ReviewBriefings in bioinformatics2012
Bioinformatic approaches for functional annotation and pathway inference in metagenomics data.
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 32 papers.
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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.
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Who cites it
32 citing papers in PubMed.
- Towards standardization in pig microbiome research based on a comprehensive twenty-year review.Animal microbiome · 2026Review
- Article
- Multiple Profile Models Extract Features from Protein Sequence Data and Resolve Functional Diversity of Very Different Protein Families.Molecular biology and evolution · 2022Article
- The role of microbial ecology in improving the performance of anaerobic digestion of sewage sludge.Frontiers in microbiology · 2022Review
- UPIMAPI, reCOGnizer and KEGGCharter: Bioinformatics tools for functional annotation and visualization of (meta)-omics datasets.Computational and structural biotechnology journal · 2022Article
- Article
- Composition and Metabolic Functions of the Microbiome in Fermented Grain during Light-FlavorMicroorganisms · 2020Article
- Targeted domain assembly for fast functional profiling of metagenomic datasets with S3A.Bioinformatics (Oxford, England) · 2020Article
- CSN: unsupervised approach for inferring biological networks based on the genome alone.BMC bioinformatics · 2020Article
- Review
- Article
- The use of next generation sequencing for improving food safety: Translation into practice.Food microbiology · 2019Review
- Shotgun Metagenomics of a Water Kefir Fermentation Ecosystem Reveals a NovelFrontiers in microbiology · 2019Article
- A multi-source domain annotation pipeline for quantitative metagenomic and metatranscriptomic functional profiling.Microbiome · 2018Article
- Microbial survival strategies in ancient permafrost: insights from metagenomics.The ISME journal · 2017Article
- A Metagenomic Approach to Cyanobacterial Genomics.Frontiers in microbiology · 2017Review
- An automated system for evaluation of the potential functionome: MAPLE version 2.1.0.DNA research : an international journal for rapid publication of reports on genes and genomes · 2016Article
- An analysis of the validity and utility of the proximon proposition.Functional & integrative genomics · 2016Article
- A Bayesian inference method for the analysis of transcriptional regulatory networks in metagenomic data.Algorithms for molecular biology : AMB · 2016Article
- VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires.PLoS computational biology · 2015Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Metagenomic approaches are increasingly recognized as a baseline for understanding the ecology and evolution of microbial ecosystems. The development of methods for pathway inference from metagenomics data is of paramount importance to link a phenotype to a cascade of events stemming from a series of connected sets of genes or proteins. Biochemical and regulatory pathways have until recently been thought and modelled within one cell type, one organism, one species. This vision is being dramatically changed by the advent of whole microbiome sequencing studies, revealing the role of symbiotic microbial populations in fundamental biochemical functions. The new landscape we face requires a clear picture of the potentialities of existing tools and development of new tools to characterize, reconstruct and model biochemical and regulatory pathways as the result of integration of function in complex symbiotic interactions of ontologically and evolutionary distinct cell types.
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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.