• Block-Diagonal and LT Codes for Distributed Computing with Straggling Servers 

      Severinson, Albin; Graell i Amat, Alexandre; Rosnes, Eirik (Peer reviewed; Journal article, 2019-03)
      We propose two coded schemes for the distributed computing problem of multiplying a matrix by a set of vectors. The first scheme is based on partitioning the matrix into submatrices and applying maximum distance separable ...
    • Bounds on the nonlinearity of differentially uniform functions by means of their image set size, and on their distance to affine functions 

      Carlet, Claude Michael (Journal article; Peer reviewed, 2021)
      We revisit and take a closer look at a (not so well known) result of a 2017 paper, showing that the differential uniformity of any vectorial function is bounded from below by an expression depending on the size of its image ...
    • Building large k-cores from sparse graphs 

      Fomin, Fedor; Sagunov, Danil; Simonov, Kirill (Journal article; Peer reviewed, 2020)
      A popular model to measure network stability is the k-core, that is the maximal induced subgraph in which every vertex has degree at least k. For example, k-cores are commonly used to model the unraveling phenomena in ...
    • Caligus rogercresseyi acetylcholinesterase types and variants: a potential marker for organophosphate resistance 

      Agusti-Ridaura, Celia; Dondrup, Michael; Horsberg, Tor Einar; Leong, Jong S; Koop, Ben F; Bravo, Sandra; Mendoza, Julio; Kaur, Kiranpreet (Peer reviewed; Journal article, 2018-10-30)
      Background Control of the sea louse Caligus rogercresseyi in the Chilean salmonid industry is reliant on chemical treatments. Azamethiphos was introduced in 2013, although other organophosphates were previously used. In ...
    • Causal inference in drug discovery and development 

      Michoel, Tom; Zhang, Jitao David (Journal article; Peer reviewed, 2023)
      To discover new drugs is to seek and to prove causality. As an emerging approach leveraging human knowledge and creativity, data, and machine intelligence, causal inference holds the promise of reducing cognitive bias and ...
    • CCZ-equivalence of bent vectorial functions and related constructions 

      Budaghyan, Lilya; Carlet, Claude (Peer reviewed; Journal article, 2011-01-06)
      We observe that the CCZ-equivalence of bent vectorial functions over F2nFn2 (n even) reduces to their EA-equivalence. Then we show that in spite of this fact, CCZ-equivalence can be used for constructing bent functions ...
    • Changes in the gene expression profile during spontaneous migraine attacks 

      Kogelman, Lisette J.A.; Falkenberg, Katrine; Buil, Alfonso; Erola, Pau; Courraud, Julie; Laursen, Susan Svane; Michoel, Tom Luk Robert; Olesen, Jes; Hansen, Thomas F. (Journal article; Peer reviewed, 2021)
      Migraine attacks are delimited, allowing investigation of changes during and outside attack. Gene expression fluctuates according to environmental and endogenous events and therefore, we hypothesized that changes in RNA ...
    • Characteristics of 454 pyrosequencing data—enabling realistic simulation with flowsim 

      Balzer, Susanne Mignon; Malde, Ketil; Lanzén, Anders; Sharma, Animesh; Jonassen, Inge (Peer reviewed; Journal article, 2010)
      Motivation: The commercial launch of 454 pyrosequencing in 2005was a milestone in genome sequencing in terms of performance and cost. Throughout the three available releases, average read lengths have increased to ∼500 ...
    • CHOPCHOP v2: a web tool for the next generation of CRISPR genome engineering 

      Valen, Eivind; Labun, Kornel; Montague, Tessa G.; Gagnon, James A.; Thyme, Summer B. (Journal article; Peer reviewed, 2016)
      In just 3 years CRISPR genome editing has transformed biology, and its popularity and potency continue to grow. New CRISPR effectors and rules for locating optimum targets continue to be reported, highlighting the need for ...
    • CHOPCHOP v3: expanding the CRISPR web toolbox beyond genome editing 

      Labun, Kornel; Montague, Tessa G.; Krause, Maximilian; Torres Cleuren, Yamila Nicole; Tjeldnes, Håkon; Valen, Eivind (Peer reviewed; Journal article, 2019-07-02)
      The CRISPR–Cas system is a powerful genome editing tool that functions in a diverse array of organisms and cell types. The technology was initially developed to induce targeted mutations in DNA, but CRISPR–Cas has now been ...
    • Chromatin accessibility established by Pou5f3, Sox19b and Nanog primes genes for activity during zebrafish genome activation 

      Pálfy, Máté; Schulze, Gunnar; Valen, Eivind; Vastenhouw, Nadine L. (Journal article; Peer reviewed, 2020-01)
      In many organisms, early embryonic development is driven by maternally provided factors until the controlled onset of transcription during zygotic genome activation. The regulation of chromatin accessibility and its ...
    • Chromatin and epigenetic features of long-range gene regulation 

      Harmston, Nathan; Lenhard, Boris (Peer reviewed; Journal article, 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. ...
    • Classes of Intersection Digraphs with Good Algorithmic Properties 

      Jaffke, Lars; Kwon, O-joung; Telle, Jan Arne (Journal article; Peer reviewed, 2022)
      While intersection graphs play a central role in the algorithmic analysis of hard problems on undirected graphs, the role of intersection digraphs in algorithms is much less understood. We present several contributions ...
    • Classification of quadratic APN functions with coefficients in F2 for dimensions up to 9 

      Yu, Yuyin; Kaleyski, Nikolay Stoyanov; Budaghyan, Lilya; Li, Yongqiang (Journal article; Peer reviewed, 2020)
      Almost perfect nonlinear (APN) and almost bent (AB) functions are integral components of modern block ciphers and play a fundamental role in symmetric cryptography. In this paper, we describe a procedure for searching for ...
    • Close Relatives of Feedback Vertex Set Without Single-Exponential Algorithms Parameterized by Treewidth 

      Bergougnoux, Benjamin; Bonnet, Édouard; Brettell, Nick; Kwon, O-Joung (Journal article; Peer reviewed, 2020)
      The Cut & Count technique and the rank-based approach have lead to single-exponential FPT algorithms parameterized by treewidth, that is, running in time 2^𝒪(tw)n^𝒪(1), for Feedback Vertex Set and connected versions of ...
    • Clustering to Given Connectivities 

      Golovach, Petr; Thilikos, Dimitrios M. (Peer reviewed; Journal article, 2019)
      We define a general variant of the graph clustering problem where the criterion of density for the clusters is (high) connectivity. In Clustering to Given Connectivities, we are given an n-vertex graph G, an integer k, and ...
    • Co-Degeneracy and Co-Treewidth: Using the Complement to Solve Dense Instances 

      Duarte, Gabriel; Oliveira, Mateus De Oliveira; Souza, Uéverton S. (Journal article; Peer reviewed, 2021)
      Clique-width and treewidth are two of the most important and useful graph parameters, and several problems can be solved efficiently when restricted to graphs of bounded clique-width or treewidth. Bounded treewidth implies ...
    • Coherence for Monoidal Groupoids in HoTT 

      Piceghello, Stefano (Journal article; Peer reviewed, 2020)
      We present a proof of coherence for monoidal groupoids in homotopy type theory. An important role in the formulation and in the proof of coherence is played by groupoids with a free monoidal structure; these can be represented ...
    • Coherent Conformational Degrees of Freedom as a Structural Basis for Allosteric Communication 

      Mitternacht, Simon; Berezovsky, Igor N. (Peer reviewed; Journal article, 2011-12-08)
      Conformational changes in allosteric regulation can to a large extent be described as motion along one or a few coherent degrees of freedom. The states involved are inherent to the protein, in the sense that they are visited ...
    • Combining Aspect-Oriented and Strategic Programming 

      Kalleberg, Karl Trygve; Visser, Eelco (Peer reviewed; Journal article, 2006-01)
      Properties such as logging, persistence, debugging, tracing, distribution, performance monitoring and exception handling occur in most programming paradigms and are normally very difficult or even impossible to modularizewith ...