ArticleNature communications2022
HarmonizR enables data harmonization across independent proteomic datasets with appropriate handling of missing values.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers, 1 of them a synthesis that pooled it.
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Who cites it
43 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- Sexual Dimorphism and Intraspecific Toxin Variation in Crotalus durissus terrificus Venom: Insights from Proteomics, Peptidomics, and Structural Modeling.Journal of proteome research · 2026Article
- Best practices for using biological data in psychological research.Journal of mood and anxiety disorders · 2026Review
- Intestinal fructose catabolism promotes obesity and insulin resistance via ileal lacteal remodeling.Science advances · 2026Article
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- A sequential MAP kinase cascade regulates mechanical signalling.Nature communications · 2026Article
- Blood biomarkers predict conversion from cognitively stable to mild cognitive impairment or Alzheimer's disease in Down syndrome at 16-month follow-up in ABC-DS.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2026Article
- Identification of serum protein biomarkers for pre-cancerous lesions associated with pancreatic ductal adenocarcinoma.Molecular oncology · 2026Article
- omicsGMF: a multi-tool for dimensionality reduction, batch correction and imputation in bulk- and single-cell proteomics.Nature communications · 2026Article
- Immune cell annotation in the single-cell studies: technologies, challenges, and integrative solutions.Immunologic research · 2026Review
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- Recent advances in machine learning-enhanced extracellular vesicle omics for oncology.Journal of nanobiotechnology · 2026Review
- Explainable machine learning of PROGRESS-Plus social factors predicts cognitive trajectories after traumatic brain injury.Scientific reports · 2026Article
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- Proteomic analysis of saliva reveals changes in proteomic profiles during colorectal cancer in an Iranian cohort.Frontiers in oncology · 2026Article
- NAD⁺ Reduction in Glutamatergic Neurons Induces Lipid Catabolism and Neuroinflammation in the Brain via SARM1.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Unveiling proteomic and peptide-level modifications in cerebrospinal fluid and plasma in normal cognitive aging.Communications medicine · 2025Article
- Protein-level batch-effect correction enhances robustness in MS-based proteomics.Nature communications · 2025Article
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Authors and funding
9 authors.
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Abstract
Dataset integration is common practice to overcome limitations in statistically underpowered omics datasets. Proteome datasets display high technical variability and frequent missing values. Sophisticated strategies for batch effect reduction are lacking or rely on error-prone data imputation. Here we introduce HarmonizR, a data harmonization tool with appropriate missing value handling. The method exploits the structure of available data and matrix dissection for minimal data loss, without data imputation. This strategy implements two common batch effect reduction methods-ComBat and limma (removeBatchEffect()). The HarmonizR strategy, evaluated on four exemplarily analyzed datasets with up to 23 batches, demonstrated successful data harmonization for different tissue preservation techniques, LC-MS/MS instrumentation setups, and quantification approaches. Compared to data imputation methods, HarmonizR was more efficient and performed superior regarding the detection of significant proteins. HarmonizR is an efficient tool for missing data tolerant experimental variance reduction and is easily adjustable for individual dataset properties and user preferences.
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