ReviewBriefings in functional genomics2013
Explaining microbial phenotypes on a genomic scale: GWAS for microbes.
Review in Briefings in functional genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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
35 citing papers in PubMed.
- Comparative assessment of large language models for microbial phenotype assignment.Genome biology · 2026Article
- A versatile multi-components mixed model for bacterial-Genome Wide association studies.Nature communications · 2026Article
- Article
- Genome-resolved analysis of Serratia marcescens strain SMTT infers niche specialization as a hydrocarbon-degrader.DNA research : an international journal for rapid publication of reports on genes and genomes · 2024Article
- Use of whole genome sequencing for surveillance and control of foodborne diseases:Frontiers in microbiology · 2024Review
- Combined reference-free and multi-reference based GWAS uncover cryptic variation underlying rapid adaptation in a fungal plant pathogen.PLoS pathogens · 2023Article
- Predictive modeling of antibiotic eradication therapy success for new-onset Pseudomonas aeruginosa pulmonary infections in children with cystic fibrosis.PLoS computational biology · 2023Article
- From genotype to phenotype: computational approaches for inferring microbial traits relevant to the food industry.FEMS microbiology reviews · 2023Review
- Deciphering complex antibiotic resistance patterns inFrontiers in cellular and infection microbiology · 2023Article
- Pathogenomes and variations in Shiga toxin production among geographically distinct clones ofMicrobial genomics · 2022Article
- Potential Use of Microbial Community Genomes in Various Dimensions of Agriculture Productivity and Its Management: A Review.Frontiers in microbiology · 2022Review
- Forest and Trees: Exploring Bacterial Virulence with Genome-wide Association Studies and Machine Learning.Trends in microbiology · 2021Review
- Alphaherpesvirus Genomics: Past, Present and Future.Current issues in molecular biology · 2021Review
- Temporal encoding of bacterial identity and traits in growth dynamics.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Microbial functional diversity: From concepts to applications.Ecology and evolution · 2019Review
- Uncovering carbohydrate metabolism through a genotype-phenotype association study of 56 lactic acid bacteria genomes.Applied microbiology and biotechnology · 2019Article
- Machine Learning Approaches for Epidemiological Investigations of Food-Borne Disease Outbreaks.Frontiers in microbiology · 2019Review
- Comparative Genome Analysis ofFrontiers in microbiology · 2019Article
- Current Affairs of Microbial Genome-Wide Association Studies: Approaches, Bottlenecks and Analytical Pitfalls.Frontiers in microbiology · 2019Review
- MicroPheno: predicting environments and host phenotypes from 16S rRNA gene sequencing using a k-mer based representation of shallow sub-samples.Bioinformatics (Oxford, England) · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
There is an increasing availability of complete or draft genome sequences for microbial organisms. These data form a potentially valuable resource for genotype-phenotype association and gene function prediction, provided that phenotypes are consistently annotated for all the sequenced strains. In this review, we address the requirements for successful gene-trait matching. We outline a basic protocol for microbial functional genomics, including genome assembly, annotation of genotypes (including single nucleotide polymorphisms, orthologous groups and prophages), data pre-processing, genotype-phenotype association, visualization and interpretation of results. The methodologies for association described herein can be applied to other data types, opening up possibilities to analyze transcriptome-phenotype associations, and correlate microbial population structure or activity, as measured by metagenomics, to environmental parameters.
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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.