Rolf I. Skotheim

• Wolowczyk, Camilla; Neckmann, Ulrike; Aure, Miriam Ragle; Hall, Martina; Johannessen, Bjarne & Zhao, Sen [Show all 14 contributors for this article] (2022). NRF2 drives an oxidative stress response predictive of breast cancer. Free Radical Biology & Medicine. ISSN 0891-5849. 184, p. 170–184. doi: 10.1016/j.freeradbiomed.2022.03.029.
• Pluta, John; Pyle, Louise C.; Nead, Kevin T.; Wilf, Rona; Li, Mingyao & Mitra, Nandita [Show all 57 contributors for this article] (2021). Identification of 22 susceptibility loci associated with testicular germ cell tumors. Nature Communications. ISSN 2041-1723. 12(1), p. 1–13. doi: 10.1038/s41467-021-24334-y.
• Sveen, Anita; Johannessen, Bjarne; Eilertsen, Ina Andrassy; Røsok, Bård Ingvald; Gulla, Marie & Eide, Peter Andreas Wold [Show all 14 contributors for this article] (2021). The expressed mutational landscape of microsatellite stable colorectal cancers. Genome Medicine. ISSN 1756-994X. 13. doi: 10.1186/s13073-021-00955-2. Full text in Research Archive
• Tryggestad, Anne Merete Aaland; Axcrona, Karol; Axcrona, Ulrika; Bigalke, Iris; Brennhovd, Bjørn & Inderberg, Else Marit [Show all 19 contributors for this article] (2021). Long-term first-in-man Phase I/II study of an adjuvant dendritic cell vaccine in patients with high-risk prostate cancer after radical prostatectomy. The Prostate. ISSN 0270-4137. 82(2), p. 245–253. doi: 10.1002/pros.24267.
• Kidd, Susanne Gundersen; Carm, Kristina Totland; Bogaard, Mari; Olsen, Linn Guro; Bakken, Anne Cathrine & Løvf, Marthe [Show all 10 contributors for this article] (2021). High expression of SCHLAP1 in primary prostate cancer is an independent predictor of biochemical recurrence, despite substantial heterogeneity. Neoplasia. ISSN 1522-8002. 23(6), p. 634–641. doi: 10.1016/j.neo.2021.05.012. Full text in Research Archive
• Hoff, Andreas Midbøe; Kraggerud, Sigrid M.; Alagaratnam, Sharmini; Berg, Kaja Christine Graue; Johannessen, Bjarne & Høland, Maren [Show all 11 contributors for this article] (2020). Frequent copy number gains of SLC2A3 and ETV1 in testicular embryonal carcinomas. Endocrine-Related Cancer. ISSN 1351-0088. 27(9), p. 457–468. doi: 10.1530/ERC-20-0064. Full text in Research Archive
• Zhao, Sen; Hoff, Andreas Midbøe & Skotheim, Rolf I. (2020). ScaR - A tool for sensitive detection of known fusion transcripts: Establishing prevalence of fusions in testicular germ cell tumors. NAR Genomics and Bioinformatics. ISSN 2631-9268. 2(1). doi: 10.1093/nargab/lqz025. Show summary

  Bioinformatics tools for fusion transcript detection from RNA-sequencing data are in general developed for identification of novel fusions, which demands a high number of supporting reads and strict filters to avoid false discoveries. As our knowledge of bona fide fusion genes becomes more saturated, there is a need to establish their prevalence with high sensitivity. We present ScaR, a tool that uses a supervised scaffold realignment approach for sensitive fusion detection in RNA-seq data. ScaR detects a set of 130 synthetic fusion transcripts from simulated data at a higher sensitivity compared to established fusion finders. Applied to fusion transcripts potentially involved in testicular germ cell tumors (TGCTs), ScaR detects the fusions RCC1-ABHD12B and CLEC6A-CLEC4D in 9% and 28% of 150 TGCTs, respectively. The fusions were not detected in any of 198 normal testis tissues. Thus, we demonstrate high prevalence of RCC1-ABHD12B and CLEC6A-CLEC4D in TGCTs, and their cancer specific features. Further, we find that RCC1-ABHD12B and CLEC6A-CLEC4D are predominantly expressed in the seminoma and embryonal carcinoma histological subtypes of TGCTs, respectively. In conclusion, ScaR is useful for establishing the frequency of known and validated fusion transcripts in larger data sets and detecting clinically relevant fusion transcripts with high sensitivity.

• Neckmann, Ulrike; Wolowczyk, Camilla; Hall, Martina; Almaas, Eivind; Ren, Jiang & Zhao, Sen [Show all 11 contributors for this article] (2019). GREM1 is associated with metastasis and predicts poor prognosis in ER-negative breast cancer patients. Cell Communication and Signaling. ISSN 1478-811X. 17. doi: 10.1186/s12964-019-0467-7. Full text in Research Archive
• Carm, Kristina Totland; Hoff, Andreas Midbøe; Bakken, Anne Cathrine; Axcrona, Ulrika; Axcrona, Karol & Lothe, Ragnhild A [Show all 8 contributors for this article] (2019). Interfocal heterogeneity challenges the clinical usefulness of molecular classification of primary prostate cancer. Scientific Reports. ISSN 2045-2322. 9(1). doi: 10.1038/s41598-019-49964-7. Full text in Research Archive
• Smeby, Jørgen; Sveen, Anita; Eilertsen, Ina Andrassy; Danielsen, Stine Aske; Hoff, Andreas Midbøe & Eide, Peter Andreas Wold [Show all 12 contributors for this article] (2019). Transcriptional and functional consequences of TP53 splice mutations in colorectal cancer. Oncogenesis. ISSN 2157-9024. 8:35(6), p. 1–8. doi: 10.1038/s41389-019-0141-3. Full text in Research Archive
• Eilertsen, Ina Andrassy; Sveen, Anita; Strømme, Jonas Meier; Skotheim, Rolf I.; Nesbakken, Arild & Lothe, Ragnhild A (2018). Alternative splicing expands the prognostic impact of KRAS in microsatellite stable primary colorectal cancer . International Journal of Cancer. ISSN 0020-7136. 144(4), p. 841–847. doi: 10.1002/ijc.31809. Full text in Research Archive
• Celestino, Ricardo; Nome, Torfinn; Pestana, Ana; Hoff, Andreas Midbøe; Gonçalves, A. Pedro & Pereira, Luísa [Show all 12 contributors for this article] (2018). CRABP1, C1QL1 and LCN2 are biomarkers of differentiated thyroid carcinoma, and predict extrathyroidal extension. BMC Cancer. ISSN 1471-2407. 18:68, p. 1–16. doi: 10.1186/s12885-017-3948-3. Full text in Research Archive
• Løvf, Marthe; Zhao, Sen; Axcrona, Ulrika; Johannessen, Bjarne; Bakken, Anne Cathrine & Carm, Kristina Totland [Show all 13 contributors for this article] (2018). Multifocal primary prostate cancer exhibits high degree of genomic heterogeneity. European Urology. ISSN 0302-2838. p. 1–8. doi: 10.1016/j.eururo.2018.08.009.
• Smebye, Marianne Lislerud; Agostini, Antonio; Johannessen, Bjarne; Thorsen, Jim; Davidson, Ben & Tropé, Claes Gøran [Show all 9 contributors for this article] (2017). Involvement of DPP9 in gene fusions in serous ovarian carcinoma. BMC Cancer. ISSN 1471-2407. 17(1). doi: 10.1186/s12885-017-3625-6.
• Zhao, Sen; Løvf, Marthe; Carm, Kristina Totland; Bakken, Anne Cathrine; Hoff, Andreas Midbøe & Skotheim, Rolf I. (2017). Novel transcription-induced fusion RNAs in prostate cancer. OncoTarget. ISSN 1949-2553. 8(30), p. 49133–49143. doi: 10.18632/oncotarget.17099.
• Berg, Kaja Christine Graue; Eide, Peter Andreas Wold; Eilertsen, Ina Andrassy; Johannessen, Bjarne; Bruun, Jarle & Danielsen, Stine Aske [Show all 14 contributors for this article] (2017). Multi-omics of 34 colorectal cancer cell lines - a resource for biomedical studies. Molecular Cancer. ISSN 1476-4598. 16:116, p. 1–16. doi: 10.1186/s12943-017-0691-y.
• Sveen, Anita; Johannessen, Bjarne; Tengs, Torstein; Danielsen, Stine Aske; Eilertsen, Ina Andrassy & Lind, Guro Elisabeth [Show all 16 contributors for this article] (2017). Multilevel genomics of colorectal cancers with microsatellite instability – clinical impact of JAK1 mutations and consensus molecular subtype 1. Genome Medicine. ISSN 1756-994X. 9(1). doi: 10.1186/s13073-017-0434-0.
• Lågstad, Stian; Zhao, Sen; Hoff, Andreas Midbøe; Johannessen, Bjarne; Lingjærde, Ole Christian & Skotheim, Rolf I. (2017). Chimeraviz: A tool for visualizing chimeric RNA. Bioinformatics. ISSN 1367-4803. 33(18), p. 2954–2956. doi: 10.1093/bioinformatics/btx329. Show summary

  Advances in high-throughput RNA sequencing have enabled more efficient detection of fusion transcripts, but the technology and associated software used for fusion detection from sequencing data often yield a high false discovery rate. Good prioritization of the results is important, and this can be helped by a visualization framework that automatically integrates RNA data with known genomic features. Here we present chimeraviz, a Bioconductor package that automates the creation of chimeric RNA visualizations. The package supports input from nine different fusion-finder tools: deFuse, EricScript, InFusion, JAFFA, FusionCatcher, FusionMap, PRADA, SOAPfuse and STAR-FUSION.

• Smebye, Marianne Lislerud; Haugom, Lisbeth; Davidson, Ben; Tropé, Claes Gøran; Heim, Sverre & Skotheim, Rolf I. [Show all 7 contributors for this article] (2017). Bilateral ovarian carcinomas differ in the expression of metastasis-related genes. Oncology Letters. ISSN 1792-1074. 13(1), p. 184–190. doi: 10.3892/ol.2016.5384.
• Moen, Line Victoria; Ramberg, Håkon Andre; Zhao, Sen; Grytli, Helene Hartvedt; Sveen, Anita & Berge, Viktor [Show all 9 contributors for this article] (2017). Observed correlation between the expression levels of catalytic subunit, C?2, of cyclic adenosine monophosphate-dependent protein kinase and prostate cancer aggressiveness. Urologic Oncology. ISSN 1078-1439. 35(3), p. 111.e1–111.e8. doi: 10.1016/j.urolonc.2016.10.002. Show summary

  Background As an intracellular human pathogen, Mycobacterium tuberculosis (Mtb) is facing multiple stressful stimuli inside the macrophage and the granuloma. Understanding Mtb responses to stress is essential to identify new virulence factors and pathways that play a role in the survival of the tubercle bacillus. The main goal of this study was to map the regulatory networks of differentially expressed (DE) transcripts in Mtb upon various forms of genotoxic stress. We exposed Mtb cells to oxidative (H2O2 or paraquat), nitrosative (DETA/NO), or alkylation (MNNG) stress or mitomycin C, inducing double-strand breaks in the DNA. Total RNA was isolated from treated and untreated cells and subjected to high-throughput deep sequencing. The data generated was analysed to identify DE genes encoding mRNAs, non-coding RNAs (ncRNAs), and the genes potentially targeted by ncRNAs. Results The most significant transcriptomic alteration with more than 700 DE genes was seen under nitrosative stress. In addition to genes that belong to the replication, recombination and repair (3R) group, mainly found under mitomycin C stress, we identified DE genes important for bacterial virulence and survival, such as genes of the type VII secretion system (T7SS) and the proline-glutamic acid/proline-proline-glutamic acid (PE/PPE) family. By predicting the structures of hypothetical proteins (HPs) encoded by DE genes, we found that some of these HPs might be involved in mycobacterial genome maintenance. We also applied a state-of-the-art method to predict potential target genes of the identified ncRNAs and found that some of these could regulate several genes that might be directly involved in the response to genotoxic stress. Conclusions Our study reflects the complexity of the response of Mtb in handling genotoxic stress. In addition to genes involved in genome maintenance, other potential key players, such as the members of the T7SS and PE/PPE gene family, were identified. This plethora of responses is detected not only at the level of DE genes encoding mRNAs but also at the level of ncRNAs and their potential targets.

• Ramberg, Håkon Andre; Grytli, Helene Hartvedt; Nygård, Ståle; Wang, Wanzhong; Øgren, Hans Olav & Zhao, Sen [Show all 14 contributors for this article] (2016). PBX3 is a putative biomarker of aggressive prostate cancer. International Journal of Cancer. ISSN 0020-7136. 139(8), p. 1810–1820. doi: 10.1002/ijc.30220.
• Sveen, Anita; Kilpinen, Sami; Ruusulehto, Anja; Lothe, Ragnhild A & Skotheim, Rolf Inge (2016). Aberrant RNA splicing in cancer; Expression changes and driver mutations of splicing factor genes. Oncogene. ISSN 0950-9232. 35(19), p. 2413–2427. doi: 10.1038/onc.2015.318.
• Lorenz, Susanne; Barøy, Tale; Sun, Jinchang; Nome, Torfinn; Vodak, Daniel & Bryne, Jan Christian [Show all 21 contributors for this article] (2016). Unscrambling the genomic chaos of osteosarcoma reveals extensive transcript fusion, recurrent rearrangements and frequent novel TP53 aberrations. OncoTarget. ISSN 1949-2553. 7(5), p. 5273–5288. doi: 10.18632/oncotarget.6567. Show summary

  In contrast to many other sarcoma subtypes, the chaotic karyotypes of osteosarcoma have precluded the identification of pathognomonic translocations. We here report hundreds of genomic rearrangements in osteosarcoma cell lines, showing clear characteristics of microhomology-mediated break-induced replication (MMBIR) and end-joining repair (MMEJ) mechanisms. However, at RNA level, the majority of the fused transcripts did not correspond to genomic rearrangements, suggesting the involvement of trans-splicing, which was further supported by typical trans-splicing characteristics. By combining genomic and transcriptomic analysis, certain recurrent rearrangements were identified and further validated in patient biopsies, including a PMP22-ELOVL5 gene fusion, genomic structural variations affecting RB1, MTAP/CDKN2A and MDM2, and, most frequently, rearrangements involving TP53. Most cell lines (7/11) and a large fraction of tumor samples (10/25) showed TP53 rearrangements, in addition to somatic point mutations (6 patient samples, 1 cell line) and MDM2 amplifications (2 patient samples, 2 cell lines). The resulting inactivation of p53 was demonstrated by a deficiency of the radiation-induced DNA damage response. Thus, TP53 rearrangements are the major mechanism of p53 inactivation in osteosarcoma. Together with active MMBIR and MMEJ, this inactivation probably contributes to the exceptional chromosomal instability in these tumors. Although rampant rearrangements appear to be a phenotype of osteosarcomas, we demonstrate that among the huge number of probable passenger rearrangements, specific recurrent, possibly oncogenic, events are present. For the first time the genomic chaos of osteosarcoma is characterized so thoroughly and delivered new insights in mechanisms involved in osteosarcoma development and may contribute to new diagnostic and therapeutic strategies.

• Hoff, Andreas Midbøe; Alagaratnam, Sharmini; Zhao, Sen; Bruun, Jarle; Andrews, PW & Lothe, Ragnhild A [Show all 7 contributors for this article] (2016). Identification of novel fusion genes in testicular germ cell tumors. Cancer Research. ISSN 0008-5472. 76(1), p. 108–116. doi: 10.1158/0008-5472.CAN-15-1790.
• Cekaite, Lina; Eide, Peter Andreas Wold; Lind, Guro Elisabeth; Skotheim, Rolf I. & Lothe, Ragnhild A (2015). MicroRNAs as growth regulators, their function and biomarker status in colorectal cancer. OncoTarget. ISSN 1949-2553. 7(6), p. 6476–6505. doi: 10.18632/oncotarget.6390.
• Munkley, Jennifer; Oltean, Sebastian; Vodak, Daniel; Wilson, Brian T.; Livermore, Karen E. & Zhou, Yan [Show all 20 contributors for this article] (2015). The androgen receptor controls expression of the cancerassociated sTn antigen and cell adhesion through induction of ST6GalNAc1 in prostate cancer. OncoTarget. ISSN 1949-2553. 6(33), p. 34358–34374. doi: 10.18632/oncotarget.6024. Full text in Research Archive
• Johannessen, Bjarne; Sveen, Anita & Skotheim, Rolf Inge (2015). Tin: An R package for transcriptome instability analysis. Cancer Informatics. ISSN 1176-9351. 14, p. 109–112. doi: 10.4137/CIN.S31363.
• Rounge, Trine Ballestad; Furu, Kari; Skotheim, Rolf Inge; Haugen, Trine B.; Grotmol, Tom & Enerly, Espen (2015). Profiling of the small RNA populations in human testicular germ cell tumors shows global loss of piRNAs. Molecular Cancer. ISSN 1476-4598. 14(153). doi: 10.1186/s12943-015-0411-4. Full text in Research Archive
• Brabrand, Sigmund; Johannessen, Bjarne; Axcrona, Ulrika; Kraggerud, Sigrid M.; Berg, Kaja Christine Graue & Bakken, Anne Cathrine [Show all 11 contributors for this article] (2015). Exome sequencing of bilateral testicular germ cell tumors suggests independent development lineages. Neoplasia. ISSN 1522-8002. 17(2), p. 167–174. doi: 10.1016/j.neo.2014.12.005.
• Bruun, Jarle; Kolberg, Matthias; Ahlquist, Terje Cruickshank; Røyrvik, Ellen Christine; Nome, Torfinn & Leithe, Edward [Show all 18 contributors for this article] (2015). Regulator of chromosome condensation 2 identifies high-risk patients within both major phenotypes of colorectal cancer. Clinical Cancer Research. ISSN 1078-0432. 21(16), p. 3759–3770. doi: 10.1158/1078-0432.CCR-14-3294.
• Hoff, Andreas Midbøe; Johannessen, Bjarne; Alagaratnam, Sharmini; Zhao, Sen; Nome, Torfinn & Løvf, Marthe [Show all 11 contributors for this article] (2015). Novel RNA variants in colorectal cancers. OncoTarget. ISSN 1949-2553. 6(34), p. 36587–36602. doi: 10.18632/oncotarget.5500.
• Kolberg, Matthias; Høland, Maren; Lind, Guro Elisabeth; Ågesen, Trude Holmeide; Skotheim, Rolf Inge & Hall, Kirsten Sundby [Show all 11 contributors for this article] (2015). Protein expression of BIRC5, TK1, and TOP2A in malignant peripheral nerve sheath tumours - A prognostic test after surgical resection. Molecular Oncology. ISSN 1574-7891. 9(6), p. 1129–1139. doi: 10.1016/j.molonc.2015.02.005.
• Mesquita, Diana; Barros-Silva, João D.; Santos, Joana; Skotheim, Rolf Inge; Lothe, Ragnhild A & Paulo, Paula [Show all 7 contributors for this article] (2015). Specific and redundant activities of ETV1 and ETV4 in prostate cancer aggressiveness revealed by co-overexpression cellular contexts. OncoTarget. ISSN 1949-2553. 6(7), p. 5217–5236. doi: 10.18632/oncotarget.2847.
• Vedeld, Hege Marie; Skotheim, Rolf Inge; Lothe, Ragnhild A & Lind, Guro Elisabeth (2014). The recently suggested intestinal cancer stem cell marker DCLK1 is an epigenetic biomarker for colorectal cancer. Epigenetics. ISSN 1559-2294. 9(3), p. 346–350. doi: 10.4161/epi.27582.
• Sveen, Anita; Johannessen, Bjarne; Teixeira, Manuel; Lothe, Ragnhild A & Skotheim, Rolf Inge (2014). Transcriptome instability as a molecular pan-cancer characteristic of carcinomas. BMC Genomics. ISSN 1471-2164. 15(1). doi: 10.1186/1471-2164-15-672.
• Løvf, Marthe; Nome, Torfinn; Bruun, Jarle; Eknæs, Mette; Bakken, Anne Cathrine & Mpindi, John-Patrick [Show all 12 contributors for this article] (2014). A novel transcript, VNN1-AB, as a biomarker for colorectal cancer. International Journal of Cancer. ISSN 0020-7136. 135(9), p. 2077–2084. doi: 10.1002/ijc.28855.
• Oppelt, Angela; Haugsten, Ellen Margrethe; Zech, Tobias; Danielsen, Håvard Emil; Sveen, Anita & Lobert, Viola Helene [Show all 8 contributors for this article] (2014). PIKfyve, MTMR3 and their product PtdIns5P regulate cancer cell migration and invasion through activation of Rac1. Biochemical Journal. ISSN 0264-6021. 461(3), p. 383–390. doi: 10.1042/BJ20140132.
• Smebye, Marianne Lislerud; Sveen, Anita; Haugom, Lisbeth; Davidson, Ben; Tropé, Claes Gøran & Lothe, Ragnhild A [Show all 9 contributors for this article] (2014). Chromosome 19 rearrangements in ovarian carcinomas: Zinc finger genes are particularly targeted. Genes, Chromosomes and Cancer. ISSN 1045-2257. 53(7), p. 558–567. doi: 10.1002/gcc.22166.
• Nome, Torfinn; Hoff, Andreas Midbøe; Bakken, Anne Cathrine; Rognum, Torleiv Ole; Nesbakken, Arild & Skotheim, Rolf Inge (2014). High frequency of fusion transcripts involving TCF7L2 in colorectal cancer: Novel fusion partner and splice variants. PLOS ONE. ISSN 1932-6203. 9(3). doi: 10.1371/journal.pone.0091264. Full text in Research Archive
• Sveen, Anita; Nesbakken, Arild; Ågesen, Trude Holmeide; Guren, Marianne; Tveit, Magne Kjell & Skotheim, Rolf Inge [Show all 7 contributors for this article] (2013). Anticipating the Clinical Use of Prognostic Gene Expression-Based Tests for Colon Cancer Stage II and III: Is Godot Finally Arriving? Clinical Cancer Research. ISSN 1078-0432. 19(24), p. 6669–6677. doi: 10.1158/1078-0432.CCR-13-1769.
• Paulo, Paula; Bakken, Anne Cathrine; Cerveira, Nuno; Løvf, Marthe; Henrique, Rui & Jerónimo, Carmen [Show all 10 contributors for this article] (2013). Novel 5 ' Fusion Partners of ETV1 and ETV4 in Prostate Cancer. Neoplasia. ISSN 1522-8002. 15(7), p. 720–726. doi: 10.1593/neo.13232.
• Løvf, Marthe; Thomassen, Gard O Sundby; Mertens, Fredrik; Cerveira, Nuno; Teixeira, Manuel & Lothe, Ragnhild A [Show all 7 contributors for this article] (2013). Assessment of Fusion Gene Status in Sarcomas Using a Custom Made Fusion Gene Microarray. PLOS ONE. ISSN 1932-6203. 8(8). doi: 10.1371/journal.pone.0070649.
• Nome, Torfinn; Thomassen, Gard O Sundby; Bruun, Jarle; Ahlquist, Terje Cruickshank; Bakken, Anne Cathrine & Hoff, Andreas Midbøe [Show all 17 contributors for this article] (2013). Common fusion transcripts identified in colorectal cancer cell lines by high throughput RNA sequencing. Translational Oncology. ISSN 1944-7124. 6(5), p. 546–553. doi: 10.1593/tlo.13457. Full text in Research Archive
• Chung, Charles C.; Kanetsky, Peter A.; Wang, Zhaoming; Hildebrandt, Michelle A.T.; Koster, Roelof & Skotheim, Rolf Inge [Show all 30 contributors for this article] (2013). Meta-analysis identifies four new loci associated with testicular germ cell tumor. Nature Genetics. ISSN 1061-4036. 45(6), p. 680–685. doi: 10.1038/ng.2634.
• Schumacher, Frecrick R.; Wang, Zhaoming; Skotheim, Rolf Inge; Koster, Roelof; Chung, Charles C. & Hildebrandt, Michelle A.T. [Show all 35 contributors for this article] (2013). Testicular germ cell tumor susceptibility associated with the UCK2 locus on chromosome 1q23. Human Molecular Genetics. ISSN 0964-6906. 22(13), p. 2748–2753. doi: 10.1093/hmg/ddt109.
• Kraggerud, Sigrid M.; Høi-Hansen, Christina E.; Alagaratnam, Sharmini; Skotheim, Rolf Inge; Abeler, Vera Maria & Rajpert-De Meyts, Ewa [Show all 7 contributors for this article] (2013). Molecular characteristics of malignant ovarian germ cell tumors and comparison with testicular counterparts : implications for pathogenesis. Endocrine reviews. ISSN 0163-769X. 34(3), p. 339–376. doi: 10.1210/er.2012-1045.
• Alagaratnam, Sharmini; Harrison, Neil; Bakken, Anne Cathrine; Hoff, Andreas Midbøe; Jones, Mark & Sveen, Anita [Show all 10 contributors for this article] (2013). Transforming Pluripotency: An Exon-Level Study of Malignancy-Specific Transcripts in Human Embryonal Carcinoma and Embryonic Stem Cells. Stem Cells and Development. ISSN 1547-3287. 22(7), p. 1136–1146. doi: 10.1089/scd.2012.0369.
• Camões, Maria J; Paulo, Paula; Ribeiro, Franclim R; Barros-Silva, Joao D.; Almeida, Mafalda & Costa, Vera L [Show all 12 contributors for this article] (2012). Potential Downstream Target Genes of Aberrant ETS Transcription Factors Are Differentially Affected in Ewing's Sarcoma and Prostate Carcinoma. PLOS ONE. ISSN 1932-6203. 7(11). doi: 10.1371/journal.pone.0049819.
• Sveen, Anita; Ågesen, Trude Holmeide; Nesbakken, Arild; Meling, Gunn Iren; Rognum, Torleiv Ole & Liestøl, Knut [Show all 8 contributors for this article] (2012). ColoGuidePro: A Prognostic 7-Gene Expression Signature for Stage III Colorectal Cancer Patients. Clinical Cancer Research. ISSN 1078-0432. 18(21), p. 6001–6010. doi: 10.1158/1078-0432.CCR-11-3302.
• Paulo, Paula; Ribeiro, Franclim R; Santos, Joana; Mesquita, Diana; Almeida, Mafalda & Barros-Silva, Joao D. [Show all 14 contributors for this article] (2012). Molecular Subtyping of Primary Prostate Cancer Reveals Specific and Shared Target Genes of Different ETS Rearrangements. Neoplasia. ISSN 1522-8002. 14(7), p. 600–+. doi: 10.1593/neo.12600.
• Celestino, Ricardo; Sigstad, Eva; Løvf, Marthe; Thomassen, Gard O Sundby; Kotanska-Grøholt, Krystyna & Jørgensen, Lars Hilmar [Show all 13 contributors for this article] (2012). Survey of 548 oncogenic fusion transcripts in thyroid tumors supports the importance of the already established thyroid fusions genes. Genes, Chromosomes and Cancer. ISSN 1045-2257. 51(12), p. 1154–1164. doi: 10.1002/gcc.22003.
• Ågesen, Trude Holmeide; Sveen, Anita; Merok, Marianne Aarstad; Lind, Guro Elisabeth; Nesbakken, Arild & Skotheim, Rolf Inge [Show all 7 contributors for this article] (2012). ColoGuideEx: a robust gene classifier specific for stage II colorectal cancer prognosis. Gut. ISSN 0017-5749. 61(11), p. 1560–1567. doi: 10.1136/gutjnl-2011-301179.
• Paulo, Paula; Barros-Silva, Joao D.; Ribeiro, Franclim R; Ramalho-Carvalho, Joao; Jeronimo, Carmen & Henrique, Rui [Show all 10 contributors for this article] (2012). FLI1 is a novel ETS transcription factor involved in gene fusions in prostate cancer. Genes, Chromosomes and Cancer. ISSN 1045-2257. 51(3), p. 240–249. doi: 10.1002/gcc.20948.
• Matheu, Ander; Collado, Manuel; Wise, Clare; Manterola, Lorea; Cekaite, Lina & Tye, Angela J. [Show all 16 contributors for this article] (2012). Oncogenicity of the Developmental Transcription Factor Sox9. Cancer Research. ISSN 0008-5472. 72(5), p. 1301–1315. doi: 10.1158/0008-5472.CAN-11-3660.
• Sveen, Anita; Bakken, Anne Cathrine; Ågesen, Trude Holmeide; Lind, Guro Elisabeth; Nesbakken, Arild & Nordgård, Oddmund [Show all 10 contributors for this article] (2012). The exon-level biomarker SLC39A14 has organ-confined cancer-specificity in colorectal cancer. International Journal of Cancer. ISSN 0020-7136. 131(6), p. 1479–1485. doi: 10.1002/ijc.27399.
• Cekaite, Lina; Rantala, Juha K.; Bruun, Jarle; Guriby, Marianne; Ågesen, Trude Holmeide & Danielsen, Stine Aske [Show all 11 contributors for this article] (2012). MiR-9,-31, and-182 Deregulation Promote Proliferation and Tumor Cell Survival in Colon Cancer. Neoplasia. ISSN 1522-8002. 14(9), p. 868–U126. doi: 10.1593/neo.121094.
• Nyquist, Kaja Beate; Panagopoulos, Ioannis; Thorsen, Jim; Haugom, Lisbeth; Gorunova, Ludmila & Bjerkehagen, Bodil [Show all 13 contributors for this article] (2012). Whole-Transcriptome Sequencing Identifies Novel IRF2BP2-CDX1 Fusion Gene Brought about by Translocation t(1;5)(q42;q32) in Mesenchymal Chondrosarcoma. PLOS ONE. ISSN 1932-6203. 7(11). doi: 10.1371/journal.pone.0049705.
• Sveen, Anita; Ågesen, Trude Holmeide; Nesbakken, Arild; Rognum, Torleiv Ole; Lothe, Ragnhild A & Skotheim, Rolf Inge (2011). Transcriptome instability in colorectal cancer identified by exon microarray analyses: Associations with splicing factor expression levels and patient survival. Genome Medicine. ISSN 1756-994X. 3(5). doi: 10.1186/gm248.
• Alagaratnam, Sharmini; Lind, Guro Elisabeth; Kraggerud, Sigrid M.; Lothe, Ragnhild A & Skotheim, Rolf Inge (2011). The testicular germ cell tumour transcriptome. International Journal of Andrology. ISSN 0105-6263. 34(4pt2), p. e133–e151. doi: 10.1111/j.1365-2605.2011.01169.x.
• Ågesen, Trude Holmeide; Berg, Marianne; Clancy, Trevor; Thiis-Evensen, Espen; Cekaite, Lina & Lind, Guro Elisabeth [Show all 16 contributors for this article] (2011). CLC and IFNAR1 are differentially expressed and a global immunity score is distinct between early- and late-onset colorectal cancer. Genes and Immunity. ISSN 1466-4879. 12(8), p. 653–662. doi: 10.1038/gene.2011.43.
• Danielsen, Stine Aske; Cekaite, Lina; Ågesen, Trude Holmeide; Sveen, Anita; Nesbakken, Arild & Thiis-Evensen, Espen [Show all 9 contributors for this article] (2011). Phospholipase C Isozymes Are Deregulated in Colorectal Cancer - Insights Gained from Gene Set Enrichment Analysis of the Transcriptome. PLOS ONE. ISSN 1932-6203. 6(9). doi: 10.1371/journal.pone.0024419.
• Lind, Guro Elisabeth; Danielsen, Stine Aske; Ahlquist, Terje Cruickshank; Merok, Marianne Aarstad; Andresen, Kim & Skotheim, Rolf Inge [Show all 14 contributors for this article] (2011). Identification of an epigenetic biomarker panel with high sensitivity and specificity for colorectal cancer and adenomas. Molecular Cancer. ISSN 1476-4598. 10. doi: 10.1186/1476-4598-10-85.
• Ribeiro, Franclim R; Paulo, Paula; Costa, Vera L; Barros-Silva, Joao D.; Ramalho-Carvalho, Joao & Jeronimo, Carmen [Show all 11 contributors for this article] (2011). Cysteine-Rich Secretory Protein-3 (CRISP3) Is Strongly Up-Regulated in Prostate Carcinomas with the TMPRSS2-ERG Fusion Gene. PLOS ONE. ISSN 1932-6203. 6(7). doi: 10.1371/journal.pone.0022317.
• Sagona, Antonia; Nezis, Ioannis; Bache, Kristi Cecilie Grønvold; Haglund, Kaisa; Bakken, Anne Cathrine & Skotheim, Rolf Inge [Show all 7 contributors for this article] (2011). A Tumor-Associated Mutation of FYVE-CENT Prevents Its Interaction with Beclin 1 and Interferes with Cytokinesis. PLOS ONE. ISSN 1932-6203. 6(3). doi: 10.1371/journal.pone.0017086.
• Løvf, Marthe; Thomassen, Gard O Sundby; Bakken, Anne Cathrine; Celestino, Ricardo; Fioretos, Thoas & Lind, Guro Elisabeth [Show all 8 contributors for this article] (2011). Fusion Gene Microarray Reveals Cancer Type-Specificity Among Fusion Genes. Genes, Chromosomes and Cancer. ISSN 1045-2257. 50(5), p. 348–357. doi: 10.1002/gcc.20860.
• Costa, Vera L; Henrique, Rui; Danielsen, Stine Aske; Duarte-Pereira, S; Eknæs, Mette & Skotheim, Rolf Inge [Show all 13 contributors for this article] (2010). Three Epigenetic Biomarkers, GDF15, TMEFF2, and VIM, Accurately Predict Bladder Cancer from DNA-Based Analyses of Urine Samples. Clinical Cancer Research. ISSN 1078-0432. 16(23), p. 5842–5851. doi: 10.1158/1078-0432.CCR-10-1312.
• Auensen, Espen; Skotheim, Rolf Inge; Schjølberg, Aasa Rambæk; Røislien, Jo; Lothe, Ragnhild A & Clausen, Ole Petter Fraas (2010). Spindle proteins are differentially expressed in the various histological subtypes of testicular germ cell tumors. Journal of Carcinogenesis. ISSN 0974-6773. 9(1), p. 1–1. doi: 10.4103/1477-3163.60358.
• Micci, Francesca; Skotheim, Rolf Inge; Haugom, Lisbeth; Weimer, J; Eibak, Anne Mette E. & Abeler, Vera Maria [Show all 10 contributors for this article] (2010). Array-CGH Analysis of Microdissected Chromosome 19 Markers in Ovarian Carcinoma Identifies Candidate Target Genes. Genes, Chromosomes and Cancer. ISSN 1045-2257. 49(11), p. 1046–1053. doi: 10.1002/gcc.20813.
• Sagona, Antonia; Nezis, Jonnis P; Pedersen, Nina Marie; Liestøl, Knut; Poulton, J & Rusten, Tor Erik [Show all 9 contributors for this article] (2010). PtdIns(3)P controls cytokinesis through KIF13A-mediated recruitment of FYVE-CENT to the midbody. Nature Cell Biology. ISSN 1465-7392. 12(4), p. 362–U140. doi: 10.1038/ncb2036.
• Berg, Marianne; Ågesen, Trude Holmeide; Thiis-Evensen, Espen; Merok, Marianne Aarstad; Teixeira, Manuel & Vatn, Morten H [Show all 9 contributors for this article] (2010). Distinct high resolution genome profiles of early onset and late onset colorectal cancer integrated with gene expression data identify candidate susceptibility loci. Molecular Cancer. ISSN 1476-4598. 9. doi: 10.1186/1476-4598-9-100.
• Brekke, Helge Roar; Ribeiro, Franclim R; Kolberg, Matthias; Ågesen, Trude H.; Lind, Guro Elisabeth & Eknæs, Mette [Show all 15 contributors for this article] (2010). Genomic Changes in Chromosomes 10, 16, and X in Malignant Peripheral Nerve Sheath Tumors Identify a High-Risk Patient Group. Journal of Clinical Oncology. ISSN 0732-183X. 28(9), p. 1573–1582. doi: 10.1200/JCO.2009.24.8989.
• Skotheim, Rolf Inge; Thomassen, Gard O Sundby; Eken, Marthe; Lind, Guro Elisabeth; Micci, Francesca & Ribeiro, FR [Show all 11 contributors for this article] (2009). A universal assay for detection of oncogenic fusion transcripts by oligo microarray analysis. Molecular Cancer. ISSN 1476-4598. 8. doi: 10.1186/1476-4598-8-5. Full text in Research Archive
• Micci, Francesca; Weimer, J; Haugom, L; Skotheim, Rolf Inge; Grunewald, R & Abeler, Vera Maria [Show all 11 contributors for this article] (2009). Reverse Painting of Microidissected Chromosome 19 Markers in Ovarian Carcinoma Identifies a Complex Rearrangement Map. Genes, Chromosomes and Cancer. ISSN 1045-2257. 48(2), p. 184–193. doi: 10.1002/gcc.20628.
• Godmann, M; Gashaw, I; Eildermann, K; Schweyer, S; Bergmann, M & Skotheim, Rolf Inge [Show all 7 contributors for this article] (2009). The pluripotency transcription factor Kruppel-like factor 4 is strongly expressed in intratubular germ cell neoplasia unclassified and seminoma. Molecular human reproduction. ISSN 1360-9947. 15(8), p. 479–488. doi: 10.1093/molehr/gap040.
• Brekke, Helge Roar; Kolberg, Matthias; Skotheim, Rolf Inge; Hall, Kirsten Sundby; Bjerkehagen, Bodil & Risberg, Bjørn [Show all 13 contributors for this article] (2009). Identification of p53 as a strong predictor of survival for patients with malignant peripheral nerve sheath tumors. Neuro-Oncology. ISSN 1522-8517. 11(5), p. 514–528. doi: 10.1215/15228517-2008-127.
• Alagaratnam, Sharmini; Hardy, JR; Lothe, Ragnhild A; Skotheim, Rolf Inge & Byrne, JA (2009). TPD52, a candidate gene from genomic studies, is overexpressed in testicular germ cell tumours. Molecular and Cellular Endocrinology. ISSN 0303-7207. 306(1-2), p. 75–80. doi: 10.1016/j.mce.2008.10.043.
• Ahlquist, Terje Cruickshank; Lind, Guro Elisabeth; Costa, Vera L; Meling, Gunn Iren; Vatn, Morten H & Hoff, Geir S [Show all 10 contributors for this article] (2008). Gene methylation profiles of normal mucosa, and benign and malignant colorectal tumors identify early onset markers. Molecular Cancer. ISSN 1476-4598. 7. doi: 10.1186/1476-4598-7-94.
• Lind, Gruo Elisabeth; Ahlquist, Terje Cruickshank; Kolberg, Matthias; Berg, Marianne; Lier, Mette Eknæs & Alonso, MA [Show all 12 contributors for this article] (2008). Hypermethylated MAL gene - a silent marker of early colon tumorigenesis. Journal of Translational Medicine. ISSN 1479-5876. 6. doi: 10.1186/1479-5876-6-13.
• Skotheim, Rolf Inge & Nees, M (2007). Alternative splicing in cancer: Noise, functional, or systematic? International Journal of Biochemistry and Cell Biology. ISSN 1357-2725. 39. doi: 10.1016/j.biocel.2007.02.016.
• Lind, Gruo Elisabeth; Skotheim, Rolf Inge & Lothe, Ragnhild A (2007). The epigenome of testicular germ cell tumors. APMIS - Journal of Pathologiy, Microbiology and Immunology. ISSN 0903-4641. 115, p. 1147–1160.
• Lind, GE; Skotheim, Rolf Inge; Fraga, Mario F; Abeler, Vera Maria; Esteller, M. & Lothe, Ragnhild A (2006). Novel epigenetically deregulated genes in testicular cancer include homeobox genes and SCGB3A1 (HIN-1). Journal of Pathology. ISSN 0022-3417. 210(4), p. 441–449.
• Skotheim, Rolf Inge; Autio, R; Lind, Gruo Elisabeth; Kraggerud, Sigrid M.; Andrews, PW & Monni, Outi [Show all 8 contributors for this article] (2006). Novel genomic aberrations in testicular germ cell tumors by array-CGH, and associated gene expression changes. Cellular Oncology. ISSN 1570-5870. 28(5-6), p. 315–326.
• Lind, Gruo Elisabeth; Skotheim, Rolf Inge; Fraga, Mario F; Abeler, Vera Maria; Henrique, Rui & Saatcioglu, Fahri [Show all 9 contributors for this article] (2005). The loss of NKX3.1 expression in testicular - and prostate - cancers is not caused by promoter hypermethylation. Molecular Cancer. ISSN 1476-4598. 4(1). doi: 10.1186/1476-4598-4-8.
• Skotheim, Rolf Inge; Skotheim, Rolf Inge; Lind, Guro Elisabeth; Monni, O; Nesland, Jahn M & Abeler, Vera Maria [Show all 12 contributors for this article] (2005). Differentiation of human embryonal carcinomas in vitro and in vivo reveals expression profiles relevant to normal development. Cancer Research. ISSN 0008-5472. 65, p. 5588–5598.
• Hofer, M.D; Browne, T.J; Walsh, V; He, L; Skotheim, Rolf Inge & Lothe, Ragnhild A [Show all 7 contributors for this article] (2005). Identification of two molecular groups of seminomas by using expression and tissue microarrays. Clinical Cancer Research. ISSN 1078-0432. 11, p. 5722–5729.

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• Rajpert-De Meyts, Ewa & Skotheim, Rolf I. (2018). Complex Polygenic Nature of Testicular Germ Cell Cancer Suggests Multifactorial Aetiology. European Urology. ISSN 0302-2838. 73(6), p. 832–833. doi: 10.1016/j.eururo.2018.02.023.
• Rounge, Trine Ballestad; Furu, Kari; Skotheim, Rolf Inge; Haugen, Trine B.; Enerly, Espen & Grotmol, Tom (2015). Small RNA profiling of human testicular cancer tissue samples shows abundant tRNA fragments and global loss of piRNA.
• Skotheim, Rolf Inge; Nome, Torfinn; Thomassen, Gard O Sundby; Johannessen, Bjarne; Bakken, Anne Cathrine & Bruun, Jarle [Show all 10 contributors for this article] (2012). Identification of Fusion Transcripts in Colorectal Cancer by Combined RNA-seq and Exon Microarray Analyses. European Journal of Cancer. ISSN 0959-8049. 48, p. S121–S121.
• Skotheim, Rolf Inge; Meza-Zepeda, Leonardo Andrés; Hovig, Eivind; Lønning, Per Eystein; Lothe, Ragnhild A & Myklebost, Ola (2012). Genomsekvensering for persontilpasset kreftbehandling. Tidsskrift for Den norske legeforening. ISSN 0029-2001. 132, p. 2406–2408. doi: 10.4045/tidsskr.12.0784.
• Ågesen, Trude Holmeide; Berg, Marianne; Cekaite, Lina; Thiis-Evensen, Espen; Merok, Marianne Aarstad & Nesbakken, Arild [Show all 8 contributors for this article] (2010). Transcriptional profiling of early onset colorectal cancer identifies CLC as a potential cancer susceptibility gene. European Journal of Cancer. ISSN 0959-8049. 8(5), p. 205–205.
• Paulo, Paula; Barros-Silva, João D.; Ribeiro, Franclim R; Ramalho-Carvalho, João; Mesquita, Bárbara & Jerónimo, Carmen [Show all 10 contributors for this article] (2010). Quantitative expression analysis of nine ETS transcription factors and of the MYC and PTEN genes in a consecutive series of 200 prostate carcinomas. European Journal of Cancer. ISSN 0959-8049. 8(5), p. 169–169.
• Kolberg, Matthias; Ågesen, Trude Holmeide; Brekke, Helge Roar; Skotheim, Rolf Inge; Hall, Kirsten Sundby & van den Berg, Eva [Show all 10 contributors for this article] (2010). Prognostic value of gene expression targeted by gain of 17q sequences in malignant peripheral nerve sheath tumours. European Journal of Cancer. ISSN 0959-8049. 8(5), p. 32–32.
• Cekaite, Lina; Danielsen, Stine Aske; Ågesen, Trude Holmeide; Sveen, Anita; Thiis-Evensen, Espen & Merok, Marianne Aarstad [Show all 9 contributors for this article] (2010). New insights into molecular pathways of colorectal cancer from genome-level expression data. European Journal of Cancer. ISSN 0959-8049. 8(5), p. 223–223.
• Berg, Marianne; Ågesen, Trude Holmeide; Danielsen, Stine Aske; Ahlquist, Terje Cruickshank; Merok, Marianne Aarstad & Mala, Tom [Show all 10 contributors for this article] (2010). Genome copy number variation and gene mutation profiling show different somatic development of colorectal cancers in young and elderly patients. European Journal of Cancer. ISSN 0959-8049. 8(5), p. 201–202.
• Løvf, Marthe; Thomassen, Gard O Sundby; Lind, Guro Elisabeth; Lothe, Ragnhild A & Skotheim, Rolf Inge (2010). An oligo microarray design for detection of known and putative oncogenic fusion transcripts. European Journal of Cancer. ISSN 0959-8049. 8(5), p. 199–199.
• Burum-Auensen, E; Skotheim, Rolf Inge; Schjolberg, AR; Roislien, JO; Lothe, Ragnhild A & Clausen, Ole Petter Fraas (2009). Spindle proteins show significant changes in expression during germ cell carcinogenesis and are differently expressed in the subgroups of testicular germ cell cancer. APMIS - Journal of Pathologiy, Microbiology and Immunology. ISSN 0903-4641. 117(3), p. 236–237.
• Skotheim, Rolf Inge; Eken, Marthe; Thomassen, Gard O Sundby; Lind, Guro Elisabeth & Lothe, Ragnhild A (2009). A universal assay for detection of oncogenic fusion transcripts by oligo microarray analysis. European Journal of Cancer. ISSN 0959-8049. 7(2), p. 147–148.
• Berg, Marianne; Agesen, TH; Nesbakken, Arild; Thiis-Evensen, E; Lothe, Ragnhild A & Skotheim, Rolf Inge (2008). DNA copy number profiling of early onset colorectal cancer. Cellular Oncology. ISSN 1570-5870. 30(2), p. 153–154.
• Skotheim, Rolf Inge & Lothe, Ragnhild A (2003). The testicular germ cell tumour genome. Invited review to the 5th Workshop on Carcinoma in Situ and Testicular Cancer. APMIS - Journal of Pathologiy, Microbiology and Immunology. ISSN 0903-4641. 111, p. 136–151.
• Thorstensen, L.; Skotheim, Rolf Inge & Lothe, Ragnhild A (2003). WNT-signalisering i kreftsvulster: Genetikk og epigenetikk. NBS-nytt. ISSN 0801-3535. 27, p. 12–18.

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