List of Publications

Popitsch, N., Neumann, T., von Haeseler, A., Ameres, SL. (2024). Splice_sim: a nucleotide conversion-enabled RNA-seq simulation and evaluation framework. Genome Biol. 25(1):166

Bhat, P., Cabrera-Quio, LE., Herzog, VA (...) Pauli, A., Ameres, SL. (2023). SLAMseq resolves the kinetics of maternal and zygotic gene expression during early zebrafish embryogenesis. Cell Rep. 42(2):112070

Fasching, N., Petržílek, J., Popitsch, N., Herzog, VA., Ameres, SL. (2022). Transcriptome-Wide Profiling of RNA Stability. Methods Mol Biol. 2404:311-330

Asimi, V., Sampath Kumar, A., Niskanen, H (...) Meissner, A., Hnisz, D. (2022). Hijacking of transcriptional condensates by endogenous retroviruses. Nat Genet. 54(8):1238-1247

Huth, M., Santini, L., Galimberti, E (...) Beyer, A., Leeb, M. (2022). NMD is required for timely cell fate transitions by fine-tuning gene expression and regulating translation. Genes Dev. 36(5-6):348-367

Bhat, P., Burkard, TR., Herzog, VA., Pauli, A., Ameres, SL. (2021). Systematic refinement of gene annotations by parsing mRNA 3' end sequencing datasets. Methods Enzymol. 655:205-223

Herzog, VA., Fasching, N., Ameres, SL. (2020). Determining mRNA Stability by Metabolic RNA Labeling and Chemical Nucleoside Conversion. Methods Mol Biol. 2062:169-189

Xie, W., Sowemimo, I., Hayashi, R (...) Ameres, SL., Patel, DJ. (2020). Structure-function analysis of microRNA 3'-end trimming by Nibbler. Proc Natl Acad Sci U S A. 117(48):30370-30379

Reichholf, B., Herzog, VA., Fasching, N (...) Sowemimo, I., Ameres, SL. (2019). Time-Resolved Small RNA Sequencing Unravels the Molecular Principles of MicroRNA Homeostasis. Mol Cell. 75(4):756-768.e7

Matsushima, W., Herzog, VA., Neumann, T (...) Ameres, SL., Miska, EA. (2019). Publisher Correction: Sequencing cell-type-specific transcriptomes with SLAM-ITseq. Nat Protoc. 14(8):2597

Matsushima, W., Herzog, VA., Neumann, T (...) Ameres, SL., Miska, EA. (2019). Sequencing cell-type-specific transcriptomes with SLAM-ITseq. Nat Protoc. 14(8):2261-2278

Kroupova, A., Ivascu, A., Reimão-Pinto, MM., Ameres, SL., Jinek, M. (2019). Structural basis for acceptor RNA substrate selectivity of the 3' terminal uridylyl transferase Tailor. Nucleic Acids Res. 47(2):1030-1042

Neumann, T., Herzog, VA., Muhar, M (...) Ameres, SL., Rescheneder, P. (2019). Quantification of experimentally induced nucleotide conversions in high-throughput sequencing datasets. BMC Bioinformatics. 20(1):258

Jantsch, MF., Quattrone, A., O'Connell, M (...) Ule, J., Fray, R. (2018). Positioning Europe for the EPITRANSCRIPTOMICS challenge. RNA Biol. 15(6):829-831

Sharma, U., Sun, F., Conine, CC (...) Ameres, SL., Rando, OJ. (2018). Small RNAs Are Trafficked from the Epididymis to Developing Mammalian Sperm. Dev Cell. 46(4):481-494.e6

Matsushima, W., Herzog, VA., Neumann, T (...) Ameres, SL., Miska, EA. (2018). SLAM-ITseq: sequencing cell type-specific transcriptomes without cell sorting. Development. 145(13)

Muhar, M., Ebert, A., Neumann, T (...) Ameres, SL., Zuber, J. (2018). SLAM-seq defines direct gene-regulatory functions of the BRD4-MYC axis. Science. 360(6390):800-805

Reimão-Pinto, MM., Rodrigues-Viana, AM., Ameres, SL. (2018). Analysis of 3' End Modifications in microRNAs by High-Throughput Sequencing. Methods Mol Biol. 1823:115-139

Alberti, C., Manzenreither, RA., Sowemimo, I (...) Ameres, SL., Cochella, L. (2018). Cell-type specific sequencing of microRNAs from complex animal tissues. Nat Methods. 15(4):283-289

Herzog, VA., Reichholf, B., Neumann, T (...) Zuber, J., Ameres, SL. (2017). Thiol-linked alkylation of RNA to assess expression dynamics. Nat Methods. 14(12):1198-1204

Reimão-Pinto, MM., Manzenreither, RA., Burkard, TR (...) Mechtler, K., Ameres, SL. (2016). Molecular basis for cytoplasmic RNA surveillance by uridylation-triggered decay in Drosophila. EMBO J. 35(22):2417-2434

Hayashi, R., Schnabl, J., Handler, D (...) Ameres, SL., Brennecke, J. (2016). Genetic and mechanistic diversity of piRNA 3'-end formation. Nature. 539(7630):588-592

Herzog, VA., Ameres, SL. (2015). Approaching the Golden Fleece a Molecule at a Time: Biophysical Insights into Argonaute-Instructed Nucleic Acid Interactions. Mol Cell. 59(1):4-7

Bortolamiol-Becet, D., Hu, F., Jee, D (...) Ameres, SL., Lai, EC. (2015). Selective Suppression of the Splicing-Mediated MicroRNA Pathway by the Terminal Uridyltransferase Tailor. Mol Cell. 59(2):217-28

Reimão-Pinto, MM., Ignatova, V., Burkard, TR (...) Fariña-Lopez, S., Ameres, SL. (2015). Uridylation of RNA Hairpins by Tailor Confines the Emergence of MicroRNAs in Drosophila. Mol Cell. 59(2):203-16

Ameres, SL., Zamore, PD. (2013). Diversifying microRNA sequence and function. Nat Rev Mol Cell Biol. 14(8):475-88

Xie, J., Ameres, SL., Friedline, R (...) Zamore, PD., Gao, G. (2012). Long-term, efficient inhibition of microRNA function in mice using rAAV vectors. Nat Methods. 9(4):403-9

Xie, J., Xie, Q., Zhang, H (...) Zamore, PD., Gao, G. (2011). MicroRNA-regulated, systemically delivered rAAV9: a step closer to CNS-restricted transgene expression. Mol Ther. 19(3):526-35

Ameres, SL., Hung, JH., Xu, J., Weng, Z., Zamore, PD. (2011). Target RNA-directed tailing and trimming purifies the sorting of endo-siRNAs between the two Drosophila Argonaute proteins. RNA. 17(1):54-63

Han, BW., Hung, JH., Weng, Z., Zamore, PD., Ameres, SL. (2011). The 3'-to-5' exoribonuclease Nibbler shapes the 3' ends of microRNAs bound to Drosophila Argonaute1. Curr Biol. 21(22):1878-87

Ameres, SL., Horwich, MD., Hung, JH (...) Weng, Z., Zamore, PD. (2010). Target RNA-directed trimming and tailing of small silencing RNAs. Science. 328(5985):1534-9

Ameres, SL., Fukunaga, R. (2010). Riding in silence: a little snowboarding, a lot of small RNAs. Silence. 1(1):8

Tafer, H., Ameres, SL., Obernosterer, G (...) Martinez, J., Hofacker, IL. (2008). The impact of target site accessibility on the design of effective siRNAs. Nat Biotechnol. 26(5):578-83

Ameres, S.L. (2007). Mechanistische Analyse des humanen RNA-Interferenz-Effektor-Komplexes BioSpektrum. (7):756

Ameres, SL., Shcherbakov, D., Nikonova, E (...) Schroeder, R., Semrad, K. (2007). RNA chaperone activity of L1 ribosomal proteins: phylogenetic conservation and splicing inhibition. Nucleic Acids Res. 35(11):3752-63

Ameres, SL., Martinez, J., Schroeder, R. (2007). Molecular basis for target RNA recognition and cleavage by human RISC. Cell. 130(1):101-12

Leuschner, PJ., Ameres, SL., Kueng, S., Martinez, J. (2006). Cleavage of the siRNA passenger strand during RISC assembly in human cells. EMBO Rep. 7(3):314-20

Ameres, SL., Drueppel, L., Pfleiderer, K (...) Hillen, W., Berens, C. (2005). Inducible DNA-loop formation blocks transcriptional activation by an SV40 enhancer. EMBO J. 24(2):358-67