ArticleCell reports2022
Thousands of small, novel genes predicted in global phage genomes.
Article in Cell reports, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed.
- Genomic analysis of prophage prevalence and diversity in the bovine mastitis pathogenMicrobial genomics · 2026Article
- Isolation, Characterization, and In Vivo Evaluation Efficacy of Lytic Bacteriophage SEP1 AgainstViruses · 2026Article
- ssRNA bacteriophage metagenomes reveal a diverse set of novel protein families.Protein science : a publication of the Protein Society · 2026Article
- Article
- Viromics approaches for the study of viral diversity and ecology in microbiomes.Nature reviews. Genetics · 2026Review
- CoMPaseD: advanced planning of proteomic experiments aiming to identify small proteins.microLife · 2026Article
- Viral Dark Matter: Illuminating Protein Function, Ecology, and Biotechnological Promises.Biochemistry · 2025Review
- De novo origin of numerous microproteins in enterobacteria.Nucleic acids research · 2025Article
- Effect of an antibiotic and a probiotic on phage communities in the swine gut microbiota.BMC research notes · 2025Article
- De novo gene birth and the conundrum of ORFan genes in bacteria.Genome research · 2025Review
- Fold first, ask later: structure-informed function annotation ofbioRxiv : the preprint server for biology · 2025Article
- Viral Dark Matter: Illuminating Protein Function, Ecology, and Biotechnological Promises.ArXiv · 2025Article
- Popcorn: prediction of short coding and noncoding genomic sequences in prokaryotes.Bioinformatics (Oxford, England) · 2025Article
- The hidden bacterial microproteome.Molecular cell · 2025Article
- SProtFP: a machine learning-based method for functional classification of small ORFs in prokaryotes.NAR genomics and bioinformatics · 2025Article
- Article
- Article
- Elucidation of molecular function of phage protein responsible for optimization of host cell lysis.BMC microbiology · 2024Article
- Preclinical characterization and in silico safety assessment of three virulent bacteriophages targeting carbapenem-resistant uropathogenic Escherichia coli.International microbiology : the official journal of the Spanish Society for Microbiology · 2024Article
- A catalog of small proteins from the global microbiome.Nature communications · 2024Article
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Authors and funding
4 authors.
Funding
Abstract
Small genes (<150 nucleotides) have been systematically overlooked in phage genomes. We employ a large-scale comparative genomics approach to predict >40,000 small-gene families in ∼2.3 million phage genome contigs. We find that small genes in phage genomes are approximately 3-fold more prevalent than in host prokaryotic genomes. Our approach enriches for small genes that are translated in microbiomes, suggesting the small genes identified are coding. More than 9,000 families encode potentially secreted or transmembrane proteins, more than 5,000 families encode predicted anti-CRISPR proteins, and more than 500 families encode predicted antimicrobial proteins. By combining homology and genomic-neighborhood analyses, we reveal substantial novelty and diversity within phage biology, including small phage genes found in multiple host phyla, small genes encoding proteins that play essential roles in host infection, and small genes that share genomic neighborhoods and whose encoded proteins may share related functions.
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