Recent Submissions

  • 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
  • JASPAR 2014: An extensively expanded and updated open-access database of transcription factor binding profiles 

    Mathelier, Anthony; Zhao, Xiaobei; Zhang, Allen W.; Parcy, François; Worsley-Hunt, Rebecca; Arenillas, David J.; Buchman, Sorana; Chen, Chih-yu; Chou, Alice; Ienasescu, Hans; Lim, Jonathan; Shyr, Casper; Tan, Ge; Zhou, Michelle; Lenhard, Boris; Sandelin, Albin; Wasserman, Wyeth W. (Oxford University Press, 2014-01)
    JASPAR (http://jaspar.genereg.net) is the largest open-access database of matrix-based nucleotide profiles describing the binding preference of transcription factors from multiple species. The fifth major release greatly ...
    Journal article
  • Skaping av meirverdi gjennom opne data om kollektivtrafikk 

    Bergheim, Livar (The University of Bergen, 2015-05-04)
    Tema i denne oppgåva er opne data, med ei avgrensing mot kollektivtrafikkdata. Djupnestudien er retta mot verksemda til Skyss, det fylkeskommunale kollektivtrafikkselskapet i Hordaland. Omgrepet opne data" inneber ...
    Master thesis
  • SMS One-Time Passwords, Security in Two-Factor Authentication 

    Eide, Jan-Erik Lothe (The University of Bergen, 2015-05-29)
    In the past decade, the low price and ease of generating and sending large amounts of SMS have made it possible for many online services to create strong and affordable authentication systems. With the growth of smartphones ...
    Master thesis
  • Implementasjon av attributtbasert tilgangskontroll i elektroniske helsesystemer 

    Kristensen, André Sæ (The University of Bergen, 2015-05-28)
    Tilgangskontroll er et av de viktigste temaene innenfor informasjonssikkerhet[10]. Sensitiv data bør bare kunne aksesseres av autoriserte brukere eller programmer. Denne oppgaven har som hovedmål å undersøke den nåværende ...
    Master thesis
  • A Survey of Linear-Programming Guided Branching Parameterized Algorithms for Vertex Cover, with Experimental Results 

    Urhaug, Tobias Sørensen (The University of Bergen, 2015-06-01)
    A survey of FPT algorithms for Vertex Cover, parameterized by an above guarantee parameter.
    Master thesis
  • Maximum number of objects in graph classes. 

    Hellestø, Marit Kristine Astad (The University of Bergen, 2015-05-31)
    The focus of this thesis is the study and implementation of two exact exponential time algorihms. These algorihms finds and lists the number of minimal dominating sets and the number of minimal subset feedback vertex ...
    Master thesis
  • Projective Simulation compared to reinforcement learning 

    Bjerland, Øystein Førsund (The University of Bergen, 2015-06-01)
    This thesis explores the model of projective simulation (PS), a novel approach for an artificial intelligence (AI) agent. The model of PS learns by interacting with the environment it is situated in, and allows for ...
    Master thesis
  • Choice of parameter for DP-based FPT algorithms: four case studies 

    Sæther, Sigve Hortemo (The University of Bergen, 2015-09-07)
    This thesis studies dynamic programming algorithms and structural parameters used when solving computationally hard problems. In particular, we look at algorithms that make use of structural decompositions to overcome ...
    Doctoral thesis
  • Exact algorithms for MAX-2SAT and MAX-3SAT via multidimensional matrix multiplication 

    Petkevich, Yevgheni (The University of Bergen, 2015-06-01)
    In this thesis it is showed how an $O(n^{4-\epsilon})$ algorithm for the cube multiplication problem (that is defined in the thesis) would imply a faster than naive $O^{*}(2^{n(1-\frac{\epsilon}{4})})$ algorithm for the ...
    Master thesis
  • Localizing Cell Towers from Crowdsourced Measurements 

    Rusvik, Johan Alexander Nordstrand (The University of Bergen, 2015-06-01)
    Today, several internet sites exist that aim to provide the locations and number of cellular network antennas worldwide. For example [1],[2] and [3]. What makes this task difficult to accomplish is the lack of information ...
    Master thesis

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