Our latest publications - BMI

• Brown, Alex; Snapkov, Igor; Akbar, Rahmad; Pavlovic, Milena; Miho, Enkelejda; Sandve, Geir Kjetil & Greiff, Victor (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, s 701- 736 . doi: 10.1039/C9ME00071B
• 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, s 1- 20 . doi: 10.1155/2019/6825728
• 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), s 1- 13 . doi: 10.1371/journal.pcbi.1006731
• Mäki-Marttunen, Tuomo; Krull, Florian; Bettella, Francesco; Hagen, Espen; Næss, Solveig; Ness, Torbjørn V; Moberget, Torgeir; Elvsåshagen, Torbjørn; Metzner, Christoph; Devor, Anna; Edwards, Andrew G.; Fyhn, Marianne; Djurovic, Srdjan; Dale, Anders; Andreassen, Ole Andreas & Einevoll, Gaute (2019). Alterations in schizophrenia-associated genes can lead to increased power in delta oscillations. Cerebral Cortex.  ISSN 1047-3211.  29(2), s 875- 891 . doi: 10.1093/cercor/bhy291
• 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. . doi: 10.1080/08037051.2018.1524707
• Mariampillai, Julian Eek; Prestgaard, Erik Edvard; Kjeldsen, Sverre; Liestøl, Knut; Engeseth, Kristian; Erikssen, Jan Emil; Bodegard, Johan; Berge, Eivind; Grundvold, Irene & Skretteberg, Torger (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), s 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.  ISSN 0305-1048.  47(4), s e21 . doi: 10.1093/nar/gky1210
• 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), s 1615- 1624 . doi: 10.1093/bioinformatics/bty835 Full text in Research Archive.
• 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 Naoki Abe; Huan Liu; Xiaohua Hu; Nesreen Ahmed; Mu Qiao; Yang Song; Donald Kossmann; Bing Liu; Kisung Lee; Jiliang Tang; Jingrui He & Jeffrey Saltz (ed.),  2018 IEEE International Conference on Big Data (Big Data), Seattle, 10-13 Dec. 2018.  IEEE.  ISBN 978-1-5386-5035-6.  kapittel.
• Prestgaard, Erik Edvard; Mariampillai, Julian Eek; Engeseth, Kristian; Erikssen, Jan Emil; Bodegard, Johan; Liestøl, Knut; Gjesdal, Knut; Kjeldsen, Sverre; Grundvold, Irene & Berge, Eivind (2018). Change in Cardiorespiratory Fitness and Risk of Stroke and Death.. Stroke.  ISSN 0039-2499.  50, s 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; Solano, Angela; Carraro, Dirce Maria; Forones, Nora Manoukian; Bohorquez, Mabel; Lino‐Silva, Leonardo S.; Buleje, Jose; Spirandelli, Florencia; Abe‐Sandes, Kiyoko; Nascimento, Ivana; Sullcahuaman, Yasser; Sarroca, Carlos; Gonzalez, Maria Laura; Herrando, Alberto Ignacio; Alvarez, Karin; Neffa, Florencia; Galvão, Henrique Camposreis; Esperon, Patricia; Golubicki, Mariano; Cisterna, Daniel; Cardoso, Florencia C.; Torrezan, Giovana Tardin; Junior, Samuel Aguiar; Pimenta, Célia Aparecida Marques; Formiga, Maria Nirvana da Cruz; Santos, Erika; Sá, Caroline U.; Oliveira, Edite P.; Fujita, Ricardo; Spirandelli, Enrique; Jimenez, Geiner; Guindalini, Rodrigo Santa Cruz; de Azevedo, Renata Gondim Meira Velame; Bueno, Larissa Souza Mario; Nogueira, Sonia Tereza dos Santos; Loarte, Mariela Torres; Padron, Jorge; Castro‐Mujica, Maria del Carmen; del Monte, Julio Sanchez; Caballero, Carmelo; Peña, Carlos Mario Muñeton; Pinto, Joseph P.; Barletta‐Carrillo, Claudia; Melva, Gutiérrez Angulo; Piñero, Tamara Alejandra; Beltran, Paola Montenegro; Ashton‐Prolla, Patricia; Rodriguez, Yenni; Quispe, Richard; Rossi, Norma Teresa; Martin, Claudia; Chialina, Sergio; Kalfayan, Pablo German; Bazo‐Alvarez, Juan Carlos; Cañete, Alcides Recalde; Dominguez‐Barrera, Constantino; Nuñez, Lina; da Silva, Sabrina Daniela; Balavarca, Yesilda; Vernhoff, Patrik; Plazzer, John‐Paul; Møller, Pål; Hovig, Eivind & Dominguez-Valentin, Mev (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. Show summary

  Colorectal cancer (CRC) is one of the most common cancers in Latin America and the Caribbean, with the highest rates reported for Uruguay, Brazil and Argentina. We provide a global snapshot of the CRC patterns, how screening is performed, and compared/contrasted to the genetic profile of Lynch syndrome (LS) in the region. From the literature, we find that only nine (20%) of the Latin America and the Caribbean countries have developed guidelines for early detection of CRC, and also with a low adherence. We describe a genetic profile of LS, including a total of 2,685 suspected families, where confirmed LS ranged from 8% in Uruguay and Argentina to 60% in Peru. Among confirmed LS, path_MLH1 variants were most commonly identified in Peru (82%), Mexico (80%), Chile (60%), and path_MSH2/EPCAM variants were most frequently identified in Colombia (80%) and Argentina (47%). Path_MSH6 and path_PMS2 variants were less common, but they showed important presence in Brazil (15%) and Chile (10%), respectively. Important differences exist at identifying LS families in Latin American countries, where the spectrum of path_MLH1 and path_MSH2 variants are those most frequently identified. Our findings have an impact on the evaluation of the patients and their relatives at risk for LS, derived from the gene affected. Although the awareness of hereditary cancer and genetic testing has improved in the last decade, it is remains deficient, with 39%–80% of the families not being identified for LS among those who actually met both the clinical criteria for LS and showed MMR deficiency.

• Møller, Elen Kristine; Nord, Silje; Wedge, David C; Lingjærde, Ole Christian; Silwal-Pandit, Laxmi; Gythfeldt, Hedda; Vollan, Hans Kristian Moen; Fleischer, Thomas; Krohn, Marit; Schlichting, Ellen; Borgen, Elin; Garred, Øystein; Holmen, Marit Muri; Wist, Erik; Naume, Bjørn; Van Loo, Peter; Børresen-Dale, Anne-Lise; Engebråten, Olav & Kristensen, Vessela N. (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
• 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), s 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
• Hutin, David; Tamblyn, Laura; Gomez, Alvin; Grimaldi, Giulia; Soedling, Helen; Cho, Tiffany; Ahmed, Shaimaa; Lucas, Christin; Kanduri, Srinivasa Kalyana Chakravarthi; Grant, Denis M & Matthews, Jason (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), s 347- 360 . doi: 10.1093/toxsci/kfy136
• 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, s 74598- 74615 . doi: 10.1109/ACCESS.2018.2882270
• 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, s 1- 29 . doi: 10.3389/fphys.2018.01221
• 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), s 1- 17 . doi: 10.1371/journal.pone.0208484
• 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), s 841- 847 . doi: 10.1002/ijc.31809 Show summary

  KRAS mutation is a well‐known marker for poor response to targeted treatment and patient prognosis in microsatellite stable (MSS) colorectal cancer (CRC). However, variation in clinical outcomes among patients wild‐type for KRAS underlines that this is not a homogeneous population. Here, we evaluated the prognostic impact of KRAS alternative splicing in relation to mutation status in a single‐hospital series of primary MSS CRCs (N = 258). Using splicing‐sensitive microarrays and RNA sequencing, the relative expression of KRAS‐4A versus KRAS‐4B transcript variants was confirmed to be down‐regulated in CRC compared to normal colonic mucosa (N = 41; p ≤ 0.001). This was independent of mutation status, however, gene set enrichment analysis revealed that the effect of splicing on KRAS signaling was specific to the KRAS wild‐type subgroup, in which low relative KRAS‐4A expression was associated with a higher level of KRAS signaling (p = 0.005). In concordance, the prognostic value of KRAS splicing was also dependent on mutation status, and for patients with Stage I–III KRAS wild‐type MSS CRC, low relative KRAS‐4A expression was associated with inferior overall survival (HR: 2.36, 95% CI: 1.07–5.18, p = 0.033), a result not found in mutant cases (pinteraction = 0.026). The prognostic association in the wild‐type subgroup was independent of clinicopathological factors, including cancer stage in multivariable analysis (HR: 2.68, 95% CI: 1.18–6.09, p = 0.018). This suggests that KRAS has prognostic value beyond mutation status in MSS CRC, and highlights the importance of molecular heterogeneity in the clinically relevant KRAS wild‐type subgroup.

• Lockmer, Sandra; Østenstad, Bjørn; Hagberg, Hans; Holte, Harald; Johansson, Ann-Sofie; Wahlin, Björn Engelbrekt; Wader, Karin Fahl; Steen, Chloe Beate; Meyer, Peter Albert; Maisenhölder, Martin; Smedby, Karin Ekström; Brown, Peter & Kimby, Eva (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), s 3315- 3323 . doi: 10.1200/JCO.18.00262
• Erikssen, Gunnar; Aboulhosn, Jamil; Lin, Jeannette; Liestøl, Knut; Estensen, Mette-Elise; Gjesdal, Ola; Skulstad, Helge; Døhlen, Gaute & Lindberg, Harald L (2018). Survival in patients with univentricular hearts: The impact of right versus left ventricular morphology. Open heart.  ISSN 2053-3624.  5:e000902(2), s 1- 9 . doi: 10.1136/openhrt-2018-000902
• Varadharajan, Srinidhi; Sandve, Simen Rød; Gillard, Gareth Benjamin; Tørresen, Ole K.; Mulugeta, Teshome Dagne; Hvidsten, Torgeir Rhoden; Lien, Sigbjørn; Vøllestad, Leif Asbjørn; Jentoft, Sissel; Nederbragt, Alexander Johan & Jakobsen, Kjetill Sigurd (2018). The grayling genome reveals selection on gene expression regulation after whole-genome duplication. Genome Biology and Evolution.  ISSN 1759-6653.  10(10), s 2785- 2800 . doi: 10.1093/gbe/evy201
• Møller, Pål; Seppälä, Toni T.; Bernstein, Inge; Holinski-Feder, Elke; Sala, Paulo; Evans, D. Gareth; Lindblom, Annika; Macrae, Finlay; Blanco, Ignacio; Sijmons, Rolf H.; Jeffries, Jacqueline; Vasen, Hans F.A.; Burn, John; Nakken, Sigve; Hovig, Eivind; Rødland, Einar Andreas; Tharmaratnam, Kukatharmini; de Vos tot Nederveen Cappel, Wouter H.; Hill, James; Wijnen, Juul T.; Jenkins, Mark A.; Green, Kate; Lalloo, Fiona; Sunde, Lone; Mints, Miriam; Bertario, Lucio; Pineda, Marta; Navarro, Matilde; Morak, Monika; Renkonen-Sinisalo, Laura; Dominguez-Valentin, Mev; Frayling, Ian M.; Plazzer, John-Paul; Pylvanainen, Kirsi; Genuardi, Maurizio; Mecklin, Jukka-Pekka; Möslein, Gabriela; Sampson, Julian R. & Capella, Gabriel (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), s 1306- 1316 . doi: 10.1136/gutjnl-2017-314057
• Simovski, Boris; Kanduri, Srinivasa Kalyana Chakravarthi; Gundersen, Sveinung; Titov, Dmytro; Domanska, Diana Ewa; Bock, Christoph; Bossini-Castillo, Lara; Chikina, Maria; Favorov, Alexander; Layer, Ryan M.; Mironov, Alexandre A.; Quinlan, Aaron R.; Sheffield, Nathan C.; Trynka, Gosia & Sandve, Geir Kjetil (2018). Coloc-stats: A unified web interface to perform colocalization analysis of genomic features. Nucleic Acids Research.  ISSN 0305-1048.  46(1), s 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.; Mancia, Giuseppe; Parati, Gianfranco; Weber, Michael A. & Berge, Eivind (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), s 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), s 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; Polyak, Kornelia; Børresen-Dale, Anne-Lise; Helland, Åslaug; Markowetz, Florian & Russnes, Hege Elisabeth Giercksky (2018). Intratumor heterogeneity defines treatment-resistant HER2+ breast tumors. Molecular Oncology.  ISSN 1574-7891.  s 1- 18 . doi: 10.1002/1878-0261.12375
• 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, s 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; Bodegard, Johan; Erikssen, Jan Emil; Gjesdal, Knut & Skretteberg, Torger (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.  ISSN 2047-4873.  25(15), s 1655- 1663 . doi: 10.1177/2047487318793459
• Winje, Ivan; Sheng, Xia; Hansson, Kenth-Arne; Solbrå, Andreas Våvang; Tennøe, Simen; Saatcioglu, Fahri; Bruusgaard, Jo C. & Gundersen, Kristian (2018). Cachexia does not induce loss of myonuclei or muscle fibres during xenografted prostate cancer in mice. Acta Physiologica.  ISSN 1748-1708.  s 1- 9 . doi: 10.1111/apha.13204
• Malerød, Lene; Le Borgne, Roland; Lie-Jensen, Anette Christensen; Eikenes, Åsmund Husabø; Brech, Andreas; Liestøl, Knut; Stenmark, Harald & Haglund, Kaisa (2018). Centrosomal ALIX regulates mitotic spindle orientation by modulating astral microtubule dynamics. EMBO Journal.  ISSN 0261-4189.  37(13), s 1- 21 . doi: 10.15252/embj.201797741
• Tekle, Kidane M; Gundersen, Sveinung; Klepper, Kjetil; Bongo, Lars Ailo; Raknes, Inge Alexander; Li, Xiaxi; Zhang, Wei; Andreetta, Christian; Mulugeta, Teshome Dagne; Kalaš, Matúš; Rye, Morten Beck; Hjerde, Erik; Antony Samy, Jeevan Karloss; Fornous, Ghislain; Azab, Abdulrahman; Våge, Dag Inge; Hovig, Eivind; Willassen, Nils Peder; Drabløs, Finn; Nygård, Ståle; Petersen, Kjell & Jonassen, Inge (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; Kvaløy, Anne Sunniva; Rosenwald, Andreas; Lingjærde, Ole Christian; Rimsza, Lisa M.; Smeland, Erlend B; Scott, David W. & Kolstad, Arne (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.  s 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; Lagesen, Karin & Koch, Marcus A. (2018). Adding Complexity to Complexity: Gene Family Evolution in Polyploids. Frontiers in Ecology and Evolution.  ISSN 2296-701X.  6, s 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; Lundin, Knut Erik Aslaksen; Qiao, Shuo Wang & Sollid, Ludvig Magne (2018). Disease-driving CD4+ T cell clonotypes persist for decades in celiac disease. Journal of Clinical Investigation.  ISSN 0021-9738.  128(6), s 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.; Einarsdóttir, Margrét S.; Moore, Kristjan H. S.; Sigurðsson, Ásgeir; Magnúsdóttir, Droplaug N.; Jónsson, Hákon; Snorradóttir, Steinunn; Hovig, Eivind; Møller, Pål; Kockum, Ingrid; Olsson, Tomas; Alfredsson, Lars; Hansen, Thomas F.; Werge, Thomas; Cavalleri, Gianpiero L.; Gilbert, Edmund; Lalueza-Fox, Carles; Walser III, Joe W.; Kristjánsdóttir, Steinunn; Gopalakrishnan, Shyam; Arnadottir, Lilja; Magnússon, Ólafur Þ.; Gilbert, Marcus Thomas Pius; Stefánsson, Kári & Helgason, Agnar (2018). Ancient genomes from Iceland reveal the making of a human population. Science.  ISSN 0036-8075.  360(6392), s 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; Nissen, Anke M.; Morak, Monika; Holinski-Feder, Elke; Martins, Alexandra; Møller, Pål & Hovig, Eivind (2018). Genetic variants of prospectively demonstrated phenocopies in BRCA1/2 kindreds. Hereditary Cancer in Clinical Practice.  ISSN 1731-2302.  16:4, s 1- 14 . doi: 10.1186/s13053-018-0086-0
• Dragly, Svenn-Arne; Mobarhan, Milad; Lepperød, Mikkel Elle; Tennøe, Simen; Fyhn, Marianne; Hafting, Torkel & Malthe-Sørenssen, Anders (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; Wall, Samuel T & Rognes, Marie Elisabeth (2018). In vivo estimation of elastic heterogeneity in an infarcted human heart. Biomechanics and Modeling in Mechanobiology.  ISSN 1617-7959.  s 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; Dillard, Pierre; Theodossiou, Theodossis; Holien, Toril; Sundan, Anders; Inderberg, Else Marit; Smeland, Erlend B; Myklebust, June & Oksvold, Morten Pedersen (2018). Artesunate shows potent anti-tumor activity in B-cell lymphoma. Journal of Hematology & Oncology.  ISSN 1756-8722.  11:23, s 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; Meier, Sonnich; Edvardsen, Rolf & Jentoft, Sissel (2018). Genomic architecture of haddock (Melanogrammus aeglefinus) shows expansions of innate immune genes and short tandem repeats. BMC Genomics.  ISSN 1471-2164.  19(240), s 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; Lyngbakken, Magnus Nakrem; Orstad, Eivind Bjørkan; Enger, Steve; Nygård, Ståle; Røsjø, Helge & Tveit, Arnljot (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.  ISSN 2047-9980.  7(10) . doi: 10.1161/JAHA.118.008562
• Aqrawi, Lara Adnan; Jensen, Janicke Liaaen; Øijordsbakken, Gunnvor; Ruus, Ann-Kristin; Nygård, Ståle; Holden, Marit; Jonsson, Roland; Galtung, Hilde & Skarstein, Kathrine (2018). Signalling pathways identified in salivary glands from primary Sjögren's syndrome patients reveal enhanced adipose tissue development. Autoimmunity.  ISSN 0891-6934.  51(3), s 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), s A199- A223 . doi: 10.1137/15M1020447
• Brynildsen, Jon; Petäjä, Liisa; Pettilä, Ville; Nygård, Ståle; Vaara, Suvi T.; Linko, Rita; Okkonen, Marjatta; Hagve, Tor-Arne; Soininen, Leena; Suojaranta-Ylinen, Raili; Lyngbakken, Magnus Nakrem; Omland, Torbjørn & Røsjø, Helge (2018). The predictive value of NT-proBNP and hs-TnT for risk of death in cardiac surgical patients. Clinical Biochemistry.  ISSN 0009-9120.  53, s 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.; Morak, Monika; Holinski-Feder, Elke; Martins, Alexandra; Møller, Pål & Hovig, Eivind (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
• Lie, Kai Kristoffer; Tørresen, Ole K.; Solbakken, Monica Hongrø; Rønnestad, Ivar; Tooming-Klunderud, Ave; Nederbragt, Alexander Johan; Jentoft, Sissel & Sæle, Øystein (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), s 1- 17 . doi: 10.1186/s12864-018-4570-8 Full text in Research Archive.
• Vodak, Daniel; Lorenz, Susanne; Nakken, Sigve; Aasheim, Lars Birger; Holte, Harald; Bai, Baoyan; Myklebost, Ola; Meza, Leonardo Zepeda & Hovig, Eivind (2018). Sample-Index Misassignment Impacts Tumour Exome Sequencing. Scientific Reports.  ISSN 2045-2322.  8:5307, s 1- 6 . doi: 10.1038/s41598-018-23563-4 Full text in Research Archive.
• Finsberg, Henrik Nicolay; Xi, Ce; Tan, Ju Le; Zhong, Liang; Genet, Martin; Sundnes, Joakim; Lee, Lik Chuan & Wall, Samuel T (2018). Efficient estimation of personalized biventricular mechanical function employing gradient‐based optimization. International Journal for Numerical Methods in Biomedical Engineering.  ISSN 2040-7939.  34(7) . doi: 10.1002/cnm.2982
• Birkeland, Einar Elvbakken; Zhang, Shan; Poduval, Deepak; Geisler, Jürgen; Nakken, Sigve; Vodak, Daniel; Meza, Leonardo Zepeda; Hovig, Eivind; Myklebost, Ola; Knappskog, Stian & Lønning, Per Eystein (2018). Patterns of genomic evolution in advanced melanoma. Nature Communications.  ISSN 2041-1723.  9:2665, s 1- 12 . doi: 10.1038/s41467-018-05063-1 Full text in Research Archive.
• Finsberg, Henrik Nicolay; Balaban, Gabriel; Ross, Stian Balnagown; Håland, Trine Synnøve Fink; Odland, Hans Henrik; Sundnes, Joakim & Wall, Samuel Thomas (2018). Estimating cardiac contraction through high resolution data assimilation of a personalized mechanical model. Journal of Computational Science.  ISSN 1877-7503.  24, s 85- 90 . doi: 10.1016/j.jocs.2017.07.013 Full text in Research Archive. Show summary

  Cardiac computational models, individually personalized, can provide clinicians with useful diagnostic information and aid in treatment planning. A major bottleneck in this process can be determining model parameters to fit created models to individual patient data. However, adjoint-based data assimilation techniques can now rapidly estimate high dimensional parameter sets. This method is used on a cohort of heart failure patients, capturing cardiac mechanical information and comparing it with a healthy control group. Excellent fit (R2 ≥ 0.95) to systolic strains is obtained, and analysis shows a significant difference in estimated contractility between the two groups. Keywords Cardiac mechanics; Adjoint method; Data assimilation; PDE-constrained optimization; Contractility

• Kallhovd, Siri; Maleckar, Mary Margot Catherine & Rognes, Marie Elisabeth (2018). Inverse estimation of cardiac activation times via gradient-based optimization. International Journal for Numerical Methods in Biomedical Engineering.  ISSN 2040-7939.  34(2) . doi: 10.1002/cnm.2919
• Dean, Katharine Rose; Krauer, Fabienne; Walløe, Lars; Lingjærde, Ole Christian; Bramanti, Barbara; Stenseth, Nils Christian & Schmid, Boris Valentijn (2018). Human ectoparasites and the spread of plague in Europe during the Second Pandemic. Proceedings of the National Academy of Sciences of the United States of America.  ISSN 0027-8424.  115(6), s 1304- 1309 . doi: 10.1073/pnas.1715640115
• Danielsen, Håvard Emil; Hveem, Tarjei Sveinsgjerd; Domingo, Enric; Pradhan, Manohar; Kleppe, Andreas; Syvertsen, Rolf Anders; Kostolomov, Ilya; Nesheim, John Arne; Askautrud, Hanne Arenberg; Nesbakken, Arild; Lothe, Ragnhild A; Svindland, Aud; Shephard, Neil; Novelli, Marco; Johnstone, Elaine; Tomlinson, I; Kerr, Rachel & Kerr, David (2018). Prognostic markers for colorectal cancer: Estimating ploidy and stroma. Annals of Oncology.  ISSN 0923-7534.  29(3), s 616- 623 . doi: 10.1093/annonc/mdx794
• Prestgaard, Erik Edvard; Hodnesdal, Christian; Engeseth, Kristian; Erikssen, Jan Emil; Bodegard, Johan; Liestøl, Knut; Gjesdal, Knut; Kjeldsen, Sverre; Grundvold, Irene & Berge, Eivind (2017). Long-term predictors of stroke in healthy middle-aged men. International Journal of Stroke.  ISSN 1747-4930.  13(3), s 292- 300 . doi: 10.1177/1747493017730760
• Timmermann, Viviane; Dejgaard, Lars; Haugaa, Kristina; Edwards, Andrew; Sundnes, Joakim; McCulloch, Andrew D. & Wall, Samuel Thomas (2017). An integrative appraisal of mechano-electric feedback mechanisms in the heart. Progress in Biophysics and Molecular Biology.  ISSN 0079-6107.  130, s 404- 417 . doi: 10.1016/j.pbiomolbio.2017.08.008
• Rand, Knut Dagestad; Grytten, Ivar; Nederbragt, Alexander Johan; Storvik, Geir Olve; Glad, Ingrid Kristine & Sandve, Geir Kjetil (2017). Coordinates and intervals in graph-based reference genomes. BMC Bioinformatics.  ISSN 1471-2105.  18:263, s 1- 8 . doi: 10.1186/s12859-017-1678-9 Full text in Research Archive.
• Romaine, Andreas; Sørensen, Ida Wiig; Zeltz, Cedric; Lu, Ning; Erusappan, Pugazendhi Murugan; Melleby, Arne Olav; Zhang, Lili; Bendiksen, Bård Andre; Robinson, EL; Aronsen, Jan Magnus; Herum, Kate Louise Møller; Danielsen, Håvard Emil; Sjaastad, Ivar; Christensen, Geir Arve & Gullberg, Donald (2017). Overexpression of integrin α11 induces cardiac fibrosis in mice. Acta Physiologica Scandinavica.  ISSN 0001-6772.  222:e13025(2), s 1- 17 . doi: 10.1111/apha.12932
• Paulsen, Geir; Clark, Stuart R; Nordmoen, Bjørn; Nenakhov, Sergey; Andersson, Aron; Cai, Xing & Dahle, Hans Petter (2017). Automated Translation of MATLAB Code to C++ with Performance and Traceability, In Claus-Peter Rückemann & D Vucinic (ed.),  Proceedings of the Eleventh International Conference on Advanced Engineering Computing and Applications in Sciences (ADVCOMP 2017).  International Academy, Research and Industry Association (IARIA).  ISBN 978-1-61208-599-9.  11.  s 50 - 55
• Salvatore, Stefania; Domanska, Diana Ewa; Wood, Mollie; Nordeng, Hedvig Marie Egeland & Sandve, Geir Kjetil (2017). Complex patterns of concomitant medication use: A study among Norwegian women using paracetamol during pregnancy. PLoS ONE.  ISSN 1932-6203.  12(12) . doi: 10.1371/journal.pone.0190101 Full text in Research Archive.

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• Silwal-Pandit, Laxmi; Stålberg, Stina Margrethe; Mermelekas, G; Lothe, Inger Marie Bowitz; Skrede, Martina Landschoof; Dalsgaard, Astrid M.; Helland, Åshild; Skålhegg, Bjørn Steen; Labori, Knut Jørgen; Lingjærde, Ole Christian & Kure, Elin Wenche Hegland (2019). Proteomic Landscape of Pancreatic Ductal Adenocarcinoma.
• Fan, Qiong; Nørgaard, Rikke Christine; Grytten, Ivar; Ulven, Stine Marie; Lucas, Christin; Bindesbøll, Christian; Lemma, Roza Berhanu; Gabrielsen, Odd Stokke; Grønning-Wang, Line Mariann; Nebb, Hilde Irene & Sæther, Thomas (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), s 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 & Schmid, Boris Valentijn (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), s E7894- E7895 . doi: 10.1073/pnas.1810221115
• Blanco Gonzalez, Enrique; Jentoft, Sissel; Hansen, Michael Møller; Knutsen, Halvor; Sodeland, Marte; Mattingsdal, Morten; Stenseth, Nils Christian; Robalo, Joana I. & Jorde, Per Erik (2018). Understanding adaptation in translocating wrasses.
• Tarabichi, Maxime; Martincorena, Iñigo; Gerstung, Moritz; Leroi, Armand M.; Markowetz, Florian; Spellman, Paul; Morris, Quaid D; Lingjærde, Ole Christian; Wedge, David C. & Van Loo, Peter (2018). Neutral tumor evolution?. Nature Genetics.  ISSN 1061-4036.  50(12), s 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; Masegosa, Andres & Brodtkorb, André R. (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; Hafting, Torkel & Malthe-Sørenssen, Anders (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), s 832- 833 . doi: 10.1016/j.eururo.2018.02.023
• Kaveh, Fatemeh; Baumbusch, Lars Oliver; Nebdal, Daniel J.H.; Børresen-Dale, Anne-Lise; Lingjærde, Ole Christian; Edvardsen, Hege; Kristensen, Vessela N. & Solvang, Hiroko Kato (2018). Correction: A systematic comparison of copy number alterations in four types of female cancer. BMC Cancer.  ISSN 1471-2407.  18(80) . doi: 10.1186/s12885-017-3766-7
• Tennøe, Simen (2018). How to model effects of uncertain model parameters with Uncertainpy..
• Bjørkhaug, Steinar Traae; Aanes, Håvard; Medhus, Asle Wilhelm; Skar, Viggo Øystein; Malvik, Stine; Henriksen, Christine; Neupane, Sudan Prasad; Bramness, Jørgen Gustav & Valeur, Jørgen (2018). Tarmfloraendringer hos pasienter med forhøyet alkoholkonsum.
• Alsøe, Lene; Sarno, Antonio; Carracedo Huroz, Sergio; Domanska, Diana Ewa; Dingler, Felix; Lirussi, Lisa; Sengupta, Tanima; Tekin, Nuriye Basdag; Jobert, Laure; Alexandrov, Ludmil B.; Galashevskaya, Anastasia; Rada, Christina; Sandve, Geir Kjetil; Rognes, Torbjørn; Krokan, Hans Einar & Nilsen, Hilde Loge (2017). Uracil Accumulation and Mutagenesis Dominated by Cytosine Deamination in CpG Dinucleotides in Mice Lacking UNG and SMUG1.
• Pettersen, Klas; Holter, Karl Erik; Kehlet, Benjamin; Devor, Anna; Sejnowski, Terrence J.; Dale, Anders; Omholt, Stig William; Ottersen, Ole Petter; Mardal, Kent-Andre & Nagelhus, Erlend Arnulf (2017). Interstitial solute transport in 3D reconstructed neuropil: Diffusion predominates.
• Hagen, Espen; Næss, Solveig; Ness, Torbjørn V & Einevoll, Gaute (2017). Computing brain signals (CBra): Concurrent simulation of network activity, extracellular electric potentials and magnetic fields.
• Næss, Solveig; Ness, Torbjørn V; Halnes, Geir; Halgren, Eric; Dale, Anders M. & Einevoll, Gaute (2017). Biophysical modeling of single neuron contributions to ECoG and EEG signals.
• Hagen, Espen; Næss, Solveig; Ness, Torbjørn V & Einevoll, Gaute (2017). Computing Brain Signals: concurrent simulation of network activity, extracellular electric potentials and magnetic fields.
• Næss, Solveig; Ness, Torbjørn V; Halnes, Geir; Halgren, Eric; Dale, Anders M. & Einevoll, Gaute (2017). Biophysical modeling of single-neuron contributions to ECoG and EEG signals.
• Næss, Solveig (2017). Biophysical Modeling of Single Neuron Contributions to ECoG and EEG signals.
• Hagen, Espen; Næss, Solveig; Ness, Torbjørn V & Einevoll, Gaute (2017). Computing Brain Signals (CBra): Concurrent simulation of network activity, extracellular electric potentials and magnetic fields.
• Næss, Solveig; Ness, Torbjørn V; Halnes, Geir; Halgren, Eric; Dale, Anders & Einevoll, Gaute (2017). Biophysical modeling of single-neuron contributions toECoG, EEG and MEG signals.
• Dragly, Svenn-Arne; Mobarhan, Milad; Solbrå, Andreas Våvang; Tennøe, Simen; Hafreager, Anders; Malthe-Sørenssen, Anders; Fyhn, Marianne; Hafting, Torkel & Einevoll, Gaute (2017). Neuronify: An Educational Simulator for Neural Circuits. Show summary

  Neurons are cells in the brain that are able to rapidly change the electric field across their cell membrane. These changes allow neurons to communicate with each other and is the basis for the complex computations in the brain. Understanding how neurons communicate and the properties of neuronal networks is essential for neuroscience students. Traditionally, students draw networks with pen and paper and qualitatively deduce features of the network by analyzing the static drawings. Here, we present Neuronify, an app that allows students to draw the same networks on a computer or mobile device and run dynamic simulations without programming. The students can test their analysis by running the network and check their predictions against the outcome. Educational software (apps) can improve science education by providing an interactive way of learning about complicated topics that are hard to explain with text and static illustrations. Such software is readily available in many areas of natural science such as physics and electrical engineering. However, few educational apps are available for simulation of neural networks. Neuronify allows the user to easily create and explore neural networks in a plug-and-play simulation environment. The user can drag and drop network elements such as neurons, electrical stimulation tools and recording devices. The components can then easily be connected to one another. Building intuition for how neurons and neural networks behave has been a top priority in designing Neuronify. We aim to provide a low entry point to simulation-based neuroscience. Most undergraduate students do not have the computational experience to create their own neural simulator. Neuronify offers them an opportunity to build and experiment with neural networks in a graphical and easy-to-understand interface. By playing around with the networks, the students can develop a good understanding of their properties. To facilitate the use of Neuronify in teaching, a set of premade common network motifs is provided, performing functions such as input summation and detection of direction of stimulus movement. Neuronify is developed in C++ and QML using the cross-platform application framework Qt. It has been downloaded more than 30,000 times since its launch and is available on smart phones (Android, iOS), tablet computers as well personal computers (Windows, Mac, Linux).

• Tennøe, Simen; Mobarhan, Milad; Dragly, Svenn-Arne; Solbrå, Andreas Våvang & Nederbragt, Alexander Johan (2017). Teaching modelling to first-year biology students. Show summary

  The field of biology relies heavily on computations. This is not well reflected in education and the current undergraduate curriculum has little computational content. This results in a discontinuity between the education received by the students and the problems they face after graduation. The end result is that the students are not equipped to meet the requirements of modern research nor the tasks awaiting them in the industry. To remedy this problem, a new course, BIOS 1100 - Introduction to Modelling in Biology, will be held for the first time at the University of Oslo in fall 2017. Currently, no available book combines biology and programming at an introductory level in a satisfactory way. Most textbooks teach both topics separately or expect the reader to know either biology or programming from before. We have therefore written our own textbook to be used as curriculum in this course. This book aims to teach programming and modelling to first year biology students through examples from biology. The book is based on a philosophy of just-in-time teaching where the programming concepts are introduced just when they are needed to solve the problem in hand. This puts the programming content in an unusual order in comparison to the traditional computer science curriculum while keeping the biology students motivated by the problems they solve. The examples are mainly from the three branches of biology: population dynamics, bioinformatics and evolution. The purpose is to give biology students a practical understanding of programming and mathematical models. This will enable the understanding of mathematical models and encourage critical thinking. Programming allows much more realistic and inspiring problems to be addressed, enabling students to work on current research topics early on. The textbook is written using DocOnce (created by Hans Petter Langtangen), which enables us to compile the book to both LaTeX/PDF, HTML and Jupyter Notebooks.

• Drabløs, Finn; Nygård, Ståle; Petersen, Kjell; Våge, Dag Inge; Willassen, Nils Peder; Hovig, Eivind & Jonassen, Inge (2017). ELIXIR.NO - The national infrastructure for bioinformatics.
• Nederbragt, Alexander Johan (2017). How I got infected by fish genomics - and how you can too.
• Nederbragt, Alexander Johan (2017). Software Carpentry og Data Carpentry: opplæring i bruk og deling av forskningsdata – for forskere, av forskere, ved UiO.
• Nederbragt, Alexander Johan (2017). Teaching Researchers Basic Skills for Computational Research: the Software Carpentry Model.
• Cai, Xing & Langguth, Johannes (2017). Accelerated high-performance computing for computational cardiac electrophysiology.
• Kanduri, Chakravarthi; Domanska, Diana; Hovig, Eivind & Sandve, Geir Kjetil (2017). Genome build information is an essential part of genomic track files. Genome Biology.  ISSN 1465-6906.  18(1) . doi: 10.1186/s13059-017-1312-1

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