ArticleBMC bioinformatics2012
A novel approach for biomarker selection and the integration of repeated measures experiments from two assays.
Article in BMC bioinformatics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 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
66 citing papers in PubMed.
- Effect of Varying Quantities of Lean Beef as Part of a Mediterranean-Style Dietary Pattern on Gut Microbiota and Plasma, Fecal, and Urinary Metabolites: A Randomized Crossover Controlled Feeding Trial.Journal of the American Heart Association · 2025Trial
- Neonatal intensive care unit (NICU) exposures exert a sustained influence on the progression of gut microbiota and metabolome in the first year of life.Scientific reports · 2021Trial
- Plasma Sulphur-Containing Amino Acids, Physical Exercise and Insulin Sensitivity in Overweight Dysglycemic and Normal Weight Normoglycemic Men.Nutrients · 2018Trial
- Systems Vaccinology Identifies an Early Innate Immune Signature as a Correlate of Antibody Responses to the Ebola Vaccine rVSV-ZEBOV.Cell reports · 2017Trial
- Large-scale analysis of temporal gene expression variation in peripheral blood.Nature communications · 2026Article
- Factors Contributing to Short-Term Structural Variability in a Longitudinal MRI Dataset.Human brain mapping · 2026Article
- Expression of free fatty acid receptors in the liver of periparturient dairy cows supplemented with essential fatty acids and conjugated linoleic acid.JDS communications · 2026Article
- Longitudinal omics data analysis: approaches and applications.Computational and structural biotechnology journal · 2026Review
- Multi-Omics Signatures of Periodontitis and Periodontal Therapy on the Oral and Gut Microbiome.Journal of periodontal research · 2025Article
- Prebiotic supplementation in patients with type 1 diabetes: study protocol for a randomised controlled trial in Canada.BMJ open · 2025Article
- Destabilization of mutualistic interactions shapes the early heat stress response of the coral holobiont.Microbiome · 2025Article
- Lipidome Changes Associated with a Diet-Induced Reduction in Hepatic Fat among Adolescent Boys with Metabolic Dysfunction-Associated Steatotic Liver Disease.Metabolites · 2024Article
- Identification of Genomic Signatures for Colorectal Cancer Survival Using Exploratory Data Mining.International journal of molecular sciences · 2024Article
- New Enhancing MRI Lesions Associate with IL-17, Neutrophil Degranulation and Integrin Microparticles: Multi-Omics Combined with Frequent MRI in Multiple Sclerosis.Biomedicines · 2023Article
- Can Gait Characteristics Be Represented by Physical Activity Measured with Wrist-Worn Accelerometers?Sensors (Basel, Switzerland) · 2023Article
- Interplay between Cruciferous Vegetables and the Gut Microbiome: A Multi-Omic Approach.Nutrients · 2022Article
- A LongitudinalMetabolites · 2022Article
- Grape polyphenols decrease circulating branched chain amino acids in overfed adults.Frontiers in nutrition · 2022Article
- Multi-omic phenotyping reveals host-microbe responses to bariatric surgery, glycaemic control and obesity.Communications medicine · 2022Article
- Standardized Whole Blood Assay and Bead-Based Cytokine Profiling Reveal Commonalities and Diversity of the Response to Bacteria and TLR Ligands in Cattle.Frontiers in immunology · 2022Article
6 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundHigh throughput 'omics' experiments are usually designed to compare changes observed between different conditions (or interventions) and to identify biomarkers capable of characterizing each condition. We consider the complex structure of repeated measurements from different assays where different conditions are applied on the same subjects.
resultsWe propose a two-step analysis combining a multilevel approach and a multivariate approach to reveal separately the effects of conditions within subjects from the biological variation between subjects. The approach is extended to two-factor designs and to the integration of two matched data sets. It allows internal variable selection to highlight genes able to discriminate the net condition effect within subjects. A simulation study was performed to demonstrate the good performance of the multilevel multivariate approach compared to a classical multivariate method. The multilevel multivariate approach outperformed the classical multivariate approach with respect to the classification error rate and the selection of relevant genes. The approach was applied to an HIV-vaccine trial evaluating the response with gene expression and cytokine secretion. The discriminant multilevel analysis selected a relevant subset of genes while the integrative multilevel analysis highlighted clusters of genes and cytokines that were highly correlated across the samples.
conclusionsOur combined multilevel multivariate approach may help in finding signatures of vaccine effect and allows for a better understanding of immunological mechanisms activated by the intervention. The integrative analysis revealed clusters of genes, that were associated with cytokine secretion. These clusters can be seen as gene signatures to predict future cytokine response. The approach is implemented in the R package mixOmics (http://cran.r-project.org/) with associated tutorials to perform the analysis(a).
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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.