{
  "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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  "affiliations": [
    "Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), University Hospital Heidelberg , Im Neuenheimer Feld 669, 69120 Heidelberg ,",
    "Klaus Tschira Institute for Integrative Computational Cardiology, University of Heidelberg , Im Neuenheimer Feld 669, 69120 Heidelberg ,",
    "German Center for Cardiovascular Research (DZHK) – Partner site Heidelberg/Mannheim , Im Neuenheimer Feld 410, 69120 Heidelberg ,",
    "Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Mannheim Cancer Center, Medical Faculty Mannheim, Heidelberg University , Franz-Volhard-Str. 6, 68167 Mannheim ,",
    "Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance , 69120 Heidelberg ,",
    "Max Delbrück Center for Molecular Medicine (MDC) , Robert-Rössle-Straße 10, 13125 Berlin ,",
    "Berlin Institute of Health at Charité – Universitätsmedizin Berlin , Charitéplatz 1, 10117 Berlin ,"
  ],
  "article_type": "brief report",
  "arxiv": null,
  "author_total": 7,
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        1,
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      "name": "Etienne Boileau",
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      "name": "Maja Bencun"
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      "name": "Francesca Tuorto",
      "orcid": "0000-0003-1625-1181"
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      "name": "Isabel S Naarmann-de Vries",
      "orcid": "0000-0002-8115-5412"
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      "name": "Pauline Fahjen"
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      "name": "Philipp Mertins"
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    {
      "affs": [
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        1,
        2
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      "name": "Christoph Dieterich",
      "orcid": "0000-0001-9468-6311"
    }
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  "doi": "10.1093/nargab/lqag130",
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  "native_subjects": [
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      "heading",
      "Computational Methods for Transcriptome Analysis"
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  "pdf_url": "https://academic.oup.com/nargab/article-pdf/8/4/lqag130/72841802/lqag130.pdf",
  "pmcid": "PMC13728661",
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  "published": "2026-11-03",
  "publisher": "Oxford University Press (OUP)",
  "ris": "https://research.draconitic.com/paper/86rzvzag957tp.ris",
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  "subjects": [
    {
      "field": "biology",
      "origin": "issn:2631-9268",
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  "title": "Rp-Bp and the Ribotools box for translatome profiling",
  "title_text": "Rp-Bp and the Ribotools box for translatome profiling",
  "type": "peer-reviewed",
  "updated_at": "2026-11-07T12:21:36Z",
  "url": "https://research.draconitic.com/paper/86rzvzag957tp",
  "venue": "NAR Genomics and Bioinformatics",
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