Now showing items 41-60 of 315

    • 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 ...
    • 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 ...
    • Community curation of bioinformatics software and data resources 

      Ison, Jon; Ménager, Hervé; Brancotte, Bryan; Jaaniso, Erik; Salumets, Ahto; Raček, Tomáš; Lamprecht, Anna-Lena; Palmblad, Magnus; Kalaš, Matúš; Chmura, Piotr; Hancock, John M; Schwämmle, Veit; Ienasescu, Hans-Ioan (Peer reviewed; Journal article, 2019)
      The corpus of bioinformatics resources is huge and expanding rapidly, presenting life scientists with a growing challenge in selecting tools that fit the desired purpose. To address this, the European Infrastructure for ...
    • Community-driven development for computational biology at Sprints, Hackathons and Codefests 

      Möller, Steffen; Afgan, Enis; Banck, Michael; Bonnal, Raoul J. P.; Booth, Timothy; Chilton, John; Cock, Peter J. A.; Gumbel, Markus; Harris, Nomi; Holland, Richard; Kalaš, Matúš; Kaján, László; Kibukawa, Eri; Powel, David R.; Prins, Pjotr; Quinn, Jacqueline; Sallou, Olivier; Strozzi, Francesco; Seemann, Torsten; Sloggett, Clare; Soiland-Reyes, Stian; Spooner, William; Steinbiss, Sascha; Tille, Andreas; Travis, Anthony J.; Guimera, Roman V.; Katayama, Toshiaki; Chapman, Brad A. (Peer reviewed; Journal article, 2014-11-27)
      Background: Computational biology comprises a wide range of technologies and approaches. Multiple technologies can be combined to create more powerful workflows if the individuals contributing the data or providing tools ...
    • Comparative Visualization of Protein Secondary Structures 

      Kocincova, Lucia; Jaresova, Miroslava; Byska, Jan; Parulek, Julius; Hauser, Helwig; Kozlikova, Barbora (Peer reviewed; Journal article, 2017-02-15)
      Background: Protein function is determined by many factors, namely by its constitution, spatial arrangement, and dynamic behavior. Studying these factors helps the biochemists and biologists to better understand the protein ...
    • Comparison between instrumental variable and mediation-based methods for reconstructing causal gene networks in yeast 

      Ludl, Adriaan-Alexander; Michoel, Tom Luk Robert (Journal article; Peer reviewed, 2021)
      Causal gene networks model the flow of information within a cell. Reconstructing causal networks from omics data is challenging because correlation does not imply causation. When genomics and transcriptomics data from a ...
    • A complexity dichotomy for critical values of the b-chromatic number of graphs 

      Lima, Paloma T.; Jaffke, Lars (Journal article; Peer reviewed, 2020)
      A b-coloring of a graph G is a proper coloring of its vertices such that each color class contains a vertex that has at least one neighbor in all the other color classes. The b-Coloring problem asks whether a graph G has ...
    • A complexity dichotomy for critical values of the b-chromatic number of graphs 

      Jaffke, Lars; Lima, Paloma T. (Peer reviewed; Journal article, 2019-08-20)
      A b-coloring of a graph G is a proper coloring of its vertices such that each color class contains a vertex that has at least one neighbor in all the other color classes. The b-Coloring problem asks whether a graph G has ...
    • Complexity of the Steiner Network Problem with Respect to the Number of Terminals 

      Eiben, Eduard; Knop, Dusan; Panolan, Fahad; Suchý, Ondřej (Journal article; Peer reviewed, 2019)
      In the Directed Steiner Network problem we are given an arc-weighted digraph G, a set of terminals T subseteq V(G) with |T|=q, and an (unweighted) directed request graph R with V(R)=T. Our task is to output a subgraph H ...
    • Compressing permutation groups into grammars and polytopes. A graph embedding approach 

      Jaffke, Lars; De Oliveira Oliveira, Mateus; Tiwary, Hans Raj (Journal article; Peer reviewed, 2020)
      It can be shown that each permutation group G ⊑ 𝕊_n can be embedded, in a well defined sense, in a connected graph with O(n+|G|) vertices. Some groups, however, require much fewer vertices. For instance, 𝕊_n itself can ...
    • Computational science in the eighteenth century. Test cases for the methods of Newton, Raphson, and Halley: 1685 to 1745 

      Steihaug, Trond (Peer reviewed; Journal article, 2020)
      This is an overview of examples and problems posed in the late 1600s up to the mid 1700s for the purpose of testing or explaining the two different implementations of the Newton-Raphson method, Newton’s method as described ...
    • Computing cutwidth and pathwidth of semi-complete digraphs via degree orderings 

      Pilipczuk, Michal Pawel (Conference object; Peer reviewed; Journal article, 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, ...
    • Computing minimal triangulation in Time o(n^2.376) 

      Heggernes, Pinar; Telle, Jan Arne; Villanger, Yngve (Journal article, 2005)
    • Connecting the Dots (with Minimum Crossings) 

      Agrawal, Akanksha; Guspiel, Grzegorz; Madathil, Jayakrishnan; Saurabh, Saket; Zehavi, Meirav (Journal article; Peer reviewed, 2019)
      We study a prototype Crossing Minimization problem, defined as follows. Let F be an infinite family of (possibly vertex-labeled) graphs. Then, given a set P of (possibly labeled) n points in the Euclidean plane, a collection ...
    • Conserved BK Channel-Protein Interactions Reveal Signals Relevant to Cell Death and Survival 

      Sokolowski, Bernd; Orchard, Sandra; Harvey, Margaret; Sridhar, Settu; Sakai, Yoshihisa (Peer reviewed; Journal article, 2011-12-09)
      The large-conductance Ca2+-activated K+ (BK) channel and its b-subunit underlie tuning in non-mammalian sensory or hair cells, whereas in mammals its function is less clear. To gain insights into species differences and ...
    • Constructing APN functions through isotopic shifts 

      Budaghyan, Lilya; Calderini, Marco; Carlet, Claude; Coulter, Robert; Villa, Irene (Journal article; Peer reviewed, 2020)
      Almost perfect nonlinear (APN) functions over fields of characteristic 2 play an important role in cryptography, coding theory and, more generally, mathematics and information theory. In this paper we deduce a new method ...
    • Continuous Levels-of-Detail and Visual Abstraction for Seamless Molecular Visualization 

      Parulek, Julius; Jönsson, Daniel; Ropinski, Timo; Bruckner, Stefan; Ynnerman, Anders; Viola, Ivan (Peer reviewed; Journal article, 2014-05-06)
      Molecular visualization is often challenged with rendering of large molecular structures in real time. We introduce a novel approach that enables us to show even large protein complexes. Our method is based on the ...