta L, Liu Y, Liu C, Perno CF, Alcaro S, Zhang J. Detecting and understanding genetic and structural features in HIV-1 B subtype V3 underlying HIV-1 co-receptor usage. Bioinformatics. 2013 Feb 15; 29(4):451-60. PMID: 23297034.
      View in: PubMed
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