Publications
Selected
Sinan U. Umu et al. (2023), cellsnake: a user-friendly tool for single-cell RNA sequencing analysis, GigaScience
Sinan U. Umu et al. (2023), Accurate microRNA annotation of animal genomes using trained covariance models of curated microRNA complements in MirMachine, Cell Genomics
Sinan U. Umu et al. (2022), Serum RNAs can predict lung cancer up to 10 years prior to diagnosis eLife
Umu, S. U. et al. (2018). A comprehensive profile of circulating RNAs in human serum. RNA Biology (highly cited)
Umu, Sinan U. and Gardner, P. P. (2017). A comprehensive benchmark of RNA-RNA interaction prediction tools for all domains of life. Bioinformatics (highly cited)
Umu, Sinan U. et al., (2016). Avoidance of stochastic RNA interactions can be harnessed to control protein expression levels in bacteria and archaea. eLife (On eLife web cover)
Selected talks
Sinan U. Umu, MirMachine: accurate microRNA annotation of animal genomes using trained covariance models, Norwegian Biodiversity & Genomics Conference, February 2023, Oslo, Norway (Selected talk)
Sinan U. Umu, Spatial transcriptomics analysis of human colon; results, lessons and challenges, Genomics Open Day, 10x genomics, December 2022, Oslo, Norway (Invited speaker)
Sinan Uğur Umu et al., Accurate microRNA annotation using covariance models based on manually curated databases in MirMachine, Biodiversity Genomics 2020, Cambridge, UK (Selected talk)
Robert Lyle, Sinan Uğur Umu et al. Prediagnostic serum RNA levels are highly dynamic in lung cancer. ASHG 2019, Houston, USA (Selected talk)
Sinan Uğur Umu et al., Avoidance of crosstalk RNA interactions in prokaryotes, EMBO/EMBL Symposium The Non-Coding Genome 2017, Heidelberg, Germany, September 2017 (Selected Talk, travel grant)
Other publications
Gardner PP, Paterson JM, McGimpsey S, Ashari-Ghomi F, Umu SU, Pawlik A, Gavryushkin A, Black MA. Sustained software development, not number of citations or journal choice, is indicative of accurate bioinformatic software. Genome Biology. 2022 Feb 16;23(1):56. doi: 10.1186/s13059-022-02625-x. PMID: 35172880; PMCID: PMC8851831.
Fromm B, Høye E, Domanska D, Zhong X, Aparicio-Puerta E, Ovchinnikov V, Umu SU, Chabot PJ, Kang W, Aslanzadeh M, Tarbier M, Mármol-Sánchez E, Urgese G, Johansen M, Hovig E, Hackenberg M, Friedländer MR, Peterson KJ. MirGeneDB 2.1: toward a complete sampling of all major animal phyla. Nucleic Acids Res. 2022 Jan 7;50(D1):D204-D210. doi: 10.1093/nar/gkab1101. PMID: 34850127; PMCID: PMC8728216.
Brägelmann J, Barahona Ponce C, Marcelain K, Roessler S, Goeppert B, Gallegos I, Colombo A, Sanhueza V, Morales E, Rivera MT, de Toro G, Ortega A, Müller B, Gabler F, Scherer D, Waldenberger M, Reischl E, Boekstegers F, Garate-Calderon V, Umu SU, Rounge TB, Popanda O, Lorenzo Bermejo J. Epigenome-Wide Analysis of Methylation Changes in the Sequence of Gallstone Disease, Dysplasia, and Gallbladder Cancer. Hepatology. 2021 Jun;73(6):2293-2310. doi: 10.1002/hep.31585. Epub 2021 Jun 15. PMID: 33020926.
Sonja Lagström, Alexander Hesselberg Løvestad, Sinan Uğur Umu, Ole Herman Ambur, Mari Nygård, Trine B. Rounge, Irene Kraus Christiansen, HPV16 and HPV18 type-specific APOBEC3 and integration profiles in different diagnostic categories of cervical samples (2021) Tumour Virus Research
Joshua Burton and Sinan U. Umu et al. (2020), Serum RNA Profiling in the 10-Years Period Prior to Diagnosis of Testicular Germ Cell Tumor, Frontiers Oncology Johannes Brägelmann … Sinan U. Umu et al. (2020), Epigenome‐wide analysis of methylation changes in the sequence of gallstone disease, dysplasia, and gallbladder cancer, Hepatology
Dominique Scherer … Sinan U. Umu et al. (2020), RNA Sequencing of Hepatobiliary Cancer Cell Lines: Data and Applications to Mutational and Transcriptomic Profiling, Cancers
Sonja Lagström and Sinan Uğur Umu et al. (2019), TaME-seq: An efficient sequencing approach for characterisation of HPV genomic variability and chromosomal integration, Scientific Reports.
Trine B Rounge and Sinan U Umu et al. (2018), Circulating small non-coding RNAs associated with age, sex, smoking, body mass and physical activity, Scientific Reports, 247155; doi: https://doi.org/10.1101/247155
Tobias Fehlmann … Sinan Ugur Umu et al., (2017). A high-resolution map of the human small non-coding transcriptome. Bioinformatics, btx814. Stinus Lindgreen* and Sinan Ugur Umu* et al., (2014) Robust Identification of Noncoding RNA from Transcriptomes Requires Phylogenetically-Informed Sampling. PLoS Comput Biol 10(10): e1003907. 10.1371/journal.pcbi.1003907
H Ogul, A T Kalkan, Sinan Ugur Umu, M S Akkaya (2013), TRAINER: A General-Purpose Trainable Short Biosequence Classifer, Protein and peptide letters 20 (10), 1108-1114 H.Oğul, Sinan Ugur Umu, Y.Y.Tuncel, M.S.Akkaya, (2011), A probabilistic approach to microRNA-target binding, Biochemical and Biophysical Research Communications 413, 111-115.