Sinan Ugur Umu

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

  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. [Show all 7 contributors for this article] (2023). Accurate microRNA annotation of animal genomes using trained covariance models of curated microRNA complements in MirMachine. Cell Genomics. 3:100348(8), p. 1–15. doi: 10.1016/j.xgen.2023.100348. Full text in Research Archive
• 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. Full text in Research Archive
• Gardner, Paul P.; Paterson, James M.; McGimpsey, Stephanie; Ashari-Ghomi, Fatemeh; Umu, Sinan Ugur & Pawlik, Aleksandra [Show all 8 contributors for this article] (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 [Show all 41 contributors for this article] (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. Full text in Research Archive
• Fromm, Bastian; Høye, Eirik; Domanska, Diana; Zhong, Xiangfu; Aparicio-Puerta, Ernesto & Ovchinnikov, Vladimir [Show all 18 contributors for this article] (2022). MirGeneDB 2.1: toward a complete sampling of all major animal phyla. Nucleic Acids Research (NAR). ISSN 0305-1048. 50(D1), p. D204–D210. doi: 10.1093/nar/gkab1101. Full text in Research Archive
• Lagström, Sonja ; Løvestad, Alexander; Umu, Sinan Uğur; Ambur, Ole Herman; Nygård, Mari & Rounge, Trine Ballestad [Show all 7 contributors for this article] (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. Full text in Research Archive
• Brägelmann, Johannes; Ponce, Carol Barahona; Marcelain, Katherine; Roessler, Stephanie; Goeppert, Benjamin & Ivan, Gallegos [Show all 23 contributors for this article] (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 [Show all 13 contributors for this article] (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. Full text in Research Archive
• Burton, Joshua; Umu, Sinan Uğur; Langseth, Hilde; Grotmol, Tom; Grimsrud, Tom Kristian & Haugen, Trine B. [Show all 7 contributors for this article] (2020). Serum RNA profiling in the 10-year period prior to diagnosis of testicular germ cell tumour. Frontiers in Oncology. ISSN 2234-943X. 10, p. 1–13. doi: 10.3389/fonc.2020.574977. Full text in Research Archive
• Umu, Sinan Uğur; Langseth, Hilde; Keller, Andreas; Meese, Eckart; Helland, Åslaug & Lyle, Robert [Show all 7 contributors for this article] (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), p. 235–247. doi: 10.1002/1878-0261.12620.
• Lagström, Sonja ; Umu, Sinan Uğur; Lepistö, Maija; Ellonen, Pekka; Meisal, Roger & Christiansen, Irene Kraus [Show all 8 contributors for this article] (2019). TaME-seq: An efficient sequencing approach for characterisation of HPV genomic variability and chromosomal integration. Scientific Reports. ISSN 2045-2322. 9:524, p. 1–12. doi: 10.1038/s41598-018-36669-6. Full text in Research Archive
• Rounge, Trine Ballestad; Umu, Sinan Uğur; Keller, Andreas; Meese, Eckart; Ursin, Giske & Tretli, Steinar [Show all 8 contributors for this article] (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. Full text in Research Archive
• Fehlmann, Tobias; Backes, Christina; Alles, Julia; Fischer, Ulrike; Hart, Martin & Kern, Fabian [Show all 20 contributors for this article] (2018). A high-resolution map of the human small non-coding transcriptome. Bioinformatics. ISSN 1367-4803. 34(10), p. 1621–1628. doi: 10.1093/bioinformatics/btx814.
• Ugur Umu, Sinan; Langseth, Hilde; Bucher-Johannessen, Cecilie; Fromm, Bastian; Keller, Andreas & Meese, Eckart [Show all 10 contributors for this article] (2018). A comprehensive profile of circulating RNAs in human serum. RNA Biology. ISSN 1547-6286. 15(2), p. 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. Show summary

  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.

View all works in Cristin

• 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 [Show all 8 contributors for this article] (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 [Show all 8 contributors for this article] (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 [Show all 8 contributors for this article] (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 [Show all 8 contributors for this article] (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 [Show all 8 contributors for this article] (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 [Show all 8 contributors for this article] (2017). Human Papillomavirus whole genome sequencing reveals genetic diversity and human genome integration sites.

View all works in Cristin