Mengjiechen.com Website Review

Publication - Mengjie Chen --- University of Chicago

Not defined

SELECTED PUBLICATIONS​See my CV for a full list of publications. * Equal Contribution201816. Chen M, Zhou X: VIPER: variability-preserving imputation for accurate gene expression recovery in single-cell RNA sequencing studies. Genome Biology 2018. [journal]15. Sun W, Bunn P, Jin C, Little P, Zhabotynsky V, Perou CM, Hayes DN, Chen M, Lin DY: The ociation between copy number aberration, DNA methylation and gene expression in tumor samples. Nucleic Acids Research 2018. [journal]14. Siegel MB, He X, Hoadley KA, Hoyle A, Pearce JB, Garrett AL, Kumar S, Moylan VJ, Brady CM, Van Swearingen AE, Marron D, Gupta GP, Thorne LB, Kieran N, Livasy C, Mardis ER, Parker JS, Chen M, Anders CK, Carey LA, Perou CM: Integrated RNA and DNA sequencing reveals early drivers of metastatic breast cancer. The Journal of Clinical Investigation 2018, 128(4). [journal]201713. Chen M, Zhou X: Controlling for Confounding Effects in Single Cell RNA Sequencing Studies Using both Control and Target Genes. Scientific reports 2017, 7:13587. [journal]12. Chen M, Gao C, Ren Z: Robust Covariance Matrix Estimation via Matrix Depth. The Annals of Statistics  2017. [arXiv]11. *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 2017  [journal]10. *Chang J, *Tan W, *Lin Z, *Xi R, *Shao M, *Chen M, Luo Y, Zhao Y, Liu Y, Huang X, Xia Y, 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: Genomic ysis of oesophageal squamous-cell carcinoma identifies alcohol drinking-related mutation signature and genomic alterations Nature communications [journal] 201720169. Chen M, Gao C, Ren Z: A General Decision Theory for Huber’s -Contamination Model. Electronic Journal of Statistics 2016 [arXiv]  8. Chen M, Lin H, Zhao H: Change point ysis of histone modifications reveals epigenetic blocks with distinct regulatory activity and biological functions. The Annals of Applied Statistics. 2016. [arXiv][code]20157. Wang Tao, Chen M, Zhao H: Estimating DNA methylation levels by joint modeling of multiple methylation profiles from microarray data. Biometrics. 2015 [journal]6. Chen M, Gao C, Zhao H: Posterior contraction rate of the Phylogenetic Indian Buffet Processes. Bayesian ysis. 2015 [arXiv]5. Chen M, Ren Z, Zhao H, Zhou H: Asymptotic normal and efficient estimation of covariate- adjusted gaussian graphical model. Journal of the American Statistical ociation 2015 [arXiv]4. Lin H, Chen M, Kundaje A, Valouev A, Yin H, Liu N, Neuenkirchen N, Zhong M, Snyder M: Re essment of Piwi Binding to the Genome and Piwi Impact on RNA Polymerase II Distribution. Developmental Cell 2015, 32(6):772–7742014 and before:3. Chen M, Gunel M, Zhao H: SomatiCA: identifying, characterizing and quantifying somatic copy number aberrations from cancer genome sequencing. PLoS ONE 2013 [journal]2. Chen M, Svicher V, Artese A, Costa G, Alteri C, Ortuso F, Parrotta L, Liu Y, Liu C, Perno CF, et al.: Detecting and understanding genetic and structural features in HIV-1 B subtype V3 underlying HIV-1 co-receptor usage. Bioinformatics 2013, 29(4):451–460 [journal] [pdf]1. Saxe JP, Chen M, Zhao H, Lin H: Tdrkh is essential for spermatogenesis and participates 
in primary piRNA biogenesis in the germline. The EMBO journal 2013, 32:1869–1885 [journal] [pdf]

Software - Mengjie Chen --- University of Chicago

Not defined

My Github page: https://github.com/chenmengjieVIPER: Variability-preserving imputation for single-cell RNA-seq [Github]SynthEx: A comprehensive suite of tools for CNA detection and tumor heterogeneity profiling [Github]Citrus:A toolkit for single cell sequencing ysis [Github]Click here for more detailsANTAC: Asymptotic normal estimation of covariate-adjusted gaussian graphical model [Source]                  Click here for more detailsSomatiCA:Identifying, characterizing and quantifying somatic copy number aberrations from cancer genome sequencing [Bioconductor]Click here for more detailsBCP-mixture:A Bayesian change point method for epigenetic block identification [Source]Click here for more detailsMBAmethyl:Model-based ysis of DNA methylation data [Bioconductor]

Interests - Mengjie Chen --- University of Chicago

Not defined

links - Mengjie Chen --- University of Chicago

Not defined