High performance data integration for large-scale analyses of incomplete Omic profiles using Batch-Effect Reduction Trees (BERT)
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| Publicado en: | Nature Communications vol. 16, no. 1 (2025), p. 7104-7117 |
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| Acceso en línea: | Citation/Abstract Full Text Full Text - PDF |
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| 024 | 7 | |a 10.1038/s41467-025-62237-4 |2 doi | |
| 035 | |a 3235846086 | ||
| 045 | 2 | |b d20250101 |b d20251231 | |
| 084 | |a 145839 |2 nlm | ||
| 100 | 1 | |a Schumann, Yannis |u Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany (ROR: https://ror.org/01js2sh04) (GRID: grid.7683.a) (ISNI: 0000 0004 0492 0453) | |
| 245 | 1 | |a High performance data integration for large-scale analyses of incomplete <i>Omic</i> profiles using Batch-Effect Reduction Trees (BERT) | |
| 260 | |b Nature Publishing Group |c 2025 | ||
| 513 | |a Journal Article | ||
| 520 | 3 | |a Data from high-throughput technologies assessing global patterns of biomolecules (omic data), is often afflicted with missing values and with measurement-specific biases (batch-effects), that hinder the quantitative comparison of independently acquired datasets. This work introduces batch-effect reduction trees (BERT), a high-performance method for data integration of incomplete omic profiles. We characterize BERT on large-scale data integration tasks with up to 5000 datasets from simulated and experimental data of different quantification techniques and omic types (proteomics, transcriptomics, metabolomics) as well as other datatypes e.g., clinical data, emphasizing the broad scope of the algorithm. Compared to the only available method for integration of incomplete omic data, HarmonizR, our method (1) retains up to five orders of magnitude more numeric values, (2) leverages multi-core and distributed-memory systems for up to 11 × runtime improvement (3) considers covariates and reference measurements to account for severely imbalanced or sparsely distributed conditions (up to 2 × improvement of average-silhouette-width).This study presents BERT, an algorithm for high-performance integration of incomplete omics data with robustness to unequal phenotype distribution. It validates the method on simulated and experimental data from proteomics, metabolomics and transcriptomics. | |
| 653 | |a Experimental data | ||
| 653 | |a Trees | ||
| 653 | |a Datasets | ||
| 653 | |a Algorithms | ||
| 653 | |a Proteomics | ||
| 653 | |a Estimates | ||
| 653 | |a Metabolomics | ||
| 653 | |a Phenotypes | ||
| 653 | |a Quality control | ||
| 653 | |a Measurement techniques | ||
| 653 | |a Data integration | ||
| 653 | |a Transcriptomics | ||
| 653 | |a Distributed memory | ||
| 653 | |a Integration | ||
| 653 | |a Biomolecules | ||
| 653 | |a Environmental | ||
| 700 | 1 | |a Schlumbohm, Simon |u Chair for High Performance Computing, Helmut-Schmidt-University Hamburg, Hamburg, Germany (ROR: https://ror.org/04e8jbs38) (GRID: grid.49096.32) (ISNI: 0000 0001 2238 0831) | |
| 700 | 1 | |a Neumann, Julia E. |u Center for Molecular Neurobiology Hamburg (ZMNH), University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany (ROR: https://ror.org/01zgy1s35) (GRID: grid.13648.38) (ISNI: 0000 0001 2180 3484); Institute of Neuropathology, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany (ROR: https://ror.org/01zgy1s35) (GRID: grid.13648.38) (ISNI: 0000 0001 2180 3484) | |
| 700 | 1 | |a Neumann, Philipp |u Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany (ROR: https://ror.org/01js2sh04) (GRID: grid.7683.a) (ISNI: 0000 0004 0492 0453); High Performance Computing &amp; Data Science, University of Hamburg, Hamburg, Germany (ROR: https://ror.org/00g30e956) (GRID: grid.9026.d) (ISNI: 0000 0001 2287 2617) | |
| 773 | 0 | |t Nature Communications |g vol. 16, no. 1 (2025), p. 7104-7117 | |
| 786 | 0 | |d ProQuest |t Health & Medical Collection | |
| 856 | 4 | 1 | |3 Citation/Abstract |u https://www.proquest.com/docview/3235846086/abstract/embedded/7BTGNMKEMPT1V9Z2?source=fedsrch |
| 856 | 4 | 0 | |3 Full Text |u https://www.proquest.com/docview/3235846086/fulltext/embedded/7BTGNMKEMPT1V9Z2?source=fedsrch |
| 856 | 4 | 0 | |3 Full Text - PDF |u https://www.proquest.com/docview/3235846086/fulltextPDF/embedded/7BTGNMKEMPT1V9Z2?source=fedsrch |