ArticleNucleic acids research2017
REPARATION: ribosome profiling assisted (re-)annotation of bacterial genomes.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed, 67 citations in OpenAlex.
- Advances in Decoding Bacterial N-Terminal Proteoforms: Technologies, Challenges, and Functional Insights.Microorganisms · 2026Review
- TRAINSPOTTER: profiling nascent protein N-termini indicative of bacterial translation initiation via deformylation-assisted N-terminomics.Nucleic acids research · 2026Article
- Abridged Ribosome Profiling for Accurate Bacterial Translation Measurements.Methods and protocols · 2026Article
- Predicted bacterial uRBSs reveal translational coupling and ribosome-mediated RBS occlusion as gene-controlling mechanisms.microLife · 2026Article
- Propensity for proto-gene emergence in bacteria.Genome biology · 2025Article
- Investigation of the global translational response to oxidative stress in the model archaeonmSphere · 2025Article
- De novo gene birth and the conundrum of ORFan genes in bacteria.Genome research · 2025Review
- Complementary Ribo-seq approaches map the translatome and provide a small protein census in the foodborne pathogen Campylobacter jejuni.Nature communications · 2025Article
- Unraveling N-Terminal Proteoform Interactomes via Multiplexed Recombineering in Salmonella.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Article
- Uncovering the small proteome of Methanosarcina mazei using Ribo-seq and peptidomics under different nitrogen conditions.Nature communications · 2024Article
- Proteins à la carte: riboproteogenomic exploration of bacterial N-terminal proteoform expression.mBio · 2024Article
- Machine Learning and Deep Learning in Synthetic Biology: Key Architectures, Applications, and Challenges.ACS omega · 2024Review
- ORFeus: a computational method to detect programmed ribosomal frameshifts and other non-canonical translation events.BMC bioinformatics · 2023Article
- Exposing the small protein load of bacterial life.FEMS microbiology reviews · 2023Review
- Revealing the small proteome ofmicroLife · 2023Article
- Unraveling the small proteome of the plant symbiontmicroLife · 2023Article
- From prediction to function: Current practices and challenges towards the functional characterization of type III effectors.Frontiers in microbiology · 2023Review
- Thousands of small, novel genes predicted in global phage genomes.Cell reports · 2022Article
- RiboReport - benchmarking tools for ribosome profiling-based identification of open reading frames in bacteria.Briefings in bioinformatics · 2022Article
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Prokaryotic genome annotation is highly dependent on automated methods, as manual curation cannot keep up with the exponential growth of sequenced genomes. Current automated methods depend heavily on sequence composition and often underestimate the complexity of the proteome. We developed RibosomeE Profiling Assisted (re-)AnnotaTION (REPARATION), a de novo machine learning algorithm that takes advantage of experimental protein synthesis evidence from ribosome profiling (Ribo-seq) to delineate translated open reading frames (ORFs) in bacteria, independent of genome annotation (https://github.com/Biobix/REPARATION). REPARATION evaluates all possible ORFs in the genome and estimates minimum thresholds based on a growth curve model to screen for spurious ORFs. We applied REPARATION to three annotated bacterial species to obtain a more comprehensive mapping of their translation landscape in support of experimental data. In all cases, we identified hundreds of novel (small) ORFs including variants of previously annotated ORFs and >70% of all (variants of) annotated protein coding ORFs were predicted by REPARATION to be translated. Our predictions are supported by matching mass spectrometry proteomics data, sequence composition and conservation analysis. REPARATION is unique in that it makes use of experimental translation evidence to intrinsically perform a de novo ORF delineation in bacterial genomes irrespective of the sequence features linked to open reading frames.
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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.