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
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