ArticleBioinformatics (Oxford, England)2025
NMFProfiler: a multi-omics integration method for samples stratified in groups.
Article in Bioinformatics (Oxford, England), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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4 citing papers in PubMed.
- Integrating Omics and Pathological Imaging Data for Cancer Prognosis via a Deep Neural Network-Based Cox Model.Statistics in medicine · 2026Article
- A review of multi-omics integration techniques across five machine learning method families.Bioinformatics advances · 2026Review
- Joint similarity nonnegative matrix factorization model for identification of recurrence-related association patterns in tumor.Briefings in bioinformatics · 2025Article
- The Neuroimmune Axis in Atopic Dermatitis: From Pathogenic Mechanisms to Targeted Neuroimmunotherapy.Journal of inflammation research · 2025Review
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7 authors.
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Abstract
motivationThe development of high-throughput sequencing enabled the massive production of "omics" data for various applications in biology. By analyzing simultaneously paired datasets collected on the same samples, integrative statistical approaches allow researchers to get a global picture of such systems and to highlight existing relationships between various molecular types and levels. Here, we introduce NMFProfiler, an integrative supervised NMF that accounts for the stratification of samples into groups of biological interest.
resultsNMFProfiler was shown to successfully extract signatures characterizing groups with performances comparable to or better than state-of-the-art approaches. In particular, NMFProfiler was used in a clinical study on atopic dermatitis (AD) and to analyze a multi-omic cancer dataset. In the first case, it successfully identified signatures combining known AD protein biomarkers and novel transcriptomic biomarkers. In addition, it was also able to extract signatures significantly associated to cancer survival. AVAILABILITY AND IMPLEMENTATION: NMFProfiler is released as a Python package, NMFProfiler (v0.3.0), available on PyPI.
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