| 2023 | SLAMseq resolves the kinetics of maternal and zygotic gene expression during early zebrafish embryogenesis. | Cell Rep | Bhat, P., Cabrera-Quio, LE., Herzog, VA., Fasching, N., Pauli, A., Ameres, SL. |
| 2022 | Transcriptome-Wide Profiling of RNA Stability. | Methods Mol Biol | Fasching, N., Petržílek, J., Popitsch, N., Herzog, VA., Ameres, SL. |
| 2022 | NMD is required for timely cell fate transitions by fine-tuning gene expression and regulating translation. | Genes Dev | Huth, M., Santini, L., Galimberti, E., Ramesmayer, J., Titz-Teixeira, F., Sehlke, R., Oberhuemer, M., Stummer, S., Herzog, V., Garmhausen, M., Romeike, M., Chugunova, A., Leesch, F., Holcik, L., Weipoltshammer, K., Lackner, A., Schoefer, C., von Haeseler, A., Buecker, C., Pauli, A., Ameres, SL., Smith, A., Beyer, A., Leeb, M. |
| 2022 | Hijacking of transcriptional condensates by endogenous retroviruses. | Nat Genet | Asimi, V., Sampath Kumar, A., Niskanen, H., Riemenschneider, C., Hetzel, S., Naderi, J., Fasching, N., Popitsch, N., Du, M., Kretzmer, H., Smith, ZD., Weigert, R., Walther, M., Mamde, S., Meierhofer, D., Wittler, L., Buschow, R., Timmermann, B., Cisse, II., Ameres, SL., Meissner, A., Hnisz, D. |
| 2021 | Systematic refinement of gene annotations by parsing mRNA 3' end sequencing datasets. | Methods Enzymol | Bhat, P., Burkard, TR., Herzog, VA., Pauli, A., Ameres, SL. |
| 2020 | Determining mRNA Stability by Metabolic RNA Labeling and Chemical Nucleoside Conversion. | Methods Mol Biol | Herzog, VA., Fasching, N., Ameres, SL. |
| 2020 | Structure-function analysis of microRNA 3'-end trimming by Nibbler. | Proc Natl Acad Sci U S A | Xie, W., Sowemimo, I., Hayashi, R., Wang, J., Burkard, TR., Brennecke, J., Ameres, SL., Patel, DJ. |
| 2019 | Structural basis for acceptor RNA substrate selectivity of the 3' terminal uridylyl transferase Tailor. | Nucleic Acids Res | Kroupova, A., Ivascu, A., Reimão-Pinto, MM., Ameres, SL., Jinek, M. |
| 2019 | Quantification of experimentally induced nucleotide conversions in high-throughput sequencing datasets. | BMC Bioinformatics | Neumann, T., Herzog, VA., Muhar, M., von Haeseler, A., Zuber, J., Ameres, SL., Rescheneder, P. |
| 2019 | Sequencing cell-type-specific transcriptomes with SLAM-ITseq. | Nat Protoc | Matsushima, W., Herzog, VA., Neumann, T., Gapp, K., Zuber, J., Ameres, SL., Miska, EA. |
| 2019 | Time-Resolved Small RNA Sequencing Unravels the Molecular Principles of MicroRNA Homeostasis. | Mol Cell | Reichholf, B., Herzog, VA., Fasching, N., Manzenreither, RA., Sowemimo, I., Ameres, SL. |
| 2019 | Publisher Correction: Sequencing cell-type-specific transcriptomes with SLAM-ITseq. | Nat Protoc | Matsushima, W., Herzog, VA., Neumann, T., Gapp, K., Zuber, J., Ameres, SL., Miska, EA. |
| 2018 | Positioning Europe for the EPITRANSCRIPTOMICS challenge. | RNA Biol | Jantsch, MF., Quattrone, A., O'Connell, M., Helm, M., Frye, M., Macias-Gonzales, M., Ohman, M., Ameres, S., Willems, L., Fuks, F., Oulas, A., Vanacova, S., Nielsen, H., Bousquet-Antonelli, C., Motorin, Y., Roignant, JY., Balatsos, N., Dinnyes, A., Baranov, P., Kelly, V., Lamm, A., Rechavi, G., Pelizzola, M., Liepins, J., Holodnuka Kholodnyuk, I., Zammit, V., Ayers, D., Drablos, F., Dahl, JA., Bujnicki, J., Jeronimo, C., Almeida, R., Neagu, M., Costache, M., Bankovic, J., Banovic, B., Kyselovic, J., Valor, LM., Selbert, S., Pir, P., Demircan, T., Cowling, V., Schäfer, M., Rossmanith, W., Lafontaine, D., David, A., Carre, C., Lyko, F., Schaffrath, R., Schwartz, S., Verdel, A., Klungland, A., Purta, E., Timotijevic, G., Cardona, F., Davalos, A., Ballana, E., O Carroll, D., Ule, J., Fray, R. |
| 2018 | Cell-type specific sequencing of microRNAs from complex animal tissues. | Nat Methods | Alberti, C., Manzenreither, RA., Sowemimo, I., Burkard, TR., Wang, J., Mahofsky, K., Ameres, SL., Cochella, L. |
| 2018 | Small RNAs Are Trafficked from the Epididymis to Developing Mammalian Sperm. | Dev Cell | Sharma, U., Sun, F., Conine, CC., Reichholf, B., Kukreja, S., Herzog, VA., Ameres, SL., Rando, OJ. |
| 2018 | Analysis of 3' End Modifications in microRNAs by High-Throughput Sequencing. | Methods Mol Biol | Reimão-Pinto, MM., Rodrigues-Viana, AM., Ameres, SL. |
| 2018 | SLAM-ITseq: sequencing cell type-specific transcriptomes without cell sorting. | Development | Matsushima, W., Herzog, VA., Neumann, T., Gapp, K., Zuber, J., Ameres, SL., Miska, EA. |
| 2018 | SLAM-seq defines direct gene-regulatory functions of the BRD4-MYC axis. | Science | Muhar, M., Ebert, A., Neumann, T., Umkehrer, C., Jude, J., Wieshofer, C., Rescheneder, P., Lipp, JJ., Herzog, VA., Reichholf, B., Cisneros, DA., Hoffmann, T., Schlapansky, MF., Bhat, P., von Haeseler, A., Köcher, T., Obenauf, AC., Popow, J., Ameres, SL., Zuber, J. |
| 2017 | Thiol-linked alkylation of RNA to assess expression dynamics. | Nat Methods | Herzog, VA., Reichholf, B., Neumann, T., Rescheneder, P., Bhat, P., Burkard, TR., Wlotzka, W., von Haeseler, A., Zuber, J., Ameres, SL. |
| 2016 | Genetic and mechanistic diversity of piRNA 3'-end formation. | Nature | Hayashi, R., Schnabl, J., Handler, D., Mohn, F., Ameres, SL., Brennecke, J. |
