Bridging temporal resolution gaps to dissect RNA silencing at the molecular and genomic scale

Project Information

RiboTrace

Grant agreement ID: 866166

DOI

10.3030/866166

Project closed

EC signature date 23 January 2020

Start date 1 February 2020

End date 31 January 2026

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 1 998 476,00

EU contribution

€ 1 998 476,00

Coordinated by

UNIVERSITAT WIEN
Austria

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Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Publications

Other (2)

Hierarchical assembly and functional resilience of the mammalian RNA exosome

Author(s): Tsimafei Navalayeu, Nikolaus Beer, Monika Bebjaková, Robert W. Kalis, Karel Stejskal, Gabriela Krššáková, Nina Fasching, Veronika A. Herzog, Niko Popitsch, Elisabeth Roitinger, Johannes Zuber, Stefan L. Ameres
Published in: bioRxiv, 2026
Publisher: openRxiv
DOI: 10.1101/2025.03.14.643291

Kinetic logic of uridylation-mediated RNA decay

Author(s): Annamaria Sgromo, Benjamin M. Jordan, Andrew Aarestad, David Mörsdorf, Franziska Boneberg, Martin Jinek, Thomas R. Burkard, Niko Popitsch, Stefan L. Ameres
Published in: bioRxiv, 2026
Publisher: openRxiv
DOI: 10.64898/2026.03.27.714668

Peer reviewed articles (10)

Rnalib: a Python library for custom transcriptomics analyses

Author(s): Niko Popitsch, Stefan L Ameres
Published in: Bioinformatics, Issue 41, 2025, ISSN 1367-4811
Publisher: Oxford University Press (OUP)
DOI: 10.1093/bioinformatics/btae751

Structure-function analysis of microRNA 3′-end trimming by Nibbler

Author(s): Wei Xie, Ivica Sowemimo, Rippei Hayashi, Juncheng Wang, Thomas R. Burkard, Julius Brennecke, Stefan L. Ameres, Dinshaw J. Patel
Published in: Proceedings of the National Academy of Sciences, Issue 117/48, 2020, Page(s) 30370-30379, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.2018156117

Mime-seq 2.0: a method to sequence microRNAs from specific mouse cell types

Author(s): Ariane Mandlbauer, Qiong Sun, Niko Popitsch, Tanja Schwickert, Miroslava Spanova, Jingkui Wang, Stefan Ameres, Meinrad Busslinger, Luisa Cochella
Published in: EMBO Journal, 2025, ISSN 1460-2075
Publisher: EMBO Press (on behalf of European Molecular Biology Organization), in partnership with Nature Publishing Group
DOI: 10.1101/2023.11.06.565867

SLAMseq resolves the kinetics of maternal and zygotic gene expression in early zebrafish embryogenesis

Author(s): Pooja Bhat, Luis E. Cabrera-Quio, Veronika A. Herzog, Nina Fasching, Andrea Pauli, Stefan L. Ameres
Published in: Cell Reports, Issue 42,2, 2023, ISSN 2211-1247
Publisher: Cell Press
DOI: 10.1101/2022.06.01.494399

Separable roles for Microprocessor and its cofactors, ERH and SAFB1/2, during microRNA cluster assistance

Author(s): Renfu Shang, Niko Popitsch, Seungjae Lee, Stefan L. Ameres, Eric C. Lai
Published in: Genes & Development, Issue 40, 2026, Page(s) 517-537, ISSN 0890-9369
Publisher: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gad.353316.125

Hijacking of transcriptional condensates by endogenous retroviruses

Author(s): Vahid Asimi, Abhishek Sampath Kumar, Henri Niskanen, Christina Riemenschneider, Sara Hetzel, Julian Naderi, Nina Fasching, Niko Popitsch, Manyu Du, Helene Kretzmer, Zachary D. Smith, Raha Weigert, Maria Walther, Sainath Mamde, David Meierhofer, Lars Wittler, René Buschow, Bernd Timmermann, Ibrahim I. Cisse, Stefan L. Ameres, Alexander Meissner, Denes Hnisz
Published in: Nature Genetics, Issue 54, 2022, Page(s) 1238-1247, ISSN 1061-4036
Publisher: Nature Publishing Group
DOI: 10.1038/s41588-022-01132-w

Collective homeostasis of condensation-prone proteins via their mRNAs

Author(s): Rupert Faraway, Neve Costello Heaven, Holly Digby, Klara Kuret Hodnik, Jure Rebselj, Oscar G. Wilkins, Anob M. Chakrabarti, Ira A. Iosub, Neža Vadnjal, Rhys Dore, Lea Knez, Stefan L. Ameres, Clemens Plaschka, Jernej Ule
Published in: Nature, Issue 647, 2025, Page(s) 798-808, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-025-09568-w

Splice_sim: a nucleotide conversion-enabled RNA-seq simulation and evaluation framework

Author(s): Niko Popitsch, Tobias Neumann, Arndt von Haeseler, Stefan L. Ameres
Published in: Genome Biology, Issue 25, 2024, ISSN 1474-760X
Publisher: Springer Science and Business Media LLC
DOI: 10.1186/s13059-024-03313-8

Proteome-scale tagging and functional screening in mammalian cells by ORFtag

Author(s): Filip Nemčko, Moritz Himmelsbach, Vincent Loubiere, Ramesh Yelagandula, Michaela Pagani, Nina Fasching, Julius Brennecke, Ulrich Elling, Alexander Stark, Stefan L. Ameres
Published in: Nature Methods, 2025, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1101/2024.01.16.575827

Conformation of sister chromatids in the replicated human genome

Author(s): Michael Mitter, Catherina Gasser, Zsuzsanna Takacs, Christoph C. H. Langer, Wen Tang, Gregor Jessberger, Charlie T. Beales, Eva Neuner, Stefan L. Ameres, Jan-Michael Peters, Anton Goloborodko, Ronald Micura, Daniel W. Gerlich
Published in: Nature, Issue 586/7827, 2020, Page(s) 139-144, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-020-2744-4

Book chapters (1)

Systematic refinement of gene annotations by parsing mRNA 3′ end sequencing datasets

Author(s): Pooja Bhat, Thomas R. Burkard, Veronika A. Herzog, Andrea Pauli, Stefan L. Ameres
Published in: mRNA 3' End Processing and Metabolism, Issue 655, 2021, Page(s) 205-223, ISBN 9780128235737
Publisher: Elsevier
DOI: 10.1016/bs.mie.2021.03.016