ArticleJournal of computer science and technology2009
Metagenomics: Facts and Artifacts, and Computational Challenges*
Article in Journal of computer science and technology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 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.
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Who cites it
64 citing papers in PubMed.
- Intestinal microbiota in healthy adults: temporal analysis reveals individual and common core and relation to intestinal symptoms.PloS one · 2011Trial
- MOSHPIT: Accessible, reproducible metagenome data science on the QIIME 2 framework.Cell genomics · 2026Article
- Droplet microfluidics strategies for overcoming bottlenecks in antibiotics discovery.iScience · 2026Review
- Microbiome Single Cell Atlases Generated with a Commercial Instrument.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Endophytic Diversity inBiology · 2025Article
- Integration of unpaired single cell omics data by deep transfer graph convolutional network.PLoS computational biology · 2025Article
- Compendium of 5810 genomes of sheep and goat gut microbiomes provides new insights into the glycan and mucin utilization.Microbiome · 2024Article
- Microbiome as a biomarker and therapeutic target in pancreatic cancer.BMC microbiology · 2024Review
- Molecular diagnostic approaches for SARS-CoV-2 detection and pathophysiological consequences.Molecular biology reports · 2023Review
- Article
- Microbiome single cell atlases generated with a commercial instrument.Research square · 2023Article
- Review
- Combining Flow Cytometry and Metagenomics Improves Recovery of Metagenome-Assembled Genomes in a Cell Culture from Activated Sludge.Microorganisms · 2023Article
- Prenatal lead exposure is negatively associated with the gut microbiome in childhood.Frontiers in microbiology · 2023Article
- The human microbiome: A promising target for lung cancer treatment.Frontiers in immunology · 2023Review
- Marine Bioprospecting, Biocatalysis and Process Development.Microorganisms · 2022Review
- An Appraisal of Bacteriophage Isolation Techniques from Environment.Microbial ecology · 2022Review
- Metabarcoding of Parasitic Wasp,Tropical life sciences research · 2022Article
- A metagenomic insight into the Yangtze finless porpoise virome.Frontiers in veterinary science · 2022Article
- Cultivating marine bacteria under laboratory conditions: Overcoming the "unculturable" dogma.Frontiers in bioengineering and biotechnology · 2022Article
4 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
Abstract
Metagenomics is the study of microbial communities sampled directly from their natural environment, without prior culturing. By enabling an analysis of populations including many (so-far) unculturable and often unknown microbes, metagenomics is revolutionizing the field of microbiology, and has excited researchers in many disciplines that could benefit from the study of environmental microbes, including those in ecology, environmental sciences, and biomedicine. Specific computational and statistical tools have been developed for metagenomic data analysis and comparison. New studies, however, have revealed various kinds of artifacts present in metagenomics data caused by limitations in the experimental protocols and/or inadequate data analysis procedures, which often lead to incorrect conclusions about a microbial community. Here, we review some of the artifacts, such as overestimation of species diversity and incorrect estimation of gene family frequencies, and discuss emerging computational approaches to address them. We also review potential challenges that metagenomics may encounter with the extensive application of next-generation sequencing (NGS) techniques.
Identifiers
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.