ReviewBriefings in bioinformatics2012
Current opportunities and challenges in microbial metagenome analysis--a bioinformatic perspective.
Review in Briefings in bioinformatics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 90 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
90 citing papers in PubMed.
- Gut microbial community of patients with Parkinson's disease analyzed using metagenome-assembled genomes.Neural regeneration research · 2026Article
- Tracing non-fungal eukaryotic diversity via shotgun metagenomes in the complex mudflat intertidal zones.mSystems · 2025Article
- Article
- Benchmarking and optimizing qualitative and quantitative pipelines in environmental metatranscriptomics using mixture controlling experiments.ISME communications · 2025Article
- Effects of plants-associated microbiota on cultivation and quality of Chinese herbal medicines.Chinese herbal medicines · 2024Review
- Cyanobacterial Genomes from a Brackish Coastal Lagoon Reveal Potential for Novel Biogeochemical Functions and Their Evolution.Journal of molecular evolution · 2024Article
- MetaBIDx: a new computational approach to bacteria identification in microbiomes.Microbiome research reports · 2024Article
- Environmental Effects on Bee Microbiota.Microbial ecology · 2023Review
- Recent Advances in Metagenomic Approaches, Applications, and Challenge.Current microbiology · 2023Review
- AirDNA sampler: An efficient and simple device enabling high-yield, high-quality airborne environment DNA for metagenomic applications.PloS one · 2023Article
- LMAS: evaluating metagenomic short de novo assembly methods through defined communities.GigaScience · 2022Article
- Impact of Stagnation on the Diversity of Cyanobacteria in Drinking Water Treatment Plant Sludge.Toxins · 2022Article
- Microbiota Communities of Healthy and Bacterial Pustule Diseased Soybean.The plant pathology journal · 2022Article
- Recent Advances of Marine Sponge-Associated Microorganisms as a Source of Commercially Viable Natural Products.Marine biotechnology (New York, N.Y.) · 2022Review
- Delineation of mechanistic approaches of rhizosphere microorganisms facilitated plant health and resilience under challenging conditions.3 Biotech · 2022Review
- A Bacterial Genome and Culture Collection of Gut Microbial in Weanling Piglet.Microbiology spectrum · 2022Article
- Article
- Representing bacteria with unique genomic signatures.Frontiers in big data · 2022Article
- Reconstruction of Archaeal Genomes from Short-Read Metagenomes.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Insufficiency in functional genomics studies, data, and applications: A case study of bio-prospecting research in ruminant microbiome.Frontiers in genetics · 2022Review
30 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Metagenomics has become an indispensable tool for studying the diversity and metabolic potential of environmental microbes, whose bulk is as yet non-cultivable. Continual progress in next-generation sequencing allows for generating increasingly large metagenomes and studying multiple metagenomes over time or space. Recently, a new type of holistic ecosystem study has emerged that seeks to combine metagenomics with biodiversity, meta-expression and contextual data. Such 'ecosystems biology' approaches bear the potential to not only advance our understanding of environmental microbes to a new level but also impose challenges due to increasing data complexities, in particular with respect to bioinformatic post-processing. This mini review aims to address selected opportunities and challenges of modern metagenomics from a bioinformatics perspective and hopefully will serve as a useful resource for microbial ecologists and bioinformaticians alike.
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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.