Department of Informatics
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Towards Correct Modelling and Model Transformation in DPF
(The University of Bergen, 20160614)Modeldriven engineering (MDE) is a modelcentric software development methodology. It promotes models as firstclass entities in software de velopment. Models are used to represent software along software devel opment ...Doctoral thesis 
Model Checking Healthcare Workflows Using Alloy
(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 
Highperformance design patterns for modern Fortran
(Hindawi, 2015)This paper presents ideas for using coordinatefree 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
(Oxford University Press, 20100511)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
(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 semicomplete digraphs via degree orderings
(Dagstuhl Publishing, 2013)The notions of cutwidth and pathwidth of digraphs play a central role in the containment theory for tournaments, or more generally semicomplete digraphs, developed in a recent series of papers by Chudnovsky, Fradkin, Kim, ...Conference object 
The Proteomics Identifications database: 2010 update
(Oxford University Press (OUP), 20091111)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 longrange gene regulation
(Oxford University Press (OUP), 20130613)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 
Subexponentialtime parameterized algorithm for Steiner tree on planar graphs
(Dagstuhl Publishing, 2013)The wellknown bidimensionality theory provides a method for designing fast, subexponentialtime parameterized algorithms for a vast number of NPhard problems on sparse graph classes such as planar graphs, bounded genus ...Conference object 
The EMBRACE web service collection
(Oxford University Press (OUP), 20100510)The EMBRACE (European Model for Bioinformatics Research and Community Education) web service collection is the culmination of a 5year project that set out to investigate issues involved in developing and deploying web ...Journal article 
The Genomic HyperBrowser: an analysis web server for genomescale data
(Oxford University Press (OUP), 20130430)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 
Variants of plane diameter completion
(Dagstuhl Publishing, 2015)The Plane Diameter Completion problem asks, given a plane graph G and a positive integer d, if it is a spanning subgraph of a plane graph H that has diameter at most d. We examine two variants of this problem where the ...Conference object 
Tight bounds for parameterized complexity of Cluster Editing
(Dagstuhl Publishing, 2013)In the Correlation Clustering problem, also known as Cluster Editing, we are given an undirected graph G and a positive integer k; the task is to decide whether G can be transformed into a cluster graph, i.e., a disjoint ...Conference object 
Minimum Fillin of Sparse Graphs: Kernelization and Approximation
(Dagstuhl Publishing, 2011)The Minimum Fillin problem is to decide if a graph can be triangulated by adding at most k edges. The problem has important applications in numerical algebra, in particular in sparse matrix computations. We develop ...Conference object 
Finding Induced Subgraphs via Minimal Triangulations
(Dagstuhl Publishing, 2010)Potential maximal cliques and minimal separators are combinatorial objects which were introduced and studied in the realm of minimal triangulation problems in cluding Minimum Fillin and Treewidth. We discover unexpected ...Conference object 
Subexponential Algorithms for Partial Cover Problems
(Dagstuhl Publishing, 2009)Partial Cover problems are optimization versions of fundamental and well studied problems like {\sc Vertex Cover} and {\sc Dominating Set}. Here one is interested in covering (or dominating) the maximum number of edges (or ...Conference object 
Finding even subgraphs even faster
(Dagstuhl Publishing, 2015)Problems of the following kind have been the focus of much recent research in the realm of parameterized complexity: Given an input graph (digraph) on n vertices and a positive integer parameter k, find if there exist k ...Conference object 
Maximum matching width: New characterizations and a fast algorithm for dominating set
(Dagstuhl Publishing, 2015)We give alternative definitions for maximum matching width, e.g., a graph G has mmw(G) <= k if and only if it is a subgraph of a chordal graph H and for every maximal clique X of H there exists A,B,C \subseteq X with A ...Conference object 
Fast biclustering by dual parameterization
(Dagstuhl Publishing, 2015)We study two clustering problems, Starforest Editing, the problem of adding and deleting edges to obtain a disjoint union of stars, and the generalization Bicluster Editing. We show that, in addition to being NPhard, none ...Conference object 
Parameterized complexity of secluded connectivity problems
(Dagstuhl Publishing, 2015)The Secluded Path problem introduced by Chechik et al. in [ESA 2013] models a situation where a sensitive information has to be transmitted between a pair of nodes along a path in a network. The measure of the quality of ...Conference object