Selected Publications
See my CV for a full list of publications.
* Equal Contribution
2021
m6A RNA modifications are measured at single-base resolution across the mammalian transcriptome.
Hu L,$ Liu S$, Peng Y $, ..., Chen M*, Chen J*, He C*. Nature Biotechnology. 2021.
Effective and scalable single-cell data alignment with non-linear canonical correlation analysis.
Hu J, Chen M*, Zhou X*. Nucleic Acids Research. 2021.
2020
Demystifying "drop-outs" in single cell UMI data.
Kim T, Zhou X, Chen M. Genome Biology. 2020 August 06;21(196).
Integrative differential expression and gene set enrichment analysis using summary statistics for scRNA-Seq studies.
Ma Y, Sun S, Shang X, Keller E, Chen M, Zhou X. Nature Communications. 2020 March 27; 11(1585).
Alignment of single-cell RNA-seq samples without over-correction using density matching.
Chen M, Zhan Q, Mu Z, Wang L, Zheng Z, Miao J, Zhu P, Li IY. Genome Research. 2021 March 19. [bioRxiv]
2019
REPIC: A database for exploring N6-methyladenosine methylome.
Liu S, He C, Chen M. Genome Biology. 2020 April 28;21(1):100.
RADAR: Differential analysis of MeRIP-seq with a random effect model.
Zhang Z, Eckret MA, Zhu A, Chryplewicz A, De Jesus DF, Ren D, Kulkarni R, Lengyel E, He C, Chen M. Genome Biology. 2019, 20 (294).
m6A mRNA methylation regulates human β-cell biology in physiological states and in type 2 diabetes.
De Jesus DF, Zhang Z, Kahraman S, Brown NK, Chen M, Hu J, Gupta MK, He C, Kulkarni RN. Nature Metabolism. 2019 Aug;1(8):765-74.
2018
VIPER: variability-preserving imputation for accurate gene expression recovery in single-cell RNA sequencing studies.
Chen M , Zhou X: Genome Biology 2018, 19(1), 196.
The association between copy number aberration, DNA methylation and gene expression in tumor samples.
Sun W, Bunn P, Jin C, Little P, Zhabotynsky V, Perou CM, Hayes DN, Chen M, Lin DY: Nucleic Acids Research 2018, 46(6), 3009-3018.
Integrated RNA and DNA sequencing reveals early drivers of metastatic breast cancer.
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: The Journal of Clinical Investigation 2018, 128(4).
2017
Controlling for confounding effects in single cell RNA sequencing studies using both control and target genes.
Chen M, Zhou X: Scientific reports 2017, 7:13587.
Robust covariance matrix estimation via matrix depth.
Chen M, Gao C, Ren Z: The Annals of Statistics. [arXiv]
SynthEx: A Synthetic- normal based DNA sequencing tool for copy number alteration detection and tumor heterogeneity profiling.
*Silva G, *Siegel MB, Mose LE, Parker JS, Sun W, Perou CM, Chen M: Genome Biology 2017, 18(1), 66.
Genomic analysis of oesophageal squamous-cell carcinoma identifies alcohol drinking-related mutation signature and genomic alterations.
*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: Nature Communications 2017, 8, 15290.
2016
A general decision theory for Huber’s - contamination model.
Chen M, Gao C, Ren Z: Electronic Journal of Statistics. [arXiv]
Change point analysis of histone modifications reveals epigenetic blocks with distinct regulatory activity and biological functions.
Chen M, Lin H, Zhao H: The Annals of Applied Statistics. [arXiv][code]
2015
Estimating DNA methylation levels by joint modeling of multiple methylation profiles from microarray data.
Wang Tao, Chen M, Zhao H: Biometrics. [journal]
Posterior contraction rate of the phylogenetic Indian Buffet Processes.
Chen M, Gao C, Zhao H: Bayesian Analysis. [arXiv]
Asymptotic normal and efficient estimation of covariate- adjusted gaussian graphical model.
Chen M, Ren Z, Zhao H, Zhou H: Journal of the American Statistical Association. [arXiv]
Reassessment of Piwi binding to the genome and Piwi impact on RNA polymerase II distribution.
Lin H, Chen M, Kundaje A, Valouev A, Yin H, Liu N, Neuenkirchen N, Zhong M, Snyder M: Developmental Cell 2015, 32(6):772–774
2014 and before:
SomatiCA: identifying, characterizing and quantifying somatic copy number aberrations from cancer genome sequencing.
Chen M, Gunel M, Zhao H: PLoS ONE 2013, 8(11), e78143.
Detecting and understanding genetic and structural features in HIV-1 B subtype V3 underlying HIV-1 co-receptor usage.
Chen M, Svicher V, Artese A, Costa G, Alteri C, Ortuso F, Parrotta L, Liu Y, Liu C, Perno CF, et al.: Bioinformatics 2013, 29(4):451–460
Tdrkh is essential for spermatogenesis and participates in primary piRNA biogenesis in the germline.
Saxe JP, Chen M, Zhao H, Lin H: The EMBO journal 2013, 32:1869–1885
See my CV for a full list of publications.
* Equal Contribution
2021
m6A RNA modifications are measured at single-base resolution across the mammalian transcriptome.
Hu L,$ Liu S$, Peng Y $, ..., Chen M*, Chen J*, He C*. Nature Biotechnology. 2021.
Effective and scalable single-cell data alignment with non-linear canonical correlation analysis.
Hu J, Chen M*, Zhou X*. Nucleic Acids Research. 2021.
2020
Demystifying "drop-outs" in single cell UMI data.
Kim T, Zhou X, Chen M. Genome Biology. 2020 August 06;21(196).
Integrative differential expression and gene set enrichment analysis using summary statistics for scRNA-Seq studies.
Ma Y, Sun S, Shang X, Keller E, Chen M, Zhou X. Nature Communications. 2020 March 27; 11(1585).
Alignment of single-cell RNA-seq samples without over-correction using density matching.
Chen M, Zhan Q, Mu Z, Wang L, Zheng Z, Miao J, Zhu P, Li IY. Genome Research. 2021 March 19. [bioRxiv]
2019
REPIC: A database for exploring N6-methyladenosine methylome.
Liu S, He C, Chen M. Genome Biology. 2020 April 28;21(1):100.
RADAR: Differential analysis of MeRIP-seq with a random effect model.
Zhang Z, Eckret MA, Zhu A, Chryplewicz A, De Jesus DF, Ren D, Kulkarni R, Lengyel E, He C, Chen M. Genome Biology. 2019, 20 (294).
m6A mRNA methylation regulates human β-cell biology in physiological states and in type 2 diabetes.
De Jesus DF, Zhang Z, Kahraman S, Brown NK, Chen M, Hu J, Gupta MK, He C, Kulkarni RN. Nature Metabolism. 2019 Aug;1(8):765-74.
2018
VIPER: variability-preserving imputation for accurate gene expression recovery in single-cell RNA sequencing studies.
Chen M , Zhou X: Genome Biology 2018, 19(1), 196.
The association between copy number aberration, DNA methylation and gene expression in tumor samples.
Sun W, Bunn P, Jin C, Little P, Zhabotynsky V, Perou CM, Hayes DN, Chen M, Lin DY: Nucleic Acids Research 2018, 46(6), 3009-3018.
Integrated RNA and DNA sequencing reveals early drivers of metastatic breast cancer.
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: The Journal of Clinical Investigation 2018, 128(4).
2017
Controlling for confounding effects in single cell RNA sequencing studies using both control and target genes.
Chen M, Zhou X: Scientific reports 2017, 7:13587.
Robust covariance matrix estimation via matrix depth.
Chen M, Gao C, Ren Z: The Annals of Statistics. [arXiv]
SynthEx: A Synthetic- normal based DNA sequencing tool for copy number alteration detection and tumor heterogeneity profiling.
*Silva G, *Siegel MB, Mose LE, Parker JS, Sun W, Perou CM, Chen M: Genome Biology 2017, 18(1), 66.
Genomic analysis of oesophageal squamous-cell carcinoma identifies alcohol drinking-related mutation signature and genomic alterations.
*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: Nature Communications 2017, 8, 15290.
2016
A general decision theory for Huber’s - contamination model.
Chen M, Gao C, Ren Z: Electronic Journal of Statistics. [arXiv]
Change point analysis of histone modifications reveals epigenetic blocks with distinct regulatory activity and biological functions.
Chen M, Lin H, Zhao H: The Annals of Applied Statistics. [arXiv][code]
2015
Estimating DNA methylation levels by joint modeling of multiple methylation profiles from microarray data.
Wang Tao, Chen M, Zhao H: Biometrics. [journal]
Posterior contraction rate of the phylogenetic Indian Buffet Processes.
Chen M, Gao C, Zhao H: Bayesian Analysis. [arXiv]
Asymptotic normal and efficient estimation of covariate- adjusted gaussian graphical model.
Chen M, Ren Z, Zhao H, Zhou H: Journal of the American Statistical Association. [arXiv]
Reassessment of Piwi binding to the genome and Piwi impact on RNA polymerase II distribution.
Lin H, Chen M, Kundaje A, Valouev A, Yin H, Liu N, Neuenkirchen N, Zhong M, Snyder M: Developmental Cell 2015, 32(6):772–774
2014 and before:
SomatiCA: identifying, characterizing and quantifying somatic copy number aberrations from cancer genome sequencing.
Chen M, Gunel M, Zhao H: PLoS ONE 2013, 8(11), e78143.
Detecting and understanding genetic and structural features in HIV-1 B subtype V3 underlying HIV-1 co-receptor usage.
Chen M, Svicher V, Artese A, Costa G, Alteri C, Ortuso F, Parrotta L, Liu Y, Liu C, Perno CF, et al.: Bioinformatics 2013, 29(4):451–460
Tdrkh is essential for spermatogenesis and participates in primary piRNA biogenesis in the germline.
Saxe JP, Chen M, Zhao H, Lin H: The EMBO journal 2013, 32:1869–1885
