ArticleNucleic acids research2019
DeepRibo: a neural network for precise gene annotation of prokaryotes by combining ribosome profiling signal and binding site patterns.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed, 88 citations in OpenAlex.
- Inferring translational efficiency from transcriptomes improves noncanonical neoantigen prioritization and cancer patient stratification.NPJ precision oncology · 2026Article
- Bridging single-molecule and genome-wide studies of cellular mRNA translation.RNA (New York, N.Y.) · 2026Review
- 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
- Microproteins in Metabolic Biology: Emerging Functions and Potential Roles as Nutrient-Linked Biomarkers.International journal of molecular sciences · 2025Review
- RiboMicrobe: An Integrated Translatome Atlas for Microorganism.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Recent advances of muconic acid production using microbial synthetic biology.Archives of microbiology · 2025Review
- Machine Learning Empowering Microbial Cell Factory: A Comprehensive Review.Applied biochemistry and biotechnology · 2025Review
- Complementary Ribo-seq approaches map the translatome and provide a small protein census in the foodborne pathogen Campylobacter jejuni.Nature communications · 2025Article
- The hidden bacterial microproteome.Molecular cell · 2025Article
- Uncovering the small proteome of Methanosarcina mazei using Ribo-seq and peptidomics under different nitrogen conditions.Nature communications · 2024Article
- A Comprehensive Review of Bioinformatics Tools for Genomic Biomarker Discovery Driving Precision Oncology.Genes · 2024Review
- 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
- The Cryptic Bacterial Microproteome.bioRxiv : the preprint server for biology · 2024Article
- Review
- Integrated sequence and -omic features reveal novel small proteome ofFrontiers in microbiology · 2024Article
- Ribosome profiling reveals the fine-tuned response ofmSystems · 2023Article
- Principles, challenges, and advances in ribosome profiling: from bulk to low-input and single-cell analysis.Advanced biotechnology · 2023Review
- Small proteins in Gram-positive bacteria.FEMS microbiology reviews · 2023Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Annotation of gene expression in prokaryotes often finds itself corrected due to small variations of the annotated gene regions observed between different (sub)-species. It has become apparent that traditional sequence alignment algorithms, used for the curation of genomes, are not able to map the full complexity of the genomic landscape. We present DeepRibo, a novel neural network utilizing features extracted from ribosome profiling information and binding site sequence patterns that shows to be a precise tool for the delineation and annotation of expressed genes in prokaryotes. The neural network combines recurrent memory cells and convolutional layers, adapting the information gained from both the high-throughput ribosome profiling data and ribosome binding translation initiation sequence region into one model. DeepRibo is designed as a single model trained on a variety of ribosome profiling experiments, used for the identification of open reading frames in prokaryotes without a priori knowledge of the translational landscape. Through extensive validation of the model trained on various sets of data, multiple species sequence similarity, mass spectrometry and Edman degradation verified proteins, the effectiveness of DeepRibo is highlighted.
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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.