Mengjie Chen
Title | Assistant Professor |
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Institution | University of Chicago |
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Department | Medicine-Genetic Medicine |
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Address | Chicago IL 60637
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Email |  |
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vCard | Download vCard |
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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.
Biography Yale University, New Haven, CT, USA | PhD | 05/2014 | Computational Biology |
2015 | Junior Faculty Development Award, University of North Carolina - Chapel Hill | 2014 | Student Marshal, Yale Graduate School of Arts and Sciences | 2009 - 2012 | China Scholarship Council-Yale World Scholarship, Yale University | 2007 - 2008 | National Scholarship, HUST, China |
ORNG Applications Research 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 |
Bibliographic
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
This graph shows the total number of publications by year, by first, middle/unknown, or last author.
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Year | Publications |
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2013 | 3 | 2014 | 5 | 2015 | 5 | 2016 | 3 | 2017 | 4 | 2018 | 1 |
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