Browsing Department of Informatics by Document Types "Peer reviewed"

Now showing items 1-20 of 516

    • A (2 + ε)-Factor Approximation Algorithm for Split Vertex Deletion 

      Lokshtanov, Daniel; Misra, Pranabendu; Panolan, Fahad; Philip, Geevarghese; Saurabh, Saket (Journal article; Peer reviewed, 2020)
      In the Split Vertex Deletion (SVD) problem, the input is an n-vertex undirected graph G and a weight function w: V(G) → ℕ, and the objective is to find a minimum weight subset S of vertices such that G-S is a split graph ...

    • Accuracy and efficiency of germline variant calling pipelines for human genome data 

      Zhao, Sen; Agafonov, Oleg; Azab, Abdulrahman; Stokowy, Tomasz; Hovig, Eivind (Journal article; Peer reviewed, 2020)
      Advances in next-generation sequencing technology have enabled whole genome sequencing (WGS) to be widely used for identification of causal variants in a spectrum of genetic-related disorders, and provided new insight into ...

    • Accurate analysis of genuine CRISPR editing events with ampliCan 

      Labun, Kornel; Guo, Xiaoge; Chavez, Alejandro; Church, George M.; Gagnon, James A.; Valen, Eivind (Peer reviewed; Journal article, 2019)
      We present ampliCan, an analysis tool for genome editing that unites highly precise quantification and visualization of genuine genome editing events. ampliCan features nuclease-optimized alignments, filtering of experimental ...

    • Acyclic, star, and injective colouring: bounding the diameter∗ 

      Brause, Christoph; Golovach, Petr; Martin, Barnaby; Ochem, Pascal; Paulusma, Daniël; Smith, Siani (Journal article; Peer reviewed, 2022)
      We examine the effect of bounding the diameter for a number of natural and well-studied variants of the COLOURING problem. A colouring is acyclic, star, or injective if any two colour classes induce a forest, star forest ...

    • An adaptive heuristic for Feeder Network Design with optional transshipment 

      Bergmann, Morten; Msakni, Mohamed Kais; Hemmati, Ahmad; Fagerholt, Kjetil (Journal article; Peer reviewed, 2023)
      This paper studies the Feeder Network Design Problem (FNDP), which considers the design of a minimum cost liner shipping network for the transportation of cargo (containers) between a given hub port and a set of feeder ...

    • Additive Schwarz preconditioner for the finite volume element discretization of symmetric elliptic problems 

      Marcinkowski, Leszek; Rahman, Talal; Loneland, Atle; Valdman, Jan (Peer reviewed; Journal article, 2015-09-25)
      A symmetric and a nonsymmetric variant of the additive Schwarz preconditioner are proposed for the solution of a class of finite volume element discretization of the symmetric elliptic problem in two dimensions, with large ...

    • Algebraic Reasoning About Timeliness 

      Haeri, Seyed Hossein; Thompson, Peter W; Van Roy, Peter; Haveraaen, Magne; Davies, Neil J; Barash, Mikhail; Hammond, Kevin; Chapman, James (Journal article; Peer reviewed, 2023)
      Designing distributed systems to have predictable performance under high load is difficult because of resource exhaustion, non-linearity, and stochastic behaviour. Timeliness, i.e., delivering results within defined time ...

    • An Algorithmic Meta-Theorem for Graph Modification to Planarity and FOL 

      Fomin, Fedor; Golovach, Petr; Stamoulis, Giannos; Thilikos, Dimitrios M. (Journal article; Peer reviewed, 2020)
      In general, a graph modification problem is defined by a graph modification operation ⊠ and a target graph property 𝒫. Typically, the modification operation ⊠ may be vertex removal, edge removal, edge contraction, or edge ...

    • Algorithms for covering multiple submodular constraints and applications 

      Chekuri, Chandra; Inamdar, Tanmay Nitin; Quanrud, Kent; Varadarajan, Kasturi; Zhang, Zhao (Journal article; Peer reviewed, 2022)
      We consider the problem of covering multiple submodular constraints. Given a finite ground set N, a weight function \(w: N \rightarrow \mathbb {R}_+\), r monotone submodular functions \(f_1,f_2,\ldots ,f_r\) over N and ...

    • Algorithms for the Rainbow Vertex Coloring Problem on Graph Classes 

      Lima, Paloma T.; van Leeuwen, Erik Jan; van der Wegen, Marieke (Journal article; Peer reviewed, 2020)
      Given a vertex-colored graph, we say a path is a rainbow vertex path if all its internal vertices have distinct colors. The graph is rainbow vertex-connected if there is a rainbow vertex path between every pair of its ...

    • Analysis of Trivium Using Compressed Right Hand Side Equations 

      Schilling, Thorsten Ernst; Raddum, Håvard (Chapter; Peer reviewed, 2012)
      We study a new representation of non-linear multivariate equations for algebraic cryptanalysis. Using a combination of multiple right hand side equations and binary decision diagrams, our new representation allows a very ...

    • 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 ...

    • An Approach to Flexible Multilevel Modelling 

      Macias, Fernando; Rutle, Adrian; Stolz, Volker; Rodriguez-Echeverria, Roberto; Wolter, Uwe Egbert (Peer reviewed; Journal article, 2018-07-12)
      Multilevel modelling approaches tackle issues related to lack of flexibility and mixed levels of abstraction by providing features like deep modelling and linguistic extension. However, the lack of a clear consensus on ...

    • Approximating Acyclicity Parameters of Sparse Hypergraphs 

      Fomin, Fedor; Golovach, Petr; Thilikos, Dimitrios (Peer reviewed; Journal article, 2009)
      The notions of hypertree width and generalized hypertree width were introduced by Gottlob, Leone, and Scarcello (PODS'99, PODS'01) in order to extend the concept of hypergraph acyclicity. These notions were further generalized ...

    • Approximating cube roots of integers, after Heron’s Metrica III.20 

      Steihaug, Trond; Rogers, D. G. (Peer reviewed; Journal article, 2013)

    • Approximation algorithms in combinatorial scientific computing 

      Pothen, Alex; Ferdous, SM; Manne, Fredrik (Journal article; Peer reviewed, 2019)
      We survey recent work on approximation algorithms for computing degreeconstrained subgraphs in graphs and their applications in combinatorial scientific computing. The problems we consider include maximization versions of ...

    • Approximation in (poly-) logarithmic space 

      Biswas, Arindam; Raman, Venkatesh; Saurabh, Saket (Journal article; Peer reviewed, 2020)
      We develop new approximation algorithms for classical graph and set problems in the RAM model under space constraints. As one of our main results, we devise an algorithm for d–Hitting Set that runs in time nO(d2+(d/ε)), ...

    • Associations Between Natural Physiological and Supraphysiological Estradiol Levels and Stress Perception 

      Leeners, Brigitte; Krüger, Tillman H.C.; Geraedts, Kirsten; Tronci, Enrico; Mancini, Toni; Egli, Marcel; Röblitz, Susanna; Saleh, Lanja; Spanaus, Katharina; Schippert, Cordula; Zhang, Y; Ille, Fabian (Peer reviewed; Journal article, 2019-06-11)
      Stress is a risk factor for impaired general, mental, and reproductive health. The role of physiological and supraphysiological estradiol concentrations in stress perception and stress processing is less well understood. ...

    • 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 ...

    • Attacks on Integer-RLWE 

      Budroni, Alessandro; Chetioui, Benjamin; Franch, Ermes (Journal article; Peer reviewed, 2020)
      In 2019, Gu Chunsheng introduced Integer-RLWE, a variant of RLWE devoid of some of its efficiency flaws. Most notably, he proposes a setting where n can be an arbitrary positive integer, contrarily to the typical construction ...