ArticleNature communications2024
Rp3: Ribosome profiling-assisted proteogenomics improves coverage and confidence during microprotein discovery.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Large-scale mapping of microproteins in the aged human brain.Nature aging · 2026Article
- A microprotein atlas of the human frontal cortex in Alzheimer's disease.Nature aging · 2026Article
- Ribo-ITP enables identification of translons from limited input samples.Nature communications · 2026Article
- Identification of unannotated microproteins involved in endothelial cell homeostasis, dysfunction, and vascular disease.Cardiovascular research · 2026Article
- Computational identification and characterization of noncoding RNA-encoded peptides: tools, databases, and in silico strategies.Amino acids · 2026Review
- An Artificial Antibody-Based Toolbox Accelerates Validation of Hidden Microproteins Encoded by the Dark Genome.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Microproteins in Human Physiology and Pathology.Biochemistry · 2026Review
- Immunoproteomics: The Evolution from Classical Methods to Emerging Techniques.Methods in molecular biology (Clifton, N.J.) · 2026Review
- The 'non-conventional' peptidome: A new layer in plant regulatory mechanisms.Plant communications · 2025Review
- Upstream open reading frame translation enhances immunogenic peptide presentation in mitotically arrested cancer cells.Nature communications · 2025Article
- Pharmaceutical perspectives on oligonucleotide therapeutics and delivery systems.Pharmacological reviews · 2025Review
- ShortStop: a machine learning framework for microprotein discovery.BMC methods · 2025Article
- Small ORFs, Big Insights:Cells · 2024Review
- Rp3: Ribosome profiling-assisted proteogenomics improves coverage and confidence during microprotein discovery.Nature communications · 2024Article
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8 authors.
Funding
Abstract
There has been a dramatic increase in the identification of non-canonical translation and a significant expansion of the protein-coding genome. Among the strategies used to identify unannotated small Open Reading Frames (smORFs) that encode microproteins, Ribosome profiling (Ribo-Seq) is the gold standard for the annotation of novel coding sequences by reporting on smORF translation. In Ribo-Seq, ribosome-protected footprints (RPFs) that map to multiple genomic sites are removed since they cannot be unambiguously assigned to a specific genomic location. Furthermore, RPFs necessarily result in short (25-34 nucleotides) reads, increasing the chance of multi-mapping alignments, such that smORFs residing in these regions cannot be identified by Ribo-Seq. Moreover, it has been challenging to identify protein evidence for Ribo-Seq. To solve this, we developed Rp3, a pipeline that integrates proteogenomics and Ribosome profiling to provide unambiguous evidence for a subset of microproteins missed by current Ribo-Seq pipelines. Here, we show that Rp3 maximizes proteomics detection and confidence of microprotein-encoding smORFs.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.