Sinan Ugur Umu

• Umu, Sinan Ugur; Vander-Elst, Karoline Rapp; Karlsen, Victoria; Chouliara, Manto; Bækkevold, Espen Sønderaal & Jahnsen, Frode Lars [Vis alle 7 forfattere av denne artikkelen] (2023). Cellsnake: a user-friendly tool for single-cell RNA sequencing analysis. GigaScience. ISSN 2047-217X. 12, s. 1–10. doi: 10.1093/gigascience/giad091. Fulltekst i vitenarkiv
• Birkeland, Einar Elvbakken; Ferrero, Giulio; Pardini, Barbara; Umu, Sinan Ugur; Tarallo, Sonia & Bulfamante, Sara [Vis alle 10 forfattere av denne artikkelen] (2023). Profiling small RNAs in fecal immunochemical tests: is it possible? Molecular Cancer. ISSN 1476-4598. 22:161(1), s. 1–7. doi: 10.1186/s12943-023-01869-w. Fulltekst i vitenarkiv Vis sammendrag

  Fecal microRNAs represent promising molecules with potential clinical interest as non-invasive diagnostic and prognostic biomarkers. Colorectal cancer (CRC) screening based on the fecal immunochemical test (FIT) is an effective tool for prevention of cancer development. However, due to the poor sensitivity of FIT especially for premalignant lesions, there is a need for implementation of complementary tests. Improving the identification of individuals who would benefit from further investigation with colonoscopy using molecular analysis, such as miRNA profiling of FIT samples, would be ideal due to their widespread use. In the present study, we assessed the feasibility of applying small RNA sequencing to measure human miRNAs in FIT leftover buffer in samples from two European screening populations. We showed robust detection of miRNAs with profiles similar to those obtained from specimens sampled using the established protocol of RNA stabilizing buffers, or in long-term archived samples. Detected miRNAs exhibited differential abundances for CRC, advanced adenoma, and control samples that were consistent for FIT and RNA-stabilizing buffers. Interestingly, the sequencing data also allowed for concomitant evaluation of small RNA-based microbial profiles. We demonstrated that it is possible to explore the human miRNome in FIT leftover samples across populations and envision that the analysis of small RNA biomarkers can complement the FIT in large scale screening settings.

• Umu, Sinan Ugur; Paynter, Vanessa Molin; Trondsen, Håvard; Buschmann, Tilo; Rounge, Trine Ballestad & Peterson, Kevin J. [Vis alle 7 forfattere av denne artikkelen] (2023). Accurate microRNA annotation of animal genomes using trained covariance models of curated microRNA complements in MirMachine. Cell Genomics. 3:100348(8), s. 1–15. doi: 10.1016/j.xgen.2023.100348. Fulltekst i vitenarkiv
• Umu, Sinan Ugur; Langseth, Hilde; Zuber, Verena; Helland, Åslaug; Lyle, Robert & Rounge, Trine Ballestad (2022). Serum RNAs can predict lung cancer up to 10 years prior to diagnosis. eLIFE. ISSN 2050-084X. 11. doi: 10.7554/ELIFE.71035. Fulltekst i vitenarkiv
• Gardner, Paul P.; Paterson, James M.; McGimpsey, Stephanie; Ashari-Ghomi, Fatemeh; Umu, Sinan Ugur & Pawlik, Aleksandra [Vis alle 8 forfattere av denne artikkelen] (2022). Sustained software development, not number of citations or journal choice, is indicative of accurate bioinformatic software. Genome Biology. ISSN 1465-6906. 23(1). doi: 10.1186/s13059-022-02625-x.
• Blandino, Alice; Scherer, Dominique; Rounge, Trine Ballestad; Umu, Sinan Ugur; Boekstegers, Felix & Barahona Ponce, Carol [Vis alle 41 forfattere av denne artikkelen] (2022). Identification of Circulating lncRNAs Associated with Gallbladder Cancer Risk by Tissue-Based Preselection, Cis-eQTL Validation, and Analysis of Association with Genotype-Based Expression. Cancers. ISSN 2072-6694. 14(3). doi: 10.3390/cancers14030634. Fulltekst i vitenarkiv
• Fromm, Bastian; Høye, Eirik; Domanska, Diana; Zhong, Xiangfu; Aparicio-Puerta, Ernesto & Ovchinnikov, Vladimir [Vis alle 18 forfattere av denne artikkelen] (2022). MirGeneDB 2.1: toward a complete sampling of all major animal phyla. Nucleic Acids Research (NAR). ISSN 0305-1048. 50(D1), s. D204–D210. doi: 10.1093/nar/gkab1101. Fulltekst i vitenarkiv
• Lagström, Sonja ; Løvestad, Alexander; Umu, Sinan Uğur; Ambur, Ole Herman; Nygård, Mari & Rounge, Trine Ballestad [Vis alle 7 forfattere av denne artikkelen] (2021). HPV16 and HPV18 type-specific APOBEC3 and integration profiles in different diagnostic categories of cervical samples. Tumour Virus Research. ISSN 2666-6790. 12. doi: 10.1016/j.tvr.2021.200221. Fulltekst i vitenarkiv
• Brägelmann, Johannes; Ponce, Carol Barahona; Marcelain, Katherine; Roessler, Stephanie; Goeppert, Benjamin & Ivan, Gallegos [Vis alle 23 forfattere av denne artikkelen] (2020). Epigenome‐wide analysis of methylation changes in the sequence of gallstone disease, dysplasia, and gallbladder cancer . Hepatology. ISSN 0270-9139. doi: 10.1002/hep.31585.
• Scherer, Dominique; López, Marcela Dávila; Goeppert, Benjamin; Abrahamsson, Sanna; Silos, Rosa González & Nova, Igor [Vis alle 13 forfattere av denne artikkelen] (2020). RNA Sequencing of Hepatobiliary Cancer Cell Lines: Data and Applications to Mutational and Transcriptomic Profiling. Cancers. ISSN 2072-6694. 12(9). doi: 10.3390/cancers12092510. Fulltekst i vitenarkiv
• Burton, Joshua; Umu, Sinan Uğur; Langseth, Hilde; Grotmol, Tom; Grimsrud, Tom Kristian & Haugen, Trine B. [Vis alle 7 forfattere av denne artikkelen] (2020). Serum RNA profiling in the 10-year period prior to diagnosis of testicular germ cell tumour. Frontiers in Oncology. ISSN 2234-943X. 10, s. 1–13. doi: 10.3389/fonc.2020.574977. Fulltekst i vitenarkiv
• Umu, Sinan Uğur; Langseth, Hilde; Keller, Andreas; Meese, Eckart; Helland, Åslaug & Lyle, Robert [Vis alle 7 forfattere av denne artikkelen] (2019). A 10-year prediagnostic follow-up study shows that serum RNA signals are highly dynamic in lung carcinogenesis. Molecular Oncology. ISSN 1574-7891. 14(2), s. 235–247. doi: 10.1002/1878-0261.12620.
• Lagström, Sonja ; Umu, Sinan Uğur; Lepistö, Maija; Ellonen, Pekka; Meisal, Roger & Christiansen, Irene Kraus [Vis alle 8 forfattere av denne artikkelen] (2019). TaME-seq: An efficient sequencing approach for characterisation of HPV genomic variability and chromosomal integration. Scientific Reports. ISSN 2045-2322. 9:524, s. 1–12. doi: 10.1038/s41598-018-36669-6. Fulltekst i vitenarkiv
• Rounge, Trine Ballestad; Umu, Sinan Uğur; Keller, Andreas; Meese, Eckart; Ursin, Giske & Tretli, Steinar [Vis alle 8 forfattere av denne artikkelen] (2018). Circulating small non-coding RNAs associated with age, sex, smoking, body mass and physical activity. Scientific Reports. ISSN 2045-2322. 8( ). doi: 10.1038/s41598-018-35974-4. Fulltekst i vitenarkiv
• Fehlmann, Tobias; Backes, Christina; Alles, Julia; Fischer, Ulrike; Hart, Martin & Kern, Fabian [Vis alle 20 forfattere av denne artikkelen] (2018). A high-resolution map of the human small non-coding transcriptome. Bioinformatics. ISSN 1367-4803. 34(10), s. 1621–1628. doi: 10.1093/bioinformatics/btx814.
• Ugur Umu, Sinan; Langseth, Hilde; Bucher-Johannessen, Cecilie; Fromm, Bastian; Keller, Andreas & Meese, Eckart [Vis alle 10 forfattere av denne artikkelen] (2018). A comprehensive profile of circulating RNAs in human serum. RNA Biology. ISSN 1547-6286. 15(2), s. 242–250. doi: 10.1080/15476286.2017.1403003.
• Umu, Sinan Uğur & Gardner, Paul P. (2016). A comprehensive benchmark of RNA–RNA interaction prediction tools for all domains of life. Bioinformatics. ISSN 1367-4803. doi: 10.1093/bioinformatics/btw728. Vis sammendrag

  Motivation The aim of this study is to assess the performance of RNA–RNA interaction prediction tools for all domains of life. Results Minimum free energy (MFE) and alignment methods constitute most of the current RNA interaction prediction algorithms. The MFE tools that include accessibility (i.e. RNAup, IntaRNA and RNAplex) to the final predicted binding energy have better true positive rates (TPRs) with a high positive predictive values (PPVs) in all datasets than other methods. They can also differentiate almost half of the native interactions from background. The algorithms that include effects of internal binding energies to their model and alignment methods seem to have high TPR but relatively low associated PPV compared to accessibility based methods. Availability and Implementation We shared our wrapper scripts and datasets at Github (github.com/UCanCompBio/RNA_Interactions_Benchmark). All parameters are documented for personal use. Supplementary information Supplementary data are available at Bioinformatics online.

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• Umu, Sinan Ugur (2023). An introduction to Snakemake and Snakemake workflows.
• Umu, Sinan Ugur & Fromm, Bastian (2023). MirMachine: accurate microRNA annotation of animal genomes using trained covariance models.
• Umu, Sinan Ugur (2022). An introduction to Snakemake and Bioinformatics workflows.
• Lagström, Sonja ; Løvestad, Alexander; Umu, Sinan Uğur; Ambur, Ole Herman; Rounge, Trine Ballestad & Christiansen, Irene Kraus (2020). Chromosomal integration and APOBEC profiles differ between HPV16 and HPV18 positive cervical samples .
• Burton, Joshua; Hammer, Hugo Lewi; Umu, Sinan Uğur; Langseth, Hilde; Grotmol, Tom & Grimsrud, Tom Kristian [Vis alle 8 forfattere av denne artikkelen] (2018). Differentially expressed small non-coding RNA in serum from testicular germ cell tumour patients and controls.
• Burton, Joshua; Hammer, Hugo Lewi; Umu, Sinan Uğur; Langseth, Hilde; Grotmol, Tom & Grimsrud, Tom Kristian [Vis alle 8 forfattere av denne artikkelen] (2018). Differentially expressed small non-coding RNA in serum from testicular germ cell tumour patients and controls.
• Lagström, Sonja; Umu, Sinan Uğur; Lepistö, Maija; Ellonen, Pekka; Meisal, Roger & Christiansen, Irene Kraus [Vis alle 8 forfattere av denne artikkelen] (2018). TaME-seq: An efficient sequencing approach to characterise HPV genomic variability and chromosomal integration.
• Lagström, Sonja; Umu, Sinan Uğur; Lepistö, Maija; Ellonen, Pekka; Meisal, Roger & Christiansen, Irene Kraus [Vis alle 8 forfattere av denne artikkelen] (2018). TaME-seq: An efficient sequencing approach to characterize human papillomavirus genomic variability and chromosomal integration.
• Burton, Joshua; Hammer, Hugo Lewi; Umu, Sinan Uğur; Langseth, Hilde; Grotmol, Tom & Grimsrud, Tom Kristian [Vis alle 8 forfattere av denne artikkelen] (2018). Small non-coding RNA in serum from testicular germ cell tumour patients identified by machine learning.
• Lagström, Sonja; Umu, Sinan Uğur; Lepistö, Maija; Ellonen, Pekka; Meisal, Roger & Christiansen, Irene Kraus [Vis alle 8 forfattere av denne artikkelen] (2017). Human Papillomavirus whole genome sequencing reveals genetic diversity and human genome integration sites.

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