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Recent Submissions

  • Editing to Eulerian Graphs 

    Dabrowski, Konrad K.; Golovach, Petr; van' t Hof, Pim; Paulusma, Daniël (Schloss Dagstuhl – Leibniz-Zentrum für Informatik GmbH, 2014)
    We investigate the problem of modifying a graph into a connected graph in which the degree of each vertex satisfies a prescribed parity constraint. Let ea, ed and vd denote the operations edge addition, edge deletion and ...
    Conference object
  • Connecting Vertices by Independent Trees 

    Basavaraju, Manu; Fomin, Fedor; Golovach, Petr; Saurabh, Saket (Schloss Dagstuhl – Leibniz-Zentrum für Informatik GmbH, 2014)
    We study the paramereteized complexity of the following connectivity problem. For a vertex subset U of a graph G, trees T1, . . . , Ts of G are completely independent spanning trees of U if each of them contains U , and ...
    Conference object
  • Largest chordal and interval subgraphs faster than 2n 

    Bliznets, Ivan; Fomin, Fedor; Pilipczuk, Michal Pawel; Villanger, Yngve (Springer, 2015-08-22)
    We prove that in a graph with n vertices, induced chordal and interval subgraphs with the maximum number of vertices can be found in time O(2λn) for some λ< 1. These are the first algorithms breaking the trivial 2nnO(1) ...
    Journal article
  • Non-Constructivity in Kan Simplicial Sets 

    Bezem, Marc; Coquand, Thierry; Parmann, Erik (Dagstuhl Publishing, 2015)
    We give an analysis of the non-constructivity of the following basic result: if X and Y are simplicial sets and Y has the Kan extension property, then Y X also has the Kan extension property. By means of Kripke countermodels ...
    Journal article
  • Investigating Streamless Sets 

    Parmann, Erik (Dagstuhl Publishing, 2015)
    In this paper we look at streamless sets, recently investigated by Coquand and Spiwack. A set is streamless if every stream over that set contain a duplicate. It is an open question in constructive mathematics whether the ...
    Journal article
  • Case Studies in Constructive Mathematics 

    Parmann, Erik (The University of Bergen, 2016-01-22)
    The common theme in this thesis is the study of constructive provability: in particular we investigate aspects of finite sets and Kan simplicial sets from a constructive perspective. There are numerous definitions of ...
    Doctoral thesis
  • Generating software for MUB complementary sequence constructions 

    Roodashty, Hanieh (The University of Bergen, 2015-11-18)
    This master thesis has been performed at the Department of Informatics, University of Bergen between February and November 2015. The work has been supervised by Professor Matthew G. Parker as a part of the research interest ...
    Master thesis
  • A 43k Kernel for Planar Dominating Set using Computer-Aided Reduction Rule Discovery 

    Halseth, Johan Torås (The University of Bergen, 2016-02-15)
    In this thesis we explore the technique of Region Decomposition for finding kernels for Planar Dominating Set. We redefine some concepts used in earlier work, fixing some ambiguities on the way. From those concepts we ...
    Master thesis
  • Axis patterning by BMPs: cnidarian network reveals evolutionary constraints 

    Genikhovich, Grigory; Fried, Patrick; Prünster, M. Mandela; Schinko, Johannes B.; Gilles, Anna F.; Fredman, David; Meier, Karin; Iber, Dagmar; Technau, Ulrich (Elsevier, 2015-03)
    BMP signaling plays a crucial role in the establishment of the dorso-ventral body axis in bilaterally symmetric animals. However, the topologies of the bone morphogenetic protein (BMP) signaling networks vary drastically ...
    Journal article
  • Efficient CRISPR-Cas9-mediated generation of knockin human pluripotent stem cells lacking undesired mutations at the targeted locus 

    Merkle, Florian T.; Neuhausser, Werner M.; Santos, David; Valen, Eivind; Gagnon, James A.; Maas, Kristi; Sandoe, Jackson; Schier, Alexander F.; Eggan, Kevin (Elsevier, 2015-05)
    The CRISPR-Cas9 system has the potential to revolutionize genome editing in human pluripotent stem cells (hPSCs), but its advantages and pitfalls are still poorly understood. We systematically tested the ability of CRISPR-Cas9 ...
    Journal article
  • FreeContact: Fast and free software for protein contact prediction from residue co-evolution 

    Kaján, László; Hopf, Thomas A.; Kalaš, Matúš; Marks, Debora S.; Rost, Burkhard (BioMed Central, 2014-03-26)
    Background: 20 years of improved technology and growing sequences now renders residue-residue contact constraints in large protein families through correlated mutations accurate enough to drive de novo predictions of protein ...
    Journal article
  • Independent Set on P5-free graphs, an empirical study 

    Haug, Håvard Karim (The University of Bergen, 2015-11-20)
    We implement the recent polynomial time algorithm for the independent set problem on P5-free graphs, and study the performance of this algorithm on graphs of size up to 50. Our empirical results show that the algorithm ...
    Master thesis
  • Parameterized Graph Modification Algorithms 

    Drange, Pål Grønås (The University of Bergen, 2015-12-10)
    Graph modification problems form an important class of algorithmic problems in computer science. In this thesis, we study edge modification problems towards classes related to chordal graphs, with the main focus on trivially ...
    Doctoral thesis
  • Security in cloud computing and virtual environments 

    Aarseth, Raymond (The University of Bergen, 2015-09-14)
    Cloud computing is a big buzzwords today. Just watch the commercials on TV and I can promise that you will hear the word cloud service at least once. With the growth of cloud technology steadily rising, and everything ...
    Master thesis
  • 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 (Oxford University Press, 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 ...
    Journal article
  • 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 (Oxford University Press, 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 ...
    Journal article
  • Efforts towards accessible and reliable bioinformatics 

    Kalaš, Matúš (The University of Bergen, 2015-11-19)
    The aim of the presented work was contributing to making scientific computing more accessible, reliable, and thus more efficient for researchers, primarily computational biologists and molecular biologists. Many approaches ...
    Doctoral thesis
  • Towards a Secure Framework for mHealth. A Case Study in Mobile Data Collection Systems 

    Gejibo, Samson Hussien (The University of Bergen, 2015-11-05)
    The rapid growth in the mobile communications technology and wide cellular coverage created an opportunity to satisfy the demand for low-cost health care solutions. Mobile Health (a.k.a. mHealth) is a promising health ...
    Doctoral thesis
  • Interactive Visual Analysis of Streaming Data 

    Smestad, Geir (Universitetet i Bergen (UiB), 2014-09-23)
    Interactive Visual Analysis (IVA) has proven to be a robust set of methods for visually exploring complex data sets and generating hypotheses from data. Datasets and techniques where the temporal aspect is central has been ...
    Master thesis
  • The genome sequence of Atlantic cod reveals a unique immune system 

    Star, Bastiaan; Nederbragt, Alexander Johan; Jentoft, Sissel; Grimholt, Unni; Malmstrøm, Martin; Gregers, Tone Fredsvik; Rounge, Trine Ballestad; Paulsen, Jonas; Solbakken, Monica Hongrø; Sharma, Animesh; Wetten, Ola Frang; Lanzén, Anders; Winer, Roger; Knight, James; Vogel, Jan-Hinnerk; Aken, Bronwen; Andersen, Øivind; Lagesen, Karin; Tooming-Klunderud, Ave; Edvardsen, Rolf; Kirubakaran, G. Tina; Espelund, Mari; Nepal, Chirag; Previti, A. Christopher; Karlsen, Bård Ove; Moum, Truls; Skage, Morten; Berg, Paul Ragnar; Gjøen, Tor; Kuhl, Heiner; Thorsen, Jim; Malde, Ketil; Reinhardt, Richard; Du, Lei; Johansen, Steinar Daae; Searle, Steve; Lien, Sigbjørn; Nilsen, Frank; Jonassen, Inge; Omholt, Stig W; Stenseth, Nils Christian; Jakobsen, Kjetill Sigurd (Nature Publishing Group, 2011-09)
    Atlantic cod (Gadus morhua) is a large, cold-adapted teleost that sustains long-standing commercial fisheries and incipient aquaculture. Here we present the genome sequence of Atlantic cod, showing evidence for complex ...
    Journal article

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