ArticleCell host & microbe2021
Automated Prediction and Annotation of Small Open Reading Frames in Microbial Genomes.
Article in Cell host & microbe, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed, 57 citations in OpenAlex.
- Artificial Intelligence-Driven Antimicrobial Peptide Discovery: Prediction, Generation, Mining and Optimization.Probiotics and antimicrobial proteins · 2026Review
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- Dual Activity Microbial Peptides Catalog.Scientific data · 2026Article
- High-resolution multi-omics enhances prediction and detection of smORF-encoded proteins in the human gut microbiome.Nature communications · 2026Article
- Harnessing toxin-mediated ribosome stalling as a complementary tool to annotate bacterial ORFs.Nucleic acids research · 2026Article
- SGAC: a graph neural network framework for imbalanced and structure-aware AMP classification.Briefings in bioinformatics · 2026Article
- TPT: a compact CNN-transformer encoder for efficient microbial small protein modeling.Frontiers in microbiology · 2026Article
- MetaPepticon: automated prediction of anticancer peptides from microbial genomes and metagenomes.PeerJ · 2026Article
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- Propensity for proto-gene emergence in bacteria.Genome biology · 2025Article
- A deep reinforcement learning platform for antibiotic discovery.bioRxiv : the preprint server for biology · 2025Article
- De novo gene birth and the conundrum of ORFan genes in bacteria.Genome research · 2025Review
- Cutting-edge deep-learning based tools for metagenomic research.National science review · 2025Review
- Eukaryotic Microproteins.Annual review of biochemistry · 2025Review
- Genomic insights into the spread of methicillin-resistant Staphylococcus aureus involved in ear infections.BMC infectious diseases · 2025Article
- 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
- ShortStop: a machine learning framework for microprotein discovery.BMC methods · 2025Article
- Article
- Origins of Life: The Protein Folding Problem all over again?Proceedings of the National Academy of Sciences of the United States of America · 2024Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Small open reading frames (smORFs) and their encoded microproteins play central roles in microbes. However, there is a vast unexplored space of smORFs within human-associated microbes. A recent bioinformatic analysis used evolutionary conservation signals to enhance prediction of small protein families. To facilitate the annotation of specific smORFs, we introduce SmORFinder. This tool combines profile hidden Markov models of each smORF family and deep learning models that better generalize to smORF families not seen in the training set, resulting in predictions enriched for Ribo-seq translation signals. Feature importance analysis reveals that the deep learning models learn to identify Shine-Dalgarno sequences, deprioritize the wobble position in each codon, and group codon synonyms found in the codon table. A core-genome analysis of 26 bacterial species identifies several core smORFs of unknown function. We pre-compute smORF annotations for thousands of RefSeq isolate genomes and Human Microbiome Project metagenomes and provide these data through a public web portal.
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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.