Our latest publications - BMI

• Mehlum, Maria Hollund; Liestøl, Knut; Kjeldsen, Sverre; Wyller, Torgeir Bruun; Julius, Stevo & Rothwell, Peter M. [Show all 10 contributors for this article] (2020). Blood pressure-lowering profiles and clinical effects of angiotensin receptor blockers versus calcium channel blockers. Hypertension. ISSN 0194-911X. 75(6), p. 1584–1592. doi: 10.1161/HYPERTENSIONAHA.119.14443.
• 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.
• Gemmell, Philip M.; Gillette, Karli; Balaban, Gabriel; Rajani, Ronak; Vigmond, Edward J. & Plank, Gernot [Show all 7 contributors for this article] (2020). A computational investigation into rate-dependant vectorcardiogram changes due to specific fibrosis patterns in non-ischæmic dilated cardiomyopathy. Computers in Biology and Medicine. ISSN 0010-4825. 123:103895, p. 1–13. doi: 10.1016/j.compbiomed.2020.103895.
• Lund-Andersen, Christin; Nakken, Sigve; Nygård, Ståle; Fromm, Bastian; Aasheim, Lars Birger & Davidson, Ben [Show all 13 contributors for this article] (2019). Integrative genomic analysis of peritoneal malignant mesothelioma: Understanding a case with extraordinary chemotherapy response. Cold Spring Harbor Molecular Case Studies. ISSN 2373-2873. 5:a003566(2), p. 1–15. doi: 10.1101/mcs.a003566. Full text in Research Archive
• Tellum, Tina; Nygård, Ståle & Lieng, Marit (2019). Non-invasive diagnosis of adenomyosis: a structured review and meta-analysis of diagnostic accuracy. Journal of minimally invasive gynecology. ISSN 1553-4650. 27(2), p. 408–418. doi: 10.1016/j.jmig.2019.11.001.
• Strøm, Thea Bismo; Vinje, Terje; Bjune, Katrine; da Costa, Luís Teixeira; Lærdahl, Jon Kristen & Leren, Trond Paul (2019). Lysosomal acid lipase does not have a propeptide and should not be considered being a proprotein. Proteins: Structure, Function, and Bioinformatics. ISSN 0887-3585. p. 440–449. doi: 10.1002/prot.25821.
• 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
• Varadharajan, Srinidhi; Rastas, Pasi; Löytynoja, Ari; Matschiner, Michael; Calboli, Federico C. F. & Guo, Baocheng [Show all 9 contributors for this article] (2019). A High-Quality Assembly of the Nine-Spined Stickleback (Pungitius pungitius) Genome . Genome Biology and Evolution (GBE). ISSN 1759-6653. 11(11), p. 3291–3308. doi: 10.1093/gbe/evz240. 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.
• Hagberg, Guri; Fure, Brynjar; Thommessen, Bente; Ihle-Hansen, Håkon; Øksengård, Anne Rita & Nygård, Ståle [Show all 10 contributors for this article] (2019). Predictors for Favorable Cognitive Outcome Post-Stroke: A-Seven-Year Follow-Up Study. Dementia and Geriatric Cognitive Disorders. ISSN 1420-8008. p. 1–11. doi: 10.1159/000501850.
• Hamfjord, Julian; Guren, Tormod Kyrre; Dajani, Olav; Johansen, Julia Sidenius; Glimelius, Bengt & Sorbye, Halfdan [Show all 12 contributors for this article] (2019). Total circulating cell-free DNA as a prognostic biomarker in metastatic colorectal cancer before first-line oxaliplatin-based chemotherapy. Annals of Oncology. ISSN 0923-7534. 30(7), p. 1088–1095. doi: 10.1093/annonc/mdz139. Full text in Research Archive
• 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
• Øjlert, Åsa Kristina; Halvorsen, Ann Rita; Nebdal, Daniel J.H.; Lund-Iversen, Marius; Solberg, Steinar & Brustugun, Odd Terje [Show all 8 contributors for this article] (2019). The immune microenvironment in non‐small cell lung cancer is predictive of prognosis after surgery. Molecular Oncology. ISSN 1574-7891. 13(5), p. 1166–1179. doi: 10.1002/1878-0261.12475. Full text in Research Archive
• Lindholm, Evita Maria; Aure, Miriam Ragle; Haugen, Mads Haugland; Sahlberg, Kristine Kleivi; Kristensen, Vessela N. & Nebdal, Daniel J.H. [Show all 9 contributors for this article] (2019). miRNA expression changes during the course of neoadjuvant bevacizumab and chemotherapy treatment in breast cancer. Molecular Oncology. ISSN 1574-7891. 13(10), p. 2278–2296. doi: 10.1002/1878-0261.12561. Full text in Research Archive
• Vinje, Terje; Lærdahl, Jon Kristen; Bjune, Katrine; Leren, Trond Paul & Strøm, Thea Bismo (2019). Characterization of the mechanisms by which missense mutations in the lysosomal acid lipase gene disrupt enzymatic activity . Human Molecular Genetics. ISSN 0964-6906. 28(18), p. 3043–3052. doi: 10.1093/hmg/ddz114.
• Mohammadzadeh, Naiyereh; Lunde, Ida Gjervold; Andenæs, Kine; Strand, Mari Elen; Aronsen, Jan Magnus & Skrbic, Biljana [Show all 15 contributors for this article] (2019). The extracellular matrix proteoglycan lumican improves survival and counteracts cardiac dilatation and failure in mice subjected to pressure overload. Scientific Reports. ISSN 2045-2322. 9:9206, p. 1–13. doi: 10.1038/s41598-019-45651-9. Full text in Research Archive
• Jarvis, Chad; Lines, Glenn Terje; Langguth, Johannes; Nakajima, Kengo & Cai, Xing (2019). Combining algorithmic rethinking and AVX-512 intrinsics for efficient simulation of subcellular calcium signaling. In Rodrigues, João M. F.; Cardoso, Pedro; Monteiro, Jânio; Lam, Roberto; Krzhizhanovskaya, Valeria V.; Lees, Michael H.; Dongarra, Jack & Sloot, Peter M.A. (Ed.), Proceedings of 19th International Conference on Computational Science, ICCS2019, Part V. Springer. ISSN 978-3-030-22749-4. p. 681–687. doi: 10.1007/978-3-030-22750-0_66.
• Mäki-Marttunen, Tuomo; Kaufmann, Tobias; Elvsåshagen, Torbjørn; Devor, Anna; Djurovic, Srdjan & Westlye, Lars Tjelta [Show all 23 contributors for this article] (2019). Biophysical Psychiatry—How Computational Neuroscience Can Help to Understand the Complex Mechanisms of Mental Disorders. Frontiers in Psychiatry. ISSN 1664-0640. 10. doi: 10.3389/fpsyt.2019.00534. Full text in Research Archive
• Brown, Alex; Snapkov, Igor; Akbar, Rahmad; Pavlovic, Milena; Miho, Enkelejda & Sandve, Geir Kjetil [Show all 7 contributors for this article] (2019). Augmenting adaptive immunity: progress and challenges in the quantitative engineering and analysis of adaptive immune receptor repertoires. Molecular Systems Design & Engineering. ISSN 2058-9689. 4(4), p. 701–736. doi: 10.1039/c9me00071b.
• Ihle-Hansen, Håkon; Vigen, Thea; Berge, Trygve; Hagberg, Guri; Engedal, Knut & Rønning, Ole M. [Show all 12 contributors for this article] (2019). Carotid Atherosclerosis and Cognitive Function in a General Population Aged 63-65 Years: Data from the Akershus Cardiac Examination (ACE) 1950 Study. Journal of Alzheimer's Disease. ISSN 1387-2877. 70(4), p. 1041–1049. doi: 10.3233/JAD-190327. Full text in Research Archive
• Lagraviere, Jeremie Alexandre Emilien; Langguth, Johannes; Prugger, Martina; Einkemmer, Lukas; Ha, Hoai Phuong & Cai, Xing (2019). Performance optimization and modeling of fine-grained irregular communication in UPC. Scientific Programming. ISSN 1058-9244. 2019:6825728, p. 1–20. doi: 10.1155/2019/6825728. Full text in Research Archive
• Grytten, Ivar; Rand, Knut Dagestad; Nederbragt, Alexander Johan; Storvik, Geir Olve; Glad, Ingrid Kristine & Sandve, Geir Kjetil (2019). Graph Peak Caller: Calling ChIP-seq peaks on graph-based reference genomes. PLoS Computational Biology. ISSN 1553-734X. 15(2), p. 1–13. doi: 10.1371/journal.pcbi.1006731. Full text in Research Archive
• Mäki-Marttunen, Tuomo; Krull, Florian; Bettella, Francesco; Hagen, Espen; Næss, Solveig & Ness, Torbjørn V [Show all 16 contributors for this article] (2019). Alterations in schizophrenia-associated genes can lead to increased power in delta oscillations. Cerebral Cortex. ISSN 1047-3211. 29(2), p. 875–891. doi: 10.1093/cercor/bhy291. Full text in Research Archive
• Mehlum, Maria Hollund; Liestøl, Knut; Wyller, Torgeir Bruun; Hua, Tsushung A.; Rostrup, Morten & Berge, Eivind (2019). Blood pressure variability in hypertensive patients with atrial fibrillation in the VALUE trial. Blood Pressure. ISSN 0803-7051. 28(2), p. 77–83. doi: 10.1080/08037051.2018.1524707.
• Mariampillai, Julian Eek; Prestgaard, Erik Edvard; Kjeldsen, Sverre; Liestøl, Knut; Engeseth, Kristian & Erikssen, Jan Emil [Show all 10 contributors for this article] (2019). SBP above 180 mmHg at moderate exercise workload increases coronary heart disease risk in healthy men during 28-year follow-up. Journal of Hypertension. ISSN 0263-6352. 37(5), p. 949–955. doi: 10.1097/HJH.0000000000001959.
• Gheorghe, Marius; Sandve, Geir Kjetil; Khan, Aziz; Cheneby, Jeanne; Ballester, Benoit & Mathelier, Anthony (2019). A map of direct TF–DNA interactions in the human genome. Nucleic Acids Research (NAR). ISSN 0305-1048. 47(4). doi: 10.1093/nar/gky1210. Full text in Research Archive
• Kanduri, Srinivasa Kalyana Chakravarthi; Bock, Christoph; Gundersen, Sveinung; Hovig, Eivind & Sandve, Geir Kjetil (2019). Colocalization analyses of genomic elements: approaches, recommendations and challenges. Bioinformatics. ISSN 1367-4803. 35(9), p. 1615–1624. doi: 10.1093/bioinformatics/bty835. Full text in Research Archive
• Langguth, Johannes; Cai, Xing & Sourouri, Mohammed (2018). Memory bandwidth contention: Communication vs computation Tradeoffs in supercomputers with multicore architectures. In Li, Mo & Tan, Kian-Lee (Ed.), Proceedings 2018 IEEE 24th International Conference on Parallel and Distributed Systems ICPADS 2018. IEEE Sarnoff Symposium. ISSN 978-1-5386-7308-9. p. 497–506. doi: 10.1109/PADSW.2018.8644601.
• Azab, Abdulrahman; Meling, Hein; Hovig, Eivind & Pursula, Antti (2018). Filesystem Front-end for Seamless Job Management in Sensitive Data e-Infrastructures and Cloud Federation. In Abe, Naoki; Liu, Huan; Hu, Xiaohua; Ahmed, Nesreen; Qiao, Mu; Song, Yang; Kossmann, Donald; Liu, Bing; Lee, Kisung; Tang, Jiliang; He, Jingrui & Saltz, Jeffrey (Ed.), 2018 IEEE International Conference on Big Data (Big Data), Seattle, 10-13 Dec. 2018. IEEE. ISSN 978-1-5386-5035-6. doi: 10.1109/BigData.2018.8622144.
• Prestgaard, Erik Edvard; Mariampillai, Julian Eek; Engeseth, Kristian; Erikssen, Jan Emil; Bodegard, Johan & Liestøl, Knut [Show all 10 contributors for this article] (2018). Change in Cardiorespiratory Fitness and Risk of Stroke and Death. Stroke. ISSN 0039-2499. 50, p. 155–161. doi: 10.1161/STROKEAHA.118.021798.
• Vaccaro, Carlos Alberto; López‐Kostner, Francisco; Della Valle, Adriana; Palmero, Edenir Inêz; Rossi, Benedito Mauro & Antelo, Marina [Show all 69 contributors for this article] (2018). From colorectal cancer pattern to the characterization of individuals at risk: Picture for genetic research in Latin America. International Journal of Cancer. ISSN 0020-7136. doi: 10.1002/ijc.31920. Full text in Research Archive
• Møller, Elen Kristine; Nord, Silje; Wedge, David C; Lingjærde, Ole Christian; Silwal-Pandit, Laxmi & Gythfeldt, Hedda [Show all 19 contributors for this article] (2018). Time series analysis of neoadjuvant chemotherapy and bevacizumab-treated breast carcinomas reveals a systemic shift in genomic aberrations. Genome Medicine. ISSN 1756-994X. 10:92. doi: 10.1186/s13073-018-0601-y. Full text in Research Archive
• Hagen, Espen; Næss, Solveig; Ness, Torbjørn V & Einevoll, Gaute (2018). Multimodal Modeling of Neural Network Activity: Computing LFP, ECoG, EEG, and MEG Signals With LFPy 2.0. Frontiers in Neuroinformatics. ISSN 1662-5196. 12(92), p. 1–36. doi: 10.3389/fninf.2018.00092. Full text in Research Archive Show summary

  Recordings of extracellular electrical, and later also magnetic, brain signals have been the dominant technique for measuring brain activity for decades. The interpretation of such signals is however nontrivial, as the measured signals result from both local and distant neuronal activity. In volume-conductor theory the extracellular potentials can be calculated from a distance-weighted sum of contributions from transmembrane currents of neurons. Given the same transmembrane currents, the contributions to the magnetic field recorded both inside and outside the brain can also be computed. This allows for the development of computational tools implementing forward models grounded in the biophysics underlying electrical and magnetic measurement modalities. LFPy (LFPy.readthedocs.io) incorporated a well-established scheme for predicting extracellular potentials of individual neurons with arbitrary levels of biological detail. It relies on NEURON (neuron.yale.edu) to compute transmembrane currents of multicompartment neurons which is then used in combination with an electrostatic forward model. Its functionality is now extended to allow for modeling of networks of multicompartment neurons with concurrent calculations of extracellular potentials and current dipole moments. The current dipole moments are then, in combination with suitable volume-conductor head models, used to compute non-invasive measures of neuronal activity, like scalp potentials (electroencephalographic recordings; EEG) and magnetic fields outside the head (magnetoencephalographic recordings; MEG). One such built-in head model is the four-sphere head model incorporating the different electric conductivities of brain, cerebrospinal fluid, skull and scalp. We demonstrate the new functionality of the software by constructing a network of biophysically detailed multicompartment neuron models from the Neocortical Microcircuit Collaboration (NMC) Portal (bbp.epfl.ch/nmc-portal) with corresponding statistics of connections and synapses, and compute in vivo-like extracellular potentials (local field potentials, LFP; electrocorticographical signals, ECoG) and corresponding current dipole moments. From the current dipole moments we estimate corresponding EEG and MEG signals using the four-sphere head model. We also show strong scaling performance of LFPy with different numbers of message-passing interface (MPI) processes, and for different network sizes with different density of connections. The open-source software LFPy is equally suitable for execution on laptops and in parallel on high-performance computing (HPC) facilities and is publicly available on GitHub.com.

• Domanska, Diana Ewa; Kanduri, Srinivasa Kalyana Chakravarthi; Simovski, Boris & Sandve, Geir Kjetil (2018). Mind the gaps: overlooking inaccessible regions confounds statistical testing in genome analysis. BMC Bioinformatics. ISSN 1471-2105. 19(481). doi: 10.1186/s12859-018-2438-1. Full text in Research Archive
• Hutin, David; Tamblyn, Laura; Gomez, Alvin; Grimaldi, Giulia; Soedling, Helen & Cho, Tiffany [Show all 11 contributors for this article] (2018). Hepatocyte-Specific Deletion of TIPARP, a Negative Regulator of the Aryl Hydrocarbon Receptor, Is Sufficient to Increase Sensitivity to Dioxin-Induced Wasting Syndrome. Toxicological Sciences. ISSN 1096-6080. 165(2), p. 347–360. doi: 10.1093/toxsci/kfy136. Full text in Research Archive
• Kristiansen, Stein; Sønsteby Hugaas, Mari; Goebel, Vera Hermine; Plagemann, Thomas Peter; Nikolaidis, Konstantinos & Liestøl, Knut (2018). Data Mining for Patient Friendly Apnea Detection. IEEE Access. ISSN 2169-3536. 6, p. 74598–74615. doi: 10.1109/ACCESS.2018.2882270. Full text in Research Archive
• Vagos, Marcia Raquel da Silva e Sousa; Van Herck, Ilsbeth Gerarda Maria; Sundnes, Joakim; Arevalo, Hermenegild; Edwards, Andrew & Koivumäki, Jussi (2018). Computational modeling of electrophysiology and pharmacotherapy of atrial fibrillation: Recent advances and future challenges. Frontiers in Physiology. ISSN 1664-042X. 9:1221, p. 1–29. doi: 10.3389/fphys.2018.01221. Full text in Research Archive
• Yao, Ying; Zia, Asima; Wyrozemski, Lukasz Adam; Lindeman, Ida; Sandve, Geir Kjetil & Qiao, Shuo Wang (2018). Exploiting antigen receptor information to quantify index switching in single-cell transcriptome sequencing experiments. PLOS ONE. ISSN 1932-6203. 13(12), p. 1–17. doi: 10.1371/journal.pone.0208484. 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
• Lockmer, Sandra; Østenstad, Bjørn; Hagberg, Hans; Holte, Harald; Johansson, Ann-Sofie & Wahlin, Björn Engelbrekt [Show all 13 contributors for this article] (2018). Chemotherapy-free initial treatment of advanced indolent lymphoma has durable effect with low toxicity: Results from two Nordic lymphoma group trials with more than 10 years of follow-up. Journal of Clinical Oncology. ISSN 0732-183X. 36(33), p. 3315–3323. doi: 10.1200/JCO.18.00262.
• Erikssen, Gunnar; Aboulhosn, Jamil; Lin, Jeannette; Liestøl, Knut; Estensen, Mette-Elise & Gjesdal, Ola [Show all 9 contributors for this article] (2018). Survival in patients with univentricular hearts: The impact of right versus left ventricular morphology. Open heart. ISSN 2053-3624. 5:e000902(2), p. 1–9. doi: 10.1136/openhrt-2018-000902. Full text in Research Archive
• Varadharajan, Srinidhi; Sandve, Simen Rød; Gillard, Gareth Benjamin; Tørresen, Ole K.; Mulugeta, Teshome Dagne & Hvidsten, Torgeir Rhoden [Show all 11 contributors for this article] (2018). The grayling genome reveals selection on gene expression regulation after whole-genome duplication. Genome Biology and Evolution (GBE). ISSN 1759-6653. 10(10), p. 2785–2800. doi: 10.1093/gbe/evy201. Full text in Research Archive
• Møller, Pål; Seppälä, Toni T.; Bernstein, Inge; Holinski-Feder, Elke; Sala, Paulo & Evans, D. Gareth [Show all 38 contributors for this article] (2018). Cancer risk and survival in path_MMR carriers by gene and gender up to 75 years of age: a report from the Prospective Lynch Syndrome Database. Gut. ISSN 0017-5749. 67(7), p. 1306–1316. doi: 10.1136/gutjnl-2017-314057. Full text in Research Archive
• Simovski, Boris; Kanduri, Srinivasa Kalyana Chakravarthi; Gundersen, Sveinung; Titov, Dmytro; Domanska, Diana Ewa & Bock, Christoph [Show all 15 contributors for this article] (2018). Coloc-stats: A unified web interface to perform colocalization analysis of genomic features. Nucleic Acids Research (NAR). ISSN 0305-1048. 46(1), p. W186–W193. doi: 10.1093/nar/gky474. Full text in Research Archive
• Mehlum, Maria Hollund; Liestøl, Knut; Kjeldsen, Sverre; Julius, Stevo; Hua, Tsushung A. & Rothwell, Peter M. [Show all 10 contributors for this article] (2018). Blood pressure variability and risk of cardiovascular events and death in patients with hypertension and different baseline risks. European Heart Journal. ISSN 0195-668X. 39(24), p. 2243–2251. doi: 10.1093/eurheartj/ehx760.
• Tellum, Tina; Nygård, Ståle; Skovholt, Else K.; Qvigstad, Erik & Lieng, Marit (2018). Development of a clinical prediction model for diagnosing adenomyosis. Fertility and Sterility. ISSN 0015-0282. 110(5), p. 957–964.e3. doi: 10.1016/j.fertnstert.2018.06.009.
• Rye, Inga Hansine; Trinh, Anne; Sætersdal, Anna Barbro; Nebdal, Daniel J.H.; Lingjærde, Ole Christian & Almendro, Vanessa [Show all 11 contributors for this article] (2018). Intratumor heterogeneity defines treatment-resistant HER2+ breast tumors. Molecular Oncology. ISSN 1574-7891. p. 1–18. doi: 10.1002/1878-0261.12375. Full text in Research Archive
• Tennøe, Simen; Halnes, Geir & Einevoll, Gaute (2018). Uncertainpy: A Python toolbox for uncertainty quantification and sensitivity analysis in computational neuroscience. Frontiers in Neuroinformatics. ISSN 1662-5196. 12:49, p. 1–29. doi: 10.3389/fninf.2018.00049. Full text in Research Archive
• Engeseth, Kristian; Prestgaard, Erik Edvard; Mariampillai, Julian Eek; Grundvold, Irene; Liestøl, Knut & Kjeldsen, Sverre [Show all 10 contributors for this article] (2018). Physical fitness is a modifiable predictor of early cardiovascular death: A 35-year follow-up study of 2014 healthy middle-aged men. European Journal of Preventive Cardiology (EJPC). ISSN 2047-4873. 25(15), p. 1655–1663. doi: 10.1177/2047487318793459.
• Winje, Ivan; Sheng, Xia; Hansson, Kenth-Arne; Solbrå, Andreas Våvang; Tennøe, Simen & Saatcioglu, Fahri [Show all 8 contributors for this article] (2018). Cachexia does not induce loss of myonuclei or muscle fibres during xenografted prostate cancer in mice. Acta Physiologica. ISSN 1748-1708. p. 1–9. doi: 10.1111/apha.13204.
• Malerød, Lene; Le Borgne, Roland; Lie-Jensen, Anette Christensen; Eikenes, Åsmund Husabø; Brech, Andreas & Liestøl, Knut [Show all 8 contributors for this article] (2018). Centrosomal ALIX regulates mitotic spindle orientation by modulating astral microtubule dynamics. EMBO Journal. ISSN 0261-4189. 37(13), p. 1–21. doi: 10.15252/embj.201797741.
• Tekle, Kidane M; Gundersen, Sveinung; Klepper, Kjetil; Bongo, Lars Ailo; Raknes, Inge Alexander & Li, Xiaxi [Show all 22 contributors for this article] (2018). Norwegian e-Infrastructure for Life Sciences (NeLS). F1000 Research. ISSN 2046-1402. 7:968. doi: 10.5256/f1000research.16472.r35600. Full text in Research Archive
• Holte, Harald; Beiske, Klaus; Boyle, Merrill; Trøen, Gunhild; Blaker, Yngvild Nuvin & Myklebust, June [Show all 13 contributors for this article] (2018). The MCL35 gene expression proliferation assay predicts high-risk MCL patients in a Norwegian cohort of younger patients given intensive first line therapy. British Journal of Haematology. ISSN 0007-1048. p. 1–10. doi: 10.1111/bjh.15518.
• Mable, Barbara K.; Brysting, Anne Krag; Jørgensen, Marte Holten; Carbonell, Anna K.Z.; Kiefer, Christiane & Ruiz-Duarte, Paola [Show all 8 contributors for this article] (2018). Adding Complexity to Complexity: Gene Family Evolution in Polyploids. Frontiers in Ecology and Evolution. ISSN 2296-701X. 6, p. 1–20. doi: 10.3389/fevo.2018.00114. Full text in Research Archive
• Risnes, Louise Fremgaard; Christophersen, Asbjørn; Dahal-Koirala, Shiva; Neumann, Ralf Stefan; Sandve, Geir Kjetil & Sarna, Vikas Kumar [Show all 9 contributors for this article] (2018). Disease-driving CD4+ T cell clonotypes persist for decades in celiac disease. Journal of Clinical Investigation. ISSN 0021-9738. 128(6), p. 2642–2650. doi: 10.1172/JCI98819. Full text in Research Archive
• Ebenesersdóttir, Sigríður Sunna; Sandoval-Velasco, Marcela; Gunnarsdóttir, Ellen D.; Jagadeesan, Anuradha; Guðmundsdóttir, Valdís B. & Thordardóttir, Elísabet L. [Show all 30 contributors for this article] (2018). Ancient genomes from Iceland reveal the making of a human population. Science. ISSN 0036-8075. 360(6392), p. 1028–1032. doi: 10.1126/science.aar2625. Full text in Research Archive
• Dominguez Valentin, Mev; Evans, D. Gareth R.; Nakken, Sigve; Tubeuf, Hélène; Vodak, Daniel & Ekstrøm, Per Olaf [Show all 12 contributors for this article] (2018). Genetic variants of prospectively demonstrated phenocopies in BRCA1/2 kindreds. Hereditary Cancer in Clinical Practice. ISSN 1731-2302. 16:4, p. 1–14. doi: 10.1186/s13053-018-0086-0. Full text in Research Archive
• Dragly, Svenn-Arne; Mobarhan, Milad; Lepperød, Mikkel Elle; Tennøe, Simen; Fyhn, Marianne & Hafting, Torkel [Show all 7 contributors for this article] (2018). Experimental directory structure (Exdir): An alternative to HDF5 without introducing a new file format. Frontiers in Neuroinformatics. ISSN 1662-5196. 12. doi: 10.3389/fninf.2018.00016.
• Balaban, Gabriel; Finsberg, Henrik Nicolay; Funke, Simon Wolfgang; Håland, Trine Synnøve Fink; Hopp, Einar & Sundnes, Joakim [Show all 8 contributors for this article] (2018). In vivo estimation of elastic heterogeneity in an infarcted human heart. Biomechanics and Modeling in Mechanobiology. ISSN 1617-7959. p. 1–13. doi: 10.1007/s10237-018-1028-5. Full text in Research Archive
• Våtsveen, Thea Kristin; Myhre, Marit Renee; Steen, Chloe Beate; Wälchli, Sébastien; Lingjærde, Ole Christian & Bai, Baoyan [Show all 14 contributors for this article] (2018). Artesunate shows potent anti-tumor activity in B-cell lymphoma. Journal of Hematology & Oncology. ISSN 1756-8722. 11:23, p. 1–12. doi: 10.1186/s13045-018-0561-0. Full text in Research Archive
• Tørresen, Ole K.; Brieuc, Marine Servane; Solbakken, Monica Hongrø; Sørhus, Elin; Nederbragt, Alexander Johan & Jakobsen, Kjetill Sigurd [Show all 9 contributors for this article] (2018). Genomic architecture of haddock (Melanogrammus aeglefinus) shows expansions of innate immune genes and short tandem repeats. BMC Genomics. ISSN 1471-2164. 19(240), p. 1–17. doi: 10.1186/s12864-018-4616-y. Full text in Research Archive
• Ihle-Hansen, Håkon; Vigen, Thea; Ihle-Hansen, Hege; Rønning, Ole M.; Berge, Trygve & Thommessen, Bente [Show all 12 contributors for this article] (2018). Prevalence of carotid plaque in a 63- to 65-Year-Old Norwegian cohort from the general population: The ACE (Akershus Cardiac Examination) 1950 study. Journal of the American Heart Association (JAHA). ISSN 2047-9980. 7(10). doi: 10.1161/JAHA.118.008562. Full text in Research Archive
• Aqrawi, Lara Adnan; Jensen, Janicke Liaaen; Øijordsbakken, Gunnvor; Ruus, Ann-Kristin; Nygård, Ståle & Holden, Marit [Show all 9 contributors for this article] (2018). Signalling pathways identified in salivary glands from primary Sjögren's syndrome patients reveal enhanced adipose tissue development. Autoimmunity. ISSN 0891-6934. 51(3), p. 135–146. doi: 10.1080/08916934.2018.1446525. Show summary

  A characteristic feature of primary Sjögren’s syndrome (pSS) is the destruction of salivary and lacrimal glands mediated by mononuclear cell infiltration. Adipocytes can also occupy a large portion of the salivary gland (SG) tissue area, although little is known about their significance in pSS. We have previously investigated adipose tissue infiltration in SG biopsies from pSS patients and non-SS sicca controls. Our findings indicated the distinct incidence of adipose tissue replacement in pSS patients, where adipocytes were detected in interleukin (IL) 6 rich regions. We now aimed to examine the development of adipocytes in the SG microenvironment, and delineate their possible involvement in immune reactions. A microarray analysis was performed on SG from 6 pSS patients and 6 non-SS controls, where the expression levels of genes involved in adipose tissue development, inflammatory responses, and lymphoma development were assessed. Real-time PCR was carried out on SG from 14 pSS patients and 15 non-SS controls to account for IL6, IL10, and IL17 mRNA levels. Immunohistochemical staining of frozen SG tissue using IL17 was also conducted. Our results indicate signalling pathways identified in SG of pSS patients displayed genes leading to prominent adipose tissue development and reduced mitochondrial fatty acid beta-oxidation (ARID5B, OXCT1, BDH1, SOX8, HMGCS2, FTO, ECHS1, PCCA, ACADL and ACADVL), inflammatory responses (IL1R1, IL7R, IL10RA, IL15, IL18RAP, CCL2, CCL5, CCL22, CXCR6, CD14, and CD48), and lymphoma development via JAK-STAT signalling (STAT2, TYK2, EBI3, FAS, TNFRSF1B, MAP3K8, HMOX1, LTB, TNF, STAT1, and BAK1). Genes involved in interferon production and signalling were also detected (IRF1, IRF9, and IRF7), in addition to IL6, IL10, and IL17. Higher mRNA levels of IL6, IL17 and IL10 were observed in the SG of pSS patients compared to controls. Moreover, IL17 positive cells were detected mostly interstitially in the SG and around adipocytes, also within the focal infiltrates. In conclusion, adipocyte development seems to be more prominent in the SG of pSS patients, where adipose tissue replacement is also evident. Whether this is due to disease progression, or the repair process, remains to be investigated. Detection of IL17 positive adipocytes in the target organ suggests their involvement in immune reactions.

• Campos, Joventino Oliveira; dos Santos, Rodrigo Weber; Sundnes, Joakim & Rocha, Bernardo Martins (2018). Preconditioned augmented Lagrangian formulation for nearly incompressible cardiac mechanics. International Journal for Numerical Methods in Biomedical Engineering. ISSN 2040-7939. 34(4). doi: 10.1002/cnm.2948.
• Feinberg, Jonathan; Eck, Vinzenz Gregor & Langtangen, Hans Petter (2018). Multivariate polynomial chaos expansions with dependent variables. SIAM Review. ISSN 0036-1445. 40(1), p. A199–A223. doi: 10.1137/15M1020447.
• Brynildsen, Jon; Petäjä, Liisa; Pettilä, Ville; Nygård, Ståle; Vaara, Suvi T. & Linko, Rita [Show all 13 contributors for this article] (2018). The predictive value of NT-proBNP and hs-TnT for risk of death in cardiac surgical patients. Clinical Biochemistry. ISSN 0009-9120. 53, p. 65–71. doi: 10.1016/j.clinbiochem.2018.01.012.
• Dominguez Valentin, Mev; Nakken, Sigve; Tubeuf, Hélène; Vodak, Daniel; Ekstrøm, Per Olaf & Nissen, Anke M. [Show all 11 contributors for this article] (2018). Identification of genetic variants for clinical management of familial colorectal tumors. BMC Medical Genetics. ISSN 1471-2350. 19(1). doi: 10.1186/s12881-018-0533-9. Full text in Research Archive
• Lie, Kai Kristoffer; Tørresen, Ole K.; Solbakken, Monica Hongrø; Rønnestad, Ivar; Tooming-Klunderud, Ave & Nederbragt, Alexander Johan [Show all 8 contributors for this article] (2018). Loss of stomach, loss of appetite? Sequencing of the ballan wrasse (Labrus bergylta) genome and intestinal transcriptomic profiling illuminate the evolution of loss of stomach function in fish. BMC Genomics. ISSN 1471-2164. 19(186), p. 1–17. doi: 10.1186/s12864-018-4570-8. Full text in Research Archive

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• 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.
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• Bai, Baoyan; Vodák, Daniel; Nakken, Sigve; Wise, Jillian; Blaker, Yngvild Nuvin & Lingjærde, Ole Christian [Show all 18 contributors for this article] (2019). Deep profiling of genetic aberrations and clonal evolution in follicular lymphoma. Blood. ISSN 0006-4971. 134(1), p. 20–20. doi: 10.1182/blood-2019-128403.
• Fan, Qiong; Nørgaard, Rikke Christine; Grytten, Ivar; Ness, Cecilie Maria; Lucas, Christin & Vekterud, Kristin [Show all 15 contributors for this article] (2019). LXRα interacts with the glucose-sensing transcription factor ChREBPα to regulate its transcriptional activity.
• Hagen, Espen; Stasik, Alexander Johannes; Billeh, Yazan N.; Siegle, Joshua H.; Dai, Kael & Rimehaug, Atle Eskeland [Show all 14 contributors for this article] (2019). Comparing spikes and the local field potential (LFP) in V1 between experimental data and a comprehensive biophysical model.
• Hagen, Espen; Stasik, Alexander Johannes; Billeh, Yazan; Siegle, Joshua H.; Dai, Kael & Rimehaug, Atle Eskeland [Show all 14 contributors for this article] (2019). Comparing spikes and the local field potential (LFP) in V1 between experimental data and a comprehensive biophysical model.
• Trotter, James David; Cai, Xing; Funke, Simon Wolfgang & Langguth, Johannes (2019). Compiling finite element variational forms for GPU-based assembly.
• Thune, Andreas & Cai, Xing (2019). Balancing the numerical and parallel performance for reservoir simulations.
• Cai, Xing (2019). Unstructured computational meshes and data locality.
• Cai, Xing (2019). Heterogeneous computing for cardiac electrophysiology.
• Langguth, Johannes; Arevalo, Hermenegild; Hustad, Kristian Gregorius & Cai, Xing (2019). Towards detailed real-time simulations of cardiac arrhythmia.
• Silwal-Pandit, Laxmi; Stålberg, Stina Margrethe; Mermelekas, G; Lothe, Inger Marie Bowitz; Skrede, Martina Landschoof & Dalsgaard, Astrid M. [Show all 11 contributors for this article] (2019). Proteomic Landscape of Pancreatic Ductal Adenocarcinoma.
• Fan, Qiong; Nørgaard, Rikke Christine; Grytten, Ivar; Ulven, Stine Marie; Lucas, Christin & Bindesbøll, Christian [Show all 11 contributors for this article] (2018). LXRα interacts with the glucose-sensing transcription factor ChREBPα and increases its transcriptional activity.
• Mehlum, Maria Hollund; Liestøl, Knut; Kjeldsen, Sverre & Berge, Eivind (2018). Response to letters from Torp-Pedersen and colleagues and de Courson and colleagues. European Heart Journal. ISSN 0195-668X. 39(47), p. 4221–4221. doi: 10.1093/eurheartj/ehy605.
• Næss, Solveig; Ness, Torbjørn V; Hagen, Espen & Einevoll, Gaute (2018). Biophysical modelling of EEG signals from large neural populations.
• Dean, Katharine Rose; Krauer, Fabienne; Walløe, Lars; Lingjærde, Ole Christian; Bramanti, Barbara & Stenseth, Nils Christian [Show all 7 contributors for this article] (2018). Reply to Park et al.: Human ectoparasite transmission of plague during the Second Pandemic is still plausible. Proceedings of the National Academy of Sciences of the United States of America. ISSN 0027-8424. 115(34), p. E7894–E7895. doi: 10.1073/pnas.1810221115.
• Blanco Gonzalez, Enrique ; Jentoft, Sissel; Hansen, Michael Møller; Knutsen, Halvor; Sodeland, Marte & Mattingsdal, Morten [Show all 9 contributors for this article] (2018). Understanding adaptation in translocating wrasses.
• Tarabichi, Maxime; Martincorena, Iñigo; Gerstung, Moritz; Leroi, Armand M.; Markowetz, Florian & Spellman, Paul [Show all 10 contributors for this article] (2018). Neutral tumor evolution? Nature Genetics. ISSN 1061-4036. 50(12), p. 1630–1633. doi: 10.1038/s41588-018-0258-x.
• Tennøe, Simen; Halnes, Geir & Einevoll, Gaute (2018). Uncertainpy: A Python toolbox for uncertainty quantification and sensitivity analysis of computational neuroscience models.
• Reinar, William Brynildsen; Tørresen, Ole K.; Matschiner, Michael; Jentoft, Sissel; Nederbragt, Alexander Johan & Jakobsen, Kjetill Sigurd (2018). The impact of repetitive DNA on speciation rates in teleost fish.
• Tabib, Mandar; Khan, Malik Muhammad Zaki Murtaza; Lingjærde, Ole Christian; Johannessen, Kjetil Andre; Rasheed, Adil & Fonn, Eivind [Show all 8 contributors for this article] (2018). Geilo Winter School in eScience on Artificial Intelligence.
• Langguth, Johannes; Hermenegild, Arevalo; Jarvis, Chad & Cai, Xing (2018). Towards Detailed Organ-Scale Simulations in Cardiac Electrophysiology.
• Cai, Xing (2018). Heterogeneous Computing: Programming, Performance and Applications.
• Trotter, James David; Langguth, Johannes & Cai, Xing (2018). Quantifying data traffic of sparse matrix-vector multiplication in a multi-level memory hierarchy.
• Cai, Xing (2018). Education in HPC and Data Science at Simula Research Lab and UiO.
• Thune, Andreas & Cai, Xing (2018). Unstructured mesh partitioning in the presence of strong coefficient heterogeneity.
• Dragly, Svenn-Arne; Mobarhan, Milad; Lepperød, Mikkel Elle; Tennøe, Simen; Stasik, Alexander Johannes & Fyhn, Marianne [Show all 8 contributors for this article] (2018). Exdir An alternative to HDF5 that uses Numpy files for data, YAML for metadata and simple directories to define the hierarchy.
• Hagen, Espen; Næss, Solveig; Ness, Torbjørn V & Einevoll, Gaute (2018). Multimodal modeling of neural network activity: computing LFP, ECoG, EEG and MEG signals with LFPy 2.0.
• Hagen, Espen; Næss, Solveig; Ness, Torbjørn V & Einevoll, Gaute (2018). Multimodal modeling of neural network activity: computing LFP, ECoG, EEG and MEG signals with LFPy2.0.
• 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.
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