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1. Guided extraction of genome-scale metabolic models for the integration and analysis of omics data
Andrew Walakira, Damjana Rozman, Tadeja Režen, Miha Mraz, Miha Moškon, 2021, original scientific article

Keywords: genome-scale metabolic model, model extraction methods, context-specific metabolic model, omics data integration, subsystem enrichment analysis, model interpretability
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2. Towards a data-integrated cell
Noël Malod-Dognin, Julia Petschnigg, Sam F. L. Windels, Janez Povh, Harry Hemmingway, Robin Ketteler, Nataša Pržulj, 2019, original scientific article

Keywords: non-negative matrix factorization, data integration, cancer-related genes, pan-cancer genes, integrated cell, biological networks
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3. Embedding to Reference t-SNE Space Addresses Batch Effects in Single-Cell Classification
Pavlin Gregor Poličar, 2019, master's thesis/paper

Keywords: batch effects, embedding, t-SNE, visualization, single-cell transcriptomics, data integration, domain adaptation
Full text (file, 16,34 MB)

4. Transcriptomics of receptive endometrium in women with sonographic features of adenomyosis
Erika Prašnikar, Tanja Kunej, Mario Gorenjak, Uroš Potočnik, Borut Kovačič, Jure Knez, 2022, original scientific article

Keywords: adenomyosis, assisted reproductive techniques (ART), data integration, endometrial receptivity, enrichment pathway analysis, omics approaches, RNA-seq, systems biology, transcriptomics, window of implantation
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5. Bioinformatics integration of microbiome and metabolomics data in the translational context
Leon Deutsch, 2022, doctoral dissertation

Keywords: bioinformatics, metabolomics, metagenomcis, physical inactivity, data integration, systems biology, microbiome, urine, nuclear magnetic spectrometry
Full text (file, 30,37 MB)
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