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| Item Type: | Article |
|---|---|
| Title: | Rp-Bp and the Ribotools box for translatome profiling |
| Creators: |
Boileau, Etienne  ORCID: https://orcid.org/0000-0001-9355-0973, Bencun, Maja, Tuorto, Francesca ORCID: https://orcid.org/0000-0003-1625-1181, Vries, Isabel S Naarmann-de ORCID: https://orcid.org/0000-0002-8115-5412, Fahjen, Pauline ORCID: https://orcid.org/0000-0002-5015-0643, Mertins, Philipp ORCID: https://orcid.org/0000-0002-2245-528X and Dieterich, Christoph ORCID: https://orcid.org/0000-0001-9468-6311
|
| 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. |
| Keywords: | Cardiac Myocytes, Cell Differentiation, Induced Pluripotent Stem Cells, Open Reading Frames, Protein Biosynthesis, Proteomics, Ribosome Profiling, Software |
| Source: | NAR Genomics and Bioinformatics |
| ISSN: | 2631-9268 |
| Publisher: | Oxford University Press |
| Volume: | 8 |
| Number: | 4 |
| Page Range: | lqag130 |
| Date: | December 2026 |
| Official Publication: | https://doi.org/10.1093/nargab/lqag130 |
| PubMed: | View item in PubMed |
| Related to: |
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