Publications by Year
* Equal Contribution
2022
m6A RNA modifications are measured at single-base resolution across the mammalian transcriptome.
Hu L, Liu S, Peng Y, …, Chen M*, Chen J*, Chuan He*: Nature Biotechnology. (2022): 1-10. [link]
KAS-seq: genome-wide sequencing of single-stranded DNA by N3-kethoxal-assisted labeling.
Lyu R, Wu T, Zhu A, West-Szymanski D, Weng X, Chen M and He C: Nature Protocols. (2022): 1-19. [link]
Genomic and transcriptomic changes induced by neoadjuvant chemotherapy in ovarian cancer.
Javellana M, Eckert MA, Heide J, Zawieracz K, Weigert M, Ashley S, Stock E, Chapel D, Huang L, Yamada SD, Ahmed AA., Lastra R, Chen M, and Lengyel E: Cancer Research. 2022. 82(1), 169-176. [link]
2021
Effective and scalable single-cell data alignment with non-linear canonical correlation analysis.
Hu J, Chen M*, Zhou X*: Nucleic Acids Research. 2021. Dec 6. [link] [software]
Whole-genome Analysis of Nigerian Patients with Breast Cancer Reveals Ethnic-driven Somatic Evolution and Distinct Genomic Subtypes.
Ansari-Pour N et al, …, Chen M, … and Olopade O: Nature Communications. 2021. Nov 26;12(1):1-5. [link]
Alignment of single-cell RNA-seq samples without overcorrection using kernel density matching.
Chen M, Zhan Q, Mu Z, Wang L, Zhu P and Li Y: Genome Research. 2021 March 19, doi:10.1101/gr.261115.120 [link][software]
Cell Type Aware analysis of RNA-seq data (CARseq) reveals difference and similarities of the molecular mechanisms of Schizophrenia and Autism.
Jin C, Chen M, Lin D and Sun W: Nature Computational Science. 2021 April, 1(4):1-9 [link][software]
Extensive pleiotropism and allelic heterogeneity mediate metabolic effects of IRX3 and IRX5.
Sobreira D, Joslin AC, Zhan Q, …, Chen M, Aneas I, Nóbrega MA: Science. 372.6546 (2021): 1085-1091. [link]
2020
Integrative Differential Expression and Gene Set Enrichment Analysis for Single Cell RNA-seq Studies.
Sun S, Ying M, Shang X, Keller E, Chen M and Zhou X: Nature Communications. 2020 Mar 27;11(1):1585. [link][software]
REPIC: A database for exploring N6-methyladenosine methylome.
Liu S, He C and Chen M: Genome Biology. 2020 Apr 28;21(1):100 [link][website]
Allele-specific open chromatin in human iPSC neurons elucidates functional noncoding disease variants.
Zhang S, Zhang H, Zhou Y, Qiao M, Zhao S, Kozlova A, Shi J, Sanders A, Wang G, Luo K, Sengupta S, West S, Qian S, Strait M, Avramopoulos D, Cowan C, Chen M, Pang Z, Gejman P, He X, and Duan J: Science. 2020, Jul 31, 369(6503): 561-565 [link]
Demystifying "drop-outs" in single cell UMI data.
Kim T, Zhou X* and Chen M*: Genome Biology. 2020 Aug 06, 21(196) [link][software]
Selected work before 2020
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
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
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
* Equal Contribution
2022
m6A RNA modifications are measured at single-base resolution across the mammalian transcriptome.
Hu L, Liu S, Peng Y, …, Chen M*, Chen J*, Chuan He*: Nature Biotechnology. (2022): 1-10. [link]
KAS-seq: genome-wide sequencing of single-stranded DNA by N3-kethoxal-assisted labeling.
Lyu R, Wu T, Zhu A, West-Szymanski D, Weng X, Chen M and He C: Nature Protocols. (2022): 1-19. [link]
Genomic and transcriptomic changes induced by neoadjuvant chemotherapy in ovarian cancer.
Javellana M, Eckert MA, Heide J, Zawieracz K, Weigert M, Ashley S, Stock E, Chapel D, Huang L, Yamada SD, Ahmed AA., Lastra R, Chen M, and Lengyel E: Cancer Research. 2022. 82(1), 169-176. [link]
2021
Effective and scalable single-cell data alignment with non-linear canonical correlation analysis.
Hu J, Chen M*, Zhou X*: Nucleic Acids Research. 2021. Dec 6. [link] [software]
Whole-genome Analysis of Nigerian Patients with Breast Cancer Reveals Ethnic-driven Somatic Evolution and Distinct Genomic Subtypes.
Ansari-Pour N et al, …, Chen M, … and Olopade O: Nature Communications. 2021. Nov 26;12(1):1-5. [link]
Alignment of single-cell RNA-seq samples without overcorrection using kernel density matching.
Chen M, Zhan Q, Mu Z, Wang L, Zhu P and Li Y: Genome Research. 2021 March 19, doi:10.1101/gr.261115.120 [link][software]
Cell Type Aware analysis of RNA-seq data (CARseq) reveals difference and similarities of the molecular mechanisms of Schizophrenia and Autism.
Jin C, Chen M, Lin D and Sun W: Nature Computational Science. 2021 April, 1(4):1-9 [link][software]
Extensive pleiotropism and allelic heterogeneity mediate metabolic effects of IRX3 and IRX5.
Sobreira D, Joslin AC, Zhan Q, …, Chen M, Aneas I, Nóbrega MA: Science. 372.6546 (2021): 1085-1091. [link]
2020
Integrative Differential Expression and Gene Set Enrichment Analysis for Single Cell RNA-seq Studies.
Sun S, Ying M, Shang X, Keller E, Chen M and Zhou X: Nature Communications. 2020 Mar 27;11(1):1585. [link][software]
REPIC: A database for exploring N6-methyladenosine methylome.
Liu S, He C and Chen M: Genome Biology. 2020 Apr 28;21(1):100 [link][website]
Allele-specific open chromatin in human iPSC neurons elucidates functional noncoding disease variants.
Zhang S, Zhang H, Zhou Y, Qiao M, Zhao S, Kozlova A, Shi J, Sanders A, Wang G, Luo K, Sengupta S, West S, Qian S, Strait M, Avramopoulos D, Cowan C, Chen M, Pang Z, Gejman P, He X, and Duan J: Science. 2020, Jul 31, 369(6503): 561-565 [link]
Demystifying "drop-outs" in single cell UMI data.
Kim T, Zhou X* and Chen M*: Genome Biology. 2020 Aug 06, 21(196) [link][software]
Selected work before 2020
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
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
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
