Publications 2025

Clarke AW, Høye E, Hembrom AA, Paynter VM, Vinther J, Wyrożemski Ł, Biryukova I, Formaggioni A, Ovchinnikov V, Herlyn H, Pierce A, Wu C, Aslanzadeh M, Cheneby J, Martinez P, Friedländer MR, Hovig E, Hackenberg M, Umu SU, Johansen M, Peterson KJ, Fromm B (2025)
MirGeneDB 3.0: improved taxonomic sampling, uniform nomenclature of novel conserved microRNA families and updated covariance models
Nucleic Acids Res, 53 (D1), D116-D128
DOI 10.1093/nar/gkae1094, PubMed 39673268

Publications 2024

Stawiski K, Fortner RT, Pestarino L, Umu SU, Kaaks R, Rounge TB, Elias KM, Fendler W, Langseth H (2024)
Validation of miRNA signatures for ovarian cancer earlier detection in the pre-diagnosis setting using machine learning approaches
Front Oncol, 14, 1389066
DOI 10.3389/fonc.2024.1389066, PubMed 38983926

Publications 2023

Birkeland E, Ferrero G, Pardini B, Umu SU, Tarallo S, Bulfamante S, Hoff G, Senore C, Rounge TB, Naccarati A (2023)
Profiling small RNAs in fecal immunochemical tests: is it possible?
Mol Cancer, 22 (1), 161
DOI 10.1186/s12943-023-01869-w, PubMed 37789383

Umu SU, Paynter VM, Trondsen H, Buschmann T, Rounge TB, Peterson KJ, Fromm B (2023)
Accurate microRNA annotation of animal genomes using trained covariance models of curated microRNA complements in MirMachine
Cell Genom, 3 (8), 100348
DOI 10.1016/j.xgen.2023.100348, PubMed 37601971

Publications 2022

Blandino A, Scherer D, Rounge TB, Umu SU, Boekstegers F, Barahona Ponce C, Marcelain K, Gárate-Calderón V, Waldenberger M, Morales E, Rojas A, Munoz C, Retamales J, de Toro G, Barajas O, Rivera MT, Cortés A, Loader D, Saavedra J, Gutiérrez L, Ortega A, Bertrán ME, Gabler F, Campos M, Alvarado J et al. (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 (Basel), 14 (3)
DOI 10.3390/cancers14030634, PubMed 35158906

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 (2022)
MirGeneDB 2.1: toward a complete sampling of all major animal phyla
Nucleic Acids Res, 50 (D1), D204-D210
DOI 10.1093/nar/gkab1101, PubMed 34850127

Gardner PP, Paterson JM, McGimpsey S, Ashari-Ghomi F, Umu SU, Pawlik A, Gavryushkin A, Black MA (2022)
Sustained software development, not number of citations or journal choice, is indicative of accurate bioinformatic software
Genome Biol, 23 (1), 56
DOI 10.1186/s13059-022-02625-x, PubMed 35172880

Umu SU, Langseth H, Zuber V, Helland Å, Lyle R, Rounge TB (2022)
Serum RNAs can predict lung cancer up to 10 years prior to diagnosis
Elife, 11
DOI 10.7554/eLife.71035, PubMed 35147498

Umu SU, Rapp Vander-Elst K, Karlsen VT, Chouliara M, Bækkevold ES, Jahnsen FL, Domanska D (2022)
Cellsnake: a user-friendly tool for single-cell RNA sequencing analysis
Gigascience, 12
DOI 10.1093/gigascience/giad091, PubMed 37889009

Publications 2021

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 (2021)
Epigenome-Wide Analysis of Methylation Changes in the Sequence of Gallstone Disease, Dysplasia, and Gallbladder Cancer
Hepatology, 73 (6), 2293-2310
DOI 10.1002/hep.31585, PubMed 33020926

Lagström S, Løvestad AH, Umu SU, Ambur OH, Nygård M, Rounge TB, Christiansen IK (2021)
HPV16 and HPV18 type-specific APOBEC3 and integration profiles in different diagnostic categories of cervical samples
Tumour Virus Res, 12, 200221
DOI 10.1016/j.tvr.2021.200221, PubMed 34175494

Publications 2020

Burton J, Umu SU, Langseth H, Grotmol T, Grimsrud TK, Haugen TB, Rounge TB (2020)
Serum RNA Profiling in the 10-Years Period Prior to Diagnosis of Testicular Germ Cell Tumor
Front Oncol, 10, 574977
DOI 10.3389/fonc.2020.574977, PubMed 33251139

Scherer D, Dávila López MD, Goeppert B, Abrahamsson S, González Silos RG, Nova I, Marcelain K, Roa JC, Ibberson D, Umu SU, Rounge TB, Roessler S, Bermejo JL (2020)
RNA Sequencing of Hepatobiliary Cancer Cell Lines: Data and Applications to Mutational and Transcriptomic Profiling
Cancers (Basel), 12 (9)
DOI 10.3390/cancers12092510, PubMed 32899426

Umu SU, Langseth H, Keller A, Meese E, Helland Å, Lyle R, Rounge TB (2020)
A 10-year prediagnostic follow-up study shows that serum RNA signals are highly dynamic in lung carcinogenesis
Mol Oncol, 14 (2), 235-247
DOI 10.1002/1878-0261.12620, PubMed 31851411

Publications 2019

Lagström S, Umu SU, Lepistö M, Ellonen P, Meisal R, Christiansen IK, Ambur OH, Rounge TB (2019)
TaME-seq: An efficient sequencing approach for characterisation of HPV genomic variability and chromosomal integration
Sci Rep, 9 (1), 524
DOI 10.1038/s41598-018-36669-6, PubMed 30679491

Publications 2018

Fehlmann T, Backes C, Alles J, Fischer U, Hart M, Kern F, Langseth H, Rounge T, Umu SU, Kahraman M, Laufer T, Haas J, Staehler C, Ludwig N, Hübenthal M, Meder B, Franke A, Lenhof HP, Meese E, Keller A (2018)
A high-resolution map of the human small non-coding transcriptome
Bioinformatics, 34 (10), 1621-1628
DOI 10.1093/bioinformatics/btx814, PubMed 29281000

Rounge TB, Umu SU, Keller A, Meese E, Ursin G, Tretli S, Lyle R, Langseth H (2018)
Circulating small non-coding RNAs associated with age, sex, smoking, body mass and physical activity
Sci Rep, 8 (1), 17650
DOI 10.1038/s41598-018-35974-4, PubMed 30518766

Publications 2017

Umu SU, Gardner PP (2017)
A comprehensive benchmark of RNA-RNA interaction prediction tools for all domains of life
Bioinformatics, 33 (7), 988-996
DOI 10.1093/bioinformatics/btw728, PubMed 27993777

Umu SU, Langseth H, Bucher-Johannessen C, Fromm B, Keller A, Meese E, Lauritzen M, Leithaug M, Lyle R, Rounge TB (2017)
A comprehensive profile of circulating RNAs in human serum
RNA Biol, 15 (2), 242-250
DOI 10.1080/15476286.2017.1403003, PubMed 29219730

Publications 2016

Umu SU, Poole AM, Dobson RC, Gardner PP (2016)
Avoidance of stochastic RNA interactions can be harnessed to control protein expression levels in bacteria and archaea
Elife, 5
DOI 10.7554/eLife.13479, PubMed 27642845

Publications 2014

Lindgreen S, Umu SU, Lai AS, Eldai H, Liu W, McGimpsey S, Wheeler NE, Biggs PJ, Thomson NR, Barquist L, Poole AM, Gardner PP (2014)
Robust identification of noncoding RNA from transcriptomes requires phylogenetically-informed sampling
PLoS Comput Biol, 10 (10), e1003907
DOI 10.1371/journal.pcbi.1003907, PubMed 25357249

Publications 2013

Ogul H, Kalkan AT, Umu SU, Akkaya MS (2013)
TRAINER: a general-purpose trainable short biosequence classifer
Protein Pept Lett, 20 (10), 1108-14
DOI 10.2174/0929866511320100004, PubMed 23544665

Publications 2011

Oğul H, Umu SU, Tuncel YY, Akkaya MS (2011)
A probabilistic approach to microRNA-target binding
Biochem Biophys Res Commun, 413 (1), 111-5
DOI 10.1016/j.bbrc.2011.08.065, PubMed 21875575