Dong X - Search Results

1

Benchmarking UMI-based single-cell RNA-seq preprocessing workflows.

You Y, Tian L, Su S, Dong X, Jabbari JS, Hickey PF, Ritchie ME. You Y, et al. Among authors: dong x. Genome Biol. 2021 Dec 14;22(1):339. doi: 10.1186/s13059-021-02552-3. Genome Biol. 2021. PMID: 34906205 Free PMC article.

2

RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR.

Law CW, Alhamdoosh M, Su S, Dong X, Tian L, Smyth GK, Ritchie ME. Law CW, et al. Among authors: dong x. F1000Res. 2016 Jun 17;5:ISCB Comm J-1408. doi: 10.12688/f1000research.9005.3. eCollection 2016. F1000Res. 2016. PMID: 27441086 Free PMC article.

3

scPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data.

Tian L, Su S, Dong X, Amann-Zalcenstein D, Biben C, Seidi A, Hilton DJ, Naik SH, Ritchie ME. Tian L, et al. Among authors: dong x. PLoS Comput Biol. 2018 Aug 10;14(8):e1006361. doi: 10.1371/journal.pcbi.1006361. eCollection 2018 Aug. PLoS Comput Biol. 2018. PMID: 30096152 Free PMC article.

4

Benchmarking single cell RNA-sequencing analysis pipelines using mixture control experiments.

Tian L, Dong X, Freytag S, Lê Cao KA, Su S, JalalAbadi A, Amann-Zalcenstein D, Weber TS, Seidi A, Jabbari JS, Naik SH, Ritchie ME. Tian L, et al. Among authors: dong x. Nat Methods. 2019 Jun;16(6):479-487. doi: 10.1038/s41592-019-0425-8. Epub 2019 May 27. Nat Methods. 2019. PMID: 31133762

5

Distinct initiating events underpin the immune and metabolic heterogeneity of KRAS-mutant lung adenocarcinoma.

Best SA, Ding S, Kersbergen A, Dong X, Song JY, Xie Y, Reljic B, Li K, Vince JE, Rathi V, Wright GM, Ritchie ME, Sutherland KD. Best SA, et al. Among authors: dong x. Nat Commun. 2019 Sep 13;10(1):4190. doi: 10.1038/s41467-019-12164-y. Nat Commun. 2019. PMID: 31519898 Free PMC article.

6

CellBench: R/Bioconductor software for comparing single-cell RNA-seq analysis methods.

Su S, Tian L, Dong X, Hickey PF, Freytag S, Ritchie ME. Su S, et al. Among authors: dong x. Bioinformatics. 2020 Apr 1;36(7):2288-2290. doi: 10.1093/bioinformatics/btz889. Bioinformatics. 2020. PMID: 31778143 Free PMC article.

7

Opportunities and challenges in long-read sequencing data analysis.

Amarasinghe SL, Su S, Dong X, Zappia L, Ritchie ME, Gouil Q. Amarasinghe SL, et al. Among authors: dong x. Genome Biol. 2020 Feb 7;21(1):30. doi: 10.1186/s13059-020-1935-5. Genome Biol. 2020. PMID: 32033565 Free PMC article. Review.

8

Harnessing Natural Killer Immunity in Metastatic SCLC.

Best SA, Hess JB, Souza-Fonseca-Guimaraes F, Cursons J, Kersbergen A, Dong X, Rautela J, Hyslop SR, Ritchie ME, Davis MJ, Leong TL, Irving L, Steinfort D, Huntington ND, Sutherland KD. Best SA, et al. Among authors: dong x. J Thorac Oncol. 2020 Sep;15(9):1507-1521. doi: 10.1016/j.jtho.2020.05.008. Epub 2020 May 26. J Thorac Oncol. 2020. PMID: 32470639 Free article.

9

A guide to creating design matrices for gene expression experiments.

Law CW, Zeglinski K, Dong X, Alhamdoosh M, Smyth GK, Ritchie ME. Law CW, et al. Among authors: dong x. F1000Res. 2020 Dec 10;9:1444. doi: 10.12688/f1000research.27893.1. eCollection 2020. F1000Res. 2020. PMID: 33604029 Free PMC article.

10

The long and the short of it: unlocking nanopore long-read RNA sequencing data with short-read differential expression analysis tools.

Dong X, Tian L, Gouil Q, Kariyawasam H, Su S, De Paoli-Iseppi R, Prawer YDJ, Clark MB, Breslin K, Iminitoff M, Blewitt ME, Law CW, Ritchie ME. Dong X, et al. NAR Genom Bioinform. 2021 Apr 26;3(2):lqab028. doi: 10.1093/nargab/lqab028. eCollection 2021 Jun. NAR Genom Bioinform. 2021. PMID: 33937765 Free PMC article.

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