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Co-transcriptional gene regulation in eukaryotes and prokaryotes.
Shine M, Gordon J, Schärfen L, Zigackova D, Herzel L, Neugebauer KM. Shine M, et al. Among authors: scharfen l. Nat Rev Mol Cell Biol. 2024 Mar 20. doi: 10.1038/s41580-024-00706-2. Online ahead of print. Nat Rev Mol Cell Biol. 2024. PMID: 38509203 Review.
Extensible benchmarking of methods that identify and quantify polyadenylation sites from RNA-seq data.
Bryce-Smith S, Burri D, Gazzara MR, Herrmann CJ, Danecka W, Fitzsimmons CM, Wan YK, Zhuang F, Fansler MM, Fernández JM, Ferret M, Gonzalez-Uriarte A, Haynes S, Herdman C, Kanitz A, Katsantoni M, Marini F, McDonnel E, Nicolet B, Poon CL, Rot G, Schärfen L, Wu PJ, Yoon Y, Barash Y, Zavolan M. Bryce-Smith S, et al. Among authors: scharfen l. RNA. 2023 Dec;29(12):1839-1855. doi: 10.1261/rna.079849.123. Epub 2023 Oct 10. RNA. 2023. PMID: 37816550 Free PMC article. Review.
Extensible benchmarking of methods that identify and quantify polyadenylation sites from RNA-seq data.
Bryce-Smith S, Burri D, Gazzara MR, Herrmann CJ, Danecka W, Fitzsimmons CM, Wan YK, Zhuang F, Fansler MM, Fernández JM, Ferret M, Gonzalez-Uriarte A, Haynes S, Herdman C, Kanitz A, Katsantoni M, Marini F, McDonnel E, Nicolet B, Poon CL, Rot G, Schärfen L, Wu PJ, Yoon Y, Barash Y, Zavolan M. Bryce-Smith S, et al. Among authors: scharfen l. bioRxiv [Preprint]. 2023 Jun 26:2023.06.23.546284. doi: 10.1101/2023.06.23.546284. bioRxiv. 2023. PMID: 37425672 Free PMC article. Updated. Preprint.
Transcriptome-wide mapping reveals a diverse dihydrouridine landscape including mRNA.
Draycott AS, Schaening-Burgos C, Rojas-Duran MF, Wilson L, Schärfen L, Neugebauer KM, Nachtergaele S, Gilbert WV. Draycott AS, et al. Among authors: scharfen l. PLoS Biol. 2022 May 24;20(5):e3001622. doi: 10.1371/journal.pbio.3001622. eCollection 2022 May. PLoS Biol. 2022. PMID: 35609439 Free PMC article.
Transcription Regulation Through Nascent RNA Folding.
Schärfen L, Neugebauer KM. Schärfen L, et al. J Mol Biol. 2021 Jul 9;433(14):166975. doi: 10.1016/j.jmb.2021.166975. Epub 2021 Apr 1. J Mol Biol. 2021. PMID: 33811916 Free PMC article. Review.