1. Beer spoiling mechanisms of Lactobacillus brevisMateja Govže, 2017, master's thesis Keywords: beer, hop, Humulus lupulus, beer spoilage, lactic acid bacteria, Lactobacillus brevis, genome, genome sequencing, genome analysis, RNA sequencing, transcriptomic analysis, gene expression analysis, fenotypic analysis
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2. Dissection of dynamic transcriptome landscape of leaf, bract, and lupulin gland in hop (Humulus lupulus L.)Ajay Kumar Mishra, Tomáš Kocábek, Vishnu Sukumari Nath, Praveen Awasthi, Ankita Shrestha, Uday Kumar Killi, Jernej Jakše, Josef Patzak, Karel Krofta, Jaroslav Matoušek, 2020, original scientific article Keywords: bitter acids, prenylflavonoids, terpenoids, trichome, Humulus lupulus, lupulin glands, RNA sequencing
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3. Integrated proteo-transcriptomic analyses reveal insights into regulation of pollen development stages and dynamics of cellular response to apple fruit crinkle viroid (AFCVd)-infection in Nicotiana tabacumAnkita Shrestha, Ajay Kumar Mishra, Jaroslav Matoušek, Lenka Steinbachová, David Potěšil, Vishnu Sukumari Nath, Praveen Awasthi, Tomáš Kocábek, Jernej Jakše, Lenka Záveská Drábková, Zbyněk Zdráhal, David Honys, Gerhard Steger, 2020, original scientific article Keywords: AFCVd propagation and eradication, viroid replication, viroid degradation, Nicotiana tabacum, male gametophyte, proteome, RNA sequencing, RT qPCR
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4. Adipose tissue gene expression of entire male, immunocastrated and surgically castrated pigsKlavdija Poklukar Žnidaršič, Marjeta Čandek-Potokar, Milka Vrecl, Nina Batorek Lukač, Gregor Fazarinc, Kevin Kress, Volker Stefanski, Martin Škrlep, 2021, original scientific article Keywords: pigs, adipose tissue, entire males, immunocastration, surgical castration, RNA-sequencing, expression
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5. Large-scale transcriptomics-driven approach revealed overexpression of CRNDE as a poor survival prognosis biomarker in glioblastomaMaxim Sorokin, Mikhail Raevskiy, Alja Zottel, Neja Šamec, Marija Skoblar Vidmar, Alenka Matjašič, Andrej Zupan, Jernej Mlakar, Maria Suntsova, Denis V. Kuzmin, Anton A. Buzdin, Ivana Jovchevska, 2021, original scientific article Keywords: glioblastoma, noncoding RNA, long-term survival, CRNDE, RNA sequencing
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6. Single cell RNA sequencing in autoimmune inflammatory rheumatic diseasesTadeja Kuret, Snežna Sodin-Šemrl, Branimir Leskošek, Polonca Ferk, 2022, review article Keywords: rheumatoid arthritis, systemic lupus erythematosus, RNA sequencing, single cell, systemic sclerosis, precision medicine
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7. Comprehensive transcriptome profiling of urothelial cells following TNFα stimulation in an in vitro interstitial cystitis/bladder pain syndrome modelTadeja Kuret, Dominika Peskar, Mateja Erdani-Kreft, Andreja Erman, Peter Veranič, 2022, original scientific article Keywords: interstitial cystitis, bladder pain syndrome, urothelial cells, inflammation, RNA sequencing, transcriptomics, proinflammatory cytokines
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8. Molecular profiling of inflammatory processes in a mouse model of IC/BPSDominika Peskar, Tadeja Kuret, Katja Lakota, Andreja Erman, 2023, original scientific article Keywords: interstitial cystitis, inflammation, RNA sequencing, bladder pain syndrome, animal model, cyclophosphamide
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9. Integration and analysis of scRNAseq data using genome-scale metabolic modelsJurij Nastran, 2024, master's thesis Keywords: genome-scale metabolic models, model extraction methods, context-specific metabolic models, omics data integration, metabolism, cancer, single-cell RNA sequencing data
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