Browsing Bergen Open Research Archive by Author "Jonassen, Inge"

Now showing items 1-20 of 53

    • Application of quantitative transcriptomics in evaluating the ex vivo effects of per- and polyfluoroalkyl substances on Atlantic cod (Gadus morhua) ovarian physiology 

      Khan, Essa Ahsan; Zhang, Xiaokang; Hanna, Eileen Marie; Yadetie, Fekadu; Jonassen, Inge; Goksøyr, Anders; Arukwe, Augustine (Journal article; Peer reviewed, 2021)
      Because of their global consumption and persistence, per- and polyfluoroalkyl substances (PFASs), are ubiquitously distributed in the environment, as well as in wildlife and humans. In the present study, we have employed ...

    • The Atlantic salmon genome provides insights into rediploidization 

      Lien, Sigbjørn; Koop, Ben F; Sandve, Simen Rød; Miller, Jason R.; Kent, Matthew Peter; Nome, Torfinn; Hvidsten, Torgeir Rhoden; Leong, Jong; Minkley, David R.; Zimin, Aleksey; Grammes, Fabian; Grove, Harald; Gjuvsland, Arne Bjørke; Walenz, Brian; Hermansen, Russell A.; von Schalburg, Kristian R.; Rondeau, Eric; Genova, Alex Di; Antony Samy, Jeevan Karloss; Vik, Jon Olav; Vigeland, Magnus Dehli; Caler, Lis; Grimholt, Unni; Jentoft, Sissel; Våge, Dag Inge; de Jong, Pieter J.; Moen, Thomas; Baranski, Matthew; Palti, Yniv; Smith, Douglas W.; Yorke, James A.; Nederbragt, Alexander J.; Tooming-Klunderud, Ave; Jakobsen, Kjetill Sigurd; Jiang, Xuanting; Fan, Dingding; Hu, Yan; Liberles, David A.; Vidal, Rodrigo; Iturra, Patricia; Jones, Steven J.M.; Jonassen, Inge; Maass, Alejandro; Omholt, Stig William; Davidson, William S (Peer reviewed; Journal article, 2016-05)
      The whole-genome duplication 80 million years ago of the common ancestor of salmonids (salmonid-specific fourth vertebrate whole-genome duplication, Ss4R) provides unique opportunities to learn about the evolutionary fate ...

    • The bio.tools registry of software tools and data resources for the life sciences 

      Ison, Jon; Ienasescu, Hans-Ioan; Chmura, Piotr; Rydza, Emil; Ménager, Hervé; Kalaš, Matúš; Schwämmle, Veit; Grüning, Björn A.; Beard, Niall; Lopez, Rodrigo; Duvaud, Severine; Stockinger, Heinz; Persson, Bengt; Svobodová Vařeková, Radka; Raček, Tomáš; Vondrášek, Jiří; Peterson, Hedi; Salumets, Ahto; Jonassen, Inge; et al., +18 authors (total 37) (Peer reviewed; Journal article, 2019-08-12)
      Bioinformaticians and biologists rely increasingly upon workflows for the flexible utilization of the many life science tools that are needed to optimally convert data into knowledge. We outline a pan-European enterprise ...

    • BioXSD: the common data-exchange format for everyday bioinformatics web services 

      Kalaš, Matúš; Puntervoll, Pål; Joseph, Alexandre; Bartaševičiūtė, Edita; Töpfer, Armin; Venkataraman, Prabakar; Pettifer, Steve; Bryne, Jan Christian; Ison, Jon; Blanchet, Christophe; Rapacki, Kristoffer; Jonassen, Inge (Peer reviewed; Journal article, 2010)
      Motivation: The world-wide community of life scientists has access to a large number of public bioinformatics databases and tools, which are developed and deployed using diverse technologies and designs. More and more of ...

    • Characteristics of 454 pyrosequencing data—enabling realistic simulation with flowsim 

      Balzer, Susanne Mignon; Malde, Ketil; Lanzén, Anders; Sharma, Animesh; Jonassen, Inge (Peer reviewed; Journal article, 2010)
      Motivation: The commercial launch of 454 pyrosequencing in 2005was a milestone in genome sequencing in terms of performance and cost. Throughout the three available releases, average read lengths have increased to ∼500 ...

    • Characterization of the 18s rRNA gene for designing universal eukaryote specific primers 

      Hadziavdic, Kenan; Lekang, Katrine; Lanzén, Anders; Jonassen, Inge; Thompson, Eric; Troedsson, Christofer (Peer reviewed; Journal article, 2014-02-07)
      High throughput sequencing technology has great promise for biodiversity studies. However, an underlying assumption is that the primers used in these studies are universal for the prokaryotic or eukaryotic groups of interest. ...

    • The chemical defensome of five model teleost fish 

      Eide, Marta; Zhang, Xiaokang; Karlsen, Odd André; Goldstone, Jared V.; Stegeman, John; Jonassen, Inge; Goksøyr, Anders (Journal article; Peer reviewed, 2021)
      How an organism copes with chemicals is largely determined by the genes and proteins that collectively function to defend against, detoxify and eliminate chemical stressors. This integrative network includes receptors and ...

    • Common gene expression signatures in Parkinson’s disease are driven by changes in cell composition 

      Sanchez Nido, Gonzalo; Dick, Fiona; Toker, Lilah; Petersen, Kjell; Alves, Guido Werner; Tysnes, Ole-Bjørn; Jonassen, Inge; Haugarvoll, Kristoffer; Tzoulis, Charalampos (Journal article; Peer reviewed, 2020-04-21)
      The etiology of Parkinson’s disease is largely unknown. Genome-wide transcriptomic studies in bulk brain tissue have identified several molecular signatures associated with the disease. While these studies have the potential ...

    • A Comparative Analysis of Feature Selection Methods for Biomarker Discovery in Study of Toxicant-Treated Atlantic Cod (Gadus Morhua) Liver 

      Zhang, Xiaokang; Jonassen, Inge (Communications in Computer and Information Science; 1056, Chapter; Peer reviewed, 2019)
      Univariate and multivariate feature selection methods can be used for biomarker discovery in analysis of toxicant exposure. Among the univariate methods, differential expression analysis (DEA) is often applied for its ...

    • Comprehensive characterization of copy number variation (CNV) called from array, long- and short-read data 

      Lavrichenko, Ksenia; Johansson, Stefan; Jonassen, Inge (Journal article; Peer reviewed, 2021)
      Background SNP arrays, short- and long-read genome sequencing are genome-wide high-throughput technologies that may be used to assay copy number variants (CNVs) in a personal genome. Each of these technologies comes with ...

    • CREST – Classification Resources for Environmental Sequence Tags 

      Lanzén, Anders; Jørgensen, Steffen Leth; Huson, Daniel H.; Gorfer, Markus; Grindhaug, Svenn Helge; Jonassen, Inge; Øvreås, Lise; Urich, Tim (Peer reviewed; Journal article, 2012-11-08)
      Sequencing of taxonomic or phylogenetic markers is becoming a fast and efficient method for studying environmental microbial communities. This has resulted in a steadily growing collection of marker sequences, most notably ...

    • Disentangling genetic and epigenetic determinants of ultrafast adaptation 

      Gjuvsland, Arne Bjørke; Zörgö, Enikö Beatrix; Antony Samy, Jeevan Karloss; Stenberg, Simon; Demirsoy, Ibrahim H; Roque, Francisco; Maciaszczyk-Dziubinska, Ewa; Migocka, Magdalena; Alonso-Perez, Elisa; Zackrisson, Martin; Wysocki, Robert; Tamas, Markus J; Jonassen, Inge; Omholt, Stig William; Warringer, Jonas (Peer reviewed; Journal article, 2016)
      A major rationale for the advocacy of epigenetically mediated adaptive responses is that they facilitate faster adaptation to environmental challenges. This motivated us to develop a theoretical–experimental framework for ...

    • Early response evaluation by single cell signaling profiling in acute myeloid leukemia 

      Tislevoll, Benedicte Sjo; Hellesøy, Monica; Fagerholt, Oda Helen Eck; Gullaksen, Stein-Erik; Srivastava, Aashish; Birkeland, Even; Kleftogiannis, Dimitrios; Ayuda Duran, Pilar; Piechaczyk, Laure Isabelle; Tadele, Dagim Shiferaw; Skavland, Jørn; Panagiotis, Baliakas; Hovland, Randi; Andresen, Vibeke; Seternes, Ole Morten; Tvedt, Tor Henrik Anderson; Aghaeepour, Nima; Gavasso, Sonia; Porkka, Kimmo; Jonassen, Inge; Fløisand, Yngvar; Enserink, Jorrit; Blaser, Nello; Gjertsen, Bjørn Tore (Journal article; Peer reviewed, 2023)
      Aberrant pro-survival signaling is a hallmark of cancer cells, but the response to chemotherapy is poorly understood. In this study, we investigate the initial signaling response to standard induction chemotherapy in a ...

    • EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats 

      Ison, Jon; Kalaš, Matúš; Jonassen, Inge; Bolser, Dan; Uludag, Mahmut; McWilliam, Hamish; Malone, James; Lopez, Rodrigo; Pettifer, Steve; Rice, Peter (Peer reviewed; Journal article, 2013)
      Motivation: Advancing the search, publication and integration of bioinformatics tools and resources demands consistent machine-understandable descriptions. A comprehensive ontology allowing such descriptions is therefore ...

    • The EMBRACE web service collection 

      Pettifer, Steve; Ison, Jon; Kalaš, Matúš; Thorne, David; McDermott, Philip; Jonassen, Inge; Ali, Liaquat; Fernandez, Jose M; Rodriguez, Jose M; Pisano, David G; Blanchet, Christophe; Uludag, Mahmut; Rice, Peter; Bartaseviciute, Edita; Rapacki, Kristoffer; Hekkelman, Maarten; Sand, Olivier; Stockinger, Heinz; Clegg, Andrew B; Bongcam-Rudloff, Eric; Salzemann, Jean; Breton, Vincent; Attwood, Teresa K; Cameron, Graham; Vriend, Gert (Peer reviewed; Journal article, 2010-05-10)
      The EMBRACE (European Model for Bioinformatics Research and Community Education) web service collection is the culmination of a 5-year project that set out to investigate issues involved in developing and deploying web ...

    • An Ensemble Feature Selection Framework Integrating Stability 

      Zhang, Xiaokang; Jonassen, Inge (Chapter; Peer reviewed, 2019)
      Ensemble feature selection has drawn more and more attention in recent years. There are mainly two strategies for ensemble feature selection, namely data perturbation and function perturbation. Data perturbation performs ...

    • Evaluation of a eukaryote phylogenetic microarray for environmental monitoring of marine sediments 

      Lekang, Katrine; Lanzén, Anders; Jonassen, Inge; Thompson, Eric; Troedsson, Christofer (Journal article; Peer reviewed, 2020)
      Increased exploitation of resources in sensitive marine ecosystems emphasizes the importance of knowledge regarding ecological impacts. However, current bio-monitoring practices are limited in terms of target-organisms and ...

    • Exome Sequencing and Genetic Testing for MODY 

      Johansson, Stefan; Irgens, Henrik; Chudasama, Kishan K.; Molnes, Janne; Aerts, Jan; Knappskog, Per; Njølstad, Pål Rasmus; Roque, Francisco S.; Jonassen, Inge; Molven, Anders (Peer reviewed; Journal article, 2012-05-25)
      Context: Genetic testing for monogenic diabetes is important for patient care. Given the extensive genetic and clinical heterogeneity of diabetes, exome sequencing might provide additional diagnostic potential when standard ...

    • Filtering duplicate reads from 454 pyrosequencing data 

      Balzer, Susanne Mignon; Malde, Ketil; Grohme, Markus A.; Jonassen, Inge (Peer reviewed; Journal article, 2013)
      Motivation: Throughout the recent years, 454 pyrosequencing has emerged as an efficient alternative to traditional Sanger sequencing and is widely used in both de novo whole-genome sequencing and metagenomics. Especially ...

    • GBA2 mutations cause a Marinesco-Sjogren-like syndrome: Genetic and biochemical studies 

      Haugarvoll, Kristoffer; Johansson, Stefan; Rodriguez, Carlos E.; Boman, Helge; Haukanes, Bjørn Ivar; Bruland, Ove; Roque, Francisco; Jonassen, Inge; Blomqvist, Maria; Telstad, Wenche; Månsson, Jan-Eric; Knappskog, Per; Bindoff, Laurence (Peer reviewed; Journal article, 2017-01-04)
      Background: With the advent new sequencing technologies, we now have the tools to understand the phenotypic diversity and the common occurrence of phenocopies. We used these techniques to investigate two Norwegian families ...