ReviewBriefings in bioinformatics2024
Current approaches and outstanding challenges of functional annotation of metabolites: a comprehensive review.
Review in Briefings in bioinformatics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 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
16 citing papers in PubMed.
- Comparative genomics approaches to identify genomic regions associated with the antimicrobial activity ofMicrobial genomics · 2026Article
- Application of Metabolomics in the Exploration of Bioactive Compounds and Drug Development from Medicinal Fungi.Metabolites · 2026Review
- PMconv: How to Compare Proteomes and Metabolomes?International journal of molecular sciences · 2026Article
- Plasma Metabolomics Reveals a Shared Metabolomic Profile in Experimental and Human Chronic Kidney Disease.Toxins · 2026Article
- TidyMass2: advancing LC-MS untargeted metabolomics through metabolite origin inference and metabolic feature-based functional module analysis.Nature communications · 2026Article
- Metabolite coupling analysis and metabolite-flux coupling analysis of genome-scale metabolic models.Frontiers in bioinformatics · 2026Article
- Multiomics Approaches for Bacteriophage-Based Biocontrol Applications: A Review of Metabolomics, Transcriptomics, and Proteomics.BioMed research international · 2026Review
- Applications of Metabolomics in the Development of Biomedicine and Biotechnology.Advances in experimental medicine and biology · 2026Review
- The data substrate of exposome intelligence: an interoperability profile for untargeted metabolomics.Frontiers in artificial intelligence · 2026Article
- Beyond Bulk Metabolomics: Emerging Technologies for Defining Cell-Type Specific Metabolic Pathways in Health and Disease.Biomolecules · 2025Review
- Multi-omic data integration and exploiting metabolic models using systems biology approach increase precision in subtyping and early diagnosis of cancer.Quantitative biology (Beijing, China) · 2025Article
- Advances in Functional Genomics for Exploring Abiotic Stress Tolerance Mechanisms in Cereals.Plants (Basel, Switzerland) · 2025Review
- The Future of a Myriad of Accelerated Biodiscoveries Lies in AI-Powered Mass Spectrometry and Multiomics Integration.Journal of mass spectrometry : JMS · 2025Article
- Gene-Embedded Multi-Modal Networks for Population-Scale Multi-Omics Discovery.bioRxiv : the preprint server for biology · 2025Article
- NeuroFANN: identification of neuropathological subtypes in dementia with plasma proteins by using functionally annotated neural network.Briefings in bioinformatics · 2025Article
- Functional Annotation of Altered Root Metabolites and Metabolic Pathways in Spring Wheat Cultivars Under Varying Salinity and Photoperiod.Physiologia plantarumArticle
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
Metabolite profiling is a powerful approach for the clinical diagnosis of complex diseases, ranging from cardiometabolic diseases, cancer, and cognitive disorders to respiratory pathologies and conditions that involve dysregulated metabolism. Because of the importance of systems-level interpretation, many methods have been developed to identify biologically significant pathways using metabolomics data. In this review, we first describe a complete metabolomics workflow (sample preparation, data acquisition, pre-processing, downstream analysis, etc.). We then comprehensively review 24 approaches capable of performing functional analysis, including those that combine metabolomics data with other types of data to investigate the disease-relevant changes at multiple omics layers. We discuss their availability, implementation, capability for pre-processing and quality control, supported omics types, embedded databases, pathway analysis methodologies, and integration techniques. We also provide a rating and evaluation of each software, focusing on their key technique, software accessibility, documentation, and user-friendliness. Following our guideline, life scientists can easily choose a suitable method depending on method rating, available data, input format, and method category. More importantly, we highlight outstanding challenges and potential solutions that need to be addressed by future research. To further assist users in executing the reviewed methods, we provide wrappers of the software packages at https://github.com/tinnlab/metabolite-pathway-review-docker.
Indexed as
Identifiers
What Socratic 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 Socratic graph.