Our latest publications - BMI

• Khadse, Anand; Haakensen, Vilde Drageset; Silwal-Pandit, Laxmi; Hamfjord, Julian; Micke, Patrick & Botling, Johan [Show all 10 contributors for this article] (2022). Prognostic Significance of the Loss of Heterozygosity of KRAS in Early-Stage Lung Adenocarcinoma. Frontiers in Oncology. ISSN 2234-943X. 12. doi: 10.3389/fonc.2022.873532.
• Kidd, Susanne Gundersen; Bogaard, Mari; Carm, Kristina Totland; Bakken, Anne Cathrine; Maltau, Aase Margrethe Victoria & Løvf, Marthe [Show all 10 contributors for this article] (2022). In situ expression of ERG protein in the context of tumor heterogeneity identifies prostate cancer patients with inferior prognosis. Molecular Oncology. ISSN 1574-7891. 16(15), p. 2810–2822. doi: 10.1002/1878-0261.13225. Full text in Research Archive
• Trotter, James David; Cai, Xing & Funke, Simon Wolfgang (2022). On Memory Traffic and Optimisations for Low-order Finite Element Assembly Algorithms on Multi-core CPUs. ACM Transactions on Mathematical Software. ISSN 0098-3500. 48(2). doi: 10.1145/3503925.
• Olstad, Emilie Willoch; Nordeng, Hedvig Marie Egeland; Sandve, Geir Kjetil Ferkingstad; Lyle, Robert & Gervin, Kristina (2022). Low reliability of DNA methylation across Illumina Infinium platforms in cord blood: implications for replication studies and meta-analyses of prenatal exposures. Clinical Epigenetics. ISSN 1868-7075. 14(1). doi: 10.1186/s13148-022-01299-3.
• Minotto, Thomas; Haff, Ingrid Hobæk & Sandve, Geir Kjetil Ferkingstad (2022). Detecting statistical interactions in immune receptor datasets. In Torelli, Nicola; BELLIO, RUGGERO & MUGGEO, VITO (Ed.), Proceedings of the 36th International Workshop on Statistical Modelling. EUT Edizioni Università di Trieste. ISSN 978-88-5511-309-0. p. 253–257.
• Rognes, Torbjørn; Scheffer, Lonneke; Greiff, Victor & Sandve, Geir Kjetil (2022). CompAIRR: ultra-fast comparison of adaptive immune receptor repertoires by exact and approximate sequence matching. Bioinformatics. ISSN 1367-4803. doi: 10.1093/bioinformatics/btac505. Full text in Research Archive
• Silwat-Pandit, Laxmi; Stålberg, Stina M.; Johansson, Henrik J.; Mermelekas, Georgios; Lothe, Inger Marie Bowitz & Skrede, Martina Landschoof [Show all 14 contributors for this article] (2022). Proteome Analysis of Pancreatic Tumors Implicates Extracellular Matrix in Patient Outcome. Cancer Treatment and Research Communications. ISSN 2468-2942. doi: 10.1158/2767-9764.CRC-21-0100. Full text in Research Archive
• Kanduri, Chakravarthi; Pavlović, Milena; Scheffer, Lonneke; Motwani, Keshav; Chernigovskaya, Maria & Greiff, Victor [Show all 7 contributors for this article] (2022). Profiling the baseline performance and limits of machine learning models for adaptive immune receptor repertoire classification. GigaScience. ISSN 2047-217X. 11(05). doi: 10.1093/gigascience/giac046. Full text in Research Archive
• Fontugne, Jacqueline; Cai, Peter Y.; Alnajar, Hussein; Bhinder, Bhavneet; Park, Kyung & Ye, Huihui [Show all 26 contributors for this article] (2022). Collision tumors revealed by prospectively assessing subtype-defining molecular alterations in 904 individual prostate cancer foci. JCI Insight. ISSN 2379-3708. 7(4). doi: 10.1172/jci.insight.155309.
• Strømme, Jonas Meier; Johannessen, Bjarne; Kidd, Susanne Gundersen; Bogaard, Mari; Carm, Kristina Totland & Zhang, Xiaokang [Show all 12 contributors for this article] (2022). Expressed prognostic biomarkers for primary prostate cancer independent of multifocality and transcriptome heterogeneity. Cancer Gene Therapy. ISSN 0929-1903. p. 1–9. doi: 10.1038/s41417-022-00444-7.
• Akbar, Rahmad; Robert, Philippe Paul Auguste; Weber, Cédric R.; Widrich, Michael; Frank, Robert & Pavlovic, Milena [Show all 19 contributors for this article] (2022). In silico proof of principle of machine learning-based antibody design at unconstrained scale. mAbs. ISSN 1942-0862. 14:e2031482(1), p. 1–18. doi: 10.1080/19420862.2022.2031482.
• Lervik, Anders; Svenum, Ingeborg-Helene; Wang, Zhaohui; Cabriolu, Raffaela; Riccardi, Enrico & Andersson, Stefan (2022). The role of pressure and defects in the wurtzite to rock salt transition in cadmium selenide. Physical Chemistry, Chemical Physics - PCCP. ISSN 1463-9076. 24(14), p. 8378–8386. doi: 10.1039/d1cp05051f.
• Dahal-Koirala, Shiva; Balaban, Gabriel; Neumann, Ralf Stefan; Scheffer, Lonneke; Lundin, Knut & Greiff, Victor [Show all 9 contributors for this article] (2022). TCRpower: quantifying the detection power of T-cell receptor sequencing with a novel computational pipeline calibrated by spike-in sequences. Briefings in Bioinformatics. ISSN 1467-5463. doi: 10.1093/bib/bbab566.
• Aarøen, Ola; Riccardi, Enrico; van Erp, Titus Sebastiaan & Sletmoen, Marit (2022). Thin film breakage in oil–in–water emulsions, a multidisciplinary study. Colloids and Surfaces A: Physicochemical and Engineering Aspects. ISSN 0927-7757. 632. doi: 10.1016/j.colsurfa.2021.127808. Full text in Research Archive
• 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.
• Haugen, Mads Haugland; Lingjærde, Ole Christian; Hedenfalk, Ingrid; Garred, Øystein; Borgen, Elin & Loman, Niklas [Show all 12 contributors for this article] (2021). Protein signature predicts response to neoadjuvant treatment with chemotherapy and bevacizumab in HER2-negative breast cancers. JCO Precision Oncology (JCO PO). 5, p. 286–306. doi: 10.1200/PO.20.00086. Full text in Research Archive
• Burchard, Luk; Cai, Xing & Langguth, Johannes (2021). iPUG for Multiple Graphcore IPUs: Optimizing Performance and Scalability of Parallel Breadth-First Search. In Sur, Chiranjib & Kothapalli, Kishore (Ed.), 2021 IEEE 28th International Conference on High Performance Computing, Data, and Analytics (HiPC). IEEE (Institute of Electrical and Electronics Engineers). ISSN 978-1-6654-1016-8. p. 162–171. doi: 10.1109/HiPC53243.2021.00030. Full text in Research Archive
• Thune, Andreas; Cai, Xing & Rustad, Alf Birger (2021). On the impact of heterogeneity-aware mesh partitioning and non-contributing computation removal on parallel reservoir simulations. Journal of Mathematics in Industry. ISSN 2190-5983. 11(1). doi: 10.1186/s13362-021-00108-5.
• Jæger, Karoline Horgmo; Wall, Samuel Thomas & Tveito, Aslak (2021). Computational prediction of drug response in short QT syndrome type 1 based on measurements of compound effect in stem cell-derived cardiomyocytes. PLoS Computational Biology. ISSN 1553-734X. 17(2). doi: 10.1371/JOURNAL.PCBI.1008089.
• Fischer-Holzhausen, Sophie; Yamamoto, Kei; Fjeldstad, Maria Perona & Maleckar, Mary Margot Catherine (2021). Probing the Putative Role of KATP Channels and Biological Variability in a Mathematical Model of Chondrocyte Electrophysiology. Bioelectricity. ISSN 2576-3105. 3(4), p. 272–281. doi: 10.1089/bioe.2021.0034.
• Hamfjord, Julian; Guren, Tormod Kyrre; Glimelius, Bengt; Sorbye, Halfdan; Pfeiffer, Per & Dajani, Olav [Show all 11 contributors for this article] (2021). Clinicopathological factors associated with tumour-specific mutation detection in plasma of patients with RAS-mutated or BRAF-mutated metastatic colorectal cancer. International Journal of Cancer. ISSN 0020-7136. 149(6), p. 1385–1397. doi: 10.1002/ijc.33672. Full text in Research Archive
• 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
• Yao, Ying; Wyrozemski, Lukasz Adam; Lundin, Knut; Sandve, Geir Kjetil Ferkingstad & Qiao, Shuo Wang (2021). Differential expression profile of gluten-specific T cells identified by single-cell RNA-seq. PLOS ONE. ISSN 1932-6203. 16:e0258029(10), p. 1–17. doi: 10.1371/journal.pone.0258029. Full text in Research Archive
• Slabodkin, Andrei; Chernigovskaia, Maria; Mikocziova, Ivana; Akbar, Rahmad; Scheffer, Lonneke & Pavlović, Milena [Show all 16 contributors for this article] (2021). Individualized VDJ recombination predisposes the available Ig sequence space. Genome Research. ISSN 1088-9051. p. 2209–2224. doi: 10.1101/gr.275373.121. Full text in Research Archive
• Lien, Tonje Gulbrandsen; Ohnstad, Hege Oma; Lingjærde, Ole Christian; Vallon-Christersson, Johan; Aaserud, Marit & Sveli, My Anh Tu [Show all 12 contributors for this article] (2021). Sample preparation approach influences pam50 risk of recurrence score in early breast cancer. Cancers. ISSN 2072-6694. 13(23). doi: 10.3390/cancers13236118. Full text in Research Archive
• Gundersen, Sveinung; Boddu, Sanjay; Capella-Gutierrez, Salvador; Drabløs, Finn; Fernández, José M. & Kompova, Radmila [Show all 10 contributors for this article] (2021). Recommendations for the FAIRification of genomic track metadata. F1000 Research. ISSN 2046-1402. 10. doi: 10.12688/f1000research.28449.1.
• Pavlović, Milena; Scheffer, Lonneke; Motwani, Keshav; Kanduri, Chakravarthi; Kompova, Radmila & Vazov, Nikolay Aleksandrov [Show all 41 contributors for this article] (2021). The immuneML ecosystem for machine learning analysis of adaptive immune receptor repertoires. Nature Machine Intelligence. 3(11), p. 936–944. doi: 10.1038/s42256-021-00413-z.
• Roet, Sander; Daub, Christopher David & Riccardi, Enrico (2021). Chemistrees: Data-Driven Identification of Reaction Pathways via Machine Learning. Journal of Chemical Theory and Computation. ISSN 1549-9618. 17(10), p. 1–10. doi: 10.1021/acs.jctc.1c00458.
• Alwash, Mostafa; Savarimuthu, Bastin Tony Roy & Parackal, Mathew (2021). Mining brand value propositions on Twitter: exploring the link between marketer-generated content and eWOM outcomes. Social Network Analysis and Mining. ISSN 1869-5450. 11(1). doi: 10.1007/s13278-021-00790-8.
• Jiang, Xiaojun; Bergquist, Annika; Löscher, Britt-Sabina; Venkatesh, Geetha; Mold, Jeff E. & Holm, Kristian [Show all 15 contributors for this article] (2021). A heterozygous germline CD100 mutation in a family with primary sclerosing cholangitis. Science Translational Medicine. ISSN 1946-6234. 13(582). doi: 10.1126/scitranslmed.abb0036.
• Arnaout, Ramy A.; Luning Prak, Eline T.; Schwab, Nicholas; Rubelt, Florian; Greiff, Victor & Pavlović, Milena [Show all 32 contributors for this article] (2021). The Future of Blood Testing Is the Immunome. Frontiers in Immunology. ISSN 1664-3224. 12:626793, p. 1–6. doi: 10.3389/fimmu.2021.626793. Full text in Research Archive
• Greiff, Victor & Sandve, Geir Kjetil Ferkingstad (2021). Profiling the baseline performance and limits of machine learning models for adaptive immune receptor repertoire classification . BioRxiv. ISSN 0362-4331.
• Greiff, Victor & Sandve, Geir Kjetil Ferkingstad (2021). immuneML: an ecosystem for machine learning analysis of adaptive immune receptor repertoires. BioRxiv. ISSN 0362-4331.
• Greiff, Victor & Sandve, Geir Kjetil Ferkingstad (2021). One billion synthetic 3D-antibody-antigen complexes enable unconstrained machine-learning formalized investigation of antibody specificity prediction . BioRxiv. ISSN 0362-4331. doi: 10.1101/2021.07.06.451258.
• Akbar, Rahmad; Robert, Philippe Paul Auguste; Pavlović, Milena; Jeliazkov, Jeliazko R.; Snapkov, Igor & Slabodkin, Andrei [Show all 15 contributors for this article] (2021). A compact vocabulary of paratope-epitope interactions enables predictability of antibody-antigen binding. Cell reports. ISSN 2211-1247. 34:108856(11), p. 1–21. doi: 10.1016/j.celrep.2021.108856. Full text in Research Archive
• Mattingsdal, Morten; Ebenesersdóttir, Sigríður Sunna; Moore, Kristjan H. S.; Andreassen, Ole Andreas; Hansen, Thomas F. & Werge, Thomas [Show all 12 contributors for this article] (2021). The genetic structure of Norway. European Journal of Human Genetics. ISSN 1018-4813. doi: 10.1038/s41431-021-00899-6. Full text in Research Archive
• Mahé, Frédéric; Czech, Lucas; Stamatakis, Alexandros; Quince, Christopher; de Vargas, Colomban & Dunthorn, Micah [Show all 7 contributors for this article] (2021). Swarm v3: towards tera-scale amplicon clustering. Bioinformatics. ISSN 1367-4803. 38(1), p. 267–269. doi: 10.1093/bioinformatics/btab493. Full text in Research Archive
• Yao, Ying; Zia, Asima; Neumann, Ralf Stefan; Pavlović, Milena; Balaban, Gabriel & Lundin, Knut Erik Aslaksen [Show all 8 contributors for this article] (2021). T cell receptor repertoire as a potential diagnostic marker for celiac disease. Clinical Immunology. ISSN 1521-6616. 222:108621, p. 1–7. doi: 10.1016/j.clim.2020.108621. Full text in Research Archive
• 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
• Eriksson, Anna Maria; Leikfoss, Ingvild Sørum; Abrahamsen, Greger; Gjerstad, Vibeke Sundvold; Mesel Isom, Martine & Keshari, Pankaj [Show all 12 contributors for this article] (2021). Exploring the role of the multiple sclerosis susceptibility gene CLEC16A in T cells. Scandinavian Journal of Immunology. ISSN 0300-9475. 94(1). doi: 10.1111/sji.13050. Full text in Research Archive
• Snipen, Lars; Angell, Inga-Leena; Rognes, Torbjørn & Rudi, Knut (2021). Reduced metagenome sequencing for strain-resolution taxonomic profiles. Microbiome. ISSN 2049-2618. 9(1). doi: 10.1186/s40168-021-01019-8. Full text in Research Archive
• Lemma, Roza Berhanu; Ledsaak, Marit; Fuglerud, Bettina Maria; Sandve, Geir Kjetil; Eskeland, Ragnhild & Gabrielsen, Odd Stokke (2021). Chromatin occupancy and target genes of the haematopoietic master transcription factor MYB. Scientific Reports. ISSN 2045-2322. 11(9008). doi: 10.1038/s41598-021-88516-w. Full text in Research Archive Show summary

  The transcription factor MYB is a master regulator in haematopoietic progenitor cells and a pioneer factor affecting differentiation and proliferation of these cells. Leukaemic transformation may be promoted by high MYB levels. Despite much accumulated molecular knowledge of MYB, we still lack a comprehensive understanding of its target genes and its chromatin action. In the present work, we performed a ChIP-seq analysis of MYB in K562 cells accompanied by detailed bioinformatics analyses. We found that MYB occupies both promoters and enhancers. Five clusters (C1–C5) were found when we classified MYB peaks according to epigenetic profiles. C1 was enriched for promoters and C2 dominated by enhancers. C2-linked genes were connected to hematopoietic specific functions and had GATA factor motifs as second in frequency. C1 had in addition to MYB-motifs a significant frequency of ETS-related motifs. Combining ChIP-seq data with RNA-seq data allowed us to identify direct MYB target genes. We also compared ChIP-seq data with digital genomic footprinting. MYB is occupying nearly a third of the super-enhancers in K562. Finally, we concluded that MYB cooperates with a subset of the other highly expressed TFs in this cell line, as expected for a master regulator

• Balaban, Gabriel; Halliday, Brian P.; Porter, Bradley; Bai, Wenjia; Nygård, Ståle & Owen, Ruth [Show all 18 contributors for this article] (2021). Late-Gadolinium Enhancement Interface Area and Electrophysiological Simulations Predict Arrhythmic Events in Patients With Nonischemic Dilated Cardiomyopathy. JACC: Clinical Electrophysiology. ISSN 2405-500X. 7(2), p. 238–249. doi: 10.1016/j.jacep.2020.08.036.
• Jæger, Karoline Horgmo; Charwat, Verena; Wall, Samuel; Healy, Kevin E. & Tveito, Aslak (2021). Identifying drug response by combining measurements of the membrane potential, the cytosolic calcium concentration, and the extracellular potential in microphysiological systems. Frontiers in Pharmacology. ISSN 1663-9812. 11:569489, p. 1–16. doi: 10.3389/fphar.2020.569489.
• Aarøen, Ola; Riccardi, Enrico & Sletmoen, Marit (2021). Exploring the effects of approach velocity on depletion force and coalescence in oil-in-water emulsions. RSC Advances. ISSN 2046-2069. 11(15), p. 8730–8740. doi: 10.1039/d1ra00661d. Full text in Research Archive
• Jæger, Karoline Horgmo; Hustad, Kristian Gregorius; Cai, Xing & Tveito, Aslak (2021). Efficient numerical solution of the EMI model representing the extracellular space (E), cell membrane (M) and intracellular space (I) of a collection of cardiac cells. Frontiers in Physics. ISSN 2296-424X. 8(579461). doi: 10.3389/fphy.2020.579461. Full text in Research Archive
• Ask, Eivind Heggernes; Tschan-Plessl, Astrid; Gjerdingen, Thea Johanne; Hoel, Hanna Julie; Sætersmoen, Michelle Lu & Wiiger, Merete Thune [Show all 16 contributors for this article] (2021). A Systemic Protein Deviation Score Linked to PD-1+ CD8+ T Cell Expansion That Predicts Overall Survival in Diffuse Large B Cell Lymphoma. Med. ISSN 2666-6359. 2(2), p. 180–195. doi: 10.1016/j.medj.2020.10.006.
• Næss, Solveig; Halnes, Geir; Hagen, Espen; Hagler, Donald J.; Dale, Anders M. & Einevoll, Gaute [Show all 7 contributors for this article] (2021). Biophysically detailed forward modeling of the neural origin of EEG and MEG signals. NeuroImage. ISSN 1053-8119. 225. doi: 10.1016/j.neuroimage.2020.117467. Full text in Research Archive
• Riccardi, Enrico; Daub, Christopher David; Hänninen, vesa & Halonen, Lauri (2020). Path sampling for atmospheric reactions: formic acid catalysed conversion of SO3+ H2O to H2SO4. PeerJ. ISSN 2167-8359. 2. doi: 10.7717/peerj-pchem.7.
• Liu, Jingjing; van der Smissen, Wendy J. C. Prager; Collee, Margriet J.; Bolla, Manjeet K.; Wang, Qin & Kristensen, Vessela N. [Show all 82 contributors for this article] (2020). Germline HOXB13 mutations p.G84E and p.R217C do not confer an increased breast cancer risk. Scientific Reports. ISSN 2045-2322. 10:9688(1), p. 1–14. doi: 10.1038/s41598-020-65665-y. Full text in Research Archive
• Bailey, Matthew H.; Meyerson, William U.; Dursi, L. Jonathan; Wang, Liang-Bo; Dong, Guanlan & Aure, Miriam Ragle [Show all 51 contributors for this article] (2020). Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. Nature Communications. ISSN 2041-1723. 11:4748, p. 1–27. doi: 10.1038/s41467-020-18151-y. Full text in Research Archive
• Li, Constance H.; Prokopec, Stephenie D.; Sun, Ren X.; Yousif, Fouad; Schmitz, Nathaniel & Aure, Miriam Ragle [Show all 51 contributors for this article] (2020). Sex differences in oncogenic mutational processes. Nature Communications. ISSN 2041-1723. 11:4330, p. 1–24. doi: 10.1038/s41467-020-17359-2. Full text in Research Archive
• Wise, Jillian; Nakken, Sigve; Steen, Chloe Beate; Vodak, Daniel; Trøen, Gunhild & Johannessen, Bjarne [Show all 24 contributors for this article] (2020). Mutational dynamics and immune evasion in diffuse large B-cell lymphoma explored in a relapse-enriched patient series. Blood Advances. ISSN 2473-9529. 4(9), p. 1859–1866. doi: 10.1182/bloodadvances.2019001325. Show summary

  • Diagnostic and relapse diffuse large B-cell lymphoma (DLBCL) biopsies reveal increased mutational burden/loss of heterozygosity in HLA-A. • Serially sampled tumor biopsies provide insight into therapeutic targets and evolutionary divergence in relapsed/refractory DLBCL.

• Jæger, Karoline Horgmo; Hustad, Kristian Gregorius; Cai, Xing & Tveito, Aslak (2020). Operator Splitting and Finite Difference Schemes for Solving the EMI Model. In Tveito, Aslak; Mardal, Kent-Andre & Rognes, Marie (Ed.), Modeling Excitable Tissue -- The EMI Framework. Springer. ISSN 978-3-030-61156-9. p. 44–55. doi: 10.1007/978-3-030-61157-6_4.
• Trotter, James David; Langguth, Johannes & Cai, Xing (2020). Cache simulation for irregular memory traffic on multi-core CPUs: Case study on performance models for sparse matrix–vector multiplication. Journal of Parallel and Distributed Computing. ISSN 0743-7315. 144, p. 189–205. doi: 10.1016/j.jpdc.2020.05.020.
• 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.

• Ness, Torbjørn Vefferstad; Halnes, Geir; Næss, Solveig; Pettersen, Klas Henning & Einevoll, Gaute (2020). Computing extracellular electric potentials from neuronal simulations. arXiv.org. ISSN 2331-8422.
• Næss, Solveig; Halnes, Geir; Hagen, Espen; Hagler, Donald J.; Dale, Anders M. & Einevoll, Gaute [Show all 7 contributors for this article] (2020). Biophysical modeling of the neural origin of EEG and MEG signals. BioRxiv. ISSN 0362-4331. doi: 10.1101/2020.07.01.181875.
• Backe, Paul Hoff; Lærdahl, Jon Kristen; Kittelsen, Lene Svendsen; Dalhus, Bjørn; Mørkrid, Lars & Bjørås, Magnar (2020). Structural basis for substrate and product recognition in human phosphoglucomutase-1 (PGM1) isoform 2, a member of the α-D-phosphohexomutase superfamily. Scientific Reports. ISSN 2045-2322. 10(1). doi: 10.1038/s41598-020-62548-0. Full text in Research Archive
• Dai, Kael; Gratiy, Sergey L.; Billeh, Yazan; Xu, Richard; Cai, Binghuang & Cain, Nicholas [Show all 12 contributors for this article] (2020). Brain Modeling ToolKit: An open source software suite for multiscale modeling of brain circuits. PLoS Computational Biology. ISSN 1553-734X. 16(11). doi: 10.1371/journal.pcbi.1008386. Full text in Research Archive
• Kyte, Jon A; Andresen, Nikolai Kragøe; Russnes, Hege Elisabeth Giercksky; Fretland, Signe Øien; Falk, Ragnhild Sørum & Lingjærde, Ole Christian [Show all 7 contributors for this article] (2020). ICON: A randomized phase IIb study evaluating immunogenic chemotherapy combined with ipilimumab and nivolumab in patients with metastatic hormone receptor positive breast cancer. Journal of Translational Medicine. ISSN 1479-5876. 18(1). doi: 10.1186/s12967-020-02421-w. Full text in Research Archive
• ICGC/TCGA Pan-Cancer Analysis, of Whole Genomes Consortium; Campbell, Peter J.; Getz, Gad; Korbel, Jan O.; Stuart, Joshua M. & Jennings, Jennifer L. [Show all 54 contributors for this article] (2020). Pan-cancer analysis of whole genomes. Nature. ISSN 0028-0836. 578(7793), p. 82–93. doi: 10.1038/s41586-020-1969-6. Full text in Research Archive
• Grytten, Ivar; Rand, Knut Dagestad; Nederbragt, Alexander Johan & Sandve, Geir Kjetil (2020). Assessing graph-based read mappers against a baseline approach highlights strengths and weaknesses of current methods. BMC Genomics. ISSN 1471-2164. 21. doi: 10.1186/s12864-020-6685-y. Full text in Research Archive
• Balaban, Gabriel; Costa, Caroline Mendonca; Porter, Bradley; Halliday, Brian; Rinaldi, Christopher A. & Prasad, Sanjay K. [Show all 9 contributors for this article] (2020). 3D Electrophysiological Modeling of Interstitial Fibrosis Networks and Their Role in Ventricular Arrhythmias in Non-Ischemic Cardiomyopathy. IEEE Transactions on Biomedical Engineering. ISSN 0018-9294. 67(11), p. 3125–3133. doi: 10.1109/TBME.2020.2976924.
• Farooq, Amna; Grønmyr, Sindre; Omer, Ali Avan; Rognes, Torbjørn; Scheffler, Katja & Bjørås, Magnar [Show all 7 contributors for this article] (2020). HMST-Seq-Analyzer: A new python tool for differential methylation and hydroxymethylation analysis in various DNA methylation sequencing data. Computational and Structural Biotechnology Journal. ISSN 2001-0370. 18, p. 2877–2889. doi: 10.1016/j.csbj.2020.09.038. Full text in Research Archive
• Khelik, Ksenia; Sandve, Geir Kjetil; Nederbragt, Alexander Johan & Rognes, Torbjørn (2020). NucBreak: location of structural errors in a genome assembly by using paired-end Illumina reads. BMC Bioinformatics. ISSN 1471-2105. 21(1). doi: 10.1186/s12859-020-3414-0. Full text in Research Archive
• Safavi, Shiva; Larouche, Ariane; Zahn, Astrid; Patenaude, Anne-Marie; Domanska, Diana Ewa & Dionne, Kiersten [Show all 17 contributors for this article] (2020). The uracil-DNA glycosylase UNG protects the fitness of normal and cancer B cells expressing AID. NAR Cancer. ISSN 2632-8674. 2(3). doi: 10.1093/narcan/zcaa019. Full text in Research Archive
• Bjørnstad, Johannes; Khan, Adil Mahboob; Røed-Undlien, Henriette; Bendz, Bjørn; Nygård, Ståle & Nilsen-Hoel, Tom [Show all 7 contributors for this article] (2020). Operative survival in patients with acute aortic disease in the era of newer oral anticoagulants. Open heart. ISSN 2053-3624. 7:e001278(2), p. 1–9. doi: 10.1136/openhrt-2020-001278. Full text in Research Archive
• Ree, Anne Hansen; Nygaard, Vigdis; Pedersen, Kjetil Boye; Heinrich, Daniel; Dueland, Svein & Bergheim, Inger Riise [Show all 25 contributors for this article] (2020). Molecularly matched therapy in the context of sensitivity, resistance, and safety; patient outcomes in end-stage cancer?the MetAction study. Acta Oncologica. ISSN 0284-186X. p. 1–10. doi: 10.1080/0284186X.2020.1742377. Full text in Research Archive
• Fan, Qiong; Nørgaard, Rikke Christine; Grytten, Ivar; Ness, Cecilie; Lucas, Christin & Vekterud, Kristin [Show all 15 contributors for this article] (2020). LXRα Regulates ChREBPα Transactivity in a Target Gene-Specific Manner through an Agonist-Modulated LBD-LID Interaction. Cells. ISSN 2073-4409. 9(5), p. 1–26. doi: 10.3390/cells9051214. Full text in Research Archive Show summary

  The cholesterol-sensing nuclear receptor liver X receptor (LXR) and the glucose-sensing transcription factor carbohydrate responsive element-binding protein (ChREBP) are central players in regulating glucose and lipid metabolism in the liver. More knowledge of their mechanistic interplay is needed to understand their role in pathological conditions like fatty liver disease and insulin resistance. In the current study, LXR and ChREBP co-occupancy was examined by analyzing ChIP-seq datasets from mice livers. LXR and ChREBP interaction was determined by Co-immunoprecipitation (CoIP) and their transactivity was assessed by real-time quantitative polymerase chain reaction (qPCR) of target genes and gene reporter assays. Chromatin binding capacity was determined by ChIP-qPCR assays. Our data show that LXRα and ChREBPα interact physically and show a high co-occupancy at regulatory regions in the mouse genome. LXRα co-activates ChREBPα and regulates ChREBP-specific target genes in vitro and in vivo. This co-activation is dependent on functional recognition elements for ChREBP but not for LXR, indicating that ChREBPα recruits LXRα to chromatin in trans. The two factors interact via their key activation domains; the low glucose inhibitory domain (LID) of ChREBPα and the ligand-binding domain (LBD) of LXRα. While unliganded LXRα co-activates ChREBPα, ligand-bound LXRα surprisingly represses ChREBPα activity on ChREBP-specific target genes. Mechanistically, this is due to a destabilized LXRα:ChREBPα interaction, leading to reduced ChREBP-binding to chromatin and restricted activation of glycolytic and lipogenic target genes. This ligand-driven molecular switch highlights an unappreciated role of LXRα in responding to nutritional cues that was overlooked due to LXR lipogenesis-promoting function.

• Weber, Cédric R.; Akbar, Rahmad; Yermanos, Alexander; Pavlovic, Milena; Snapkov, Igor & Sandve, Geir Kjetil [Show all 8 contributors for this article] (2020). immuneSIM: tunable multi-feature simulation of B- and T-cell receptor repertoires for immunoinformatics benchmarking. Bioinformatics. ISSN 1367-4803. 36(11), p. 3594–3596. doi: 10.1093/bioinformatics/btaa158. Full text in Research Archive
• du Pré, Fleur; Blazevski, Jana; Dewan, Alisa Elinsdatter; Stamnæs, Jorunn; Kanduri, Srinivasa Kalyana Chakravarthi & Sandve, Geir Kjetil [Show all 13 contributors for this article] (2020). B cell tolerance and antibody production to the celiac disease autoantigen transglutaminase 2. Journal of Experimental Medicine (JEM). ISSN 0022-1007. 217:e20190860.(2), p. 1–14. doi: 10.1084/jem.20190860. Full text in Research Archive
• Fan, Qiong; Nørgaard, Rikke Christine; Grytten, Ivar; Ness, Cecilie Maria; Lucas, Christin & Vekterud, Kristin [Show all 15 contributors for this article] (2019). Open the LID: LXRα regulates ChREBPα transactivity in a target gene-specific manner through an agonist-modulated LBD-LID interaction. BioRxiv. ISSN 0362-4331. doi: 10.1101/2019.12.20.869974. Show summary

  The cholesterol-sensing nuclear receptor liver X receptor (LXR) and the glucose-sensing transcription factor carbohydrate responsive element-binding protein (ChREBP) are central players in regulating glucose and lipid metabolism in liver. We have previously shown that LXR regulates ChREBP transcription and activity; however, the underlying mechanisms are unclear. In the current study, we demonstrate that LXRα and ChREBPα interact physically, and show a high co-occupancy at regulatory regions in the mouse genome. LXRα co-activates ChREBPα, and regulates ChREBP-specific target genes in vitro and in vivo. This co-activation is dependent on functional recognition elements for ChREBP, but not for LXR, indicating that ChREBPα recruits LXRα to chromatin in trans. The two factors interact via their key activation domains; ChREBPα’s low glucose inhibitory domain (LID) and the ligand-binding domain (LBD) of LXRα. While unliganded LXRα co-activates ChREBPα, ligand-bound LXRα surprisingly represses ChREBPα activity on ChREBP-specific target genes. Mechanistically, this is due to a destabilized LXRα:ChREBPα interaction, leading to reduced ChREBP-binding to chromatin and restricted activation of glycolytic and lipogenic target genes. This ligand-driven molecular switch highlights an unappreciated role of LXRα that was overlooked due to LXR lipogenesis-promoting function.

• Mariampillai, Julian Eek; Liestøl, Knut; Kjeldsen, Sverre; Prestgaard, Erik Edvard; Engeseth, Kristian & Bodegard, Johan [Show all 11 contributors for this article] (2019). Exercise Systolic Blood Pressure at Moderate Workload Is Linearly Associated With Coronary Disease Risk in Healthy Men. Hypertension Research. ISSN 0916-9636. 75(1), p. 44–50. doi: 10.1161/HYPERTENSIONAHA.119.13528. Full text in Research Archive
• Dominguez-Valentin, Mev; Nakken, Sigve; Tubeuf, Hélène; Vodák, Daniel; Ekstrøm, Per Olaf & Nissen, Anke M. [Show all 15 contributors for this article] (2019). Results of multigene panel testing in familial cancer cases without genetic cause demonstrated by single gene testing. Scientific Reports. ISSN 2045-2322. 9:18555, p. 1–9. doi: 10.1038/s41598-019-54517-z. Full text in Research Archive
• Salvatore, Stefania; Rand, Knut Dagestad; Grytten, Ivar; Ferkingstad, Egil; Domanska, Diana & Holden, Lars [Show all 10 contributors for this article] (2019). Beware the Jaccard: the choice of similarity measure is important and non-trivial in genomic colocalisation analysis. Briefings in Bioinformatics. ISSN 1467-5463. p. 1–8. doi: 10.1093/bib/bbz083.
• Balaban, Gabriel; Halliday, Brian P; Bai, Wenjia; Porter, Bradley; Malvuccio, Carlotta & Lamata, Pablo [Show all 11 contributors for this article] (2019). Scar shape analysis and simulated electrical instabilities in a non-ischemic dilated cardiomyopathy patient cohort. PLoS Computational Biology. ISSN 1553-734X. 15(10). doi: 10.1371/journal.pcbi.1007421. Full text in Research Archive
• Lie-Jensen, Anette; Ivanauskiene, Kristina; Malerød, Lene; Jain, Ashish; Tan, Kia Wee & Lærdahl, Jon Kristen [Show all 9 contributors for this article] (2019). Centralspindlin Recruits ALIX to the Midbody during Cytokinetic Abscission in Drosophila via a Mechanism Analogous to Virus Budding. Current Biology. ISSN 0960-9822. 29(20), p. 3538–3548.e7. doi: 10.1016/j.cub.2019.09.025.
• Steen, Chloe Beate; Leich, Ellen; Myklebust, June Helen; Lockmer, Sandra; Wise, Jillian & Wahlin, Björn Engelbrekt [Show all 14 contributors for this article] (2019). A clinico-molecular predictor identifies follicular lymphoma patients at risk of early transformation after first-line immunotherapy. Haematologica. ISSN 0390-6078. 104(10), p. 460–464. doi: 10.3324/haematol.2018.209080. Full text in Research Archive
• Tellum, Tina; MATIC, GORDANA; Dormagen, Johann Baptist; Nygård, Ståle; Viktil, Ellen & Qvigstad, Erik [Show all 7 contributors for this article] (2019). Diagnosing adenomyosis with MRI: a prospective study revisiting the junctional zone thickness cutoff of 12 mm as a diagnostic marker. European Radiology. ISSN 0938-7994. 29(12), p. 6971–6981. doi: 10.1007/s00330-019-06308-3.
• Halnes, Geir; Tennøe, Simen; Haug, Trude; Einevoll, Gaute; Weltzien, Finn-Arne & Hodne, Kjetil (2019). A computational model for gonadotropin releasing cells in the teleost fish medaka. PLoS Computational Biology. ISSN 1553-734X. 15(8), p. 1–28. doi: 10.1371/journal.pcbi.1006662. Full text in Research Archive
• Piplani, Honit; Marek-Iannucci, Stefanie; Sin, Jon; Hou, Jean; Takahashi, Toshimasa & Sharma, Ankush [Show all 17 contributors for this article] (2019). Simvastatin induces autophagic flux to restore cerulein-impaired phagosome-lysosome fusion in acute pancreatitis. Biochimica et Biophysica Acta - Molecular Basis of Disease. ISSN 0925-4439. 1865(11), p. 1–14. doi: 10.1016/j.bbadis.2019.08.006. Full text in Research Archive

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• Leoncio Netto, Waldir; Fagerland, Morten; Lydersen, Stian; Laake, Petter & Lingjærde, Ole Christian (2022). contingencytables: Statistical Analysis of Contingency Tables.
• Kanduri, Chakravarthi; Sandve, Geir Kjetil Ferkingstad; Hovig, Eivind; De, Subhajyoti & Layer, Ryan (2021). Editorial: Genomic Colocalization and Enrichment Analyses. Frontiers in Genetics. ISSN 1664-8021. 11. doi: 10.3389/fgene.2020.617876.
• Denysov, Sergiy; Bruaset, Are Magnus & Selstø, Sølve (2021). Software for Emulations of Digital Quantum Algorithms: To Build or not to Build? ERCIM News. ISSN 0926-4981.
• Sandve, Geir Kjetil Ferkingstad (2021). ImmuneML and the case for domain-tailored machine learning platforms.
• Balaban, Gabriel; Grytten, Ivar; Rand, Knut Dagestad; Scheffer, Lonneke & Sandve, Geir Kjetil (2021). Ten simple rules for quick and dirty scientific programming. PLoS Computational Biology. ISSN 1553-734X. 17:e1008549(3), p. 1–15. doi: 10.1371/journal.pcbi.1008549.
• Riccardi, Enrico; Carvalho, Barbara & Smeplass, Eli (2021). Postdoktorer blir utnyttet. Forskerforum. ISSN 0800-1715. 3.
• Bailey, Matthew H.; Meyerson, William U.; Dursi, Lewis Jonathan; Wang, Liang-Bo; Dong, Guanlan & Liang, Wen-Wei [Show all 1,451 contributors for this article] (2020). Author Correction: Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples (Nature Communications, (2020), 11, 1, (4748), 10.1038/s41467-020-18151-y). Nature Communications. ISSN 2041-1723. 11(1). doi: 10.1038/s41467-020-20128-w.
• Molyneux, Sam D.; Waterhouse, Paul D.; Shelton, Dawne; Shao, Yang W.; Watling, Christopher M. & Tang, Qing-Lian [Show all 18 contributors for this article] (2020). Author Correction: Human somatic cell mutagenesis creates genetically tractable sarcomas (Nature Genetics, (2014), 46, 9, (964-972), 10.1038/ng.3065). Nature Genetics. ISSN 1061-4036. 52(4). doi: 10.1038/s41588-020-0589-2.
• Widrich, Michael; Schäfl, Bernhard; Pavlović, Milena; Ramsauer, Hubert; Gruber, Lukas & Holzleitner, Markus [Show all 11 contributors for this article] (2020). Modern Hopfield Networks and Attention for Immune Repertoire Classification. Show summary

  A central mechanism in machine learning is to identify, store, and recognize patterns. How to learn, access, and retrieve such patterns is crucial in Hopfield networks and the more recent transformer architectures. We show that the attention mechanism of transformer architectures is actually the update rule of modern Hopfield networks that can store exponentially many patterns. We exploit this high storage capacity of modern Hopfield networks to solve a challenging multiple instance learning (MIL) problem in computational biology: immune repertoire classification. In immune repertoire classification, a vast number of immune receptors are used to predict the immune status of an individual. This constitutes a MIL problem with an unprecedentedly massive number of instances, two orders of magnitude larger than currently considered problems, and with an extremely low witness rate. Accurate and interpretable machine learning methods solving this problem could pave the way towards new vaccines and therapies, which is currently a very relevant research topic intensified by the COVID-19 crisis. In this work, we present our novel method DeepRC that integrates transformer-like attention, or equivalently modern Hopfield networks, into deep learning architectures for massive MIL such as immune repertoire classification. We demonstrate that DeepRC outperforms all other methods with respect to predictive performance on large-scale experiments including simulated and real-world virus infection data and enables the extraction of sequence motifs that are connected to a given disease class. Source code and datasets: https://github.com/ml-jku/DeepRC.

• Langguth, Johannes; Gaur, Namit; Arevalo, Hermenegild; Jarvis, Chad; Altanaite, Neringa & Lan, Qiang [Show all 7 contributors for this article] (2020). Towards detailed Organ-Scale Simulations in Cardiac Electrophysiology.
• Hustad, Kristian Gregorius; Cai, Xing; Langguth, Johannes & Arevalo, Hermenegild (2020). Efficient simulations of patient-specific electrical heart activity on the DGX-2.
• Huckins, Laura M.; Dobbyn, Amanda; Ruderfer, Douglas M.; Hoffman, Gabriel; Wang, Weiqing & Pardiñas, Antonio F. [Show all 360 contributors for this article] (2019). Publisher Correction: Gene expression imputation across multiple brain regions provides insights into schizophrenia risk (Nature Genetics, (2019), 51, 4, (659-674), 10.1038/s41588-019-0364-4). Nature Genetics. ISSN 1061-4036. 51(6). doi: 10.1038/s41588-019-0435-6.
• Nik-Zainal, Serena; Davies, Helen; Staaf, Johan; Ramakrishna, Manasa; Glodzik, Dominik & Zou, Xueqing [Show all 88 contributors for this article] (2019). Correction to: Landscape of somatic mutations in 560 breast cancer whole-genome sequences (Nature, (2016), 534, 7605, (47-54), 10.1038/nature17676). Nature. ISSN 0028-0836. 566(7742). doi: 10.1038/s41586-019-0883-2.
• Cheng, Jiqiu; Demeulemeester, Jonas; Wedge, David C.; Vollan, Hans Kristian Moen; Pitt, Jason J. & Russnes, Hege Elisabeth Giercksky [Show all 18 contributors for this article] (2019). Correction to: Pan-cancer analysis of homozygous deletions in primary tumours uncovers rare tumour suppressors (Nature Communications, (2017), 8, 1, (1221), 10.1038/s41467-017-01355-0). Nature Communications. ISSN 2041-1723. 10(1). doi: 10.1038/s41467-019-08512-7.
• Gheorghe, Marius; Sandve, Geir Kjetil Ferkingstad; Khan, Aziz; Chèneby, Jeanne; Ballester, Benoit & Mathelier, Anthony (2019). Erratum: A map of direct TF-DNA interactions in the human genome (Nucleic acids research (2019) 47 4 (e21)). Nucleic Acids Research (NAR). ISSN 0305-1048. 47(14). doi: 10.1093/nar/gkz582.
• Hagen, Espen; Næss, Solveig; Ness, Torbjørn V & Einevoll, Gaute (2019). LFPy: Multimodal Modeling of Extracellular Neuronal Recordings in Python.
• Næss, Solveig (2021). Biophysical modeling of electric and magnetic brain signals. Reprosentralen, University of Oslo. Full text in Research Archive

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