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Recent Submissions

  • WEBnm@ v2.0: Web server and services for comparing protein flexibility 

    Tiwari, Sandhya Premnath; Fuglebakk, Edvin; Hollup, Siv Midtun; Skjærven, Lars; Cragnolini, Tristan; Grindhaug, Svenn Helge; Tekle, Kidane M; Reuter, Nathalie (BioMed Central, 2014-12-30)
    Background: Normal mode analysis (NMA) using elastic network models is a reliable and cost-effective computational method to characterise protein flexibility and by extension, their dynamics. Further insight into the ...
    Journal article
  • Tools and data services registry: a community effort to document bioinformatics resources 

    Ison, Jon; Rapacki, Kristoffer; Ménager, Hervé; Kalaš, Matúš; et al., 69 authors (Oxford University Press, 2015-11-03)
    Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora of databases ...
    Journal article
  • Using registries to integrate bioinformatics tools and services into workbench environments 

    Ménager, Hervé; Kalaš, Matúš; Rapacki, Kristoffer; Ison, Jon (Springer, 2015)
    The diversity and complexity of bioinformatics resources presents significant challenges to their localisation, deployment and use, creating a need for reliable systems that address these issues. Meanwhile, users demand ...
    Journal article
  • MultiPath TCP-communication (in NorNet Core) 

    Ingebretsen, Kristian Bøckmann; Selvik, Daniel (The University of Bergen, 2016-05-31)
    Technology is constantly evolving, and we are currently witnessing a digital revolution with a tremendous growth of interconnected devices. The scale of the Internet and the amount of transported data is constantly ...
    Master thesis
  • Algorithms for Linearly Ordered Boolean Formulas 

    Egeland, Christian (The University of Bergen, 2016-06-30)
    This thesis considers a class of propositional boolean formulas on which various problems related to satisfiability are efficiently solvable by a dynamic programming algorithm. It mainly consists of two larger parts: the ...
    Master thesis
  • Incompleteness of the Inference System BNeg 

    Golid, Kjetil Midtgarden (The University of Bergen, 2016-05-31)
    Any propositional discourse can be represented as a propositional theory in a specific form in such a way that the theory is inconsistent if and only if the discourse is paradoxical. Propositional theories in this form ...
    Master thesis
  • SelGenes: a tool for selecting marker genes in heterogeneous samples 

    Samdal, Kristian Brakstad (The University of Bergen, 2016-05-31)
    SelGenes is a tool for selecting marker genes for the dominating cell type in heterogeneous samples. Based on a framework from an existing algorithm, SelGenes selects cell-type specific marker genes for the dominating ...
    Master thesis
  • Using Smart Cards to Mitigate Security Threats on Mobile Devices 

    Sivertsgård, Henrik Mathisen (The University of Bergen, 2016-05-31)
    This master thesis developed and tested the idea that smart cards are able to help mitigate security threats on mobile devices that are handling sensitive data. Investigating the limitations of smart cards is a fundamental ...
    Master thesis
  • Statistical and Algebraic Properties of DES 

    Fauskanger, Stian; Semaev, Igor A. (Springer, 2016)
    D. Davies and S. Murphy found that there are at most 660 different probability distributions on the output from any three adjacent S-boxes after 16 rounds of DES. In this paper it is shown that there are only 72 different ...
    Chapter
  • Towards Correct Modelling and Model Transformation in DPF 

    Wang, Xiaoliang (The University of Bergen, 2016-06-14)
    Model-driven engineering (MDE) is a model-centric software development methodology. It promotes models as first-class entities in software de- velopment. Models are used to represent software along software devel- opment ...
    Doctoral thesis
  • Model Checking Healthcare Workflows Using Alloy 

    Wang, Xiaoliang; Rutle, Adrian (Elsevier B.V., 2014)
    Workflows are used to organize business processes, and workflow management tools are used to guide users in which order these processes should be performed. These tools increase organizational efficiency and enable users ...
    Conference object
  • High-performance design patterns for modern Fortran 

    Haveraaen, Magne; Morris, Karla; Rouson, Damian; Radhakrishnan, Hari; Carson, Clayton (Hindawi, 2015)
    This paper presents ideas for using coordinate-free numerics in modern Fortran to achieve code flexibility in the partial differential equation (PDE) domain. We also show how Fortran, over the last few decades, has changed ...
    Journal article
  • The Ontology Lookup Service: bigger and better 

    Côté, Richard G.; Reisinger, Florian; Martens, Lennart; Barsnes, Harald; Vizcaíno, Juan Antonio; Hermjakob, Henning (Oxford University Press, 2010-05-11)
    The Ontology Lookup Service (OLS; http://www.ebi .ac.uk/ols) has been providing several means to query, browse and navigate biomedical ontologies and controlled vocabularies since it first went into production 4 years ...
    Journal article
  • Enumerating minimal connected dominating sets in graphs of bounded chordality 

    Golovach, Petr; Heggernes, Pinar; Kratsch, Dieter (Dagstuhl Publishing, 2015)
    Listing, generating or enumerating objects of specified type is one of the principal tasks in algorithmics. In graph algorithms one often enumerates vertex subsets satisfying a certain property. We study the enumeration ...
    Conference object
  • Computing cutwidth and pathwidth of semi-complete digraphs via degree orderings 

    Pilipczuk, Michal Pawel (Dagstuhl Publishing, 2013)
    The notions of cutwidth and pathwidth of digraphs play a central role in the containment theory for tournaments, or more generally semi-complete digraphs, developed in a recent series of papers by Chudnovsky, Fradkin, Kim, ...
    Conference object
  • The Proteomics Identifications database: 2010 update 

    Vizcaíno, Juan Antonio; Côté, Richard G.; Reisinger, Florian; Barsnes, Harald; Foster, JM; Rameseder, Jonathan; Hermjakob, Henning; Martens, Lennart (Oxford University Press (OUP), 2009-11-11)
    The Proteomics Identifications database (PRIDE, <a href="http://www.ebi.ac.uk/pride"target="blank">http://www.ebi.ac.uk/pride) at the European Bioinformatics Institute has become one of the main repositories of mass ...
    Journal article
  • Chromatin and epigenetic features of long-range gene regulation 

    Harmston, Nathan; Lenhard, Boris (Oxford University Press (OUP), 2013-06-13)
    The precise regulation of gene transcription during metazoan development is controlled by a complex system of interactions between transcription factors, histone modifications and modifying enzymes and chromatin conformation. ...
    Journal article
  • Subexponential-time parameterized algorithm for Steiner tree on planar graphs 

    Pilipczuk, Marcin; Pilipczuk, Michal Pawel; van Leeuwen, Erik Jan; Sankowski, Piotr (Dagstuhl Publishing, 2013)
    The well-known bidimensionality theory provides a method for designing fast, subexponential-time parameterized algorithms for a vast number of NP-hard problems on sparse graph classes such as planar graphs, bounded genus ...
    Conference object
  • 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 (Oxford University Press (OUP), 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 ...
    Journal article
  • The Genomic HyperBrowser: an analysis web server for genome-scale data 

    Sandve, Geir Kjetil; Gundersen, Sveinung; Johansen, Morten; Glad, Ingrid Kristine; Gunathasan, Krishanthi; Holden, Lars; Holden, Marit; Liestøl, Knut; Nygård, Ståle; Nygaard, Vegard; Paulsen, Jonas; Rydbeck, Halfdan; Trengereid, Kai; Clancy, Trevor; Drabløs, Finn; Ferkingstad, Egil; Kalaš, Matúš; Lien, Tonje Gulbrandsen; Rye, Morten Beck; Frigessi, Arnoldo; Hovig, Johannes Eivind (Oxford University Press (OUP), 2013-04-30)
    The immense increase in availability of genomic scale datasets, such as those provided by the ENCODE and Roadmap Epigenomics projects, presents unprecedented opportunities for individual researchers to pose novel falsifiable ...
    Journal article

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