| 2026 | Separable roles for Microprocessor and its cofactors, ERH and SAFB1/2, during microRNA cluster assistance. | Genes Dev | Shang, R., Popitsch, N., Lee, S., Ameres, SL., Lai, EC. |
| 2024 | Rnalib: a Python library for custom transcriptomics analyses. | Bioinformatics | Popitsch, N., Ameres, SL. |
| 2024 | Splice_sim: a nucleotide conversion-enabled RNA-seq simulation and evaluation framework. | Genome Biol | Popitsch, N., Neumann, T., von Haeseler, A., Ameres, SL. |
| 2023 | SLAMseq resolves the kinetics of maternal and zygotic gene expression during early zebrafish embryogenesis. | Cell Rep | Bhat, P., Cabrera-Quio, LE., Herzog, VA (...) 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 (...) Beyer, A., Leeb, M. |
| 2022 | Hijacking of transcriptional condensates by endogenous retroviruses. | Nat Genet | Asimi, V., Sampath Kumar, A., Niskanen, H (...) 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 | Structure-function analysis of microRNA 3'-end trimming by Nibbler. | Proc Natl Acad Sci U S A | Xie, W., Sowemimo, I., Hayashi, R (...) 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 | 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 (...) Ameres, SL., Miska, EA. |
| 2019 | Quantification of experimentally induced nucleotide conversions in high-throughput sequencing datasets. | BMC Bioinformatics | Neumann, T., Herzog, VA., Muhar, M (...) Ameres, SL., Rescheneder, P. |
| 2019 | Time-Resolved Small RNA Sequencing Unravels the Molecular Principles of MicroRNA Homeostasis. | Mol Cell | Reichholf, B., Herzog, VA., Fasching, N (...) Sowemimo, I., Ameres, SL. |
| 2019 | Publisher Correction: Sequencing cell-type-specific transcriptomes with SLAM-ITseq. | Nat Protoc | Matsushima, W., Herzog, VA., Neumann, T (...) Ameres, SL., Miska, EA. |
| 2018 | Cell-type specific sequencing of microRNAs from complex animal tissues. | Nat Methods | Alberti, C., Manzenreither, RA., Sowemimo, I (...) 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 | Positioning Europe for the EPITRANSCRIPTOMICS challenge. | RNA Biol | Jantsch, MF., Quattrone, A., O'Connell, M (...) Ule, J., Fray, R. |
| 2018 | SLAM-ITseq: sequencing cell type-specific transcriptomes without cell sorting. | Development | Matsushima, W., Herzog, VA., Neumann, T (...) Ameres, SL., Miska, EA. |
| 2018 | SLAM-seq defines direct gene-regulatory functions of the BRD4-MYC axis. | Science | Muhar, M., Ebert, A., Neumann, T (...) Ameres, SL., Zuber, J. |
