ArticleBioinformatics (Oxford, England)2021
HRIBO: high-throughput analysis of bacterial ribosome profiling data.
Article in Bioinformatics (Oxford, England), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 13 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
13 citing papers in PubMed, 18 citations in OpenAlex.
- Abridged Ribosome Profiling for Accurate Bacterial Translation Measurements.Methods and protocols · 2026Article
- Complementary Ribo-seq approaches map the translatome and provide a small protein census in the foodborne pathogen Campylobacter jejuni.Nature communications · 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
- Functional diversity and molecular interactions of small membrane proteins in bacteria.microLife · 2025Review
- A review of Ribosome profiling and tools used in Ribo-seq data analysis.Computational and structural biotechnology journal · 2024Review
- Uncovering the small proteome of Methanosarcina mazei using Ribo-seq and peptidomics under different nitrogen conditions.Nature communications · 2024Article
- Ribosome profiling reveals the fine-tuned response ofmSystems · 2023Article
- Characterization of the zinc finger μ-protein HVO_0758 fromFrontiers in microbiology · 2023Article
- Unraveling the small proteome of the plant symbiontmicroLife · 2023Article
- Revealing the small proteome ofmicroLife · 2023Article
- RiboReport - benchmarking tools for ribosome profiling-based identification of open reading frames in bacteria.Briefings in bioinformatics · 2022Article
- Identifying Small Open Reading Frames in Prokaryotes with Ribosome Profiling.Journal of bacteriology · 2022Article
- A global data-driven census ofmicroLife · 2020Article
Corrections and comments
- Erratum issued
Authors and funding
8 authors at 2 institutions in 1 country.
Funding
Abstract
motivationRibosome profiling (Ribo-seq) is a powerful approach based on deep sequencing of cDNA libraries generated from ribosome-protected RNA fragments to explore the translatome of a cell, and is especially useful for the detection of small proteins (50-100 amino acids) that are recalcitrant to many standard biochemical and in silico approaches. While pipelines are available to analyze Ribo-seq data, none are designed explicitly for the automatic processing and analysis of data from bacteria, nor are they focused on the discovery of unannotated open reading frames (ORFs).
resultsWe present HRIBO (High-throughput annotation by Ribo-seq), a workflow to enable reproducible and high-throughput analysis of bacterial Ribo-seq data. The workflow performs all required pre-processing and quality control steps. Importantly, HRIBO outputs annotation-independent ORF predictions based on two complementary bacteria-focused tools, and integrates them with additional feature information and expression values. This facilitates the rapid and high-confidence discovery of novel ORFs and their prioritization for functional characterization. AVAILABILITY AND IMPLEMENTATION: HRIBO is a free and open source project available under the GPL-3 license at: https://github.com/RickGelhausen/HRIBO.
Indexed as
Identifiers
What OpenQuestion holds
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.