Now showing items 1-20 of 287

    • 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 ...
    • 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 ...
    • 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 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 ...
    • 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 (Conference object; 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 ...
    • 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 ...
    • Automatic interpretation of otoliths using deep learning 

      Moen, Endre; Handegard, Nils Olav; Allken, Vaneeda; Albert, Ole Thomas; Harbitz, Alf; Malde, Ketil (Peer reviewed; Journal article, 2018-12-17)
      The age structure of a fish population has important implications for recruitment processes and population fluctuations, and is a key input to fisheries-assessment models. The current method of determining age structure ...
    • Axiom-Based Transformations: Optimisation and Testing 

      Bagge, Anya Helene; Haveraaen, Magne (Peer reviewed; Journal article, 2009-10-10)
      Programmers typically have knowledge about properties of their programs that aren't explicitly expressed in the code ­ properties that may be very useful for, e.g., compiler optimisation and automated testing. Although ...
    • 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 (Peer reviewed; Journal article, 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 ...
    • B-chromatic number: Beyond NP-hardness 

      Panolan, Fahad; Philip, Geevarghese; Saurabh, Saket (Conference object; Peer reviewed; Journal article, 2015)
      The b-chromatic number of a graph G, chi_b(G), is the largest integer k such that G has a k-vertex coloring with the property that each color class has a vertex which is adjacent to at least one vertex in each of the other ...
    • Balanced judicious bipartition is fixed-parameter tractable 

      Lokshtanov, Daniel; Saurabh, Saket; Sharma, Roohani; Zehavi, Meirav (Journal article; Peer reviewed, 2019)
      The family of judicious partitioning problems, introduced by Bollobás and Scott to the field of extremal combinatorics, has been extensively studied from a structural point of view for over two decades. This rich realm of ...
    • Bidimensionality and Kernels 

      Fomin, Fedor; Lokshtanov, Daniel; Saurabh, Saket; Thilikos, Dimitrios (Journal article; Peer reviewed, 2020)
      Bidimensionality theory was introduced by [E. D. Demaine et al., J. ACM, 52 (2005), pp. 866--893] as a tool to obtain subexponential time parameterized algorithms on H-minor-free graphs. In [E. D. Demaine and M. Hajiaghayi, ...
    • Bifurcation and sensitivity analysis reveal key drivers of multistability in a model of macrophage polarization 

      Frank, Anna-Simone; Larripa, Kamila; Ryu, Hwayeon; Snodgrass, Ryan; Röblitz, Susanna (Journal article; Peer reviewed, 2020)
      In this paper, we present and analyze a mathematical model for polarization of a single macrophage which, despite its simplicity, exhibits complex dynamics in terms of multistability. In particular, we demonstrate that an ...