Rapid folding of nascent RNA regulates eukaryotic RNA biogenesis
Schärfen L, Vock IW, Simon MD, Neugebauer KM
Mol. Cell 85(8) 1561-1574 (2025)
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Co-transcriptional gene regulation in eukaryotes and prokaryotes
Shine M, Gordon JM, Schärfen L, Zigackova D, Herzel L, Neugebauer KM
Nat. Rev. Mol. Cell Biol. 25 534-554 (2024)

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 BP, Poon CL, Rot G, Schärfen L, Wu PJ, Yoon Y, Barash Y, Zavolan M
RNA 29 1839-1855 (2023)

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
PLOS Biology 20(5) (2022)
> Primer in PLOS Biology

Identification of Alternative Polyadenylation in Cyanidioschyzon merolae Through Long-Read Sequencing of mRNA
Schärfen L*, Zigackova D*, Reimer K, Stark MR, Slat VA, Francoeur NJ, Wells ML, Zhou L, Blackshear PJ, Neugebauer KM, Rader SD
Front. Genet. 12 (2022)

Transcription regulation through nascent RNA folding
Schärfen L, Neugebauer KM
J. Mol. Biol. 433(14) (2021)

Phosphorylation of the nuclear poly(A) binding protein (PABPN1) during mitosis protects mRNA from hyperadenylation and maintains transcriptome dynamics
Gordon JM*, Phizicky DV*, Schärfen L, Brown LC, Escayola DA, Kanyo J, Lam T, Simon MD, Neugebauer KM
Nucl. Acids Res. 52(16) 9886–9903 (2024)

Identification of coilin interactors reveals coordinated control of Cajal body number and structure
Escayola DA*, Zhang C*, Nischwitz E, Schärfen L, Dörner K, Straube K, Kutay U, Butter F, Neugebauer KM
J. Cell Biol. 224(2) (2024)

Direct visualization of four LexA states controlling SOS response strength during antibiotic treatment
Schärfen L, Tišma M, Hartmann A, Schlierf M
bioRxiv (2021)

Fast, simultaneous tagging and mutagenesis of genes on bacterial chromosomes
Schärfen L*, Tišma M*, Schlierf M
ACS Synth. Biol. 9(8) 2203–2207 (2020)
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Enhancing the stability of DNA origami nanostructures: staple strand redesign versus enzymatic ligation
Ramakrishnan S*, Schärfen L*, Hunold K*, Fricke S, Grundmeier G, Schlierf M, Keller A, Krainer G
Nanoscale 11(35) 16270–16276 (2019)

Real-time monitoring of protein-induced DNA conformational changes using single-molecule FRET
Schärfen L, Schlierf M
Methods 169 11–20 (2019)