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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: mackowiak sd. 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.
Extensive identification and analysis of conserved small ORFs in animals.
Mackowiak SD, Zauber H, Bielow C, Thiel D, Kutz K, Calviello L, Mastrobuoni G, Rajewsky N, Kempa S, Selbach M, Obermayer B. Mackowiak SD, et al. Genome Biol. 2015 Sep 14;16:179. doi: 10.1186/s13059-015-0742-x. Genome Biol. 2015. PMID: 26364619 Free PMC article.
Circular RNAs are a large class of animal RNAs with regulatory potency.
Memczak S, Jens M, Elefsinioti A, Torti F, Krueger J, Rybak A, Maier L, Mackowiak SD, Gregersen LH, Munschauer M, Loewer A, Ziebold U, Landthaler M, Kocks C, le Noble F, Rajewsky N. Memczak S, et al. Among authors: mackowiak sd. Nature. 2013 Mar 21;495(7441):333-8. doi: 10.1038/nature11928. Epub 2013 Feb 27. Nature. 2013. PMID: 23446348
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: mackowiak sd. 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.
Identification of novel and known miRNAs in deep-sequencing data with miRDeep2.
Mackowiak SD. Mackowiak SD. Curr Protoc Bioinformatics. 2011 Dec;Chapter 12:Unit 12.10.. doi: 10.1002/0471250953.bi1210s36. Curr Protoc Bioinformatics. 2011. PMID: 22161567
doRiNA: a database of RNA interactions in post-transcriptional regulation.
Anders G, Mackowiak SD, Jens M, Maaskola J, Kuntzagk A, Rajewsky N, Landthaler M, Dieterich C. Anders G, et al. Among authors: mackowiak sd. Nucleic Acids Res. 2012 Jan;40(Database issue):D180-6. doi: 10.1093/nar/gkr1007. Epub 2011 Nov 15. Nucleic Acids Res. 2012. PMID: 22086949 Free PMC article.
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: mackowiak sd. 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.
Specific microRNAs regulate heat stress responses in Caenorhabditis elegans.
Nehammer C, Podolska A, Mackowiak SD, Kagias K, Pocock R. Nehammer C, et al. Among authors: mackowiak sd. Sci Rep. 2015 Mar 9;5:8866. doi: 10.1038/srep08866. Sci Rep. 2015. PMID: 25746291 Free PMC article.
Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation.
Bazzini AA, Johnstone TG, Christiano R, Mackowiak SD, Obermayer B, Fleming ES, Vejnar CE, Lee MT, Rajewsky N, Walther TC, Giraldez AJ. Bazzini AA, et al. Among authors: mackowiak sd. EMBO J. 2014 May 2;33(9):981-93. doi: 10.1002/embj.201488411. Epub 2014 Apr 4. EMBO J. 2014. PMID: 24705786 Free PMC article.
An inventory of yeast proteins associated with nucleolar and ribosomal components.
Staub E, Mackowiak S, Vingron M. Staub E, et al. Among authors: mackowiak s. Genome Biol. 2006;7(10):R98. doi: 10.1186/gb-2006-7-10-r98. Epub 2006 Oct 26. Genome Biol. 2006. PMID: 17067374 Free PMC article.
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