Chen M - Search Results

1

RADAR: differential analysis of MeRIP-seq data with a random effect model.

Zhang Z, Zhan Q, Eckert M, Zhu A, Chryplewicz A, De Jesus DF, Ren D, Kulkarni RN, Lengyel E, He C, Chen M. Zhang Z, et al. Among authors: chen m. Genome Biol. 2019 Dec 23;20(1):294. doi: 10.1186/s13059-019-1915-9. Genome Biol. 2019. PMID: 31870409 Free PMC article.

2

SynthEx: a synthetic-normal-based DNA sequencing tool for copy number alteration detection and tumor heterogeneity profiling.

Silva GO, Siegel MB, Mose LE, Parker JS, Sun W, Perou CM, Chen M. Silva GO, et al. Among authors: chen m. Genome Biol. 2017 Apr 8;18(1):66. doi: 10.1186/s13059-017-1193-3. Genome Biol. 2017. PMID: 28390427 Free PMC article.

3

Heritability estimation and differential analysis of count data with generalized linear mixed models in genomic sequencing studies.

Sun S, Zhu J, Mozaffari S, Ober C, Chen M, Zhou X. Sun S, et al. Among authors: chen m. Bioinformatics. 2019 Feb 1;35(3):487-496. doi: 10.1093/bioinformatics/bty644. Bioinformatics. 2019. PMID: 30020412 Free PMC article.

4

VIPER: variability-preserving imputation for accurate gene expression recovery in single-cell RNA sequencing studies.

Chen M, Zhou X. Chen M, et al. Genome Biol. 2018 Nov 12;19(1):196. doi: 10.1186/s13059-018-1575-1. Genome Biol. 2018. PMID: 30419955 Free PMC article.

5

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. De Jesus DF, et al. Among authors: chen m. Nat Metab. 2019 Aug;1(8):765-774. doi: 10.1038/s42255-019-0089-9. Epub 2019 Jul 29. Nat Metab. 2019. PMID: 31867565 Free PMC article.

6

REPIC: a database for exploring the N⁶-methyladenosine methylome.

Liu S, Zhu A, He C, Chen M. Liu S, et al. Among authors: chen m. Genome Biol. 2020 Apr 28;21(1):100. doi: 10.1186/s13059-020-02012-4. Genome Biol. 2020. PMID: 32345346 Free PMC article.

7

Demystifying "drop-outs" in single-cell UMI data.

Kim TH, Zhou X, Chen M. Kim TH, et al. Among authors: chen m. Genome Biol. 2020 Aug 6;21(1):196. doi: 10.1186/s13059-020-02096-y. Genome Biol. 2020. PMID: 32762710 Free PMC article.

8

Alignment of single-cell RNA-seq samples without overcorrection using kernel density matching.

Chen M, Zhan Q, Mu Z, Wang L, Zheng Z, Miao J, Zhu P, Li YI. Chen M, et al. Genome Res. 2021 Apr;31(4):698-712. doi: 10.1101/gr.261115.120. Epub 2021 Mar 19. Genome Res. 2021. PMID: 33741686 Free PMC article.

9

Neoadjuvant Chemotherapy Induces Genomic and Transcriptomic Changes 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 RR, Chen M, Lengyel E. Javellana M, et al. Among authors: chen m. Cancer Res. 2022 Jan 1;82(1):169-176. doi: 10.1158/0008-5472.CAN-21-1467. Epub 2021 Nov 4. Cancer Res. 2022. PMID: 34737212 Free PMC article.

10

KAS-seq: genome-wide sequencing of single-stranded DNA by N₃-kethoxal-assisted labeling.

Lyu R, Wu T, Zhu AC, West-Szymanski DC, Weng X, Chen M, He C. Lyu R, et al. Among authors: chen m. Nat Protoc. 2022 Feb;17(2):402-420. doi: 10.1038/s41596-021-00647-6. Epub 2022 Jan 10. Nat Protoc. 2022. PMID: 35013616 Free PMC article. Review.

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