Publications - IMBA

Year	Title	Journal	Authors
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.
2020	Determining mRNA Stability by Metabolic RNA Labeling and Chemical Nucleoside Conversion.	Methods Mol Biol	Herzog, VA., Fasching, N., 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.
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	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.
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-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	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.