ArticleJournal of bacteriology2022
Identifying Small Open Reading Frames in Prokaryotes with Ribosome Profiling.
Article in Journal of bacteriology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed, 61 citations in OpenAlex.
- Pyrrolysine supply and demand shapes the translational landscape inProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Approaches for Studying Context Specificity of Translation Inhibitor Action.International journal of molecular sciences · 2026Review
- Harnessing toxin-mediated ribosome stalling as a complementary tool to annotate bacterial ORFs.Nucleic acids research · 2026Article
- Extended Shine-Dalgarno motifs govern translation initiation in Staphylococcus aureus.Nature communications · 2026Article
- Predicted bacterial uRBSs reveal translational coupling and ribosome-mediated RBS occlusion as gene-controlling mechanisms.microLife · 2026Article
- RiboMicrobe: An Integrated Translatome Atlas for Microorganism.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Early posttranscriptional response to tetracycline exposure in a gram-negative soil bacterium reveals unexpected attenuation mechanism of a DUF1127 gene.RNA biology · 2025Article
- Comprehensive profiling of ribo-seq detected small sequences in yeast reveals robust conservation patterns and their potential mechanisms of origin.BMC genomics · 2025Article
- PIRT-Seq: a high-resolution whole-genome assay to identify protein-coding genes.Nucleic acids research · 2025Article
- Popcorn: prediction of short coding and noncoding genomic sequences in prokaryotes.Bioinformatics (Oxford, England) · 2025Article
- Complementary Ribo-seq approaches map the translatome and provide a small protein census in the foodborne pathogen Campylobacter jejuni.Nature communications · 2025Article
- RIBOSS detects novel translational events by combining long- and short-read transcriptome and translatome profiling.Briefings in bioinformatics · 2025Article
- How Small Proteins Adjust the Metabolism of Cyanobacteria Under Stress: The Role of Small Proteins in Cyanobacterial Stress Responses.BioEssays : news and reviews in molecular, cellular and developmental biology · 2025Review
- sORFdb - a database for sORFs, small proteins, and small protein families in bacteria.BMC genomics · 2025Article
- Review
- Functional diversity and molecular interactions of small membrane proteins in bacteria.microLife · 2025Review
- Uncovering the small proteome of Methanosarcina mazei using Ribo-seq and peptidomics under different nitrogen conditions.Nature communications · 2024Article
- A catalog of small proteins from the global microbiome.Nature communications · 2024Article
- A survey of experimental and computational identification of small proteins.Briefings in bioinformatics · 2024Review
- Ribosome profiling reveals downregulation of UMP biosynthesis as the major early response to phage infection.Microbiology spectrum · 2024Article
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
Abstract
Small proteins encoded by open reading frames (ORFs) shorter than 50 codons (small ORFs [sORFs]) are often overlooked by annotation engines and are difficult to characterize using traditional biochemical techniques. Ribosome profiling has tremendous potential to empirically improve the annotations of prokaryotic genomes. Recent improvements in ribosome profiling methods for bacterial model organisms have revealed many new sORFs in well-characterized genomes. Antibiotics that trap ribosomes just after initiation have played a key role in these developments by allowing the unambiguous identification of the start codons (and, hence, the reading frame) for novel ORFs. Here, we describe these new methods and highlight critical controls and considerations for adapting ribosome profiling to different prokaryotic species.
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Registered trials
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.