List of Publications

2023SLAMseq resolves the kinetics of maternal and zygotic gene expression during early zebrafish embryogenesis.Cell RepBhat, P., Cabrera-Quio, LE., Herzog, VA., Fasching, N., Pauli, A., Ameres, SL.
2022Transcriptome-Wide Profiling of RNA Stability.Methods Mol BiolFasching, N., Petržílek, J., Popitsch, N., Herzog, VA., Ameres, SL.
2022NMD is required for timely cell fate transitions by fine-tuning gene expression and regulating translation.Genes DevHuth, 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.
2022Hijacking of transcriptional condensates by endogenous retroviruses.Nat GenetAsimi, 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.
2021Systematic refinement of gene annotations by parsing mRNA 3' end sequencing datasets.Methods EnzymolBhat, P., Burkard, TR., Herzog, VA., Pauli, A., Ameres, SL.
2020Determining mRNA Stability by Metabolic RNA Labeling and Chemical Nucleoside Conversion.Methods Mol BiolHerzog, VA., Fasching, N., Ameres, SL.
2020Structure-function analysis of microRNA 3'-end trimming by Nibbler.Proc Natl Acad Sci U S AXie, W., Sowemimo, I., Hayashi, R., Wang, J., Burkard, TR., Brennecke, J., Ameres, SL., Patel, DJ.
2019Structural basis for acceptor RNA substrate selectivity of the 3' terminal uridylyl transferase Tailor.Nucleic Acids ResKroupova, A., Ivascu, A., Reimão-Pinto, MM., Ameres, SL., Jinek, M.
2019Quantification of experimentally induced nucleotide conversions in high-throughput sequencing datasets.BMC BioinformaticsNeumann, T., Herzog, VA., Muhar, M., von Haeseler, A., Zuber, J., Ameres, SL., Rescheneder, P.
2019Sequencing cell-type-specific transcriptomes with SLAM-ITseq.Nat ProtocMatsushima, W., Herzog, VA., Neumann, T., Gapp, K., Zuber, J., Ameres, SL., Miska, EA.
2019Time-Resolved Small RNA Sequencing Unravels the Molecular Principles of MicroRNA Homeostasis.Mol CellReichholf, B., Herzog, VA., Fasching, N., Manzenreither, RA., Sowemimo, I., Ameres, SL.
2019Publisher Correction: Sequencing cell-type-specific transcriptomes with SLAM-ITseq.Nat ProtocMatsushima, W., Herzog, VA., Neumann, T., Gapp, K., Zuber, J., Ameres, SL., Miska, EA.
2018Positioning Europe for the EPITRANSCRIPTOMICS challenge.RNA BiolJantsch, 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.
2018Cell-type specific sequencing of microRNAs from complex animal tissues.Nat MethodsAlberti, C., Manzenreither, RA., Sowemimo, I., Burkard, TR., Wang, J., Mahofsky, K., Ameres, SL., Cochella, L.
2018Small RNAs Are Trafficked from the Epididymis to Developing Mammalian Sperm.Dev CellSharma, U., Sun, F., Conine, CC., Reichholf, B., Kukreja, S., Herzog, VA., Ameres, SL., Rando, OJ.
2018Analysis of 3' End Modifications in microRNAs by High-Throughput Sequencing.Methods Mol BiolReimão-Pinto, MM., Rodrigues-Viana, AM., Ameres, SL.
2018SLAM-ITseq: sequencing cell type-specific transcriptomes without cell sorting.DevelopmentMatsushima, W., Herzog, VA., Neumann, T., Gapp, K., Zuber, J., Ameres, SL., Miska, EA.
2018SLAM-seq defines direct gene-regulatory functions of the BRD4-MYC axis.ScienceMuhar, 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.
2017Thiol-linked alkylation of RNA to assess expression dynamics.Nat MethodsHerzog, VA., Reichholf, B., Neumann, T., Rescheneder, P., Bhat, P., Burkard, TR., Wlotzka, W., von Haeseler, A., Zuber, J., Ameres, SL.
2016Genetic and mechanistic diversity of piRNA 3'-end formation.NatureHayashi, R., Schnabl, J., Handler, D., Mohn, F., Ameres, SL., Brennecke, J.