ReviewNature protocols2024
Web-based multi-omics integration using the Analyst software suite.
Review in Nature protocols, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 109 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
109 citing papers in PubMed, 166 citations in OpenAlex.
- Processed plant-based meat-supplemented diet versus red meat-based supplemented diet randomized cross-over trial Finding Optimal Oral Diet-1 (FOOD-1) trial.Scientific reports · 2026Trial
- Targeted Microbial Shifts and Metabolite Profiles Were Associated with Clinical Response to an Anti-Inflammatory Diet in Osteoarthritis.Nutrients · 2025Trial
- Dietary tryptophan mitigates lung ischemia-reperfusion injury in association with increased indole-3-propionate and aryl hydrocarbon receptor signaling.Gut microbes · 2026Article
- Article
- Adipose tissue as a humoral-neuronal hub in metabolic regulation.Nature reviews. Endocrinology · 2026Review
- Multi-omics integration of proteomics and metabolomics in pediatric health and disease.Communications medicine · 2026Review
- MAPA: A Semantic Network Framework for Functional Module Discovery and Interpretation in Multi-Omics Data.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Food processing-derived carbon dots disrupt male fertility via the gut-testis axis.Science China. Life sciences · 2026Article
- Peripheral nerve injury induces an immunometabolic signature involving reduced free fatty-acid pools.Metabolic brain disease · 2026Article
- Using MetaboAnalyst 6.0 for exposomics data analysis-from LC-MS2 spectra processing to dose-response modeling and causal inference.Nature protocols · 2026Review
- Proteomic Profiling of Endothelial Cells Under Laminar Shear Stress Confirms the Importance of KLF4 in the Regulation of Membrane Protein Expression Compared to Oscillatory Flow.Journal of proteome research · 2026Article
- Lipocalin-2 Is Induced by Uromodulin Aggregates without Affecting Kidney Disease Progression in Autosomal Dominant Tubulointerstitial Kidney Disease- UMOD.Journal of the American Society of Nephrology : JASN · 2026Article
- From pancreas and islet resources to diabetes insights.Diabetologia · 2026Review
- Serum peptidomic profiling identifies systemic JAK-STAT and PI3K-Akt pathway dysregulation in cats with chronic gingivostomatitis.Journal of veterinary internal medicine · 2026Article
- The human microbiome as a source of novel bioactive natural products: structures, bioactivities, and biosynthetic insights.Journal of natural medicines · 2026Review
- A lipid-immune network signature defines susceptibility to asparaginase-associated pancreatitis.JCI insight · 2026Article
- Seal and fish oils partially counteract inflammation and modulate endocannabinoidome lipid and oxylipin alterations in DSS-induced colitis.Scientific reports · 2026Article
- Novel insights into the binding mechanisms of selected aldehydes during heat-induced protein unfolding.NPJ science of food · 2026Article
- A lipidomics roadmap: from basic research to societal challenges.Nature communications · 2026Review
- Parabacteroides goldsteinii and its metabolite 7-KLCA attenuate endometriosis via TGR5 to reprogram macrophages by modulating the PPARγ/GPR132 axis.NPJ biofilms and microbiomes · 2026Article
49 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
8 authors at 3 institutions in 1 country.
Funding
Abstract
The growing number of multi-omics studies demands clear conceptual workflows coupled with easy-to-use software tools to facilitate data analysis and interpretation. This protocol covers three key components involved in multi-omics analysis, including single-omics data analysis, knowledge-driven integration using biological networks and data-driven integration through joint dimensionality reduction. Using the dataset from a recent multi-omics study of human pancreatic islet tissue and plasma samples, the first section introduces how to perform transcriptomics/proteomics data analysis using ExpressAnalyst and lipidomics data analysis using MetaboAnalyst. On the basis of significant features detected in these workflows, the second section demonstrates how to perform knowledge-driven integration using OmicsNet. The last section illustrates how to perform data-driven integration from the normalized omics data and metadata using OmicsAnalyst. The complete protocol can be executed in ~2 h. Compared with other available options for multi-omics integration, the Analyst software suite described in this protocol enables researchers to perform a wide range of omics data analysis tasks via a user-friendly web interface.
Indexed as
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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.