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Peer-reviewedCC BY 4.0NAR Genomics and Bioinformatics

Rp-Bp and the Ribotools box for translatome profiling

  • Etienne Boileau1,2,3
  • Maja Bencun1,2,3
  • Francesca Tuorto4,5
  • Isabel S Naarmann-de Vries1,2,3
  • Pauline Fahjen6
  • Philipp Mertins6,7
  • Christoph Dieterich1,2,3
7 affiliations
  1. 1Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), University Hospital Heidelberg , Im Neuenheimer Feld 669, 69120 Heidelberg ,
  2. 2Klaus Tschira Institute for Integrative Computational Cardiology, University of Heidelberg , Im Neuenheimer Feld 669, 69120 Heidelberg ,
  3. 3German Center for Cardiovascular Research (DZHK) – Partner site Heidelberg/Mannheim , Im Neuenheimer Feld 410, 69120 Heidelberg ,
  4. 4Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Mannheim Cancer Center, Medical Faculty Mannheim, Heidelberg University , Franz-Volhard-Str. 6, 68167 Mannheim ,
  5. 5Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance , 69120 Heidelberg ,
  6. 6Max Delbrück Center for Molecular Medicine (MDC) , Robert-Rössle-Straße 10, 13125 Berlin ,
  7. 7Berlin Institute of Health at Charité – Universitätsmedizin Berlin , Charitéplatz 1, 10117 Berlin ,
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Abstract

We present the Ribotools “box” for the analysis of matched ribosome profiling (Ribo-seq) and RNA sequencing data. Ribotools can be used in standalone mode or in combination with Rp-Bp for Ribo-seq quality control, open reading frames discovery, translation efficiency, and differential expression analyses. In this work, we use Ribotools to profile the differentiation of human induced pluripotent stem cells (hiPSCs) into cardiomyocytes to reveal a remarkably coherent transition from plastic, signaling-driven to stable, structurally committed cardiac cells, staged through multiple layers of translational control. Together with complementary proteomics, the resulting dataset provides a rich multi-omics resource for investigating the hiPSC model of cardiac lineage commitment. Additionally, we present a reproducible and extensible pipeline for benchmarking translation efficiency analysis tools. Ribotools and Rp-Bp are available on Bioconda and help to make research accessible and reproducible. Detailed documentation, test datasets, and tutorials are available at https://ribotools.readthedocs.io and https://rp-bp.readthedocs.io.

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Cite

BibTeXRIS
BibTeX
@article{boileau2026rpbp,
  title = {{Rp-Bp and the Ribotools box for translatome profiling}},
  author = {Etienne Boileau and Maja Bencun and Francesca Tuorto and Isabel S Naarmann-de Vries and Pauline Fahjen and Philipp Mertins and Christoph Dieterich},
  journal = {NAR Genomics and Bioinformatics},
  year = {2026},
  month = nov,
  doi = {10.1093/nargab/lqag130},
  url = {https://academic.oup.com/nargab/article/doi/10.1093/nargab/lqag130/9010720},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - Rp-Bp and the Ribotools box for translatome profiling
AU  - Etienne Boileau
AU  - Maja Bencun
AU  - Francesca Tuorto
AU  - Isabel S Naarmann-de Vries
AU  - Pauline Fahjen
AU  - Philipp Mertins
AU  - Christoph Dieterich
PY  - 2026
DA  - 2026/11/03
JO  - NAR Genomics and Bioinformatics
DO  - 10.1093/nargab/lqag130
UR  - https://academic.oup.com/nargab/article/doi/10.1093/nargab/lqag130/9010720
AB  - We present the Ribotools “box” for the analysis of matched ribosome profiling (Ribo-seq) and RNA sequencing data. Ribotools can be used in standalone mode or in combination with Rp-Bp for Ribo-seq quality control, open reading frames discovery, translation efficiency, and differential expression analyses. In this work, we use Ribotools to profile the differentiation of human induced pluripotent stem cells (hiPSCs) into cardiomyocytes to reveal a remarkably coherent transition from plastic, signaling-driven to stable, structurally committed cardiac cells, staged through multiple layers of translational control. Together with complementary proteomics, the resulting dataset provides a rich multi-omics resource for investigating the hiPSC model of cardiac lineage commitment. Additionally, we present a reproducible and extensible pipeline for benchmarking translation efficiency analysis tools. Ribotools and Rp-Bp are available on Bioconda and help to make research accessible and reproducible. Detailed documentation, test datasets, and tutorials are available at https://ribotools.readthedocs.io and https://rp-bp.readthedocs.io.
SN  - 2631-9268
ER  -