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miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades.
Friedländer MR, Mackowiak SD, Li N, Chen W, Rajewsky N. Friedländer MR, et al. Among authors: chen w. Nucleic Acids Res. 2012 Jan;40(1):37-52. doi: 10.1093/nar/gkr688. Epub 2011 Sep 12. Nucleic Acids Res. 2012. PMID: 21911355 Free PMC article.
Discovering microRNAs from deep sequencing data using miRDeep.
Friedländer MR, Chen W, Adamidi C, Maaskola J, Einspanier R, Knespel S, Rajewsky N. Friedländer MR, et al. Among authors: chen w. Nat Biotechnol. 2008 Apr;26(4):407-15. doi: 10.1038/nbt1394. Nat Biotechnol. 2008. PMID: 18392026
MicroRNAs in brain function and disease.
Kuss AW, Chen W. Kuss AW, et al. Among authors: chen w. Curr Neurol Neurosci Rep. 2008 May;8(3):190-7. doi: 10.1007/s11910-008-0031-0. Curr Neurol Neurosci Rep. 2008. PMID: 18541114 Review.
De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics.
Adamidi C, Wang Y, Gruen D, Mastrobuoni G, You X, Tolle D, Dodt M, Mackowiak SD, Gogol-Doering A, Oenal P, Rybak A, Ross E, Sánchez Alvarado A, Kempa S, Dieterich C, Rajewsky N, Chen W. Adamidi C, et al. Among authors: chen w. Genome Res. 2011 Jul;21(7):1193-200. doi: 10.1101/gr.113779.110. Epub 2011 May 2. Genome Res. 2011. PMID: 21536722 Free PMC article.
An overview of the analysis of next generation sequencing data.
Gogol-Döring A, Chen W. Gogol-Döring A, et al. Among authors: chen w. Methods Mol Biol. 2012;802:249-57. doi: 10.1007/978-1-61779-400-1_16. Methods Mol Biol. 2012. PMID: 22130885
Retargeting transposon insertions by the adeno-associated virus Rep protein.
Ammar I, Gogol-Döring A, Miskey C, Chen W, Cathomen T, Izsvák Z, Ivics Z. Ammar I, et al. Among authors: chen w. Nucleic Acids Res. 2012 Aug;40(14):6693-712. doi: 10.1093/nar/gks317. Epub 2012 Apr 19. Nucleic Acids Res. 2012. PMID: 22523082 Free PMC article.
Argonaute2 regulates the pancreatic β-cell secretome.
Tattikota SG, Sury MD, Rathjen T, Wessels HH, Pandey AK, You X, Becker C, Chen W, Selbach M, Poy MN. Tattikota SG, et al. Among authors: chen w. Mol Cell Proteomics. 2013 May;12(5):1214-25. doi: 10.1074/mcp.M112.024786. Epub 2013 Jan 28. Mol Cell Proteomics. 2013. PMID: 23358505 Free PMC article.
Global profiling of miRNAs and the hairpin precursors: insights into miRNA processing and novel miRNA discovery.
Li N, You X, Chen T, Mackowiak SD, Friedländer MR, Weigt M, Du H, Gogol-Döring A, Chang Z, Dieterich C, Hu Y, Chen W. Li N, et al. Among authors: chen t, chen w. Nucleic Acids Res. 2013 Apr 1;41(6):3619-34. doi: 10.1093/nar/gkt072. Epub 2013 Feb 8. Nucleic Acids Res. 2013. PMID: 23396444 Free PMC article.
Ultra-deep profiling of alternatively spliced Drosophila Dscam isoforms by circularization-assisted multi-segment sequencing.
Sun W, You X, Gogol-Döring A, He H, Kise Y, Sohn M, Chen T, Klebes A, Schmucker D, Chen W. Sun W, et al. Among authors: chen t, chen w. EMBO J. 2013 Jul 17;32(14):2029-38. doi: 10.1038/emboj.2013.144. Epub 2013 Jun 21. EMBO J. 2013. PMID: 23792425 Free PMC article.
Neural circular RNAs are derived from synaptic genes and regulated by development and plasticity.
You X, Vlatkovic I, Babic A, Will T, Epstein I, Tushev G, Akbalik G, Wang M, Glock C, Quedenau C, Wang X, Hou J, Liu H, Sun W, Sambandan S, Chen T, Schuman EM, Chen W. You X, et al. Among authors: chen t, chen w. Nat Neurosci. 2015 Apr;18(4):603-610. doi: 10.1038/nn.3975. Epub 2015 Feb 25. Nat Neurosci. 2015. PMID: 25714049 Free PMC article.
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