ArticlePLoS computational biology2005
Bioinformatics for whole-genome shotgun sequencing of microbial communities.
Article in PLoS computational biology, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 136 papers, 1 of them a synthesis that pooled it.
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
136 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Gastrointestinal surgery and the gut microbiome: a systematic literature review.European journal of clinical nutrition · 2021Pooled it
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- Decoding extremophiles: insights from bioinformatics, machine learning, and data-driven approaches.Briefings in bioinformatics · 2026Review
- Artificial Intelligence for Microbial Isolation and Cultivation: Progress and Challenges.Microorganisms · 2026Review
- Mining Microbial Dark Matter: Advanced Cultivation Techniques for Bioactive Compound Discovery.Pharmaceuticals (Basel, Switzerland) · 2025Review
- Predicting coarse-grained representations of biogeochemical cycles from metabarcoding data.Bioinformatics (Oxford, England) · 2025Article
- Differences in Microbial Community Structure Determine the Functional Specialization of Gut Segments ofMicroorganisms · 2025Article
- Effect of folpet on hypoglycaemia, intestinal microbiota, and drug resistance genes in mice.BMC microbiology · 2025Article
- Bioinformatic Methodologies in Assessing Gut Microbiota.Microbiology research · 2024Article
- Establishing the longitudinal hemodynamic mapping framework for wearable-driven coronary digital twins.NPJ digital medicine · 2024Article
- Mechanism-guided strategies for combating antibiotic resistance.World journal of microbiology & biotechnology · 2024Review
- Breaking the Cycle: A Yeast Mannan-Rich Fraction Beneficially Modulates Egg Quality and the Antimicrobial Resistome Associated with Layer Hen Caecal Microbiomes under Commercial Conditions.Microorganisms · 2024Article
- Maternal high fat diet induces circadian clock-independent endocrine alterations impacting the metabolism of the offspring.iScience · 2024Article
- Influence ofHeliyon · 2024Article
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- Improving Bacterial Metagenomic Research through Long-Read Sequencing.Microorganisms · 2024Article
- Coffee and Microbiota: A Narrative Review.Current issues in molecular biology · 2024Review
- Metagenome and Resistome Analysis of Beta-Lactam-Resistant Bacteria Isolated from River Waters in Surabaya, Indonesia.Microorganisms · 2024Article
- Analysis on microbial communities and characteristic flavor metabolic of PXDB-meju by partially substituting wheat flour with soybean flour and gluten flour.Current research in food science · 2024Article
- Article
76 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
The application of whole-genome shotgun sequencing to microbial communities represents a major development in metagenomics, the study of uncultured microbes via the tools of modern genomic analysis. In the past year, whole-genome shotgun sequencing projects of prokaryotic communities from an acid mine biofilm, the Sargasso Sea, Minnesota farm soil, three deep-sea whale falls, and deep-sea sediments have been reported, adding to previously published work on viral communities from marine and fecal samples. The interpretation of this new kind of data poses a wide variety of exciting and difficult bioinformatics problems. The aim of this review is to introduce the bioinformatics community to this emerging field by surveying existing techniques and promising new approaches for several of the most interesting of these computational problems.
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.