ReviewMicrobiology and molecular biology reviews : MMBR2025
Computational function prediction of bacteria and phage proteins.
Review in Microbiology and molecular biology reviews : MMBR, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers, 1 of them a synthesis that pooled it.
What it found
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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
11 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Precision phage therapy in the AI/ML era: a systematic review of discovery-to-clinical translation evidence.Frontiers in microbiology · 2026Pooled it
- In silico structural and functional characterisation of two hypothetical proteins from the plant‑associated bacterium Kosakonia cowanii F52.Genomics & informatics · 2026Article
- LAMBDA: a prophage detection benchmark for genomic language models.NAR genomics and bioinformatics · 2026Article
- Phage bioinformatics tools: a review of computational approaches for bacteriophage research.Briefings in bioinformatics · 2026Review
- Decoding Viral Dark Matter: Metagenomic Prokaryotic Virus Characterization With Pharokka, Phold, and Phynteny.Current protocols · 2026Article
- Computational prediction resolves thousands of homooligomeric phage protein structures.bioRxiv : the preprint server for biology · 2026Article
- LAMBDA: A Prophage Detection Benchmark for Genomic Language Models.bioRxiv : the preprint server for biology · 2026Article
- A Century-Old Solution for 21st Century Challenges: Current Applications with a Focus on Biocontrol, Environmental Impacts, and Regulatory Perspectives.Antibiotics (Basel, Switzerland) · 2026Review
- The Role of Genomics in Advancing and Standardising Bacteriophage Therapy.Antibiotics (Basel, Switzerland) · 2026Review
- The lung microbiome and asthma: from inflammatory phenotype differentiation to microbe-based immunomodulatory strategies.Frontiers in immunology · 2026Review
- Genomic and functional analysis of stress-responsive prophages inFrontiers in microbiology · 2026Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
SUMMARYUnderstanding protein functions is crucial for interpreting microbial life; however, reliable function annotation remains a major challenge in computational biology. Despite significant advances in bioinformatics methods, ~30% of all bacterial and ~65% of all bacteriophage (phage) protein sequences cannot be confidently annotated. In this review, we examine state-of-the-art bioinformatics tools and methodologies for annotating bacterial and phage proteins, particularly those of unknown or poorly characterized function. We describe the process of identifying protein-coding regions and the systems to classify protein functionalities. Additionally, we explore a range of protein annotation methods, from traditional homology-based methods to cutting-edge machine learning models. In doing so, we provide a toolbox for confidently annotating previously unknown bacterial and phage proteins, advancing the discovery of novel functions and our understanding of microbial systems.
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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.