Crossley MP, Bocek MJ, Hamperl S, Swigut T, Cimprich KA. qDRIP: a method to quantitatively assess RNA-DNA hybrid formation genome-wide. Nucleic Acids Res. PMID: 32544226. DOI: 10.1093/nar/gkaa500.

Ummethum, H. , Hamperl, S. (2020). Proximity labeling techniques to study chromatin. Front Genet.  PMID: 32477404. DOI: 10.3389/fgene.2020.00450.  

Pich D, Mrozek-Gorska P, Bouvet M, Sugimoto A, Akidil E, Grundhoff A, Hamperl S, Ling PD, Hammerschmidt W (2019). First Days in the Life of Naive Human B Lymphocytes Infected with Epstein-Barr Virus. Mbio. PMID: 31530670. PII: e01723-19. DOI: 10.1128/mBio.01723-19.

Hamperl, S., Bocek M., Saldivar, J. C., Swigut T., and Cimprich, K. A. (2017). Transcription-replication conflict orientation modulates R-loop levels and activates distinct DNA damage responses. Cell 170, 774–786.

Hamperl, S., and Cimprich, K. A. (2016). Conflict Resolution in the Genome: How Transcription and Replication Make It Work. Cell 167, 1455–1467

Brown, C.R., Eskin, J.A., Hamperl, S., Griesenbeck, J., Jurica, M.S., and Boeger, H. (2015). Chromatin structure analysis of single gene molecules by psoralen cross-linking and electron microscopy. Methods Mol. Biol. 1228, 93–121

Hamperl, S., and Cimprich, K.A. (2014). The contribution of co-transcriptional RNA:DNA hybrid structures to DNA damage and genome instability. DNA Repair (Amst.) 19, 84–94.

Hamperl, S., Brown, C.R., Perez-Fernandez, J., Huber, K., Wittner, M., Babl, V., Stöckl, U., Boeger, H., Tschochner, H., Milkereit, P., Griesenbeck J., (2014). Purification of specific chromatin domains from single-copy gene loci in Saccharomyces cerevisiae. Methods Mol. Biol. 1094, 329–341.

Hamperl, S., Brown, C.R., Garea, A.V., Perez-Fernandez, J., Bruckmann, A., Huber, K., Wittner, M., Babl, V., Stoeckl, U., Deutzmann, R., Boeger, H., Tschochner H., Milkereit P., Griesenbeck J. (2014). Compositional and structural analysis of selected chromosomal domains from Saccharomyces cerevisiae. Nucleic Acids Res. 42, e2.

Hamperl, S., Wittner, M., Babl, V., Perez-Fernandez, J., Tschochner, H., and Griesenbeck, J. (2013). Chromatin states at ribosomal DNA loci. Biochim. Biophys. Acta 1829, 405–417. 

Hierlmeier, T., Merl, J., Sauert, M., Perez-Fernandez, J., Schultz, P., Bruckmann, A., Hamperl, S., Ohmayer, U., Rachel, R., Jacob, A., Hergert K., Deutzmann R., Griesenbeck J., Hurt E., Milkereit P., Baßler J., Tschochner H. (2013). Rrp5p, Noc1p and Noc2p form a protein module which is part of early large ribosomal subunit precursors in S. cerevisiae. Nucleic Acids Res. 41, 1191–1210.

Reiter, A.*, Hamperl, S.*, Seitz, H., Merkl, P., Perez-Fernandez, J., Williams, L., Gerber, J., Németh, A., Léger, I., Gadal, O., Milkereit P., Griesenbeck J., Tschochner H. (2012). The Reb1-homologue Ydr026c/Nsi1 is required for efficient RNA polymerase I termination in yeast. EMBO J. 31, 3480–3493 *equal contribution

Wittner, M., Hamperl, S., Stöckl, U., Seufert, W., Tschochner, H., Milkereit, P., and Griesenbeck, J. (2011). Establishment and maintenance of alternative chromatin states at a multicopy gene locus. Cell 145, 543–554.

Goetze, H., Wittner, M., Hamperl, S., Hondele, M., Merz, K., Stoeckl, U., and Griesenbeck, J. (2010). Alternative chromatin structures of the 35S rRNA genes in Saccharomyces cerevisiae provide a molecular basis for the selective recruitment of RNA polymerases I and II. Mol. Cell. Biol. 30, 2028–2045.