Sinan U. Umu, PhD

Sinan U. Umu, PhD

Computational Biology, Bioinformatics, Biostatistics

Publications

My publications span molecular and cancer epidemiology, RNA biomarkers, single-cell analysis, microbial genomics, and bioinformatics software. The complete list from my current CV is below, ordered from newest to oldest.

Google Scholar · PubMed

Full publication list

  1. Rapp E, Berset IP, Umu SU, et al. Longitudinal transcriptomic analysis of mucosa in ulcerative colitis after anti-tumor necrosis factor withdrawal compared to continued treatment. Journal of Crohn’s and Colitis. 2026;20(8):jjag121.

  2. Clarke AW, Høye E, Hembrom AA, et al., Umu SU, et al. MirGeneDB 3.0: improved taxonomic sampling, uniform nomenclature of novel conserved microRNA families and updated covariance models. Nucleic Acids Research. 2025;53(D1):D116-D128.

  3. Stawiski K, Fortner RT, Pestarino L, Umu SU, et al. Validation of miRNA signatures for ovarian cancer earlier detection in the pre-diagnosis setting using machine learning approaches. Frontiers in Oncology. 2024;14:1389066.

  4. Umu SU, Rapp Vander-Elst K, Karlsen VT, et al. Cellsnake: a user-friendly tool for single-cell RNA sequencing analysis. GigaScience. 2023;12:giad091.

  5. Birkeland E, Ferrero G, Pardini B, Umu SU, et al. Profiling small RNAs in fecal immunochemical tests: is it possible? Molecular Cancer. 2023;22(1):161.

  6. Umu SU, Paynter VM, Trondsen H, et al. Accurate microRNA annotation of animal genomes using trained covariance models of curated microRNA complements in MirMachine. Cell Genomics. 2023;3(8):100348.

  7. Gardner PP, Paterson JM, McGimpsey S, Ashari-Ghomi F, Umu SU, et al. Sustained software development, not number of citations or journal choice, is indicative of accurate bioinformatic software. Genome Biology. 2022;23(1):56.

  8. Blandino A, Scherer D, Rounge TB, Umu SU, et al. 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. 2022;14(3):634.

  9. Umu SU, Langseth H, Zuber V, Helland Å, Lyle R, Rounge TB. Serum RNAs can predict lung cancer up to 10 years prior to diagnosis. eLife. 2022;11:e71035.

  10. Fromm B, Høye E, Domanska D, et al., Umu SU, et al. MirGeneDB 2.1: toward a complete sampling of all major animal phyla. Nucleic Acids Research. 2022;50(D1):D204-D210.

  11. Lagström S, Løvestad AH, Umu SU, et al. HPV16 and HPV18 type-specific APOBEC3 and integration profiles in different diagnostic categories of cervical samples. Tumour Virus Research. 2021;12:200221.

  12. Brägelmann J, Barahona Ponce C, Marcelain K, et al., Umu SU, et al. Epigenome-wide analysis of methylation changes in the sequence of gallstone disease, dysplasia, and gallbladder cancer. Hepatology. 2021;73(6):2293-2310.

  13. Burton J, Umu SU, Langseth H, et al. Serum RNA profiling in the 10-years period prior to diagnosis of testicular germ cell tumor. Frontiers in Oncology. 2020;10:574977.

  14. Scherer D, Dávila López MD, Goeppert B, et al., Umu SU, et al. RNA sequencing of hepatobiliary cancer cell lines: data and applications to mutational and transcriptomic profiling. Cancers. 2020;12(9):2510.

  15. Umu SU, Langseth H, Keller A, et al. A 10-year prediagnostic follow-up study shows that serum RNA signals are highly dynamic in lung carcinogenesis. Molecular Oncology. 2020;14(2):235-247.

  16. Lagström S, Umu SU, Lepistö M, et al. TaME-seq: an efficient sequencing approach for characterisation of HPV genomic variability and chromosomal integration. Scientific Reports. 2019;9(1):524.

  17. Rounge TB, Umu SU, Keller A, et al. Circulating small non-coding RNAs associated with age, sex, smoking, body mass and physical activity. Scientific Reports. 2018;8(1):17650.

  18. Fehlmann T, Backes C, Alles J, et al., Umu SU, et al. A high-resolution map of the human small non-coding transcriptome. Bioinformatics. 2018;34(10):1621-1628.

  19. Umu SU, Langseth H, Bucher-Johannessen C, et al. A comprehensive profile of circulating RNAs in human serum. RNA Biology. 2018;15(2):242-250.

  20. Umu SU, Gardner PP. A comprehensive benchmark of RNA-RNA interaction prediction tools for all domains of life. Bioinformatics. 2017;33(7):988-996.

  21. Umu SU, Poole AM, Dobson RC, Gardner PP. Avoidance of stochastic RNA interactions can be harnessed to control protein expression levels in bacteria and archaea. eLife. 2016;5:e13479.

  22. Lindgreen S, Umu SU, Lai AS, et al. Robust identification of noncoding RNA from transcriptomes requires phylogenetically informed sampling. PLOS Computational Biology. 2014;10(10):e1003907.

  23. Ogul H, Kalkan AT, Umu SU, Akkaya MS. TRAINER: a general-purpose trainable short biosequence classifier. Protein & Peptide Letters. 2013;20(10):1108-1114.

  24. Oğul H, Umu SU, Tuncel YY, Akkaya MS. A probabilistic approach to microRNA-target binding. Biochemical and Biophysical Research Communications. 2011;413(1):111-115.