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Publications

Year Title Journal Authors
2020 Determining mRNA Stability by Metabolic RNA Labeling and Chemical Nucleoside Conversion. Methods Mol Biol Herzog, VA., Fasching, N., Ameres, SL.
2020 Conformation of sister chromatids in the replicated human genome. Nature Mitter, M., Gasser, C., Takacs, Z., Langer, CCH., Tang, W., Jessberger, G., Beales, CT., Neuner, E., Ameres, SL., Peters, JM., Goloborodko, A., Micura, R., Gerlich, DW.
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 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.
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 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 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.
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 Analysis of 3' End Modifications in microRNAs by High-Throughput Sequencing. Methods Mol Biol Reimão-Pinto, MM., Rodrigues-Viana, AM., Ameres, SL.
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.
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 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 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.
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 Molecular basis for cytoplasmic RNA surveillance by uridylation-triggered decay in Drosophila. EMBO J Reimão-Pinto, MM., Manzenreither, RA., Burkard, TR., Sledz, P., Jinek, M., Mechtler, K., 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.
2015 Approaching the Golden Fleece a Molecule at a Time: Biophysical Insights into Argonaute-Instructed Nucleic Acid Interactions. Mol Cell Herzog, VA., Ameres, SL.
2015 Uridylation of RNA Hairpins by Tailor Confines the Emergence of MicroRNAs in Drosophila. Mol Cell Reimão-Pinto, MM., Ignatova, V., Burkard, TR., Hung, JH., Manzenreither, RA., Sowemimo, I., Herzog, VA., Reichholf, B., Fariña-Lopez, S., Ameres, SL.
2015 Selective Suppression of the Splicing-Mediated MicroRNA Pathway by the Terminal Uridyltransferase Tailor. Mol Cell Bortolamiol-Becet, D., Hu, F., Jee, D., Wen, J., Okamura, K., Lin, CJ., Ameres, SL., Lai, EC.